diff -Naur lammps-21Feb17/bench/FERMI/README lammps-7Mar17/bench/FERMI/README --- lammps-21Feb17/bench/FERMI/README 2015-01-09 09:16:10.000000000 -0700 +++ lammps-7Mar17/bench/FERMI/README 2017-03-07 09:48:20.062786000 -0700 @@ -14,7 +14,7 @@ lmp_linux_double The precision (single, mixed, double) refers to the GPU and USER-CUDA -pacakge precision. See the README files in the lib/gpu and lib/cuda +package precision. See the README files in the lib/gpu and lib/cuda directories for instructions on how to build the packages with different precisions. The GPU and USER-CUDA sub-sections of the doc/Section_accelerate.html file also describes this process. diff -Naur lammps-21Feb17/doc/Makefile lammps-7Mar17/doc/Makefile --- lammps-21Feb17/doc/Makefile 2016-11-22 08:52:42.000000000 -0700 +++ lammps-7Mar17/doc/Makefile 2017-03-07 09:48:20.062786000 -0700 @@ -22,7 +22,7 @@ SOURCES=$(wildcard src/*.txt) OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) -.PHONY: help clean-all clean epub html pdf old venv +.PHONY: help clean-all clean epub html pdf old venv spelling # ------------------------------------------ @@ -44,6 +44,10 @@ clean: rm -rf $(RSTDIR) html + rm -rf spelling + +clean-spelling: + rm -rf spelling html: $(OBJECTS) @(\ @@ -64,6 +68,17 @@ @rm -rf html/USER/*/*.[sg]* @echo "Build finished. The HTML pages are in doc/html." +spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt + @(\ + . $(VENV)/bin/activate ;\ + pip install sphinxcontrib-spelling ;\ + cp -r src/* $(RSTDIR)/ ;\ + cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\ + sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\ + deactivate ;\ + ) + @echo "Spell check finished." + epub: $(OBJECTS) @mkdir -p epub @rm -f LAMMPS.epub diff -Naur lammps-21Feb17/doc/html/.buildinfo lammps-7Mar17/doc/html/.buildinfo --- lammps-21Feb17/doc/html/.buildinfo 2017-02-21 16:45:34.000000000 -0700 +++ lammps-7Mar17/doc/html/.buildinfo 2017-03-07 10:19:52.849393853 -0700 @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 77d5ad299193c453aca4fdf1c8ee5ba9 +config: d048617944d275a01e769de640ed37af tags: 645f666f9bcd5a90fca523b33c5a78b7 diff -Naur lammps-21Feb17/doc/html/USER/atc/man_consistent_fe_initialization.html lammps-7Mar17/doc/html/USER/atc/man_consistent_fe_initialization.html --- lammps-21Feb17/doc/html/USER/atc/man_consistent_fe_initialization.html 2017-02-21 16:45:34.000000000 -0700 +++ lammps-7Mar17/doc/html/USER/atc/man_consistent_fe_initialization.html 2017-03-07 10:19:52.857394092 -0700 @@ -27,7 +27,7 @@ syntax

fix_modify AtC consistent_fe_initialization <on | off>

examples

diff -Naur lammps-21Feb17/doc/html/bond_oxdna.html lammps-7Mar17/doc/html/bond_oxdna.html --- lammps-21Feb17/doc/html/bond_oxdna.html 1969-12-31 17:00:00.000000000 -0700 +++ lammps-7Mar17/doc/html/bond_oxdna.html 2017-03-07 10:19:52.858394121 -0700 @@ -0,0 +1,178 @@ + + + + + + + + + + + <no title> — LAMMPS documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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LAMMPS Documentation :c,h3 -21 Feb 2017 version :c,h4 +7 Mar 2017 version :c,h4 Version info: :h4 diff -Naur lammps-21Feb17/doc/src/Section_commands.txt lammps-7Mar17/doc/src/Section_commands.txt --- lammps-21Feb17/doc/src/Section_commands.txt 2017-02-21 16:02:21.000000000 -0700 +++ lammps-7Mar17/doc/src/Section_commands.txt 2017-03-07 09:48:20.062786000 -0700 @@ -281,12 +281,12 @@ 3.4 Commands listed by category :link(cmd_4),h4 -This section lists all LAMMPS commands, grouped by category. The -"next section"_#cmd_5 lists the same commands alphabetically. The +This section lists core LAMMPS commands, grouped by category. +The "next section"_#cmd_5 lists all commands alphabetically. The next section also includes (long) lists of style options for entries that appear in the following categories as a single command (fix, compute, pair, etc). Commands that are added by user packages are not -included in these categories, but they are in the next section. +included in the categories here, but they are in the next section. Initialization: @@ -361,7 +361,7 @@ "timer"_timer.html, "timestep"_timestep.html -Operations within timestepping (fixes) and diagnositics (computes): +Operations within timestepping (fixes) and diagnostics (computes): "compute"_compute.html, "compute_modify"_compute_modify.html, @@ -1016,6 +1016,7 @@ "eff/cut"_pair_eff.html, "exp6/rx"_pair_exp6_rx.html, "gauss/cut"_pair_gauss.html, +"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, "lennard/mdf"_pair_mdf.html, "list"_pair_list.html, "lj/charmm/coul/long/soft (o)"_pair_charmm.html, @@ -1091,7 +1092,7 @@ "harmonic/shift (o)"_bond_harmonic_shift.html, "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, -"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c) +"oxdna/fene"_bond_oxdna.html :tb(c=4,ea=c) :line diff -Naur lammps-21Feb17/doc/src/Section_errors.txt lammps-7Mar17/doc/src/Section_errors.txt --- lammps-21Feb17/doc/src/Section_errors.txt 2017-02-10 09:24:27.000000000 -0700 +++ lammps-7Mar17/doc/src/Section_errors.txt 2017-03-07 09:48:20.062786000 -0700 @@ -574,11 +574,11 @@ {Bad quadratic solve for particle/line collision} :dt -This is an internal error. It should nornally not occur. :dd +This is an internal error. It should normally not occur. :dd {Bad quadratic solve for particle/tri collision} :dt -This is an internal error. It should nornally not occur. :dd +This is an internal error. It should normally not occur. :dd {Bad real space Coulomb cutoff in fix tune/kspace} :dt @@ -912,7 +912,7 @@ {Cannot append atoms to a triclinic box} :dt -The simulation box must be defined with edges alligned with the +The simulation box must be defined with edges aligned with the Cartesian axes. :dd {Cannot balance in z dimension for 2d simulation} :dt @@ -992,7 +992,7 @@ LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6 factor that partitions the computation between real space and k-space -for Disptersion interactions. :dd +for Dispersion interactions. :dd {Cannot create an atom map unless atoms have IDs} :dt @@ -1327,7 +1327,7 @@ This file is created when you use some LAMMPS features, to indicate what paper you should cite on behalf of those who implemented -the feature. Check that you have write priveleges into the directory +the feature. Check that you have write privileges into the directory you are running in. :dd {Cannot open log.lammps for writing} :dt @@ -2005,7 +2005,7 @@ {Cannot use fix reax/bonds without pair_style reax} :dt -Self-explantory. :dd +Self-explanatory. :dd {Cannot use fix rigid npt/nph and fix deform on same component of stress tensor} :dt @@ -2088,7 +2088,7 @@ {Cannot use lines with fix srd unless overlap is set} :dt -This is because line segements are connected to each other. :dd +This is because line segments are connected to each other. :dd {Cannot use multiple fix wall commands with pair brownian} :dt @@ -2131,7 +2131,7 @@ {Cannot use newton pair with born/gpu pair style} :dt -Self-explantory. :dd +Self-explanatory. :dd {Cannot use newton pair with buck/coul/cut/gpu pair style} :dt @@ -2291,7 +2291,7 @@ {Cannot use newton pair with zbl/gpu pair style} :dt -Self-explantory. :dd +Self-explanatory. :dd {Cannot use non-zero forces in an energy minimization} :dt @@ -2641,11 +2641,11 @@ {Compute chunk/atom bin/cylinder radius is too large for periodic box} :dt -Radius cannot be bigger than 1/2 of a non-axis periodic dimention. :dd +Radius cannot be bigger than 1/2 of a non-axis periodic dimension. :dd {Compute chunk/atom bin/sphere radius is too large for periodic box} :dt -Radius cannot be bigger than 1/2 of any periodic dimention. :dd +Radius cannot be bigger than 1/2 of any periodic dimension. :dd {Compute chunk/atom compute array is accessed out-of-range} :dt @@ -2706,15 +2706,15 @@ {Compute chunk/atom stores no coord1 for compute property/chunk} :dt -Only certain binning options for comptue chunk/atom store coordinates. :dd +Only certain binning options for compute chunk/atom store coordinates. :dd {Compute chunk/atom stores no coord2 for compute property/chunk} :dt -Only certain binning options for comptue chunk/atom store coordinates. :dd +Only certain binning options for compute chunk/atom store coordinates. :dd {Compute chunk/atom stores no coord3 for compute property/chunk} :dt -Only certain binning options for comptue chunk/atom store coordinates. :dd +Only certain binning options for compute chunk/atom store coordinates. :dd {Compute chunk/atom variable is not atom-style variable} :dt @@ -2735,11 +2735,11 @@ {Compute cna/atom cutoff is longer than pairwise cutoff} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute cna/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute com/chunk does not use chunk/atom compute} :dt @@ -2747,7 +2747,7 @@ {Compute contact/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute contact/atom requires atom style sphere} :dt @@ -2760,7 +2760,7 @@ {Compute coord/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute damage/atom requires peridynamic potential} :dt @@ -2790,7 +2790,7 @@ {Compute erotate/asphere requires extended particles} :dt -This compute cannot be used with point paritlces. :dd +This compute cannot be used with point particles. :dd {Compute erotate/rigid with non-rigid fix-ID} :dt @@ -2835,7 +2835,7 @@ {Compute hexorder/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute improper/local used when impropers are not allowed} :dt @@ -2881,11 +2881,11 @@ {Compute orientorder/atom requires a pair style be defined} :dt -Self-explantory. :dd +Self-explanatory. :dd {Compute pair must use group all} :dt -Pair styles accumlate energy on all atoms. :dd +Pair styles accumulate energy on all atoms. :dd {Compute pe must use group all} :dt @@ -2935,7 +2935,7 @@ {Compute property/local cannot use these inputs together} :dt Only inputs that generate the same number of datums can be used -togther. E.g. bond and angle quantities cannot be mixed. :dd +together. E.g. bond and angle quantities cannot be mixed. :dd {Compute property/local does not (yet) work with atom_style template} :dt @@ -3079,7 +3079,7 @@ {Compute temp/asphere requires extended particles} :dt -This compute cannot be used with point paritlces. :dd +This compute cannot be used with point particles. :dd {Compute temp/body requires atom style body} :dt @@ -3524,12 +3524,12 @@ {Could not process Python file} :dt -The Python code in the specified file was not run sucessfully by +The Python code in the specified file was not run successfully by Python, probably due to errors in the Python code. :dd {Could not process Python string} :dt -The Python code in the here string was not run sucessfully by Python, +The Python code in the here string was not run successfully by Python, probably due to errors in the Python code. :dd {Coulomb PPPMDisp order has been reduced below minorder} :dt @@ -3638,7 +3638,7 @@ {Cutoffs missing in pair_style buck/long/coul/long} :dt -Self-exlanatory. :dd +Self-explanatory. :dd {Cutoffs missing in pair_style lj/long/coul/long} :dt @@ -4385,7 +4385,7 @@ {Fix ave/chunk does not use chunk/atom compute} :dt -The specified conpute is not for a compute chunk/atom command. :dd +The specified compute is not for a compute chunk/atom command. :dd {Fix ave/chunk fix does not calculate a per-atom array} :dt @@ -4617,11 +4617,11 @@ {Fix ave/time compute does not calculate a scalar} :dt -Self-explantory. :dd +Self-explanatory. :dd {Fix ave/time compute does not calculate a vector} :dt -Self-explantory. :dd +Self-explanatory. :dd {Fix ave/time compute does not calculate an array} :dt @@ -4970,7 +4970,7 @@ {Fix langevin angmom requires extended particles} :dt -This fix option cannot be used with point paritlces. :dd +This fix option cannot be used with point particles. :dd {Fix langevin omega is not yet implemented with kokkos} :dt @@ -6171,7 +6171,7 @@ {Initial temperatures not all set in fix ttm} :dt -Self-explantory. :dd +Self-explanatory. :dd {Input line quote not followed by whitespace} :dt @@ -6199,7 +6199,7 @@ {Insufficient Jacobi rotations for triangle} :dt -The calculation of the intertia tensor of the triangle failed. This +The calculation of the inertia tensor of the triangle failed. This should not happen if it is a reasonably shaped triangle. :dd {Insufficient memory on accelerator} :dt @@ -6463,15 +6463,15 @@ {Invalid attribute in dump custom command} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid attribute in dump local command} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid attribute in dump modify command} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid basis setting in create_atoms command} :dt @@ -6737,7 +6737,7 @@ Filenames used with the dump xyz style cannot be binary or cause files to be written by each processor. :dd -{Invalid dump_modify threshhold operator} :dt +{Invalid dump_modify threshold operator} :dt Operator keyword used for threshold specification in not recognized. :dd @@ -6751,7 +6751,7 @@ {Invalid fix ave/time off column} :dt -Self-explantory. :dd +Self-explanatory. :dd {Invalid fix box/relax command for a 2d simulation} :dt @@ -7313,7 +7313,7 @@ {LJ6 off not supported in pair_style buck/long/coul/long} :dt -Self-exlanatory. :dd +Self-explanatory. :dd {Label wasn't found in input script} :dt @@ -7361,7 +7361,7 @@ Lost atoms are checked for each time thermo output is done. See the thermo_modify lost command for options. Lost atoms usually indicate bad dynamics, e.g. atoms have been blown far out of the simulation -box, or moved futher than one processor's sub-domain away before +box, or moved further than one processor's sub-domain away before reneighboring. :dd {MEAM library error %d} :dt @@ -7526,7 +7526,7 @@ {Molecule template ID for create_atoms does not exist} :dt -Self-explantory. :dd +Self-explanatory. :dd {Molecule template ID for fix deposit does not exist} :dt @@ -7552,7 +7552,7 @@ Self-explanatory. :dd -{Molecule toplogy/atom exceeds system topology/atom} :dt +{Molecule topology/atom exceeds system topology/atom} :dt The number of bonds, angles, etc per-atom in the molecule exceeds the system setting. See the create_box command for how to specify these @@ -7792,7 +7792,7 @@ {Must use variable energy with fix addforce} :dt -Must define an energy vartiable when applyting a dynamic +Must define an energy variable when applying a dynamic force during minimization. :dd {Must use variable energy with fix efield} :dt @@ -8042,7 +8042,7 @@ {Non digit character between brackets in variable} :dt -Self-explantory. :dd +Self-explanatory. :dd {Non integer # of swaps in temper command} :dt @@ -8663,7 +8663,7 @@ {Pair style does not support compute group/group} :dt The pair_style does not have a single() function, so it cannot be -invokded by the compute group/group command. :dd +invoked by the compute group/group command. :dd {Pair style does not support compute pair/local} :dt @@ -8948,11 +8948,11 @@ {Pair yukawa/colloid requires atom style sphere} :dt -Self-explantory. :dd +Self-explanatory. :dd {Pair yukawa/colloid requires atoms with same type have same radius} :dt -Self-explantory. :dd +Self-explanatory. :dd {Pair yukawa/colloid/gpu requires atom style sphere} :dt @@ -9166,7 +9166,7 @@ {Python function evaluation failed} :dt -The Python function did not run succesfully and/or did not return a +The Python function did not run successfully and/or did not return a value (if it is supposed to return a value). This is probably due to some error condition in the function. :dd @@ -10025,7 +10025,7 @@ {Threshhold for an atom property that isn't allocated} :dt -A dump threshhold has been requested on a quantity that is +A dump threshold has been requested on a quantity that is not defined by the atom style used in this simulation. :dd {Timestep must be >= 0} :dt @@ -10087,7 +10087,7 @@ {Too many atom triplets for pair bop} :dt The number of three atom groups for angle determinations exceeds the -expected number. Check your atomic structrure to ensure that it is +expected number. Check your atomic structure to ensure that it is realistic. :dd {Too many atoms for dump dcd} :dt @@ -10155,7 +10155,7 @@ {Too many timesteps} :dt -The cummulative timesteps must fit in a 64-bit integer. :dd +The cumulative timesteps must fit in a 64-bit integer. :dd {Too many timesteps for NEB} :dt @@ -10654,7 +10654,7 @@ {Variable for region cylinder is invalid style} :dt -Only equal-style varaibles are allowed. :dd +Only equal-style variables are allowed. :dd {Variable for region is invalid style} :dt @@ -10666,7 +10666,7 @@ {Variable for region sphere is invalid style} :dt -Only equal-style varaibles are allowed. :dd +Only equal-style variables are allowed. :dd {Variable for restart is invalid style} :dt @@ -10707,7 +10707,7 @@ {Variable has circular dependency} :dt A circular dependency is when variable "a" in used by variable "b" and -variable "b" is also used by varaible "a". Circular dependencies with +variable "b" is also used by variable "a". Circular dependencies with longer chains of dependence are also not allowed. :dd {Variable name between brackets must be alphanumeric or underscore characters} :dt @@ -10796,7 +10796,7 @@ {Variable name for fix deform does not exist} :dt -Self-explantory. :dd +Self-explanatory. :dd {Variable name for fix efield does not exist} :dt @@ -11083,7 +11083,7 @@ {Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt -Self-explantory. :dd +Self-explanatory. :dd {Calling write_dump before a full system init.} :dt @@ -11414,7 +11414,7 @@ Lost atoms are checked for each time thermo output is done. See the thermo_modify lost command for options. Lost atoms usually indicate bad dynamics, e.g. atoms have been blown far out of the simulation -box, or moved futher than one processor's sub-domain away before +box, or moved further than one processor's sub-domain away before reneighboring. :dd {MSM mesh too small, increasing to 2 points in each direction} :dt @@ -11452,7 +11452,7 @@ {Molecule template for fix shake has multiple molecules} :dt -The fix shake command will only recoginze molecules of a single +The fix shake command will only recognize molecules of a single type, i.e. the first molecule in the template. :dd {More than one compute centro/atom} :dt @@ -11537,7 +11537,7 @@ If a thermo_style command is used after a thermo_modify command, the settings changed by the thermo_modify command will be reset to their -default values. This is because the thermo_modify commmand acts on +default values. This is because the thermo_modify command acts on the currently defined thermo style, and a thermo_style command creates a new style. :dd @@ -11589,7 +11589,7 @@ {One or more dynamic groups may not be updated at correct point in timestep} :dt -If there are other fixes that act immediately after the intitial stage +If there are other fixes that act immediately after the initial stage of time integration within a timestep (i.e. after atoms move), then the command that sets up the dynamic group should appear after those fixes. This will insure that dynamic group assignments are made @@ -11886,7 +11886,7 @@ {Using largest cutoff for buck/long/coul/long} :dt -Self-exlanatory. :dd +Self-explanatory. :dd {Using largest cutoff for lj/long/coul/long} :dt diff -Naur lammps-21Feb17/doc/src/Section_history.txt lammps-7Mar17/doc/src/Section_history.txt --- lammps-21Feb17/doc/src/Section_history.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/Section_history.txt 2017-03-07 09:48:20.062786000 -0700 @@ -37,7 +37,7 @@ Please see some of the closed issues for examples of how to suggest code enhancements, submit proposed changes, or report -possible bugs and how they are resoved. +possible bugs and how they are resolved. As an alternative to using GitHub, you may e-mail the "core developers"_http://lammps.sandia.gov/authors.html or send diff -Naur lammps-21Feb17/doc/src/Section_howto.txt lammps-7Mar17/doc/src/Section_howto.txt --- lammps-21Feb17/doc/src/Section_howto.txt 2017-02-21 15:56:21.000000000 -0700 +++ lammps-7Mar17/doc/src/Section_howto.txt 2017-03-07 09:48:20.062786000 -0700 @@ -573,7 +573,7 @@ LJ sigma of O-O = 3.16435 LJ epsilon, sigma of OH, HH = 0.0 :all(b),p -Note that the when using the TIP4P pair style, the neighobr list +Note that the when using the TIP4P pair style, the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2 * (OM distance), to account for the offset distance of the fictitious charges on O atoms in water molecules. Thus it is @@ -618,7 +618,7 @@ that mode of usage. The SPC/E (extended) water model is the same, except -the partial charge assignemnts change: +the partial charge assignments change: O charge = -0.8476 H charge = 0.4238 :all(b),p @@ -863,7 +863,7 @@ for details. The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the -time the simluation box is created. This happens in one of 3 ways. +time the simulation box is created. This happens in one of 3 ways. If the "create_box"_create_box.html command is used with a region of style {prism}, then a triclinic box is setup. See the "region"_region.html command for details. If the @@ -982,10 +982,10 @@ tile a triclinic simulation box via the "create_atoms"_create_atoms.html command. -A second use is to run Parinello-Rahman dyanamics via the "fix +A second use is to run Parinello-Rahman dynamics via the "fix npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt factors to compensate for off-diagonal components of the pressure -tensor. The analalog for an "energy minimization"_minimize.html is +tensor. The analog for an "energy minimization"_minimize.html is the "fix box/relax"_fix_box_relax.html command. A third use is to shear a bulk solid to study the response of the @@ -1392,7 +1392,7 @@ There is also a "dump local"_dump.html format where the user specifies what local values to output. A pre-defined index keyword can be -specified to enumuerate the local values. Two additional kinds of +specified to enumerate the local values. Two additional kinds of keywords can also be specified (c_ID, f_ID), where a "compute"_compute.html or "fix"_fix.html or "variable"_variable.html provides the values to be output. In each case, the compute or fix @@ -1525,7 +1525,7 @@ "Variables"_variable.html defined in an input script can store one or more strings. But equal-style, vector-style, and atom-style or atomfile-style variables generate a global scalar value, global vector -or values, or a per-atom vector, resepctively, when accessed. The +or values, or a per-atom vector, respectively, when accessed. The formulas used to define these variables can contain references to the thermodynamic keywords and to global and per-atom data generated by computes, fixes, and other variables. The values generated by @@ -1585,7 +1585,7 @@ degrees of freedom (and the Boltzmann constant). Since kinetic energy is a function of particle velocity, there is often a need to distinguish between a particle's advection velocity (due to some -aggregate motiion of particles) and its thermal velocity. The sum of +aggregate motion of particles) and its thermal velocity. The sum of the two is the particle's total velocity, but the latter is often what is wanted to compute a temperature. @@ -1640,14 +1640,14 @@ velocities but also rotational velocities for spherical and aspherical particles. -DPD thermostatting alters pairwise interactions in a manner analagous +DPD thermostatting alters pairwise interactions in a manner analogous to the per-particle thermostatting of "fix langevin"_fix_langevin.html. Any of the thermostatting fixes can use temperature computes that remove bias which has two effects. First, the current calculated temperature, which is compared to the requested target temperature, is -caluclated with the velocity bias removed. Second, the thermostat +calculated with the velocity bias removed. Second, the thermostat adjusts only the thermal temperature component of the particle's velocities, which are the velocities with the bias removed. The removed bias is then added back to the adjusted velocities. See the @@ -1888,7 +1888,7 @@ The lammps_open_no_mpi() function is similar except that no MPI communicator is passed from the caller. Instead, MPI_COMM_WORLD is -used to instantiate LAMMPS, and MPI is initialzed if necessary. +used to instantiate LAMMPS, and MPI is initialized if necessary. The lammps_close() function is used to shut down an instance of LAMMPS and free all its memory. @@ -1976,7 +1976,7 @@ the system and can be used by the caller to allocate space for the lammps_gather_atoms() and lammps_scatter_atoms() functions. The gather function collects atom info of the requested type (atom coords, -types, forces, etc) from all procsesors, orders them by atom ID, and +types, forces, etc) from all processors, orders them by atom ID, and returns a full list to each calling processor. The scatter function does the inverse. It distributes the same kinds of values, passed by the caller, to each atom owned by individual processors. @@ -2013,7 +2013,7 @@ section"_Section_howto.html#howto_21 of the manual for an analogous discussion for viscosity. -The thermal conducitivity tensor kappa is a measure of the propensity +The thermal conductivity tensor kappa is a measure of the propensity of a material to transmit heat energy in a diffusive manner as given by Fourier's law @@ -2099,7 +2099,7 @@ moving in another direction, normal to the area through which the momentum flows. Viscosity thus has units of pressure-time. -The first method is to perform a non-equlibrium MD (NEMD) simulation +The first method is to perform a non-equilibrium MD (NEMD) simulation by shearing the simulation box via the "fix deform"_fix_deform.html command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to thermostat the fluid via the SLLOD equations of motion. @@ -2125,7 +2125,7 @@ swapped between atoms in two different layers of the simulation box in a different dimension. This induces a velocity gradient which can be monitored with the "fix ave/chunk"_fix_ave_chunk.html command. -The fix tallies the cummulative momentum transfer that it performs. +The fix tallies the cumulative momentum transfer that it performs. See the "fix viscosity"_fix_viscosity.html command for details. The fourth method is based on the Green-Kubo (GK) formula which @@ -2268,7 +2268,7 @@ Note that chunk IDs are integer values, so for atom properties or computes that produce a floating point value, they will be truncated to an integer. You could also use the compute in a variable that -scales the floating point value to spread it across multiple intergers. +scales the floating point value to spread it across multiple integers. Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = pencils, 3d bins = boxes, spherical bins, cylindrical bins. @@ -2353,7 +2353,7 @@ Example calculations with chunks :h5 -Here are eaxmples using chunk commands to calculate various +Here are examples using chunk commands to calculate various properties: (1) Average velocity in each of 1000 2d spatial bins: @@ -2424,7 +2424,7 @@ The first approach is to set desired real-space an kspace accuracies via the {kspace_modify force/disp/real} and {kspace_modify force/disp/kspace} commands. Note that the accuracies have to be -specified in force units and are thus dependend on the chosen unit +specified in force units and are thus dependent on the chosen unit settings. For real units, 0.0001 and 0.002 seem to provide reasonable accurate and efficient computations for the real-space and kspace accuracies. 0.002 and 0.05 work well for most systems using lj @@ -2444,7 +2444,7 @@ simulation. However, it is sensitive to errors: A combination of parameters that will perform well for one system might result in far-from-optimal conditions for other simulations. For example, -parametes that provide accurate and fast computations for +parameters that provide accurate and fast computations for all-atomistic force fields can provide insufficient accuracy or united-atomistic force fields (which is related to that the latter typically have larger dispersion coefficients). @@ -2478,7 +2478,7 @@ The computational overhead can be reduced using the {kspace_modify mix/disp geom} and {kspace_modify splittol} commands. The first command simply enforces geometric mixing of the dispersion -coeffiecients in kspace computations. This introduces some error in +coefficients in kspace computations. This introduces some error in the computations but will also significantly speed-up the simulations. The second keyword sets the accuracy with which the dispersion coefficients are approximated using a matrix factorization @@ -2497,7 +2497,7 @@ 6.25 Polarizable models :link(howto_25),h4 In polarizable force fields the charge distributions in molecules and -materials respond to their electrostatic environements. Polarizable +materials respond to their electrostatic environments. Polarizable systems can be simulated in LAMMPS using three methods: the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html @@ -2551,7 +2551,7 @@ charge-on-spring models by the methods outlined in the next two sections. The assignment of masses to the additional degrees of freedom can lead to unphysical trajectories if care is not exerted in -choosing the parameters of the poarizable models and the simulation +choosing the parameters of the polarizable models and the simulation conditions. In the core-shell model the vibration of the shells is kept faster @@ -2727,18 +2727,18 @@ relative motion of the core and the shell should in theory be stable. However numerical fluctuation can introduce a small momentum to the system, which is noticable over long trajectories. -Therefore it is recomendable to use the "fix +Therefore it is recommendable to use the "fix momentum"_fix_momentum.html command in combination with "compute temp/cs"_compute_temp_cs.html when equilibrating the system to prevent any drift. -When intializing the velocities of a system with core/shell pairs, it +When initializing the velocities of a system with core/shell pairs, it is also desirable to not introduce energy into the relative motion of the core/shell particles, but only assign a center-of-mass velocity to the pairs. This can be done by using the {bias} keyword of the "velocity create"_velocity.html command and assigning the "compute temp/cs"_compute_temp_cs.html command to the {temp} keyword of the -"velocity"_velocity.html commmand, e.g. +"velocity"_velocity.html command, e.g. velocity all create 1427 134 bias yes temp CSequ velocity all scale 1427 temp CSequ :pre @@ -2808,7 +2808,7 @@ 6.27 Drude induced dipoles :link(howto_27),h4 The thermalized Drude model, similarly to the "core-shell"_#howto_26 -model, representes induced dipoles by a pair of charges (the core atom +model, represents induced dipoles by a pair of charges (the core atom and the Drude particle) connected by a harmonic spring. The Drude model has a number of features aimed at its use in molecular systems ("Lamoureux and Roux"_#howto-Lamoureux): diff -Naur lammps-21Feb17/doc/src/Section_modify.txt lammps-7Mar17/doc/src/Section_modify.txt --- lammps-21Feb17/doc/src/Section_modify.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/Section_modify.txt 2017-03-07 09:48:20.062786000 -0700 @@ -159,17 +159,17 @@ pack_comm_hybrid: store extra info unique to this atom style (optional) unpack_comm: retrieve an atom's info from the buffer (required) unpack_comm_vel: also retrieve velocity info (required) -unpack_comm_hybrid: retreive extra info unique to this atom style (optional) +unpack_comm_hybrid: retrieve extra info unique to this atom style (optional) pack_reverse: store an atom's info in a buffer communicating partial forces (required) pack_reverse_hybrid: store extra info unique to this atom style (optional) unpack_reverse: retrieve an atom's info from the buffer (required) -unpack_reverse_hybrid: retreive extra info unique to this atom style (optional) +unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional) pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required) pack_border_vel: add velocity info to buffer (required) pack_border_hybrid: store extra info unique to this atom style (optional) unpack_border: retrieve an atom's info from the buffer (required) unpack_border_vel: also retrieve velocity info (required) -unpack_border_hybrid: retreive extra info unique to this atom style (optional) +unpack_border_hybrid: retrieve extra info unique to this atom style (optional) pack_exchange: store all an atom's info to migrate to another processor (required) unpack_exchange: retrieve an atom's info from the buffer (required) size_restart: number of restart quantities associated with proc's atoms (required) @@ -369,7 +369,7 @@ post_force_respa: same as post_force, but for rRESPA (optional) final_integrate_respa: same as final_integrate, but for rRESPA (optional) min_pre_force: called after pair & molecular forces are computed in minimizer (optional) -min_post_force: called after pair & molecular forces are computed and communicated in minmizer (optional) +min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional) min_store: store extra data for linesearch based minimization on a LIFO stack (optional) min_pushstore: push the minimization LIFO stack one element down (optional) min_popstore: pop the minimization LIFO stack one element up (optional) @@ -517,7 +517,7 @@ inside: determine whether a point is in the region surface_interior: determine if a point is within a cutoff distance inside of surc surface_exterior: determine if a point is within a cutoff distance outside of surf -shape_update : change region shape if set by time-depedent variable :tb(s=:) +shape_update : change region shape if set by time-dependent variable :tb(s=:) :line @@ -601,16 +601,16 @@ "here"_Section_modify.html#mod_13 on this page. Adding a new math function of one or two arguments can be done by -editing one section of the Variable::evaulate() method. Search for +editing one section of the Variable::evaluate() method. Search for the word "customize" to find the appropriate location. Adding a new group function can be done by editing one section of the -Variable::evaulate() method. Search for the word "customize" to find +Variable::evaluate() method. Search for the word "customize" to find the appropriate location. You may need to add a new method to the Group class as well (see the group.cpp file). Accessing a new atom-based vector can be done by editing one section -of the Variable::evaulate() method. Search for the word "customize" +of the Variable::evaluate() method. Search for the word "customize" to find the appropriate location. Adding new "compute styles"_compute.html (whose calculated values can @@ -740,7 +740,7 @@ contribute several individual features. :l If you want your contribution to be added as a user-contribution and -it is several related featues, it is probably best to make it a user +it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief @@ -785,10 +785,10 @@ the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The -prerequiste for building the HTML format files are Python 3.x and +prerequisite for building the HTML format files are Python 3.x and virtualenv, the requirement for generating the PDF format manual is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least -"make html" and carefully inspect and proofread the resuling HTML format +"make html" and carefully inspect and proofread the resulting HTML format doc page before submitting your code. :l For a new package (or even a single command) you should include one or diff -Naur lammps-21Feb17/doc/src/Section_packages.txt lammps-7Mar17/doc/src/Section_packages.txt --- lammps-21Feb17/doc/src/Section_packages.txt 2017-01-18 13:07:25.000000000 -0700 +++ lammps-7Mar17/doc/src/Section_packages.txt 2017-03-07 09:48:20.062786000 -0700 @@ -94,7 +94,7 @@ :tb(ea=c) The "Authors" column lists a name(s) if a specific person is -responible for creating and maintaining the package. +responsible for creating and maintaining the package. (1) The COLLOID package includes Fast Lubrication Dynamics pair styles which were created by Amit Kumar and Michael Bybee from Jonathan @@ -462,7 +462,7 @@ acceleration, or Intel Xeon Phi. (You can build multiple times to create LAMMPS executables for different hardware.) It also requires a C++11 compatible compiler. For GPUs, the NVIDIA "nvcc" compiler is -used, and an appopriate KOKKOS_ARCH setting should be made in your +used, and an appropriate KOKKOS_ARCH setting should be made in your Makefile.machine for your GPU hardware and NVIDIA software. The simplest way to do this is to use Makefile.kokkos_cuda or @@ -955,8 +955,8 @@ in the package are nudged elastic band (NEB), parallel replica dynamics (PRD), temperature accelerated dynamics (TAD), parallel tempering, and a verlet/split algorithm for performing long-range -Coulombics on one set of processors, and the remainded of the force -field calcalation on another set. +Coulombics on one set of processors, and the remainder of the force +field calculation on another set. To install via make or Make.py: @@ -1176,7 +1176,7 @@ :link(VMD,http://www.ks.uiuc.edu/Research/vmd) The "Authors" column lists a name(s) if a specific person is -responible for creating and maintaining the package. +responsible for creating and maintaining the package. (1) The ATC package was created by Reese Jones, Jeremy Templeton, and Jon Zimmerman (Sandia). @@ -1295,13 +1295,13 @@ See these doc pages to get started: -"bond_style oxdna_fene"_bond_oxdna_fene.html -"pair_style oxdna_excv"_pair_oxdna_excv.html +"bond_style oxdna/fene"_bond_oxdna.html +"pair_style oxdna/..."_pair_oxdna.html "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul Supporting info: /src/USER-CGDNA/README, "bond_style -oxdna_fene"_bond_oxdna_fene.html, "pair_style -oxdna_excv"_pair_oxdna_excv.html, "fix +oxdna/fene"_bond_oxdna.html, "pair_style +oxdna/..."_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich @@ -1778,7 +1778,7 @@ should also be easier to build and use since there are no complicating issues with Fortran memory allocation or linking to a Fortran library. -For technical details about this implemention of ReaxFF, see +For technical details about this implementation of ReaxFF, see this paper: Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods @@ -1848,7 +1848,7 @@ The persons who created the USER-SMTBQ package are Nicolas Salles, Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at -these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact +these email addresses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact them directly if you have any questions. Examples: examples/USER/smtbq diff -Naur lammps-21Feb17/doc/src/Section_perf.txt lammps-7Mar17/doc/src/Section_perf.txt --- lammps-21Feb17/doc/src/Section_perf.txt 2016-09-23 15:04:56.000000000 -0600 +++ lammps-7Mar17/doc/src/Section_perf.txt 2017-03-07 09:48:20.062786000 -0700 @@ -69,7 +69,7 @@ For all the benchmarks, a useful metric is the CPU cost per atom per timestep. Since performance scales roughly linearly with problem size -and timesteps for all LAMMPS models (i.e. inteatomic or coarse-grained +and timesteps for all LAMMPS models (i.e. interatomic or coarse-grained potentials), the run time of any problem using the same model (atom style, force field, cutoff, etc) can then be estimated. diff -Naur lammps-21Feb17/doc/src/Section_python.txt lammps-7Mar17/doc/src/Section_python.txt --- lammps-21Feb17/doc/src/Section_python.txt 2016-11-22 08:52:42.000000000 -0700 +++ lammps-7Mar17/doc/src/Section_python.txt 2017-03-07 09:48:20.062786000 -0700 @@ -97,7 +97,7 @@ Section 11.8 gives some examples of coupling LAMMPS to other tools via Python. For example, LAMMPS can easily be coupled to a GUI or other visualization tools that display graphs or animations in real time as -LAMMPS runs. Examples of such scripts are inlcluded in the python +LAMMPS runs. Examples of such scripts are included in the python directory. Two advantages of using Python to run LAMMPS are how concise the @@ -177,7 +177,7 @@ lib/python/README file for more info. If you want to write Python code with callbacks to LAMMPS, then you -must also follow the steps overviewed in the preceeding section (11.1) +must also follow the steps overviewed in the preceding section (11.1) for running LAMMPS from Python. I.e. you must build LAMMPS as a shared library and insure that Python can find the python/lammps.py file and the shared library. @@ -325,7 +325,7 @@ Again, the "sudo" is only needed if required to copy PyPar files into your Python distribution's site-packages directory. -If you have successully installed PyPar, you should be able to run +If you have successfully installed PyPar, you should be able to run Python and type import pypar :pre @@ -369,7 +369,7 @@ python setup.py install --user :pre -If you have successully installed mpi4py, you should be able to run +If you have successfully installed mpi4py, you should be able to run Python and type from mpi4py import MPI :pre @@ -610,7 +610,7 @@ create an instance of LAMMPS, wrapped in a Python class by the lammps Python module, and return an instance of the Python class as lmp. It -is used to make all subequent calls to the LAMMPS library. +is used to make all subsequent calls to the LAMMPS library. Additional arguments to lammps() can be used to tell Python the name of the shared library to load or to pass arguments to the LAMMPS @@ -662,7 +662,7 @@ data type via the type argument. For extract_compute() and extract_fix(), the global, per-atom, or -local data calulated by the compute or fix can be accessed. What is +local data calculated by the compute or fix can be accessed. What is returned depends on whether the compute or fix calculates a scalar or vector or array. For a scalar, a single double value is returned. If the compute or fix calculates a vector or array, a pointer to the @@ -774,7 +774,7 @@ simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp, split.py, same as simple.py but running in parallel on a subset of procs, gui.py, GUI go/stop/temperature-slider to control LAMMPS, -plot.py, real-time temeperature plot with GnuPlot via Pizza.py, +plot.py, real-time temperature plot with GnuPlot via Pizza.py, viz_tool.py, real-time viz via some viz package, vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2) diff -Naur lammps-21Feb17/doc/src/Section_start.txt lammps-7Mar17/doc/src/Section_start.txt --- lammps-21Feb17/doc/src/Section_start.txt 2017-02-13 08:54:46.000000000 -0700 +++ lammps-7Mar17/doc/src/Section_start.txt 2017-03-07 09:48:20.062786000 -0700 @@ -80,7 +80,7 @@ Read this first :h5,link(start_2_1) -If you want to avoid building LAMMPS yourself, read the preceeding +If you want to avoid building LAMMPS yourself, read the preceding section about options available for downloading and installing executables. Details are discussed on the "download"_download page. @@ -251,7 +251,7 @@ clean options). The LMP_INC variable is used to include options that turn on ifdefs -within the LAMMPS code. The options that are currently recogized are: +within the LAMMPS code. The options that are currently recognized are: -DLAMMPS_GZIP -DLAMMPS_JPEG @@ -362,7 +362,7 @@ usual place (under /usr/local), you also may not need to specify these 3 variables, assuming /usr/local is in your path. On some large parallel machines which use "modules" for their compile/link -environements, you may simply need to include the correct module in +environments, you may simply need to include the correct module in your build environment, before building LAMMPS. Or the parallel machine may have a vendor-provided MPI which the compiler has no trouble finding. @@ -430,7 +430,7 @@ You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables, so the compiler and linker can find the needed FFT header and library files. Note that on some large parallel machines which use "modules" -for their compile/link environements, you may simply need to include +for their compile/link environments, you may simply need to include the correct module in your build environment. Or the parallel machine may have a vendor-provided FFT library which the compiler has no trouble finding. @@ -450,7 +450,7 @@ The FFT_INC variable also allows for a -DFFT_SINGLE setting that will use single-precision FFTs with PPPM, which can speed-up long-range -calulations, particularly in parallel or on GPUs. Fourier transform +calculations, particularly in parallel or on GPUs. Fourier transform and related PPPM operations are somewhat insensitive to floating point truncation errors and thus do not always need to be performed in double precision. Using the -DFFT_SINGLE setting trades off a little @@ -682,7 +682,7 @@ If you use a command in a LAMMPS input script that is part of a package, you must have built LAMMPS with that package, else you will get an error that the style is invalid or the command is unknown. -Every command's doc page specfies if it is part of a package. You can +Every command's doc page specifies if it is part of a package. You can also type lmp_machine -h :pre @@ -1008,7 +1008,7 @@ rename if desired. Likewise it creates an executable named src/lmp_auto, which you can rename using the -o switch if desired. -The most recently executed Make.py commmand is saved in +The most recently executed Make.py command is saved in src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke the last command, or you can save a sequence of one or more Make.py commands to a file and invoke the file of commands using "-r". You @@ -1064,7 +1064,7 @@ Obj_shared_foo. This is so that each file can be compiled with the -fPIC flag which is required for inclusion in a shared library. The build will create the file liblammps_foo.so which another application -can link to dyamically. It will also create a soft link liblammps.so, +can link to dynamically. It will also create a soft link liblammps.so, which will point to the most recently built shared library. This is the file the Python wrapper loads by default. @@ -1416,8 +1416,8 @@ numa Nm :pre This option is only relevant when using pthreads with hwloc support. -In this case Nm defines the number of NUMA regions (typicaly sockets) -on a node which will be utilizied by a single MPI rank. By default Nm +In this case Nm defines the number of NUMA regions (typically sockets) +on a node which will be utilized by a single MPI rank. By default Nm = 1. If this option is used the total number of worker-threads per MPI rank is threads*numa. Currently it is always almost better to assign at least one MPI rank per NUMA region, and leave numa set to @@ -1481,7 +1481,7 @@ installed on a machine (e.g. your desktop), you can run on more (virtual) processors than you have physical processors. -To run multiple independent simulatoins from one input script, using +To run multiple independent simulations from one input script, using multiple partitions, see "Section 6.4"_Section_howto.html#howto_4 of the manual. World- and universe-style "variables"_variable.html are useful in this context. @@ -1760,7 +1760,7 @@ is the total wall time for the section. The {Performance} line is provided for convenience to help predicting the number of loop continuations required and for comparing performance with other, -similar MD codes. The {CPU use} line provides the CPU utilzation per +similar MD codes. The {CPU use} line provides the CPU utilization per MPI task; it should be close to 100% times the number of OpenMP threads (or 1 of no OpenMP). Lower numbers correspond to delays due to file I/O or insufficient thread utilization. diff -Naur lammps-21Feb17/doc/src/Section_tools.txt lammps-7Mar17/doc/src/Section_tools.txt --- lammps-21Feb17/doc/src/Section_tools.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/Section_tools.txt 2017-03-07 09:48:20.062786000 -0700 @@ -471,7 +471,7 @@ restart2data tool :h4,link(restart) NOTE: This tool is now obsolete and is not included in the current -LAMMPS distribution. This is becaues there is now a +LAMMPS distribution. This is because there is now a "write_data"_write_data.html command, which can create a data file from within an input script. Running LAMMPS with the "-r" "command-line switch"_Section_start.html#start_7 as follows: diff -Naur lammps-21Feb17/doc/src/USER/atc/man_consistent_fe_initialization.html lammps-7Mar17/doc/src/USER/atc/man_consistent_fe_initialization.html --- lammps-21Feb17/doc/src/USER/atc/man_consistent_fe_initialization.html 2016-05-09 16:05:30.000000000 -0600 +++ lammps-7Mar17/doc/src/USER/atc/man_consistent_fe_initialization.html 2017-03-07 09:48:20.062786000 -0700 @@ -27,7 +27,7 @@ syntax

fix_modify AtC consistent_fe_initialization <on | off>

    -
  • <on|off> = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field
  • +
  • <on|off> = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field

examples

diff -Naur lammps-21Feb17/doc/src/accelerate_intel.txt lammps-7Mar17/doc/src/accelerate_intel.txt --- lammps-21Feb17/doc/src/accelerate_intel.txt 2017-01-09 13:29:27.000000000 -0700 +++ lammps-7Mar17/doc/src/accelerate_intel.txt 2017-03-07 09:48:20.062786000 -0700 @@ -20,7 +20,7 @@ calculations to the Phi. The same C++ code is used in both cases. When offloading to a coprocessor from a CPU, the same routine is run twice, once on the CPU and once with an offload flag. This allows -LAMMPS to run on the CPU cores and coprocessor cores simulataneously. +LAMMPS to run on the CPU cores and coprocessor cores simultaneously. [Currently Available USER-INTEL Styles:] @@ -115,7 +115,7 @@ recommended version of the Intel compiler is 14.0.1.106 or versions 15.0.2.044 and higher. -Although any compiler can be used with the USER-INTEL pacakge, +Although any compiler can be used with the USER-INTEL package, currently, vectorization directives are disabled by default when not using Intel compilers due to lack of standard support and observations of decreased performance. The OpenMP standard now @@ -428,7 +428,7 @@ with computation on the coprocessor when the "newton"_newton.html setting is "on". The default is dependent on the style being used, however, better performance may be achieved by setting this option -explictly. +explicitly. When using offload with CPU Hyper-Threading disabled, it may help performance to use fewer MPI tasks and OpenMP threads than available diff -Naur lammps-21Feb17/doc/src/accelerate_kokkos.txt lammps-7Mar17/doc/src/accelerate_kokkos.txt --- lammps-21Feb17/doc/src/accelerate_kokkos.txt 2017-01-17 09:44:40.000000000 -0700 +++ lammps-7Mar17/doc/src/accelerate_kokkos.txt 2017-03-07 09:48:20.062786000 -0700 @@ -217,7 +217,7 @@ KOKKOS_ARCH setting that matches the compute capability of your NVIDIA hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note the minimal required compute capability is 2.0, but this will give -signicantly reduced performance compared to Kepler generation GPUs +significantly reduced performance compared to Kepler generation GPUs with compute capability 3.x. For the LINK setting, "nvcc" should not be used; instead use g++ or another compiler suitable for linking C++ applications. Often you will want to use your MPI compiler wrapper @@ -234,7 +234,7 @@ threads to hardware cores. More info on binding threads to cores is given in "Section 5.3"_Section_accelerate.html#acc_3. -KOKKOS_ARCH=KNC enables compiler switches needed when compling for an +KOKKOS_ARCH=KNC enables compiler switches needed when compiling for an Intel Phi processor. KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism @@ -272,7 +272,7 @@ per coprocessor, and choose the number of coprocessor threads to use per MPI task (via the "-k" command-line switch discussed below). The product of MPI tasks * coprocessor threads/task should not exceed the -maximum number of threads the coproprocessor is designed to run, +maximum number of threads the coprocessor is designed to run, otherwise performance will suffer. This value is 240 for current generation Xeon Phi(TM) chips, which is 60 physical cores * 4 threads/core. Note that with the KOKKOS package you do not need to @@ -333,7 +333,7 @@ You must still use the "-k on" "command-line switch"_Section_start.html#start_7 to enable the KOKKOS package, and -specify its additional arguments for hardware options appopriate to +specify its additional arguments for hardware options appropriate to your system, as documented above. Use the "suffix kk"_suffix.html command, or you can explicitly add a diff -Naur lammps-21Feb17/doc/src/angle_hybrid.txt lammps-7Mar17/doc/src/angle_hybrid.txt --- lammps-21Feb17/doc/src/angle_hybrid.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/angle_hybrid.txt 2017-03-07 09:48:20.062786000 -0700 @@ -81,7 +81,7 @@ Unlike other angle styles, the hybrid angle style does not store angle coefficient info for individual sub-styles in a "binary restart -files"_restart.html. Thus when retarting a simulation from a restart +files"_restart.html. Thus when restarting a simulation from a restart file, you need to re-specify angle_coeff commands. [Related commands:] diff -Naur lammps-21Feb17/doc/src/atom_modify.txt lammps-7Mar17/doc/src/atom_modify.txt --- lammps-21Feb17/doc/src/atom_modify.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/atom_modify.txt 2017-03-07 09:48:20.062786000 -0700 @@ -103,7 +103,7 @@ It is OK to use the {first} keyword with a group that has not yet been defined, e.g. to use the atom_modify first command at the beginning of -your input script. LAMMPS does not use the group until a simullation +your input script. LAMMPS does not use the group until a simulation is run. The {sort} keyword turns on a spatial sorting or reordering of atoms @@ -116,7 +116,7 @@ effective at speeding up simulations of liquids as opposed to solids. In tests we have done, the speed-up can range from zero to 3-4x. -Reordering is peformed every {Nfreq} timesteps during a dynamics run +Reordering is performed every {Nfreq} timesteps during a dynamics run or iterations during a minimization. More precisely, reordering occurs at the first reneighboring that occurs after the target timestep. The reordering is performed locally by each processor, @@ -130,7 +130,7 @@ The goal of this procedure is for atoms to put atoms close to each other in the processor's one-dimensional list of atoms that are also near to each other spatially. This can improve cache performance when -pairwise intereractions and neighbor lists are computed. Note that if +pairwise interactions and neighbor lists are computed. Note that if bins are too small, there will be few atoms/bin. Likewise if bins are too large, there will be many atoms/bin. In both cases, the goal of cache locality will be undermined. @@ -138,7 +138,7 @@ NOTE: Running a simulation with sorting on versus off should not change the simulation results in a statistical sense. However, a different ordering will induce round-off differences, which will lead -to diverging trajectories over time when comparing two simluations. +to diverging trajectories over time when comparing two simulations. Various commands, particularly those which use random numbers (e.g. "velocity create"_velocity.html, and "fix langevin"_fix_langevin.html), may generate (statistically identical) diff -Naur lammps-21Feb17/doc/src/atom_style.txt lammps-7Mar17/doc/src/atom_style.txt --- lammps-21Feb17/doc/src/atom_style.txt 2016-10-24 08:19:10.000000000 -0600 +++ lammps-7Mar17/doc/src/atom_style.txt 2017-03-07 09:48:20.062786000 -0700 @@ -115,7 +115,7 @@ For the {ellipsoid} style, the particles are ellipsoids and each stores a flag which indicates whether it is a finite-size ellipsoid or a point particle. If it is an ellipsoid, it also stores a shape -vector with the 3 diamters of the ellipsoid and a quaternion 4-vector +vector with the 3 diameters of the ellipsoid and a quaternion 4-vector with its orientation. For the {dipole} style, a point dipole is defined for each point @@ -149,7 +149,7 @@ store the mass and volume of an integration point, a kernel diameter used for calculating the field variables (e.g. stress and deformation) and a contact radius for calculating repulsive forces which prevent -individual physical bodies from penetretating each other. +individual physical bodies from penetrating each other. The {wavepacket} style is similar to {electron}, but the electrons may consist of several Gaussian wave packets, summed up with coefficients @@ -165,7 +165,7 @@ stores a per-particle mass and size and orientation (i.e. the corner points of the triangle). -The {template} style allows molecular topolgy (bonds,angles,etc) to be +The {template} style allows molecular topology (bonds,angles,etc) to be defined via a molecule template using the "molecule"_molecule.html command. The template stores one or more molecules with a single copy of the topology info (bonds,angles,etc) of each. Individual atoms @@ -195,7 +195,7 @@ such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. -The "body"_body.html doc page descibes the body styles LAMMPS +The "body"_body.html doc page describes the body styles LAMMPS currently supports, and provides more details as to the kind of body particles they represent. For all styles, each body particle stores moments of inertia and a quaternion 4-vector, so that its orientation @@ -280,7 +280,7 @@ particle dynamics (DPD). The {meso} style is part of the USER-SPH package for smoothed particle -hydrodyanmics (SPH). See "this PDF +hydrodynamics (SPH). See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. The {wavepacket} style is part of the USER-AWPMD package for the diff -Naur lammps-21Feb17/doc/src/balance.txt lammps-7Mar17/doc/src/balance.txt --- lammps-21Feb17/doc/src/balance.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/balance.txt 2017-03-07 09:48:20.062786000 -0700 @@ -12,7 +12,7 @@ balance thresh style args ... keyword args ... :pre -thresh = imbalance threshhold that must be exceeded to perform a re-balance :ulb,l +thresh = imbalance threshold that must be exceeded to perform a re-balance :ulb,l one style/arg pair can be used (or multiple for {x},{y},{z}) :l style = {x} or {y} or {z} or {shift} or {rcb} :l {x} args = {uniform} or Px-1 numbers between 0 and 1 @@ -30,7 +30,7 @@ {shift} args = dimstr Niter stopthresh dimstr = sequence of letters containing "x" or "y" or "z", each not more than once Niter = # of times to iterate within each dimension of dimstr sequence - stopthresh = stop balancing when this imbalance threshhold is reached + stopthresh = stop balancing when this imbalance threshold is reached {rcb} args = none :pre zero or more keyword/arg pairs may be appended :l keyword = {weight} or {out} :l @@ -76,13 +76,13 @@ Load-balancing is typically most useful if the particles in the simulation box have a spatially-varying density distribution or when -the computational cost varies signficantly between different +the computational cost varies significantly between different particles. E.g. a model of a vapor/liquid interface, or a solid with an irregular-shaped geometry containing void regions, or "hybrid pair style simulations"_pair_hybrid.html which combine pair styles with different computational cost. In these cases, the LAMMPS default of dividing the simulation box volume into a regular-spaced grid of 3d -bricks, with one equal-volume sub-domain per procesor, may assign +bricks, with one equal-volume sub-domain per processor, may assign numbers of particles per processor in a way that the computational effort varies significantly. This can lead to poor performance when the simulation is run in parallel. @@ -91,7 +91,7 @@ With no weighting, the balancing attempts to assign an equal number of particles to each processor. With weighting, the balancing attempts to assign an equal aggregate computational weight to each processor, -which typically inducces a diffrent number of atoms assigned to each +which typically induces a different number of atoms assigned to each processor. Details on the various weighting options and examples for how they can be used are "given below"_#weighted_balance. @@ -222,7 +222,7 @@ the cutting place. The left (or lower) edge of the box is 0.0, and the right (or upper) edge is 1.0. Neither of these values is specified. Only the interior Ps-1 positions are specified. Thus is -there are 2 procesors in the x dimension, you specify a single value +there are 2 processors in the x dimension, you specify a single value such as 0.75, which would make the left processor's sub-domain 3x larger than the right processor's sub-domain. @@ -266,7 +266,7 @@ the balance procedure ends. NOTE: At each rebalance operation, the bisectioning for each cutting -plane (line in 2d) typcially starts with low and high bounds separated +plane (line in 2d) typically starts with low and high bounds separated by the extent of a processor's sub-domain in one dimension. The size of this bracketing region shrinks by 1/2 every iteration. Thus if {Niter} is specified as 10, the cutting plane will typically be @@ -301,7 +301,7 @@ That is the procedure for the first cut. Subsequent cuts are made recursively, in exactly the same manner. The subset of processors assigned to each box make a new cut in the longest dimension of that -box, splitting the box, the subset of processsors, and the particles +box, splitting the box, the subset of processors, and the particles in the box in two. The recursion continues until every processor is assigned a sub-box of the entire simulation domain, and owns the particles in that sub-box. @@ -368,7 +368,7 @@ of neighbors is likely to overestimate the ideal weight. This weight style is useful for systems where there are different -cutoffs used for different pairs of interations, or the density +cutoffs used for different pairs of interactions, or the density fluctuates, or a large number of particles are in the vicinity of a wall, or a combination of these effects. If a simulation uses multiple neighbor lists, this weight style will use the first suitable @@ -402,7 +402,7 @@ decreases by {factor}. In both cases the intermediate weight values increase/decrease proportionally as well. A value = 1.0 has no effect on the {time} weights. As a rule of thumb, effective values to use -are typicall between 0.5 and 1.2. Note that the timer quantities +are typically between 0.5 and 1.2. Note that the timer quantities mentioned above can be affected by communication which occurs in the middle of the operations, e.g. pair styles with intermediate exchange of data witin the force computation, and likewise for KSpace solves. diff -Naur lammps-21Feb17/doc/src/body.txt lammps-7Mar17/doc/src/body.txt --- lammps-21Feb17/doc/src/body.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/body.txt 2017-03-07 09:48:20.062786000 -0700 @@ -82,7 +82,7 @@ then the interaction between pairs of particles is likely to be more complex than the summation of simple sub-particle interactions. An example is contact or frictional forces between particles with planar -sufaces that inter-penetrate. +surfaces that inter-penetrate. These are additional LAMMPS commands that can be used with body particles of different styles @@ -105,7 +105,7 @@ The {nparticle} body style represents body particles as a rigid body with a variable number N of sub-particles. It is provided as a -vanillia, prototypical example of a body particle, although as +vanilla, prototypical example of a body particle, although as mentioned above, the "fix rigid"_fix_rigid.html command already duplicates its functionality. @@ -140,7 +140,7 @@ The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the prinicpal axes of the +simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. The coordinates of each sub-particle are specified as its x,y,z displacement from the center-of-mass of the body particle. The @@ -218,7 +218,7 @@ The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the prinicpal axes of the +simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. The coordinates of each vertex are specified as its x,y,z displacement from the center-of-mass of the body particle. The center-of-mass diff -Naur lammps-21Feb17/doc/src/bond_hybrid.txt lammps-7Mar17/doc/src/bond_hybrid.txt --- lammps-21Feb17/doc/src/bond_hybrid.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/bond_hybrid.txt 2017-03-07 09:48:20.062786000 -0700 @@ -64,7 +64,7 @@ Unlike other bond styles, the hybrid bond style does not store bond coefficient info for individual sub-styles in a "binary restart -files"_restart.html. Thus when retarting a simulation from a restart +files"_restart.html. Thus when restarting a simulation from a restart file, you need to re-specify bond_coeff commands. [Related commands:] diff -Naur lammps-21Feb17/doc/src/bond_oxdna.txt lammps-7Mar17/doc/src/bond_oxdna.txt --- lammps-21Feb17/doc/src/bond_oxdna.txt 1969-12-31 17:00:00.000000000 -0700 +++ lammps-7Mar17/doc/src/bond_oxdna.txt 2017-03-07 09:48:20.062786000 -0700 @@ -0,0 +1,70 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +bond_style oxdna/fene command :h3 + +[Syntax:] + +bond_style oxdna/fene :pre + +[Examples:] + +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 :pre + +[Description:] + +The {oxdna/fene} bond style uses the potential + +:c,image(Eqs/bond_oxdna_fene.jpg) + +to define a modified finite extensible nonlinear elastic (FENE) potential +"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone +in the oxDNA force field for coarse-grained modelling of DNA. + +The following coefficients must be defined for the bond type via the +"bond_coeff"_bond_coeff.html command as given in the above example, or in +the data file or restart files read by the "read_data"_read_data.html +or "read_restart"_read_restart.html commands: + +epsilon (energy) +Delta (distance) +r0 (distance) :ul + +NOTE: This bond style has to be used together with the corresponding oxDNA pair styles +for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} +and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of +"pair_style oxdna/excv"_pair_oxdna.html). The coefficients +in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. + +Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/. +A simple python setup tool which creates single straight or helical DNA strands, +DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. +A technical report with more information on the model, the structure of the input file, +the setup tool and the performance of the LAMMPS-implementation of oxDNA +can be found "here"_PDF/USER-CGDNA-overview.pdf. + +:line + +[Restrictions:] + +This bond style can only be used if LAMMPS was built with the +USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info on packages. + + +[Related commands:] + +"pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html + +[Default:] none + +:line + +:link(oxdna_fene) +[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). diff -Naur lammps-21Feb17/doc/src/bond_oxdna_fene.txt lammps-7Mar17/doc/src/bond_oxdna_fene.txt --- lammps-21Feb17/doc/src/bond_oxdna_fene.txt 2017-01-18 11:33:29.000000000 -0700 +++ lammps-7Mar17/doc/src/bond_oxdna_fene.txt 1969-12-31 17:00:00.000000000 -0700 @@ -1,70 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -bond_style oxdna_fene command :h3 - -[Syntax:] - -bond_style oxdna_fene :pre - -[Examples:] - -bond_style oxdna_fene -bond_coeff * 2.0 0.25 0.7525 :pre - -[Description:] - -The {oxdna_fene} bond style uses the potential - -:c,image(Eqs/bond_oxdna_fene.jpg) - -to define a modified finite extensible nonlinear elastic (FENE) potential -"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone -in the oxDNA force field for coarse-grained modelling of DNA. - -The following coefficients must be defined for the bond type via the -"bond_coeff"_bond_coeff.html command as given in the above example, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -epsilon (energy) -Delta (distance) -r0 (distance) :ul - -NOTE: This bond style has to be used together with the corresponding oxDNA pair styles -for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk} -and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of -"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients -in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. - -Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/. -A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/. -A technical report with more information on the model, the structure of the input file, -the setup tool and the performance of the LAMMPS-implementation of oxDNA -can be found "here"_PDF/USER-CGDNA-overview.pdf. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. - - -[Related commands:] - -"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html - -[Default:] none - -:line - -:link(oxdna_fene) -[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). diff -Naur lammps-21Feb17/doc/src/bonds.txt lammps-7Mar17/doc/src/bonds.txt --- lammps-21Feb17/doc/src/bonds.txt 2017-01-18 11:33:29.000000000 -0700 +++ lammps-7Mar17/doc/src/bonds.txt 2017-03-07 09:48:20.062786000 -0700 @@ -15,7 +15,7 @@ bond_morse bond_none bond_nonlinear - bond_oxdna_fene + bond_oxdna bond_quartic bond_table bond_zero diff -Naur lammps-21Feb17/doc/src/change_box.txt lammps-7Mar17/doc/src/change_box.txt --- lammps-21Feb17/doc/src/change_box.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/change_box.txt 2017-03-07 09:48:20.062786000 -0700 @@ -258,8 +258,8 @@ :line The {ortho} and {triclinic} keywords convert the simulation box to be -orthogonal or triclinic (non-orthongonal). See "this -section"_Section_howto#howto_13 for a discussion of how non-orthongal +orthogonal or triclinic (non-orthogonal). See "this +section"_Section_howto#howto_13 for a discussion of how non-orthogonal boxes are represented in LAMMPS. The simulation box is defined as either orthogonal or triclinic when @@ -289,7 +289,7 @@ The {remap} keyword remaps atom coordinates from the last saved box size/shape to the current box state. For example, if you stretch the box in the x dimension or tilt it in the xy plane via the {x} and {xy} -keywords, then the {remap} commmand will dilate or tilt the atoms to +keywords, then the {remap} command will dilate or tilt the atoms to conform to the new box size/shape, as if the atoms moved with the box as it deformed. diff -Naur lammps-21Feb17/doc/src/comm_style.txt lammps-7Mar17/doc/src/comm_style.txt --- lammps-21Feb17/doc/src/comm_style.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/comm_style.txt 2017-03-07 09:48:20.062786000 -0700 @@ -39,7 +39,7 @@ information for nearby atoms, communication must now be done with a more complex pattern of neighboring processors. -Note that this command does not actually define a partitoining of the +Note that this command does not actually define a partitioning of the simulation box (a domain decomposition), rather it determines what kinds of decompositions are allowed and the pattern of communication used to enable the decomposition. A decomposition is created when the diff -Naur lammps-21Feb17/doc/src/compute.txt lammps-7Mar17/doc/src/compute.txt --- lammps-21Feb17/doc/src/compute.txt 2016-09-08 14:20:32.000000000 -0600 +++ lammps-7Mar17/doc/src/compute.txt 2017-03-07 09:48:20.062786000 -0700 @@ -235,7 +235,7 @@ "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component "temp/region"_compute_temp_region.html - temperature of a region of atoms "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles -"ti"_compute_ti.html - thermodyanmic integration free energy values +"ti"_compute_ti.html - thermodynamic integration free energy values "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk diff -Naur lammps-21Feb17/doc/src/compute_angmom_chunk.txt lammps-7Mar17/doc/src/compute_angmom_chunk.txt --- lammps-21Feb17/doc/src/compute_angmom_chunk.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_angmom_chunk.txt 2017-03-07 09:48:20.062786000 -0700 @@ -22,7 +22,7 @@ [Description:] -Define a computation that calculates the angular momemtum of multiple +Define a computation that calculates the angular momentum of multiple chunks of atoms. In LAMMPS, chunks are collections of atoms defined by a "compute diff -Naur lammps-21Feb17/doc/src/compute_centro_atom.txt lammps-7Mar17/doc/src/compute_centro_atom.txt --- lammps-21Feb17/doc/src/compute_centro_atom.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_centro_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -18,8 +18,8 @@ zero or more keyword/value pairs may be appended :l keyword = {axes} :l {axes} value = {no} or {yes} - {no} = do not calulate 3 symmetry axes - {yes} = calulate 3 symmetry axes :pre + {no} = do not calculate 3 symmetry axes + {yes} = calculate 3 symmetry axes :pre :ule [Examples:] @@ -108,7 +108,7 @@ columns 5-7 and 8-10. The centrosymmetry values are unitless values >= 0.0. Their magnitude -depends on the lattice style due to the number of contibuting neighbor +depends on the lattice style due to the number of contributing neighbor pairs in the summation in the formula above. And it depends on the local defects surrounding the central atom, as described above. For the {axes yes} case, the vector components are also unitless, since diff -Naur lammps-21Feb17/doc/src/compute_chunk_atom.txt lammps-7Mar17/doc/src/compute_chunk_atom.txt --- lammps-21Feb17/doc/src/compute_chunk_atom.txt 2016-11-30 13:56:54.000000000 -0700 +++ lammps-7Mar17/doc/src/compute_chunk_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -386,7 +386,7 @@ {limit} keyword, the compression operation is performed first, as described below, which resets {Nchunk}. The {limit} keyword is then applied to the new {Nchunk} value, exactly as described in the -preceeding paragraph. Note that in this case, all atoms will end up +preceding paragraph. Note that in this case, all atoms will end up with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or compute/fix/variable value) may have been > {Nc}, because of the compression operation. @@ -459,7 +459,7 @@ which outputs the original IDs as one of the columns in its global output array. For example, using the "compute cluster/atom" command discussed above, the original 5 unique chunk IDs might be atom IDs -(27,4982,58374,857838,1000000). After compresion, these will be +(27,4982,58374,857838,1000000). After compression, these will be renumbered to (1,2,3,4,5). The original values (27,...,1000000) can be output to a file by the "fix ave/chunk"_fix_ave_chunk.html command, or by using the "fix ave/time"_fix_ave_time.html command in @@ -538,7 +538,7 @@ to the first or last bin in both the radial and axis dimensions. If {discard} is set to {mixed}, which is the default, the radial dimension is treated the same as for {discard} = no. But for the axis -dimensinon, it will only have its chunk ID set to the first or last +dimension, it will only have its chunk ID set to the first or last bin if bins extend to the simulation box boundary in the axis dimension. This is the case if the {bound} keyword settings are {lower} and {upper}, which is the default. If the {bound} keyword diff -Naur lammps-21Feb17/doc/src/compute_cna_atom.txt lammps-7Mar17/doc/src/compute_cna_atom.txt --- lammps-21Feb17/doc/src/compute_cna_atom.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_cna_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -42,7 +42,7 @@ The CNA calculation can be sensitive to the specified cutoff value. You should insure the appropriate nearest neighbors of an atom are -found within the cutoff distance for the presumed crystal strucure. +found within the cutoff distance for the presumed crystal structure. E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest neighbors for perfect BCC crystals. These formulas can be used to obtain a good cutoff distance: diff -Naur lammps-21Feb17/doc/src/compute_com.txt lammps-7Mar17/doc/src/compute_com.txt --- lammps-21Feb17/doc/src/compute_com.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_com.txt 2017-03-07 09:48:20.062786000 -0700 @@ -25,7 +25,7 @@ of atoms, including all effects due to atoms passing thru periodic boundaries. -A vector of three quantites is calculated by this compute, which +A vector of three quantities is calculated by this compute, which are the x,y,z coordinates of the center of mass. NOTE: The coordinates of an atom contribute to the center-of-mass in diff -Naur lammps-21Feb17/doc/src/compute_coord_atom.txt lammps-7Mar17/doc/src/compute_coord_atom.txt --- lammps-21Feb17/doc/src/compute_coord_atom.txt 2017-01-19 08:50:18.000000000 -0700 +++ lammps-7Mar17/doc/src/compute_coord_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -70,7 +70,7 @@ orientorder/atom"_compute_orientorder/atom command is specified as {orientorderID}. The compute must invoke its {components} option to calculate components of the {Ybar_lm} vector for each atoms, as -described in its documenation. Note that orientorder/atom compute +described in its documentation. Note that orientorder/atom compute defines its own criteria for identifying neighboring atoms. If the scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the orientorder/atom compute is larger than the specified {threshold}, diff -Naur lammps-21Feb17/doc/src/compute_damage_atom.txt lammps-7Mar17/doc/src/compute_damage_atom.txt --- lammps-21Feb17/doc/src/compute_damage_atom.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_damage_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -47,7 +47,7 @@ "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The per-atom vector values are unitlesss numbers (damage) >= 0.0. +The per-atom vector values are unitless numbers (damage) >= 0.0. [Restrictions:] diff -Naur lammps-21Feb17/doc/src/compute_dilatation_atom.txt lammps-7Mar17/doc/src/compute_dilatation_atom.txt --- lammps-21Feb17/doc/src/compute_dilatation_atom.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_dilatation_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -50,7 +50,7 @@ any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom vector values are unitlesss numbers (theta) >= 0.0. +The per-atom vector values are unitless numbers (theta) >= 0.0. [Restrictions:] diff -Naur lammps-21Feb17/doc/src/compute_displace_atom.txt lammps-7Mar17/doc/src/compute_displace_atom.txt --- lammps-21Feb17/doc/src/compute_displace_atom.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_displace_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -25,7 +25,7 @@ atom in the group from its original coordinates, including all effects due to atoms passing thru periodic boundaries. -A vector of four quantites per atom is calculated by this compute. +A vector of four quantities per atom is calculated by this compute. The first 3 elements of the vector are the dx,dy,dz displacements. The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy + dz*dz). diff -Naur lammps-21Feb17/doc/src/compute_event_displace.txt lammps-7Mar17/doc/src/compute_event_displace.txt --- lammps-21Feb17/doc/src/compute_event_displace.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_event_displace.txt 2017-03-07 09:48:20.062786000 -0700 @@ -14,7 +14,7 @@ ID, group-ID are documented in "compute"_compute.html command event/displace = style name of this compute command -threshold = minimum distance anyparticle must move to trigger an event (distance units) :ul +threshold = minimum distance any particle must move to trigger an event (distance units) :ul [Examples:] @@ -37,7 +37,7 @@ NOTE: If the system is undergoing significant center-of-mass motion, due to thermal motion, an external force, or an initial net momentum, then this compute will not be able to distinguish that motion from -local atom displacements and may generate "false postives." +local atom displacements and may generate "false positives." [Output info:] diff -Naur lammps-21Feb17/doc/src/compute_global_atom.txt lammps-7Mar17/doc/src/compute_global_atom.txt --- lammps-21Feb17/doc/src/compute_global_atom.txt 2016-11-30 13:59:16.000000000 -0700 +++ lammps-7Mar17/doc/src/compute_global_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -55,7 +55,7 @@ 0.0 is assigned to the atom. An example of how this command is useful, is in the context of -"chunks" which are static or dyanmic subsets of atoms. The "compute +"chunks" which are static or dynamic subsets of atoms. The "compute chunk/atom"_compute_chunk_atom.html command assigns unique chunk IDs to each atom. It's output can be used as the {index} parameter for this command. Various other computes with "chunk" in their style @@ -192,7 +192,7 @@ atoms, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating a vector of global quantities which the {index} parameter will reference for -assignement of global values to atoms. +assignment of global values to atoms. :line @@ -207,7 +207,7 @@ LAMMPS output options. The per-atom vector or array values will be in whatever units the -corresponsing input values are in. +corresponding input values are in. [Restrictions:] none diff -Naur lammps-21Feb17/doc/src/compute_heat_flux.txt lammps-7Mar17/doc/src/compute_heat_flux.txt --- lammps-21Feb17/doc/src/compute_heat_flux.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_heat_flux.txt 2017-03-07 09:48:20.062786000 -0700 @@ -38,7 +38,7 @@ The compute takes three arguments which are IDs of other "computes"_compute.html. One calculates per-atom kinetic energy ({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the -third calcualtes per-atom stress ({stress-ID}). +third calculates per-atom stress ({stress-ID}). NOTE: These other computes should provide values for all the atoms in the group this compute specifies. That means the other computes could @@ -83,7 +83,7 @@ post-processing operation, an autocorrelation can be performed, its integral estimated, and the Green-Kubo formula above evaluated. -The "fix ave/correlate"_fix_ave_correlate.html command can calclate +The "fix ave/correlate"_fix_ave_correlate.html command can calculate the autocorrelation. The trap() function in the "variable"_variable.html command can calculate the integral. diff -Naur lammps-21Feb17/doc/src/compute_inertia_chunk.txt lammps-7Mar17/doc/src/compute_inertia_chunk.txt --- lammps-21Feb17/doc/src/compute_inertia_chunk.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_inertia_chunk.txt 2017-03-07 09:48:20.062786000 -0700 @@ -35,7 +35,7 @@ defined and examples of how they can be used to measure properties of a system. -This compute calculates the 6 components of the symmetric intertia +This compute calculates the 6 components of the symmetric inertia tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The calculation includes all effects due to atoms passing thru periodic boundaries. diff -Naur lammps-21Feb17/doc/src/compute_msd.txt lammps-7Mar17/doc/src/compute_msd.txt --- lammps-21Feb17/doc/src/compute_msd.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_msd.txt 2017-03-07 09:48:20.062786000 -0700 @@ -33,7 +33,7 @@ parameter of mean-squared displacement, see the "compute msd/nongauss"_compute_msd_nongauss.html command. -A vector of four quantites is calculated by this compute. The first 3 +A vector of four quantities is calculated by this compute. The first 3 elements of the vector are the squared dx,dy,dz displacements, summed and averaged over atoms in the group. The 4th element is the total squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and diff -Naur lammps-21Feb17/doc/src/compute_msd_chunk.txt lammps-7Mar17/doc/src/compute_msd_chunk.txt --- lammps-21Feb17/doc/src/compute_msd_chunk.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_msd_chunk.txt 2017-03-07 09:48:20.062786000 -0700 @@ -35,7 +35,7 @@ defined and examples of how they can be used to measure properties of a system. -Four quantites are calculated by this compute for each chunk. The +Four quantities are calculated by this compute for each chunk. The first 3 quantities are the squared dx,dy,dz displacements of the center-of-mass. The 4th component is the total squared displacement, i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These diff -Naur lammps-21Feb17/doc/src/compute_msd_nongauss.txt lammps-7Mar17/doc/src/compute_msd_nongauss.txt --- lammps-21Feb17/doc/src/compute_msd_nongauss.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_msd_nongauss.txt 2017-03-07 09:48:20.062786000 -0700 @@ -30,12 +30,12 @@ (MSD) and non-Gaussian parameter (NGP) of the group of atoms, including all effects due to atoms passing thru periodic boundaries. -A vector of three quantites is calculated by this compute. The first +A vector of three quantities is calculated by this compute. The first element of the vector is the total squared dx,dy,dz displacements drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the fourth power of these displacements drfourth = (dx*dx + dy*dy + dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the -group. The 3rd component is the nonGaussian diffusion paramter NGP = +group. The 3rd component is the nonGaussian diffusion parameter NGP = 3*drfourth/(5*drsquared*drsquared), i.e. :c,image(Eqs/compute_msd_nongauss.jpg) @@ -48,7 +48,7 @@ If the {com} option is set to {yes} then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the -displacment of each atom is calcluated. +displacment of each atom is calculated. See the "compute msd"_compute_msd.html doc page for further important NOTEs, which also apply to this compute. diff -Naur lammps-21Feb17/doc/src/compute_pair.txt lammps-7Mar17/doc/src/compute_pair.txt --- lammps-21Feb17/doc/src/compute_pair.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_pair.txt 2017-03-07 09:48:20.062786000 -0700 @@ -43,7 +43,7 @@ as a global scalar by this compute. This is useful when using "pair_style hybrid"_pair_hybrid.html if you want to know the portion of the total energy contributed by one sub-style. If {evalue} is -specfied as {evdwl} or {ecoul}, then just that portion of the energy +specified as {evdwl} or {ecoul}, then just that portion of the energy is stored as a global scalar. NOTE: The energy returned by the {evdwl} keyword does not include tail @@ -52,7 +52,7 @@ Some pair styles tally additional quantities, e.g. a breakdown of potential energy into a dozen or so components is tallied by the -"pair_style reax"_pair_reax.html commmand. These values (1 or more) +"pair_style reax"_pair_reax.html command. These values (1 or more) are stored as a global vector by this compute. See the doc page for "individual pair styles"_pair_style.html for info on these values. diff -Naur lammps-21Feb17/doc/src/compute_pair_local.txt lammps-7Mar17/doc/src/compute_pair_local.txt --- lammps-21Feb17/doc/src/compute_pair_local.txt 2016-07-22 16:46:14.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_pair_local.txt 2017-03-07 09:48:20.062786000 -0700 @@ -47,7 +47,7 @@ "pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html commands. -The value {dist} is the distance bewteen the pair of atoms. +The value {dist} is the distance between the pair of atoms. The value {eng} is the interaction energy for the pair of atoms. diff -Naur lammps-21Feb17/doc/src/compute_pe_atom.txt lammps-7Mar17/doc/src/compute_pe_atom.txt --- lammps-21Feb17/doc/src/compute_pe_atom.txt 2016-10-13 13:07:38.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_pe_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -51,7 +51,7 @@ The KSpace contribution is calculated using the method in "(Heyes)"_#Heyes for the Ewald method and a related method for PPPM, as specified by the "kspace_style pppm"_kspace_style.html command. -For PPPM, the calcluation requires 1 extra FFT each timestep that +For PPPM, the calculation requires 1 extra FFT each timestep that per-atom energy is calculated. This "document"_PDF/kspace.pdf describes how the long-range per-atom energy calculation is performed. diff -Naur lammps-21Feb17/doc/src/compute_plasticity_atom.txt lammps-7Mar17/doc/src/compute_plasticity_atom.txt --- lammps-21Feb17/doc/src/compute_plasticity_atom.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_plasticity_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -44,7 +44,7 @@ any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom vector values are unitlesss numbers (lambda) >= 0.0. +The per-atom vector values are unitless numbers (lambda) >= 0.0. [Restrictions:] diff -Naur lammps-21Feb17/doc/src/compute_pressure.txt lammps-7Mar17/doc/src/compute_pressure.txt --- lammps-21Feb17/doc/src/compute_pressure.txt 2016-11-17 16:10:42.000000000 -0700 +++ lammps-7Mar17/doc/src/compute_pressure.txt 2017-03-07 09:48:20.062786000 -0700 @@ -89,7 +89,7 @@ Also note that the N in the first formula above is really degrees-of-freedom divided by d = dimensionality, where the DOF value -is calcluated by the temperature compute. See the various "compute +is calculated by the temperature compute. See the various "compute temperature"_compute.html styles for details. A compute of this style with the ID of "thermo_press" is created when diff -Naur lammps-21Feb17/doc/src/compute_property_chunk.txt lammps-7Mar17/doc/src/compute_property_chunk.txt --- lammps-21Feb17/doc/src/compute_property_chunk.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_property_chunk.txt 2017-03-07 09:48:20.062786000 -0700 @@ -64,7 +64,7 @@ "compute chunk/atom"_compute_chunk_atom.html command referenced by chunkID. This means that the original chunk IDs (e.g. molecule IDs) will have been compressed to remove chunk IDs with no atoms assigned -to them. Thus a compresed chunk ID of 3 may correspond to an original +to them. Thus a compressed chunk ID of 3 may correspond to an original chunk ID (molecule ID in this case) of 415. The {id} attribute will then be 415 for the 3rd chunk. diff -Naur lammps-21Feb17/doc/src/compute_rdf.txt lammps-7Mar17/doc/src/compute_rdf.txt --- lammps-21Feb17/doc/src/compute_rdf.txt 2017-02-14 15:41:59.000000000 -0700 +++ lammps-7Mar17/doc/src/compute_rdf.txt 2017-03-07 09:48:20.062786000 -0700 @@ -73,7 +73,7 @@ which may slow down your simulation. If you specify a {Rcut} <= force cutoff, you will force an additional neighbor list to be built at every timestep this command is invoked (or every reneighboring -timestep, whichever is less frequent), which is inefficent. LAMMPS +timestep, whichever is less frequent), which is inefficient. LAMMPS will warn you if this is the case. If you specify a {Rcut} > force cutoff, you must insure ghost atom information out to {Rcut} + {skin} is communicated, via the "comm_modify cutoff"_comm_modify.html diff -Naur lammps-21Feb17/doc/src/compute_rigid_local.txt lammps-7Mar17/doc/src/compute_rigid_local.txt --- lammps-21Feb17/doc/src/compute_rigid_local.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_rigid_local.txt 2017-03-07 09:48:20.062786000 -0700 @@ -123,7 +123,7 @@ the COM velocity and force on the COM of the body. The {omegax}, {omegay}, and {omegaz} attributes are the angular -velocity componennts of the body around its COM. +velocity components of the body around its COM. The {angmomx}, {angmomy}, and {angmomz} attributes are the angular momentum components of the body around its COM. diff -Naur lammps-21Feb17/doc/src/compute_saed.txt lammps-7Mar17/doc/src/compute_saed.txt --- lammps-21Feb17/doc/src/compute_saed.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_saed.txt 2017-03-07 09:48:20.062786000 -0700 @@ -93,7 +93,7 @@ zone axis of an intersecting Ewald sphere. Diffraction intensities will only be computed at the intersection of the reciprocal lattice mesh and a {dR_Ewald} thick surface of the Ewald sphere. See the -example 3D intestiety data and the intersection of a \[010\] zone axis +example 3D intensity data and the intersection of a \[010\] zone axis in the below image. :c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg) diff -Naur lammps-21Feb17/doc/src/compute_smd_ulsph_num_neighs.txt lammps-7Mar17/doc/src/compute_smd_ulsph_num_neighs.txt --- lammps-21Feb17/doc/src/compute_smd_ulsph_num_neighs.txt 2016-11-30 14:03:35.000000000 -0700 +++ lammps-7Mar17/doc/src/compute_smd_ulsph_num_neighs.txt 2017-03-07 09:48:20.062786000 -0700 @@ -35,7 +35,7 @@ See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The per-particle values will be given dimentionless, see "units"_units.html. +The per-particle values will be given dimensionless, see "units"_units.html. [Restrictions:] diff -Naur lammps-21Feb17/doc/src/compute_stress_atom.txt lammps-7Mar17/doc/src/compute_stress_atom.txt --- lammps-21Feb17/doc/src/compute_stress_atom.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_stress_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -92,7 +92,7 @@ "(Heyes)"_#Heyes for the Ewald method and by the methodology described in "(Sirk)"_#Sirk for PPPM. The choice of KSpace solver is specified by the "kspace_style pppm"_kspace_style.html command. Note that for -PPPM, the calcluation requires 6 extra FFTs each timestep that +PPPM, the calculation requires 6 extra FFTs each timestep that per-atom stress is calculated. Thus it can significantly increase the cost of the PPPM calculation if it is needed on a large fraction of the simulation timesteps. diff -Naur lammps-21Feb17/doc/src/compute_temp_asphere.txt lammps-7Mar17/doc/src/compute_temp_asphere.txt --- lammps-21Feb17/doc/src/compute_temp_asphere.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_temp_asphere.txt 2017-03-07 09:48:20.062786000 -0700 @@ -138,7 +138,7 @@ LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -This compute requires that atoms store angular momementum and a +This compute requires that atoms store angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff -Naur lammps-21Feb17/doc/src/compute_temp_body.txt lammps-7Mar17/doc/src/compute_temp_body.txt --- lammps-21Feb17/doc/src/compute_temp_body.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_temp_body.txt 2017-03-07 09:48:20.062786000 -0700 @@ -120,7 +120,7 @@ LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -This compute requires that atoms store angular momementum and a +This compute requires that atoms store angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html command. diff -Naur lammps-21Feb17/doc/src/compute_temp_chunk.txt lammps-7Mar17/doc/src/compute_temp_chunk.txt --- lammps-21Feb17/doc/src/compute_temp_chunk.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_temp_chunk.txt 2017-03-07 09:48:20.062786000 -0700 @@ -44,7 +44,7 @@ Define a computation that calculates the temperature of a group of atoms that are also in chunks, after optionally subtracting out the center-of-mass velocity of each chunk. By specifying optional values, -it can also calulate the per-chunk temperature or energies of the +it can also calculate the per-chunk temperature or energies of the multiple chunks of atoms. In LAMMPS, chunks are collections of atoms defined by a "compute @@ -122,7 +122,7 @@ {adof} and {cdof} keywords to adjust the calculated degress of freedom appropriately, as explained below. -Note that the per-chunk temperature calulated by this compute and the +Note that the per-chunk temperature calculated by this compute and the "fix ave/chunk temp"_fix_ave_chunk.html command can be different. This compute calculates the temperature for each chunk for a single snapshot. Fix ave/chunk can do that but can also time average those @@ -208,7 +208,7 @@ of the optional values are specified. The number of rows in the array = the number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of -columns is the number of specifed values (1 or more). These values +columns is the number of specified values (1 or more). These values can be accessed by any command that uses global array values from a compute as input. Again, see "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output diff -Naur lammps-21Feb17/doc/src/compute_temp_profile.txt lammps-7Mar17/doc/src/compute_temp_profile.txt --- lammps-21Feb17/doc/src/compute_temp_profile.txt 2016-10-27 11:09:15.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_temp_profile.txt 2017-03-07 09:48:20.062786000 -0700 @@ -118,7 +118,7 @@ NOTE: When using the {out} keyword with a value of {bin}, the calculated temperature for each bin does not include the -degrees-of-freedom adjustment described in the preceeding paragraph, +degrees-of-freedom adjustment described in the preceding paragraph, for fixes that constrain molecular motion. It does include the adjustment due to the {extra} option, which is applied to each bin. diff -Naur lammps-21Feb17/doc/src/compute_vacf.txt lammps-7Mar17/doc/src/compute_vacf.txt --- lammps-21Feb17/doc/src/compute_vacf.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_vacf.txt 2017-03-07 09:48:20.062786000 -0700 @@ -27,7 +27,7 @@ contribution to the VACF is its current velocity vector dotted into its initial velocity vector at the time the compute was specified. -A vector of four quantites is calculated by this compute. The first 3 +A vector of four quantities is calculated by this compute. The first 3 elements of the vector are vx * vx0 (and similarly for the y and z components), summed and averaged over atoms in the group. Vx is the current x-component of velocity for the atom, vx0 is the initial diff -Naur lammps-21Feb17/doc/src/compute_voronoi_atom.txt lammps-7Mar17/doc/src/compute_voronoi_atom.txt --- lammps-21Feb17/doc/src/compute_voronoi_atom.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/compute_voronoi_atom.txt 2017-03-07 09:15:13.553786000 -0700 @@ -217,6 +217,10 @@ LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. +It also requiers you have a copy of the Voro++ library built and +installed on your system. See instructions on obtaining and +installing the Voro++ software in the src/VORONOI/README file. + [Related commands:] "dump custom"_dump.html, "dump local"_dump.html diff -Naur lammps-21Feb17/doc/src/create_atoms.txt lammps-7Mar17/doc/src/create_atoms.txt --- lammps-21Feb17/doc/src/create_atoms.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/create_atoms.txt 2017-03-07 09:48:20.062786000 -0700 @@ -101,7 +101,7 @@ For the {random} style, N particles are added to the system at randomly generated coordinates, which can be useful for generating an amorphous system. The particles are created one by one using the -speficied random number {seed}, resulting in the same set of particles +specified random number {seed}, resulting in the same set of particles coordinates, independent of how many processors are being used in the simulation. If the {region-ID} argument is specified as NULL, then the created particles will be anywhere in the simulation box. If a diff -Naur lammps-21Feb17/doc/src/dihedral_hybrid.txt lammps-7Mar17/doc/src/dihedral_hybrid.txt --- lammps-21Feb17/doc/src/dihedral_hybrid.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/dihedral_hybrid.txt 2017-03-07 09:48:20.062786000 -0700 @@ -82,7 +82,7 @@ Unlike other dihedral styles, the hybrid dihedral style does not store dihedral coefficient info for individual sub-styles in a "binary -restart files"_restart.html. Thus when retarting a simulation from a +restart files"_restart.html. Thus when restarting a simulation from a restart file, you need to re-specify dihedral_coeff commands. [Related commands:] diff -Naur lammps-21Feb17/doc/src/dump.txt lammps-7Mar17/doc/src/dump.txt --- lammps-21Feb17/doc/src/dump.txt 2016-10-19 08:50:50.000000000 -0600 +++ lammps-7Mar17/doc/src/dump.txt 2017-03-07 09:48:20.062786000 -0700 @@ -225,7 +225,7 @@ meaning of the 6 character flags for "xx yy zz" is the same as above. Note that the first two numbers on each line are now xlo_bound instead -of xlo, etc, since they repesent a bounding box. See "this +of xlo, etc, since they represent a bounding box. See "this section"_Section_howto.html#howto_12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, simple formulas for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are @@ -545,7 +545,7 @@ with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by the box size. Atoms that have passed through a periodic boundary will -have the corresponding cooordinate increased or decreased by 1.0. +have the corresponding coordinate increased or decreased by 1.0. The image flags can be printed directly using the {ix}, {iy}, {iz} attributes. For periodic dimensions, they specify which image of the diff -Naur lammps-21Feb17/doc/src/dump_custom_vtk.txt lammps-7Mar17/doc/src/dump_custom_vtk.txt --- lammps-21Feb17/doc/src/dump_custom_vtk.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/dump_custom_vtk.txt 2017-03-07 09:48:20.062786000 -0700 @@ -211,7 +211,7 @@ There are several options for outputting atom coordinates. The {x}, {y}, {z} attributes are used to write atom coordinates "unscaled", in the appropriate distance "units"_units.html (Angstroms, sigma, etc). -Additionaly, you can use {xs}, {ys}, {zs} if you want to also save the +Additionally, you can use {xs}, {ys}, {zs} if you want to also save the coordinates "scaled" to the box size, so that each value is 0.0 to 1.0. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. Use {xu}, {yu}, {zu} if you @@ -224,7 +224,7 @@ Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by the box size. Atoms that have passed through a periodic boundary will have the corresponding -cooordinate increased or decreased by 1.0. +coordinate increased or decreased by 1.0. The image flags can be printed directly using the {ix}, {iy}, {iz} attributes. For periodic dimensions, they specify which image of the diff -Naur lammps-21Feb17/doc/src/dump_image.txt lammps-7Mar17/doc/src/dump_image.txt --- lammps-21Feb17/doc/src/dump_image.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/dump_image.txt 2017-03-07 09:48:20.062786000 -0700 @@ -99,7 +99,7 @@ images can easily be manually converted into an animated movie of your simulation or the process can be automated without writing the intermediate files using the dump movie style; see further details -below. Other dump styles store snapshots of numerical data asociated +below. Other dump styles store snapshots of numerical data associated with atoms in various formats, as discussed on the "dump"_dump.html doc page. @@ -237,7 +237,7 @@ :line -The various kewords listed above control how the image is rendered. +The various keywords listed above control how the image is rendered. As listed below, all of the keywords have defaults, most of which you will likely not need to change. The "dump modify"_dump_modify.html also has options specific to the dump image style, particularly for @@ -261,7 +261,7 @@ The {bond} keyword allows to you to alter how bonds are drawn. A bond is only drawn if both atoms in the bond are being drawn due to being in the specified group and due to other selection criteria -(e.g. region, threshhold settings of the +(e.g. region, threshold settings of the "dump_modify"_dump_modify.html command). By default, bonds are drawn if they are defined in the input data file as read by the "read_data"_read_data.html command. Using {none} for both the bond @@ -356,7 +356,7 @@ body style. If this keyword is not used, such particles will be drawn as spheres, the same as if they were regular atoms. -The "body"_body.html doc page descibes the body styles LAMMPS +The "body"_body.html doc page describes the body styles LAMMPS currently supports, and provides more details as to the kind of body particles they represent and how they are drawn by this dump image command. For all the body styles, individual atoms can be either a @@ -442,7 +442,7 @@ The {center} keyword determines the point in simulation space that will be at the center of the image. {Cx}, {Cy}, and {Cz} are -speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is +specified as fractions of the box dimensions, so that (0.5,0.5,0.5) is the center of the simulation box. These values do not have to be between 0.0 and 1.0, if you want the simulation box to be offset from the center of the image. Note, however, that if you choose strange @@ -476,8 +476,8 @@ The {persp} keyword determines how much depth perspective is present in the image. Depth perspective makes lines that are parallel in simulation space appear non-parallel in the image. A {pfactor} value -of 0.0 means that parallel lines will meet at infininty (1.0/pfactor), -which is an orthographic rendering with no persepctive. A {pfactor} +of 0.0 means that parallel lines will meet at infinity (1.0/pfactor), +which is an orthographic rendering with no perspective. A {pfactor} value between 0.0 and 1.0 will introduce more perspective. A {pfactor} value > 1 will create a highly skewed image with a large amount of perspective. @@ -638,7 +638,7 @@ which can be safely ignored. Other warnings and errors have to be addressed according to the FFmpeg documentation. One known issue is that certain movie file formats (e.g. MPEG level 1 -and 2 format streams) have video bandwith limits that can be crossed +and 2 format streams) have video bandwidth limits that can be crossed when rendering too large of image sizes. Typical warnings look like this: diff -Naur lammps-21Feb17/doc/src/dump_modify.txt lammps-7Mar17/doc/src/dump_modify.txt --- lammps-21Feb17/doc/src/dump_modify.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/dump_modify.txt 2017-03-07 09:48:20.062786000 -0700 @@ -426,7 +426,7 @@ The {scale} keyword applies only to the dump {atom} style. A scale value of {yes} means atom coords are written in normalized units from -0.0 to 1.0 in each box dimension. If the simluation box is triclinic +0.0 to 1.0 in each box dimension. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. A value of {no} means they are written in absolute distance units (e.g. Angstroms or sigma). @@ -470,7 +470,7 @@ If an atom-style variable is used as the attribute, then it can produce continuous numeric values or effective Boolean 0/1 values -which may be useful for the comparision operator. Boolean values can +which may be useful for the comparison operator. Boolean values can be generated by variable formulas that use comparison or Boolean math operators or special functions like gmask() and rmask() and grmask(). See the "variable"_variable.html command doc page for details. diff -Naur lammps-21Feb17/doc/src/fix_ave_chunk.txt lammps-7Mar17/doc/src/fix_ave_chunk.txt --- lammps-21Feb17/doc/src/fix_ave_chunk.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_ave_chunk.txt 2017-03-07 09:48:20.062786000 -0700 @@ -67,7 +67,7 @@ [NOTE:] -If you are trying to replace a deprectated fix ave/spatial command +If you are trying to replace a deprecated fix ave/spatial command with the newer, more flexible fix ave/chunk and "compute chunk/atom"_compute_chunk_atom.html commands, you simply need to split the fix ave/spatial arguments across the two new commands. For @@ -189,7 +189,7 @@ the {ave} keyword is set to {running} or {window} then {Nchunk} must remain constant for the duration of the simulation. This fix forces the chunk/atom compute specified by chunkID to hold {Nchunk} constant -for the appropriate time windows, by not allowing it to re-calcualte +for the appropriate time windows, by not allowing it to re-calculate {Nchunk}, which can also affect how it assigns chunk IDs to atoms. More details are given on the "compute chunk/atom"_compute_chunk_atom.html doc page. @@ -301,7 +301,7 @@ of an average. If the {norm} setting is {none}, a similar computation as for the -{sample} seting is done, except the individual "average sample values" +{sample} setting is done, except the individual "average sample values" are "summed sample values". A summed sample value is simply the chunk value summed over atoms in the sample, without dividing by the number of atoms in the sample. The output value for the chunk on the @@ -410,7 +410,7 @@ column is only used if the {compress} keyword was set to {yes} for the "compute chunk/atom"_compute_chunk_atom.html command. This means that the original chunk IDs (e.g. molecule IDs) will have been compressed -to remove chunk IDs with no atoms assigned to them. Thus a compresed +to remove chunk IDs with no atoms assigned to them. Thus a compressed chunk ID of 3 may correspond to an original chunk ID or molecule ID of 415. The OrigID column will list 415 for the 3rd chunk. diff -Naur lammps-21Feb17/doc/src/fix_ave_correlate.txt lammps-7Mar17/doc/src/fix_ave_correlate.txt --- lammps-21Feb17/doc/src/fix_ave_correlate.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_ave_correlate.txt 2017-03-07 09:48:20.062786000 -0700 @@ -64,7 +64,7 @@ [Description:] Use one or more global scalar values as inputs every few timesteps, -calculate time correlations bewteen them at varying time intervals, +calculate time correlations between them at varying time intervals, and average the correlation data over longer timescales. The resulting correlation values can be time integrated by "variables"_variable.html or used by other "output @@ -219,7 +219,7 @@ value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2. :l If {type} is set -to {lower} then each input value is correlated with every preceeding +to {lower} then each input value is correlated with every preceding value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2. :l If {type} is set to {auto/upper} then each input value is correlated diff -Naur lammps-21Feb17/doc/src/fix_ave_time.txt lammps-7Mar17/doc/src/fix_ave_time.txt --- lammps-21Feb17/doc/src/fix_ave_time.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_ave_time.txt 2017-03-07 09:48:20.062786000 -0700 @@ -33,7 +33,7 @@ vector = all input values are global vectors or global arrays {ave} args = {one} or {running} or {window M} one = output a new average value every Nfreq steps - running = output cummulative average of all previous Nfreq steps + running = output cumulative average of all previous Nfreq steps window M = output average of M most recent Nfreq steps {start} args = Nstart Nstart = start averaging on this timestep @@ -223,7 +223,7 @@ If the {ave} setting is {running}, then the values produced on timesteps that are multiples of {Nfreq} are summed and averaged in a -cummulative sense before being output. Each output value is thus the +cumulative sense before being output. Each output value is thus the average of the value produced on that timestep with all preceding values. This running average begins when the fix is defined; it can only be restarted by deleting the fix via the "unfix"_unfix.html @@ -320,7 +320,7 @@ of rows = length of the input vectors and # of columns = number of inputs. -If the fix prouduces a scalar or vector, then the scalar and each +If the fix produces a scalar or vector, then the scalar and each element of the vector can be either "intensive" or "extensive", depending on whether the values contributing to the scalar or vector element are "intensive" or "extensive". If the fix produces an array, diff -Naur lammps-21Feb17/doc/src/fix_balance.txt lammps-7Mar17/doc/src/fix_balance.txt --- lammps-21Feb17/doc/src/fix_balance.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_balance.txt 2017-03-07 09:48:20.062786000 -0700 @@ -15,12 +15,12 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l balance = style name of this fix command :l Nfreq = perform dynamic load balancing every this many steps :l -thresh = imbalance threshhold that must be exceeded to perform a re-balance :l +thresh = imbalance threshold that must be exceeded to perform a re-balance :l style = {shift} or {rcb} :l shift args = dimstr Niter stopthresh dimstr = sequence of letters containing "x" or "y" or "z", each not more than once Niter = # of times to iterate within each dimension of dimstr sequence - stopthresh = stop balancing when this imbalance threshhold is reached + stopthresh = stop balancing when this imbalance threshold is reached {rcb} args = none :pre zero or more keyword/arg pairs may be appended :l keyword = {weight} or {out} :l @@ -63,14 +63,14 @@ Load-balancing is typically most useful if the particles in the simulation box have a spatially-varying density distribution or -where the computational cost varies signficantly between different +where the computational cost varies significantly between different atoms. E.g. a model of a vapor/liquid interface, or a solid with an irregular-shaped geometry containing void regions, or "hybrid pair style simulations"_pair_hybrid.html which combine pair styles with different computational cost. In these cases, the LAMMPS default of dividing the simulation box volume into a regular-spaced grid of 3d bricks, with one equal-volume sub-domain -per procesor, may assign numbers of particles per processor in a +per processor, may assign numbers of particles per processor in a way that the computational effort varies significantly. This can lead to poor performance when the simulation is run in parallel. @@ -78,7 +78,7 @@ With no weighting, the balancing attempts to assign an equal number of particles to each processor. With weighting, the balancing attempts to assign an equal aggregate computational weight to each processor, -which typically inducces a diffrent number of atoms assigned to each +which typically induces a different number of atoms assigned to each processor. NOTE: The weighting options listed above are documented with the @@ -216,7 +216,7 @@ take advantage of information from neighboring cuts if possible, as well as counts of particles at the bounds on either side of each cuts, which themselves were cuts in previous iterations. The latter is used -to infer a density of pariticles near each of the current cuts. At +to infer a density of particles near each of the current cuts. At each iteration, the count of particles on either side of each plane is tallied. If the counts do not match the target value for the plane, the position of the cut is adjusted based on the local density. The @@ -239,7 +239,7 @@ the normal reneighboring procedure. NOTE: At each rebalance operation, the bisectioning for each cutting -plane (line in 2d) typcially starts with low and high bounds separated +plane (line in 2d) typically starts with low and high bounds separated by the extent of a processor's sub-domain in one dimension. The size of this bracketing region shrinks based on the local density, as described above, which should typically be 1/2 or more every @@ -249,7 +249,7 @@ be accurate to better than 1 part in a million. Thus there is no need to set {Niter} to a large value. This is especially true if you are rebalancing often enough that each time you expect only an incremental -adjustement in the cutting planes is necessary. LAMMPS will check if +adjustment in the cutting planes is necessary. LAMMPS will check if the threshold accuracy is reached (in a dimension) is less iterations than {Niter} and exit early. @@ -275,7 +275,7 @@ That is the procedure for the first cut. Subsequent cuts are made recursively, in exactly the same manner. The subset of processors assigned to each box make a new cut in the longest dimension of that -box, splitting the box, the subset of processsors, and the atoms in +box, splitting the box, the subset of processors, and the atoms in the box in two. The recursion continues until every processor is assigned a sub-box of the entire simulation domain, and owns the atoms in that sub-box. diff -Naur lammps-21Feb17/doc/src/fix_bond_break.txt lammps-7Mar17/doc/src/fix_bond_break.txt --- lammps-21Feb17/doc/src/fix_bond_break.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_bond_break.txt 2017-03-07 09:48:20.062786000 -0700 @@ -79,8 +79,8 @@ NOTE: One data structure that is not updated when a bond breaks are the molecule IDs stored by each atom. Even though one molecule -becomes two moleclues due to the broken bond, all atoms in both new -moleclues retain their original molecule IDs. +becomes two molecules due to the broken bond, all atoms in both new +molecules retain their original molecule IDs. Computationally, each timestep this fix operates, it loops over all the bonds in the system and computes distances between pairs of bonded @@ -122,7 +122,7 @@ These are the 2 quantities: (1) # of bonds broken on the most recent breakage timestep -(2) cummulative # of bonds broken :ul +(2) cumulative # of bonds broken :ul No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff -Naur lammps-21Feb17/doc/src/fix_bond_create.txt lammps-7Mar17/doc/src/fix_bond_create.txt --- lammps-21Feb17/doc/src/fix_bond_create.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_bond_create.txt 2017-03-07 09:48:20.062786000 -0700 @@ -118,8 +118,8 @@ NOTE: One data structure that is not updated when a bond breaks are the molecule IDs stored by each atom. Even though two molecules -become one moleclue due to the created bond, all atoms in the new -moleclue retain their original molecule IDs. +become one molecule due to the created bond, all atoms in the new +molecule retain their original molecule IDs. If the {atype} keyword is used and if an angle potential is defined via the "angle_style"_angle_style.html command, then any new 3-body @@ -218,7 +218,7 @@ These are the 2 quantities: (1) # of bonds created on the most recent creation timestep -(2) cummulative # of bonds created :ul +(2) cumulative # of bonds created :ul No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff -Naur lammps-21Feb17/doc/src/fix_bond_swap.txt lammps-7Mar17/doc/src/fix_bond_swap.txt --- lammps-21Feb17/doc/src/fix_bond_swap.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_bond_swap.txt 2017-03-07 09:48:20.062786000 -0700 @@ -81,7 +81,7 @@ The criterion for matching molecule IDs is how bond swaps performed by this fix conserve chain length. To use this features you must setup the molecule IDs for your polymer chains in a certain way, typically -in the data file, read by the "read_data"_read_data.html comand. +in the data file, read by the "read_data"_read_data.html command. Consider a system of 6-mer chains. You have 2 choices. If the molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then swaps will conserve chain length. For a particular momoner there will @@ -124,7 +124,7 @@ This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the "compute_modify"_compute_modify.html command or print this temperature -during thermodyanmic output via the "thermo_style +during thermodynamic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no effect on this fix. @@ -151,8 +151,8 @@ This fix computes two statistical quantities as a global 2-vector of output, which can be accessed by various "output commands"_Section_howto.html#howto_15. The first component of the -vector is the cummulative number of swaps performed by all processors. -The second component of the vector is the cummulative number of swaps +vector is the cumulative number of swaps performed by all processors. +The second component of the vector is the cumulative number of swaps attempted (whether accepted or rejected). Note that a swap "attempt" only occurs when swap partners meeting the criteria described above are found on a particular timestep. The vector values calculated by @@ -168,7 +168,7 @@ built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -The setings of the "special_bond" command must be 0,1,1 in order to +The settings of the "special_bond" command must be 0,1,1 in order to use this fix, which is typical of bead-spring chains with FENE or harmonic bonds. This means that pairwise interactions between bonded atoms are turned off, but are turned on between atoms two or three diff -Naur lammps-21Feb17/doc/src/fix_box_relax.txt lammps-7Mar17/doc/src/fix_box_relax.txt --- lammps-21Feb17/doc/src/fix_box_relax.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_box_relax.txt 2017-03-07 09:48:20.062786000 -0700 @@ -54,7 +54,7 @@ keywords. These keywords give you the ability to specify all 6 components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are -varied together during the mimimization. +varied together during the minimization. Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable @@ -103,7 +103,7 @@ unaffected by the chosen value, except that all particles are displaced by the same amount, different on each iteration. -NOTE: Appling an external pressure to tilt dimensions {xy}, {xz}, {yz} +NOTE: Applying an external pressure to tilt dimensions {xy}, {xz}, {yz} can sometimes result in arbitrarily large values of the tilt factors, i.e. a dramatically deformed simulation box. This typically indicates that there is something badly wrong with how the simulation was @@ -122,7 +122,7 @@ function being minimized changes if the box size/shape changes. In practice this means the minimizer can get "stuck" before you have reached the desired tolerance. The solution to this is to restart the -minmizer from the new adjusted box size/shape, since that creates a +minimizer from the new adjusted box size/shape, since that creates a new objective function valid for the new box size/shape. Repeat as necessary until the box size/shape has reached its new equilibrium. diff -Naur lammps-21Feb17/doc/src/fix_cmap.txt lammps-7Mar17/doc/src/fix_cmap.txt --- lammps-21Feb17/doc/src/fix_cmap.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_cmap.txt 2017-03-07 09:48:20.062786000 -0700 @@ -44,7 +44,7 @@ The data file read by the "read_data" must contain the topology of all the CMAP interactions, similar to the topology data for bonds, angles, -dihedrals, etc. Specically it should have a line like this +dihedrals, etc. Specially it should have a line like this in its header section: N crossterms :pre diff -Naur lammps-21Feb17/doc/src/fix_colvars.txt lammps-7Mar17/doc/src/fix_colvars.txt --- lammps-21Feb17/doc/src/fix_colvars.txt 2017-01-06 10:16:03.000000000 -0700 +++ lammps-7Mar17/doc/src/fix_colvars.txt 2017-03-07 09:48:20.062786000 -0700 @@ -59,7 +59,7 @@ of the colvars fix at a time. The colvars fix will only communicate the minimum information necessary and the colvars library supports multiple, completely independent collective variables, so there is -no restriction to functionaliry by limiting the number of colvars fixes. +no restriction to functionality by limiting the number of colvars fixes. The {input} keyword allows to specify a state file that would contain the restart information required in order to continue a calculation from @@ -100,7 +100,7 @@ This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". [Restrictions:] diff -Naur lammps-21Feb17/doc/src/fix_controller.txt lammps-7Mar17/doc/src/fix_controller.txt --- lammps-21Feb17/doc/src/fix_controller.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_controller.txt 2017-03-07 09:48:20.062786000 -0700 @@ -107,7 +107,7 @@ pick a value and sign for {alpha} that is consistent with the magnitudes and signs of {pvar} and {cvar}. The magnitude of {Kp} should then be tested over a large positive range keeping {Ki}={Kd}=0. -A good value for {Kp} will produce a fast reponse in {pvar}, without +A good value for {Kp} will produce a fast response in {pvar}, without overshooting the {setpoint}. For many applications, proportional feedback is sufficient, and so {Ki}={Kd}=0 can be used. In cases where there is a substantial lag time in the response of {pvar} to a change @@ -175,7 +175,7 @@ [Restart, fix_modify, output, run start/stop, minimize info:] -Currenlty, no information about this fix is written to "binary restart +Currently, no information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. diff -Naur lammps-21Feb17/doc/src/fix_deform.txt lammps-7Mar17/doc/src/fix_deform.txt --- lammps-21Feb17/doc/src/fix_deform.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_deform.txt 2017-03-07 09:48:20.062786000 -0700 @@ -580,10 +580,10 @@ [Restrictions:] You cannot apply x, y, or z deformations to a dimension that is -shrink-wrapped via the "boundary"_boundary.html comamnd. +shrink-wrapped via the "boundary"_boundary.html command. You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in -xy) that is shrink-wrapped via the "boundary"_boundary.html comamnd. +xy) that is shrink-wrapped via the "boundary"_boundary.html command. [Related commands:] diff -Naur lammps-21Feb17/doc/src/fix_deposit.txt lammps-7Mar17/doc/src/fix_deposit.txt --- lammps-21Feb17/doc/src/fix_deposit.txt 2016-09-06 16:56:36.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_deposit.txt 2017-03-07 09:48:20.062786000 -0700 @@ -15,7 +15,7 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l deposit = style name of this fix command :l N = # of atoms or molecules to insert :l -type = atom type to assign to inserted atoms (offset for moleclue insertion) :l +type = atom type to assign to inserted atoms (offset for molecule insertion) :l M = insert a single atom or molecule every M steps :l seed = random # seed (positive integer) :l one or more keyword/value pairs may be appended to args :l @@ -140,7 +140,7 @@ If the molecule template contains more than one molecule, the relative probability of depositing each molecule can be specified by the -{molfrac} keyword. N relative probablities, each from 0.0 to 1.0, are +{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are specified, where N is the number of molecules in the template. Each time a molecule is deposited, a random number is used to sample from the list of relative probabilities. The N values must sum to 1.0. @@ -192,7 +192,7 @@ NOTE: If you are inserting finite size particles or a molecule or rigid body consisting of finite-size particles, then you should typically set R larger than the distance at which any inserted -particle may overlap with either a previouly inserted particle or an +particle may overlap with either a previously inserted particle or an existing particle. LAMMPS will issue a warning if R is smaller than this value, based on the radii of existing and inserted particles. diff -Naur lammps-21Feb17/doc/src/fix_eos_table.txt lammps-7Mar17/doc/src/fix_eos_table.txt --- lammps-21Feb17/doc/src/fix_eos_table.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_eos_table.txt 2017-03-07 09:48:20.062786000 -0700 @@ -17,7 +17,7 @@ style = {linear} = method of interpolation file = filename containing the tabulated equation of state N = use N values in {linear} tables -keyword = name of table keyword correponding to table file :ul +keyword = name of table keyword corresponding to table file :ul [Examples:] diff -Naur lammps-21Feb17/doc/src/fix_eos_table_rx.txt lammps-7Mar17/doc/src/fix_eos_table_rx.txt --- lammps-21Feb17/doc/src/fix_eos_table_rx.txt 2017-01-06 10:16:03.000000000 -0700 +++ lammps-7Mar17/doc/src/fix_eos_table_rx.txt 2017-03-07 09:48:20.062786000 -0700 @@ -17,7 +17,7 @@ style = {linear} = method of interpolation file1 = filename containing the tabulated equation of state N = use N values in {linear} tables -keyword = name of table keyword correponding to table file +keyword = name of table keyword corresponding to table file file2 = filename containing the heats of formation of each species (optional) deltaHf = heat of formation for a single species in energy units (optional) energyCorr = energy correction in energy units (optional) diff -Naur lammps-21Feb17/doc/src/fix_evaporate.txt lammps-7Mar17/doc/src/fix_evaporate.txt --- lammps-21Feb17/doc/src/fix_evaporate.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_evaporate.txt 2017-03-07 09:48:20.062786000 -0700 @@ -31,9 +31,9 @@ [Description:] Remove M atoms from the simulation every N steps. This can be used, -for example, to model evaporation of solvent particles or moleclues +for example, to model evaporation of solvent particles or molecules (i.e. drying) of a system. Every N steps, the number of atoms in the -fix group and within the specifed region are counted. M of these are +fix group and within the specified region are counted. M of these are chosen at random and deleted. If there are less than M eligible particles, then all of them are deleted. @@ -74,7 +74,7 @@ This fix computes a global scalar, which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative number of deleted atoms. The scalar value calculated by +cumulative number of deleted atoms. The scalar value calculated by this fix is "intensive". No parameter of this fix can be used with the {start/stop} keywords of diff -Naur lammps-21Feb17/doc/src/fix_gle.txt lammps-7Mar17/doc/src/fix_gle.txt --- lammps-21Feb17/doc/src/fix_gle.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_gle.txt 2017-03-07 09:48:20.062786000 -0700 @@ -62,7 +62,7 @@ optimal for a given application and the system of choice can be obtained from "(GLE4MD)"_#GLE4MD. -Equilibrium sampling a temperature T is obtained by specifiying the +Equilibrium sampling a temperature T is obtained by specifying the target value as the {Tstart} and {Tstop} arguments, so that the diffusion matrix that gives canonical sampling for a given A is computed automatically. However, the GLE framework also allow for non-equilibrium sampling, that @@ -116,7 +116,7 @@ This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". [Restrictions:] diff -Naur lammps-21Feb17/doc/src/fix_gravity.txt lammps-7Mar17/doc/src/fix_gravity.txt --- lammps-21Feb17/doc/src/fix_gravity.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_gravity.txt 2017-03-07 09:48:20.062786000 -0700 @@ -76,7 +76,7 @@ a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and its value used to determine the quantity. You should -insure that the variable calculates a result in the approriate units, +insure that the variable calculates a result in the appropriate units, e.g. force/mass or degrees. Equal-style variables can specify formulas with various mathematical diff -Naur lammps-21Feb17/doc/src/fix_indent.txt lammps-7Mar17/doc/src/fix_indent.txt --- lammps-21Feb17/doc/src/fix_indent.txt 2016-06-17 17:13:02.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_indent.txt 2017-03-07 09:48:20.062786000 -0700 @@ -107,7 +107,7 @@ "run"_run.html command and the {elaplong} keyword of "thermo_style custom"_thermo_style.html for details. -For example, if a spherical indenter's x-position is specfied as v_x, +For example, if a spherical indenter's x-position is specified as v_x, then this variable definition will keep it's center at a relative position in the simulation box, 1/4 of the way from the left edge to the right edge, even if the box size changes: @@ -121,7 +121,7 @@ variable x equal vdisplace(2.5,5) :pre If a spherical indenter's radius is specified as v_r, then these -variable definitions will grow the size of the indenter at a specfied +variable definitions will grow the size of the indenter at a specified rate. variable r0 equal 0.0 diff -Naur lammps-21Feb17/doc/src/fix_langevin.txt lammps-7Mar17/doc/src/fix_langevin.txt --- lammps-21Feb17/doc/src/fix_langevin.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_langevin.txt 2017-03-07 09:48:20.062786000 -0700 @@ -307,7 +307,7 @@ This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". Note that calculation of this quantity requires setting the {tally} keyword to {yes}. diff -Naur lammps-21Feb17/doc/src/fix_langevin_eff.txt lammps-7Mar17/doc/src/fix_langevin_eff.txt --- lammps-21Feb17/doc/src/fix_langevin_eff.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_langevin_eff.txt 2017-03-07 09:48:20.062786000 -0700 @@ -80,7 +80,7 @@ This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". Note that calculation of this quantity requires setting the {tally} keyword to {yes}. diff -Naur lammps-21Feb17/doc/src/fix_lb_fluid.txt lammps-7Mar17/doc/src/fix_lb_fluid.txt --- lammps-21Feb17/doc/src/fix_lb_fluid.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_lb_fluid.txt 2017-03-07 09:48:20.062786000 -0700 @@ -328,7 +328,7 @@ "lb/viscous"_fix_lb_viscous.html fix if the force coupling constant is set by default, or either the "lb/viscous"_fix_lb_viscous.html fix or one of the "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html or -"lb/pc"_fix_lb_pc.html integrators, if the user chooses to specifiy +"lb/pc"_fix_lb_pc.html integrators, if the user chooses to specify their own value for the force coupling constant. [Related commands:] diff -Naur lammps-21Feb17/doc/src/fix_modify.txt lammps-7Mar17/doc/src/fix_modify.txt --- lammps-21Feb17/doc/src/fix_modify.txt 2016-07-12 17:16:13.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_modify.txt 2017-03-07 09:48:20.062786000 -0700 @@ -53,7 +53,7 @@ For fixes that calculate a contribution to the potential energy of the system, the {energy} keyword will include that contribution in thermodynamic output of potential energy. This is because the {energy -yes} setting must be specfied to include the fix's global or per-atom +yes} setting must be specified to include the fix's global or per-atom energy in the calculation performed by the "compute pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html commands. See the "thermo_style"_thermo_style.html command for info diff -Naur lammps-21Feb17/doc/src/fix_move.txt lammps-7Mar17/doc/src/fix_move.txt --- lammps-21Feb17/doc/src/fix_move.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_move.txt 2017-03-07 09:48:20.062786000 -0700 @@ -58,7 +58,7 @@ periodic boundaries are appropriate with the kind of atom motion you are prescribing with this fix. -NOTE: As dicsussed below, atoms are moved relative to their initial +NOTE: As discussed below, atoms are moved relative to their initial position at the time the fix is specified. These initial coordinates are stored by the fix in "unwrapped" form, by using the image flags associated with each atom. See the "dump custom"_dump.html command @@ -131,7 +131,7 @@ where omega is its angular velocity around the rotation axis and Rperp is a perpendicular vector from the rotation axis to the atom. If the defined "atom_style"_atom_style.html assigns an angular velocity or -angular moementum or orientation to each atom ("atom +angular momentum or orientation to each atom ("atom styles"_atom_style.html sphere, ellipsoid, line, tri, body), then those properties are also updated appropriately to correspond to the atom's motion and rotation over time. diff -Naur lammps-21Feb17/doc/src/fix_mscg.txt lammps-7Mar17/doc/src/fix_mscg.txt --- lammps-21Feb17/doc/src/fix_mscg.txt 2017-01-09 11:26:52.000000000 -0700 +++ lammps-7Mar17/doc/src/fix_mscg.txt 2017-03-07 09:48:20.062786000 -0700 @@ -83,7 +83,7 @@ (step 4) outputs files defining pair and bonded interaction ranges. The force matching functionality (step 5) outputs tabulated force files for every interaction in the system. Other diagnostic files can -also be output depending on the paramters in the MS-CG library input +also be output depending on the parameters in the MS-CG library input script. Again, see the documentation provided with the MS-CG library for more info. @@ -108,7 +108,7 @@ The MS-CG library uses C++11, which may not be supported by older compilers. The MS-CG library also has some additional numeric library -dependencies, which are describd in its documentation. +dependencies, which are described in its documentation. Currently, the MS-CG library is not setup to run in parallel with MPI, so this fix can only be used in a serial LAMMPS build and run diff -Naur lammps-21Feb17/doc/src/fix_nph_asphere.txt lammps-7Mar17/doc/src/fix_nph_asphere.txt --- lammps-21Feb17/doc/src/fix_nph_asphere.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_nph_asphere.txt 2017-03-07 09:48:20.062786000 -0700 @@ -136,7 +136,7 @@ was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -This fix requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff -Naur lammps-21Feb17/doc/src/fix_nph_body.txt lammps-7Mar17/doc/src/fix_nph_body.txt --- lammps-21Feb17/doc/src/fix_nph_body.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_nph_body.txt 2017-03-07 09:48:20.062786000 -0700 @@ -135,7 +135,7 @@ was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -This fix requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html command. diff -Naur lammps-21Feb17/doc/src/fix_npt_asphere.txt lammps-7Mar17/doc/src/fix_npt_asphere.txt --- lammps-21Feb17/doc/src/fix_npt_asphere.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_npt_asphere.txt 2017-03-07 09:48:20.062786000 -0700 @@ -161,7 +161,7 @@ was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -This fix requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff -Naur lammps-21Feb17/doc/src/fix_npt_body.txt lammps-7Mar17/doc/src/fix_npt_body.txt --- lammps-21Feb17/doc/src/fix_npt_body.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_npt_body.txt 2017-03-07 09:48:20.062786000 -0700 @@ -160,7 +160,7 @@ was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -This fix requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html command. diff -Naur lammps-21Feb17/doc/src/fix_nve_asphere.txt lammps-7Mar17/doc/src/fix_nve_asphere.txt --- lammps-21Feb17/doc/src/fix_nve_asphere.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_nve_asphere.txt 2017-03-07 09:48:20.062786000 -0700 @@ -71,7 +71,7 @@ was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -This fix requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff -Naur lammps-21Feb17/doc/src/fix_nve_asphere_noforce.txt lammps-7Mar17/doc/src/fix_nve_asphere_noforce.txt --- lammps-21Feb17/doc/src/fix_nve_asphere_noforce.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_nve_asphere_noforce.txt 2017-03-07 09:48:20.062786000 -0700 @@ -25,7 +25,7 @@ angular momentum for atoms in the group each timestep. In other words, the force and torque on the atoms is ignored and their velocity and angular momentum are not updated. The atom velocities and -angularm momenta are used to update their positions and orientation. +angular momenta are used to update their positions and orientation. This is useful as an implicit time integrator for Fast Lubrication Dynamics, since the velocity and angular momentum are updated by the @@ -49,7 +49,7 @@ was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -This fix requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff -Naur lammps-21Feb17/doc/src/fix_nve_body.txt lammps-7Mar17/doc/src/fix_nve_body.txt --- lammps-21Feb17/doc/src/fix_nve_body.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_nve_body.txt 2017-03-07 09:48:20.062786000 -0700 @@ -47,7 +47,7 @@ was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -This fix requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html command. diff -Naur lammps-21Feb17/doc/src/fix_nve_limit.txt lammps-7Mar17/doc/src/fix_nve_limit.txt --- lammps-21Feb17/doc/src/fix_nve_limit.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_nve_limit.txt 2017-03-07 09:48:20.062786000 -0700 @@ -48,8 +48,8 @@ very large for overlapped configurations. NOTE: You should not use "fix shake"_fix_shake.html in conjunction -with this fix. That is because fix shake applies contraint forces -based on the predicted postitions of atoms after the next timestep. +with this fix. That is because fix shake applies constraint forces +based on the predicted positions of atoms after the next timestep. It has no way of knowing the timestep may change due to this fix, which will cause the constraint forces to be invalid. A better strategy is to turn off fix shake when performing initial dynamics diff -Naur lammps-21Feb17/doc/src/fix_nvt_asphere.txt lammps-7Mar17/doc/src/fix_nvt_asphere.txt --- lammps-21Feb17/doc/src/fix_nvt_asphere.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_nvt_asphere.txt 2017-03-07 09:48:20.062786000 -0700 @@ -137,7 +137,7 @@ was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -This fix requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html command. diff -Naur lammps-21Feb17/doc/src/fix_nvt_body.txt lammps-7Mar17/doc/src/fix_nvt_body.txt --- lammps-21Feb17/doc/src/fix_nvt_body.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_nvt_body.txt 2017-03-07 09:48:20.062786000 -0700 @@ -136,7 +136,7 @@ was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -This fix requires that atoms store torque and angular momementum and a +This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html command. diff -Naur lammps-21Feb17/doc/src/fix_nvt_sllod_eff.txt lammps-7Mar17/doc/src/fix_nvt_sllod_eff.txt --- lammps-21Feb17/doc/src/fix_nvt_sllod_eff.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_nvt_sllod_eff.txt 2017-03-07 09:48:20.062786000 -0700 @@ -35,7 +35,7 @@ Likewise the temperature calculated by the fix, using the compute it creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html doc page), is performed with a "compute -temp/deform/eff"_compute_temp_deform_eff.html commmand that includes +temp/deform/eff"_compute_temp_deform_eff.html command that includes the eFF contribution to the temperature from the electron radial velocity. diff -Naur lammps-21Feb17/doc/src/fix_orient.txt lammps-7Mar17/doc/src/fix_orient.txt --- lammps-21Feb17/doc/src/fix_orient.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_orient.txt 2017-03-07 09:48:20.062786000 -0700 @@ -31,7 +31,7 @@ grain boundary which can be used to induce grain boundary migration (in the direction perpendicular to the grain boundary plane). The motivation and explanation of this force and its application are -described in "(Janssens)"_#Janssens. The adaptiation to bcc crystals +described in "(Janssens)"_#Janssens. The adaptation to bcc crystals is described in "(Wicaksono1)"_#Wicaksono1. The computed force is only applied to atoms in the fix group. diff -Naur lammps-21Feb17/doc/src/fix_phonon.txt lammps-7Mar17/doc/src/fix_phonon.txt --- lammps-21Feb17/doc/src/fix_phonon.txt 2016-10-24 08:19:10.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_phonon.txt 2017-03-07 09:48:20.062786000 -0700 @@ -43,7 +43,7 @@ Calculate the dynamical matrix from molecular dynamics simulations based on fluctuation-dissipation theory for a group of atoms. -Consider a crystal with \(N\) unit cells in three dimensions labelled +Consider a crystal with \(N\) unit cells in three dimensions labeled \(l = (l_1, l_2, l_3)\) where \(l_i\) are integers. Each unit cell is defined by three linearly independent vectors \(\mathbf\{a\}_1\), \(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a parallelipiped, @@ -183,7 +183,7 @@ [Default:] -The option defaults are sysdim = the same dimemsion as specified by +The option defaults are sysdim = the same dimension as specified by the "dimension"_dimension.html command, and nasr = 20. :line diff -Naur lammps-21Feb17/doc/src/fix_pour.txt lammps-7Mar17/doc/src/fix_pour.txt --- lammps-21Feb17/doc/src/fix_pour.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_pour.txt 2017-03-07 09:48:20.062786000 -0700 @@ -107,7 +107,7 @@ If the molecule template contains more than one molecule, the relative probability of depositing each molecule can be specified by the -{molfrac} keyword. N relative probablities, each from 0.0 to 1.0, are +{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are specified, where N is the number of molecules in the template. Each time a molecule is inserted, a random number is used to sample from the list of relative probabilities. The N values must sum to 1.0. @@ -144,7 +144,7 @@ All other keywords are optional with defaults as shown below. -The {diam} option is only used when inserting atoms and specifes the +The {diam} option is only used when inserting atoms and specifies the diameters of inserted particles. There are 3 styles: {one}, {range}, or {poly}. For {one}, all particles will have diameter {D}. For {range}, the diameter of each particle will be chosen randomly and @@ -175,7 +175,7 @@ The {vol} option specifies what volume fraction of the insertion volume will be filled with particles. For particles with a size specified by the {diam range} keyword, they are assumed to all be of -maximum diamter {Dhi} for purposes of computing their contribution to +maximum diameter {Dhi} for purposes of computing their contribution to the volume fraction. The higher the volume fraction value, the more particles are inserted diff -Naur lammps-21Feb17/doc/src/fix_property_atom.txt lammps-7Mar17/doc/src/fix_property_atom.txt --- lammps-21Feb17/doc/src/fix_property_atom.txt 2016-10-24 08:19:10.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_property_atom.txt 2017-03-07 09:48:20.062786000 -0700 @@ -121,7 +121,7 @@ Per-atom properties that are defined by the "atom style"_atom_style.html are initialized when atoms are created, e.g. by the "read_data"_read_data.html or "create_atoms"_create_atoms.html -commands. The per-atom properaties defined by this fix are not. So +commands. The per-atom properties defined by this fix are not. So you need to initialize them explicitly. This can be done by the "read_data"_read_data.html command, using its {fix} keyword and passing it the fix-ID of this fix. diff -Naur lammps-21Feb17/doc/src/fix_qeq.txt lammps-7Mar17/doc/src/fix_qeq.txt --- lammps-21Feb17/doc/src/fix_qeq.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_qeq.txt 2017-03-07 09:48:20.062786000 -0700 @@ -71,7 +71,7 @@ produces a different model than the published versions. NOTE: The "fix qeq/comb"_fix_qeq_comb.html command must still be used -to perform charge equliibration with the "COMB +to perform charge equilibration with the "COMB potential"_pair_comb.html. The "fix qeq/reax"_fix_qeq_reax.html command can be used to perform charge equilibration with the "ReaxFF force field"_pair_reax_c.html, although fix qeq/shielded yields the @@ -81,7 +81,7 @@ The QEq method minimizes the electrostatic energy of the system (or equalizes the derivative of energy with respect to charge of all the atoms) by adjusting the partial charge on individual atoms based on -interactions with their neighbors within {cutoff}. It reqires a few +interactions with their neighbors within {cutoff}. It requires a few parameters, in {metal} units, for each atom type which provided in a file specified by {qfile}. The file has the following format @@ -91,7 +91,7 @@ Ntype chi eta gamma zeta qcore :pre There is one line per atom type with the following parameters. -Only a subset of the parameters is used by each QEq style as descibed +Only a subset of the parameters is used by each QEq style as described below, thus the others can be set to 0.0 if desired. {chi} = electronegativity in energy units @@ -167,7 +167,7 @@ NOTE: Developing QEq parameters (chi, eta, gamma, zeta, and qcore) is non-trivial. Charges on atoms are not guaranteed to equilibrate with arbitrary choices of these parameters. We do not develop these QEq -paramters. See the examples/qeq directory for some examples. +parameters. See the examples/qeq directory for some examples. [Restart, fix_modify, output, run start/stop, minimize info:] diff -Naur lammps-21Feb17/doc/src/fix_qeq_comb.txt lammps-7Mar17/doc/src/fix_qeq_comb.txt --- lammps-21Feb17/doc/src/fix_qeq_comb.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_qeq_comb.txt 2017-03-07 09:48:20.062786000 -0700 @@ -42,12 +42,12 @@ The fix relies on the pair style (COMB in this case) to calculate the per-atom electronegativity (effective force on the charges). An electronegativity equalization calculation (or QEq) is performed in an -interative fashion, which in parallel requires communication at each +iterative fashion, which in parallel requires communication at each iteration for processors to exchange charge information about nearby atoms with each other. See "Rappe_and_Goddard"_#Rappe_and_Goddard and "Rick_and_Stuart"_#Rick_and_Stuart for details. -During a run, charge equilibration is peformed every {Nevery} time +During a run, charge equilibration is performed every {Nevery} time steps. Charge equilibration is also always enforced on the first step of each run. The {precision} argument controls the tolerance for the difference in electronegativity for all atoms during charge @@ -55,7 +55,7 @@ performing charge equilibration (more iterations) and accuracy. If the {file} keyword is used, then information about each -equilibration calculation is written to the specifed file. +equilibration calculation is written to the specified file. :line diff -Naur lammps-21Feb17/doc/src/fix_qeq_reax.txt lammps-7Mar17/doc/src/fix_qeq_reax.txt --- lammps-21Feb17/doc/src/fix_qeq_reax.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_qeq_reax.txt 2017-03-07 09:48:20.062786000 -0700 @@ -33,14 +33,14 @@ implemented in the "pair_style reax/c"_pair_reax_c.html command, but it can be used with any potential in LAMMPS, so long as it defines and uses charges on each atom. The "fix qeq/comb"_fix_qeq_comb.html -command should be used to perform charge equliibration with the "COMB +command should be used to perform charge equilibration with the "COMB potential"_pair_comb.html. For more technical details about the charge equilibration performed by fix qeq/reax, see the "(Aktulga)"_#Aktulga paper. The QEq method minimizes the electrostatic energy of the system by adjusting the partial charge on individual atoms based on interactions -with their neighbors. It reqires some parameters for each atom type. +with their neighbors. It requires some parameters for each atom type. If the {params} setting above is the word "reax/c", then these are extracted from the "pair_style reax/c"_pair_reax_c.html command and the ReaxFF force field file it reads in. If a file name is specified diff -Naur lammps-21Feb17/doc/src/fix_reax_bonds.txt lammps-7Mar17/doc/src/fix_reax_bonds.txt --- lammps-21Feb17/doc/src/fix_reax_bonds.txt 2016-11-01 09:22:44.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_reax_bonds.txt 2017-03-07 09:48:20.062786000 -0700 @@ -34,7 +34,7 @@ including timestep 0. For time-averaged chemical species analysis, please see the "fix reaxc/c/species"_fix_reaxc_species.html command. -The format of the output file should be self-explantory. +The format of the output file should be self-explanatory. :line diff -Naur lammps-21Feb17/doc/src/fix_restrain.txt lammps-7Mar17/doc/src/fix_restrain.txt --- lammps-21Feb17/doc/src/fix_restrain.txt 2016-09-10 13:48:18.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_restrain.txt 2017-03-07 09:48:20.062786000 -0700 @@ -88,7 +88,7 @@ works best for a given application. For the case of finding a minimum energy structure for a single -molecule with particular restratins (e.g. for fitting forcefield +molecule with particular restraints (e.g. for fitting forcefield parameters or constructing a potential energy surface), commands such as the following may be useful: diff -Naur lammps-21Feb17/doc/src/fix_rigid.txt lammps-7Mar17/doc/src/fix_rigid.txt --- lammps-21Feb17/doc/src/fix_rigid.txt 2016-10-24 08:19:10.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_rigid.txt 2017-03-07 09:48:20.062786000 -0700 @@ -129,7 +129,7 @@ closest to the geometrical center of the body. The fix operates using local lists of rigid bodies owned by each processor and information is exchanged and summed via local communication between neighboring -processors when ghost atom info is accumlated. +processors when ghost atom info is accumulated. NOTE: To use the {rigid/small} styles the ghost atom cutoff must be large enough to span the distance between the atom that owns the body @@ -262,7 +262,7 @@ contribute to the motion. The "neigh_modify exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html commands are used to do this. If the rigid bodies have strongly -overalapping atoms, you may need to turn off these interactions to +overlapping atoms, you may need to turn off these interactions to avoid numerical problems due to large equal/opposite intra-body forces swamping the contribution of small inter-body forces. @@ -325,7 +325,7 @@ defined in "fix npt/nph"_fix_nh.html NOTE: Currently the {rigid/npt}, {rigid/nph}, {rigid/npt/small}, and -{rigid/nph/small} styles do not support triclinic (non-orthongonal) +{rigid/nph/small} styles do not support triclinic (non-orthogonal) boxes. The target pressures for each of the 6 components of the stress tensor @@ -530,7 +530,7 @@ The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the prinicpal axes of the +simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. The (vxcm,vycm,vzcm) values are the velocity of the center of mass. @@ -580,7 +580,7 @@ :line -If your simlulation is a hybrid model with a mixture of rigid bodies +If your simulation is a hybrid model with a mixture of rigid bodies and non-rigid particles (e.g. solvent) there are several ways these rigid fixes can be used in tandem with "fix nve"_fix_nve.html, "fix nvt"_fix_nh.html, "fix npt"_fix_nh.html, and "fix nph"_fix_nh.html. diff -Naur lammps-21Feb17/doc/src/fix_rx.txt lammps-7Mar17/doc/src/fix_rx.txt --- lammps-21Feb17/doc/src/fix_rx.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_rx.txt 2017-03-07 09:48:20.062786000 -0700 @@ -21,7 +21,7 @@ minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45) maxSteps = maximum number of steps for the rkf45 solver (rkf45 only) relTol = relative tolerance for the rkf45 solver (rkf45 only) -absTol = absolute tolernace for the rkf45 solver (rkf45 only) +absTol = absolute tolerance for the rkf45 solver (rkf45 only) diag = Diagnostics frequency for the rkf45 solver (optional, rkf45 only) :ul [Examples:] @@ -63,7 +63,7 @@ The rkf45 method adjusts the step-size so that the local truncation error is held within the specified absolute and relative tolerances. The initial step-size {h0} -can be specified by the user or estimated internally. It is recommeded that the user +can be specified by the user or estimated internally. It is recommended that the user specify {h0} since this will generally reduced the number of ODE integration steps required. {h0} is defined as {dt / min_steps} if min_steps >= 1. If min_steps == 0, {h0} is estimated such that an explicit Euler method would likely produce diff -Naur lammps-21Feb17/doc/src/fix_saed_vtk.txt lammps-7Mar17/doc/src/fix_saed_vtk.txt --- lammps-21Feb17/doc/src/fix_saed_vtk.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_saed_vtk.txt 2017-03-07 09:48:20.062786000 -0700 @@ -52,7 +52,7 @@ To produce output in the image data vtk format ghost data is added outside the {Kmax} range assigned in the compute saed. The ghost data is assigned a value of -1 and can be removed setting a minimum isovolume -of 0 within the vizualiziton software. SAED images can be created by +of 0 within the visualization software. SAED images can be created by visualizing a spherical slice of the data that is centered at R_Ewald*\[h k l\]/norm(\[h k l\]), where R_Ewald=1/lambda. @@ -88,7 +88,7 @@ :line -The output for fix ave/time/saed is a file writen with the 3rd generation +The output for fix ave/time/saed is a file written with the 3rd generation vtk image data formatting. The filename assigned by the {file} keyword is appended with _N.vtk where N is an index (0,1,2...) to account for multiple diffraction intensity outputs. diff -Naur lammps-21Feb17/doc/src/fix_shake.txt lammps-7Mar17/doc/src/fix_shake.txt --- lammps-21Feb17/doc/src/fix_shake.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_shake.txt 2017-03-07 09:48:20.062786000 -0700 @@ -47,7 +47,7 @@ [SHAKE vs RATTLE:] The SHAKE algorithm was invented for schemes such as standard Verlet -timesteppnig, where only the coordinates are integrated and the +timestepping, where only the coordinates are integrated and the velocities are approximated as finite differences to the trajectories ("Ryckaert et al. (1977)"_#Ryckaert). If the velocities are integrated explicitly, as with velocity Verlet which is what LAMMPS @@ -119,7 +119,7 @@ for. NOTE: This command works by using the current forces on atoms to -caculate an additional constraint force which when added will leave +calculate an additional constraint force which when added will leave the atoms in positions that satisfy the SHAKE constraints (e.g. bond length) after the next time integration step. If you define fixes (e.g. "fix efield"_fix_efield.html) that add additional force to the @@ -133,7 +133,7 @@ The {mol} keyword should be used when other commands, such as "fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html, add molecules -on-the-fly during a simulation, and you wish to contrain the new +on-the-fly during a simulation, and you wish to constrain the new molecules via SHAKE. You specify a {template-ID} previously defined using the "molecule"_molecule.html command, which reads a file that defines the molecule. You must use the same {template-ID} that the @@ -210,7 +210,7 @@ your system by running a constant NVE simulation with a particular set of SHAKE parameters and monitoring the energy versus time. -SHAKE or RATTLE should not be used to contrain an angle at 180 degrees +SHAKE or RATTLE should not be used to constrain an angle at 180 degrees (e.g. linear CO2 molecule). This causes numeric difficulties. [Related commands:] none diff -Naur lammps-21Feb17/doc/src/fix_smd_wall_surface.txt lammps-7Mar17/doc/src/fix_smd_wall_surface.txt --- lammps-21Feb17/doc/src/fix_smd_wall_surface.txt 2016-11-30 14:03:35.000000000 -0700 +++ lammps-7Mar17/doc/src/fix_smd_wall_surface.txt 2017-03-07 09:48:20.062786000 -0700 @@ -27,7 +27,7 @@ [Description:] -This fix creates reads a traingulated surface from a file in .STL format. +This fix creates reads a triangulated surface from a file in .STL format. For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions. The radius of the new particle is that of the minimum circle which encompasses the triangle vertices. diff -Naur lammps-21Feb17/doc/src/fix_spring_self.txt lammps-7Mar17/doc/src/fix_spring_self.txt --- lammps-21Feb17/doc/src/fix_spring_self.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_spring_self.txt 2017-03-07 09:48:20.062786000 -0700 @@ -30,7 +30,7 @@ the magnitude of the force on each atom is -Kr, where r is the displacement of the atom from its current position to its initial position. The distance r correctly takes into account any crossings -of periodic boundary by the atom since it was in its intitial +of periodic boundary by the atom since it was in its initial position. With the (optional) dir flag, one can select in which direction the diff -Naur lammps-21Feb17/doc/src/fix_srd.txt lammps-7Mar17/doc/src/fix_srd.txt --- lammps-21Feb17/doc/src/fix_srd.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_srd.txt 2017-03-07 09:48:20.062786000 -0700 @@ -54,18 +54,18 @@ [Description:] -Treat a group of partilces as stochastic rotation dynamics (SRD) +Treat a group of particles as stochastic rotation dynamics (SRD) particles that serve as a background solvent when interacting with big (colloidal) particles in groupbig-ID. The SRD formalism is described in "(Hecht)"_#Hecht. The key idea behind using SRD particles as a cheap coarse-grained solvent is that SRD particles do not interact with each other, but only with the solute particles, which in LAMMPS can be spheroids, ellipsoids, or line segments, or triangles, or rigid -bodies containing multiple spherioids or ellipsoids or line segments +bodies containing multiple spheriods or ellipsoids or line segments or triangles. The collision and rotation properties of the model imbue the SRD particles with fluid-like properties, including an effective viscosity. Thus simulations with large solute particles can -be run more quickly, to measure solute propoerties like diffusivity +be run more quickly, to measure solute properties like diffusivity and viscosity in a background fluid. The usual LAMMPS fixes for such simulations, such as "fix deform"_fix_deform.html, "fix viscosity"_fix_viscosity.html, and "fix nvt/sllod"_fix_nvt_sllod.html, @@ -182,7 +182,7 @@ amount {rfactor}, so that SRD particle will only collide with one big particle at a time. For example, in a Lennard-Jones system at a temperature of 1.0 (in reduced LJ units), the minimum separation -bewteen two big particles is as small as about 0.88 sigma. Thus an +between two big particles is as small as about 0.88 sigma. Thus an {rfactor} value of 0.85 should prevent dual collisions. The {bounce} keyword can be used to limit the maximum number of @@ -230,7 +230,7 @@ dimension with {hgrid} exceeds (1 +/- tolerance), then an error or warning is generated. -NOTE: The fix srd command can be used with simluations the size and/or +NOTE: The fix srd command can be used with simulations the size and/or shape of the simulation box changes. This can be due to non-periodic boundary conditions or the use of fixes such as the "fix deform"_fix_deform.html or "fix wall/srd"_fix_wall_srd.html commands @@ -241,7 +241,7 @@ integer number of bins in the current box dimension, whether it be a fixed, shrink-wrapped, or periodic boundary, as set by the "boundary"_boundary.html command. If the box size or shape changes, -then the size of the search bins must be recalculated avery +then the size of the search bins must be recalculated every reneighboring. Note that changing the SRD bin size may alter the properties of the SRD fluid, such as its viscosity. @@ -345,15 +345,15 @@ by this fix are "intensive", meaning they do not scale with the size of the simulation. Technically, the first 8 do scale with the size of the simulation, but treating them as intensive means they are not -scaled when printed as part of thermodyanmic output. +scaled when printed as part of thermodynamic output. These are the 12 quantities. All are values for the current timestep, except for quantity 5 and the last three, each of which are -cummulative quantities since the beginning of the run. +cumulative quantities since the beginning of the run. (1) # of SRD/big collision checks performed (2) # of SRDs which had a collision -(3) # of SRD/big colllisions (including multiple bounces) +(3) # of SRD/big collisions (including multiple bounces) (4) # of SRD particles inside a big particle (5) # of SRD particles whose velocity was rescaled to be < Vmax (6) # of bins for collision searching diff -Naur lammps-21Feb17/doc/src/fix_temp_berendsen.txt lammps-7Mar17/doc/src/fix_temp_berendsen.txt --- lammps-21Feb17/doc/src/fix_temp_berendsen.txt 2016-10-12 07:34:48.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_temp_berendsen.txt 2017-03-07 09:48:20.062786000 -0700 @@ -127,7 +127,7 @@ This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". This fix can ramp its target temperature over multiple runs, using the diff -Naur lammps-21Feb17/doc/src/fix_temp_csvr.txt lammps-7Mar17/doc/src/fix_temp_csvr.txt --- lammps-21Feb17/doc/src/fix_temp_csvr.txt 2016-09-08 14:20:32.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_temp_csvr.txt 2017-03-07 09:48:20.062786000 -0700 @@ -39,7 +39,7 @@ than having it determined from the time constant directly. In the case of {temp/csld} the velocities are updated to a linear combination of the current velocities with a gaussian distribution of velocities at -the desired temperature. Both termostats are applied every timestep. +the desired temperature. Both thermostats are applied every timestep. The thermostat is applied to only the translational degrees of freedom for the particles, which is an important consideration for finite-size @@ -136,7 +136,7 @@ These fixes compute a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to the fix. The scalar value +cumulative energy change due to the fix. The scalar value calculated by this fix is "extensive". [Restrictions:] diff -Naur lammps-21Feb17/doc/src/fix_temp_rescale.txt lammps-7Mar17/doc/src/fix_temp_rescale.txt --- lammps-21Feb17/doc/src/fix_temp_rescale.txt 2016-10-18 12:59:37.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_temp_rescale.txt 2017-03-07 09:48:20.062786000 -0700 @@ -44,7 +44,7 @@ beginning and end of the run. NOTE: This thermostat will generate an error if the current -temperature is zero at the end of a timestep it is inovoked on. It +temperature is zero at the end of a timestep it is invoked on. It cannot rescale a zero temperature. {Tstart} can be specified as an equal-style "variable"_variable.html. @@ -134,7 +134,7 @@ This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". This fix can ramp its target temperature over multiple runs, using the diff -Naur lammps-21Feb17/doc/src/fix_temp_rescale_eff.txt lammps-7Mar17/doc/src/fix_temp_rescale_eff.txt --- lammps-21Feb17/doc/src/fix_temp_rescale_eff.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_temp_rescale_eff.txt 2017-03-07 09:48:20.062786000 -0700 @@ -52,7 +52,7 @@ This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative energy change due to this fix. The scalar value +cumulative energy change due to this fix. The scalar value calculated by this fix is "extensive". This fix can ramp its target temperature over multiple runs, using the diff -Naur lammps-21Feb17/doc/src/fix_tfmc.txt lammps-7Mar17/doc/src/fix_tfmc.txt --- lammps-21Feb17/doc/src/fix_tfmc.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_tfmc.txt 2017-03-07 09:48:20.062786000 -0700 @@ -41,7 +41,7 @@ particular when long time scale relaxation effects must be considered; some interesting examples are given in the review by "(Neyts)"_#Neyts. An example of a typical use case would be the modelling of chemical -vapour deposition (CVD) processes on a surface, in which impacts by +vapor deposition (CVD) processes on a surface, in which impacts by gas-phase species can be performed using MD, but subsequent relaxation of the surface is too slow to be done using MD only. Using tfMC can allow for a much faster relaxation of the surface, so that higher diff -Naur lammps-21Feb17/doc/src/fix_thermal_conductivity.txt lammps-7Mar17/doc/src/fix_thermal_conductivity.txt --- lammps-21Feb17/doc/src/fix_thermal_conductivity.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_thermal_conductivity.txt 2017-03-07 09:48:20.062786000 -0700 @@ -109,10 +109,10 @@ This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative kinetic energy transferred between the bottom and middle +cumulative kinetic energy transferred between the bottom and middle of the simulation box (in the {edim} direction) is stored as a scalar quantity by this fix. This quantity is zeroed when the fix is defined -and accumlates thereafter, once every N steps. The units of the +and accumulates thereafter, once every N steps. The units of the quantity are energy; see the "units"_units.html command for details. The scalar value calculated by this fix is "intensive". @@ -141,7 +141,7 @@ When running a simulation with large, massive particles or molecules in a background solvent, you may want to only exchange kinetic energy -bewteen solvent particles. +between solvent particles. [Related commands:] diff -Naur lammps-21Feb17/doc/src/fix_ttm.txt lammps-7Mar17/doc/src/fix_ttm.txt --- lammps-21Feb17/doc/src/fix_ttm.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_ttm.txt 2017-03-07 09:48:20.062786000 -0700 @@ -106,7 +106,7 @@ specified as parameters to the fix. The other quantities are derived. The form of the heat diffusion equation used here is almost the same as that in equation 6 of "(Duffy)"_#Duffy, with the exception that the -electronic density is explicitly reprensented, rather than being part +electronic density is explicitly represented, rather than being part of the specific heat parameter. Currently, fix ttm assumes that none of the user-supplied parameters @@ -151,7 +151,7 @@ The next Nx*Ny*Nz columns contain the temperatures for the atomic subsystem, and the final Nx*Ny*Nz columns contain the temperatures for the electronic subsystem. The ordering of the Nx*Ny*Nz columns is -with the z index varing fastest, y the next fastest, and x the +with the z index varying fastest, y the next fastest, and x the slowest. These fixes do not change the coordinates of their atoms; they only @@ -300,7 +300,7 @@ info. These fixes can only be used for 3d simulations and orthogonal -simlulation boxes. You must also use periodic +simulation boxes. You must also use periodic "boundary"_boundary.html conditions. [Related commands:] diff -Naur lammps-21Feb17/doc/src/fix_vector.txt lammps-7Mar17/doc/src/fix_vector.txt --- lammps-21Feb17/doc/src/fix_vector.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_vector.txt 2017-03-07 09:48:20.062786000 -0700 @@ -136,7 +136,7 @@ The length of the vector or the number of rows in the array grows by 1 every {Nevery} timesteps. -If the fix prouduces a vector, then the entire vector will be either +If the fix produces a vector, then the entire vector will be either "intensive" or "extensive", depending on whether the values stored in the vector are "intensive" or "extensive". If the fix produces an array, then all elements in the array must be the same, either diff -Naur lammps-21Feb17/doc/src/fix_viscosity.txt lammps-7Mar17/doc/src/fix_viscosity.txt --- lammps-21Feb17/doc/src/fix_viscosity.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_viscosity.txt 2017-03-07 09:48:20.062786000 -0700 @@ -102,7 +102,7 @@ An alternative method for calculating a viscosity is to run a NEMD simulation, as described in "Section 6.13"_Section_howto.html#howto_13 of the manual. NEMD simulations -deform the simmulation box via the "fix deform"_fix_deform.html +deform the simulation box via the "fix deform"_fix_deform.html command. Thus they cannot be run on a charged system using a "PPPM solver"_kspace_style.html since PPPM does not currently support non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; @@ -116,10 +116,10 @@ This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the -cummulative momentum transferred between the bottom and middle of the +cumulative momentum transferred between the bottom and middle of the simulation box (in the {pdim} direction) is stored as a scalar quantity by this fix. This quantity is zeroed when the fix is defined -and accumlates thereafter, once every N steps. The units of the +and accumulates thereafter, once every N steps. The units of the quantity are momentum = mass*velocity. The scalar value calculated by this fix is "intensive". @@ -147,7 +147,7 @@ in a computation of alcohol molecule properties. When running a simulation with large, massive particles or molecules -in a background solvent, you may want to only exchange momenta bewteen +in a background solvent, you may want to only exchange momenta between solvent particles. [Related commands:] diff -Naur lammps-21Feb17/doc/src/fix_wall.txt lammps-7Mar17/doc/src/fix_wall.txt --- lammps-21Feb17/doc/src/fix_wall.txt 2016-06-17 17:13:02.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_wall.txt 2017-03-07 09:48:20.062786000 -0700 @@ -136,7 +136,7 @@ The {wall/colloid} interaction is derived by integrating over constituent LJ particles of size {sigma} within the colloid particle and a 3d half-lattice of Lennard-Jones 12/6 particles of size {sigma} -in the wall. As mentioned in the preceeding paragraph, the density of +in the wall. As mentioned in the preceding paragraph, the density of particles in the wall and colloid can be different, as specified by the {epsilon} pre-factor. diff -Naur lammps-21Feb17/doc/src/fix_wall_gran.txt lammps-7Mar17/doc/src/fix_wall_gran.txt --- lammps-21Feb17/doc/src/fix_wall_gran.txt 2016-10-12 07:32:56.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_wall_gran.txt 2017-03-07 09:48:20.062786000 -0700 @@ -85,7 +85,7 @@ dampflag to 1, rather than letting them be specified directly. This means you can set the values of the wall/particle coefficients appropriately in the current code to reproduce the results of a -prevoius Hertzian monodisperse calculation. For example, for the +previous Hertzian monodisperse calculation. For example, for the common case of a monodisperse system with particles of diameter 1, Kn, Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were previously. diff -Naur lammps-21Feb17/doc/src/fix_wall_gran_region.txt lammps-7Mar17/doc/src/fix_wall_gran_region.txt --- lammps-21Feb17/doc/src/fix_wall_gran_region.txt 2016-10-13 13:07:38.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_wall_gran_region.txt 2017-03-07 09:48:20.062786000 -0700 @@ -153,7 +153,7 @@ [Restart, fix_modify, output, run start/stop, minimize info:] -Similiar to "fix wall/gran"_fix_wall_gran.html command, this fix +Similar to "fix wall/gran"_fix_wall_gran.html command, this fix writes the shear friction state of atoms interacting with the wall to "binary restart files"_restart.html, so that a simulation can continue correctly if granular potentials with shear "history" effects are @@ -169,7 +169,7 @@ its motion attributes in a way that is consistent with the simulation that wrote the restart file. In particular, if you want to change the region motion attributes (e.g. its velocity), then you should ensure -the postition/orientation of the region at the initial restart +the position/orientation of the region at the initial restart timestep is the same as it was on the timestep the restart file was written. If this is not possible, you may need to ignore info in the restart file by defining a new fix wall/gran/region command in your diff -Naur lammps-21Feb17/doc/src/fix_wall_piston.txt lammps-7Mar17/doc/src/fix_wall_piston.txt --- lammps-21Feb17/doc/src/fix_wall_piston.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/fix_wall_piston.txt 2017-03-07 09:48:20.062786000 -0700 @@ -24,7 +24,7 @@ {ramp} = use a linear velocity ramp from 0 to vz {temp} args = target damp seed extent target = target velocity for region immediately ahead of the piston - damp = damping paramter (time units) + damp = damping parameter (time units) seed = random number seed for langevin kicks extent = extent of thermostated region (distance units) {units} value = {lattice} or {box} diff -Naur lammps-21Feb17/doc/src/group.txt lammps-7Mar17/doc/src/group.txt --- lammps-21Feb17/doc/src/group.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/group.txt 2017-03-07 09:48:20.062786000 -0700 @@ -144,7 +144,7 @@ For example, these lines define a variable "eatom" that calculates the potential energy of each atom and includes it in the group if its -potential energy is above the threshhold value -3.0. +potential energy is above the threshold value -3.0. compute 1 all pe/atom compute 2 all reduce sum c_1 @@ -165,7 +165,7 @@ per-atom energy via the pe/atom compute, it will only be current if a run has been performed which evaluated pairwise energies, and the pe/atom compute was actually invoked during the run. Printing the -thermodyanmic info for compute 2 insures that this is the case, since +thermodynamic info for compute 2 insures that this is the case, since it sums the pe/atom compute values (in the reduce compute) to output them to the screen. See the "Variable Accuracy" section of the "variable"_variable.html doc page for more details on insuring that diff -Naur lammps-21Feb17/doc/src/if.txt lammps-7Mar17/doc/src/if.txt --- lammps-21Feb17/doc/src/if.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/if.txt 2017-03-07 09:48:20.062786000 -0700 @@ -37,7 +37,7 @@ [Description:] This command provides an if-then-else capability within an input -script. A Boolean expression is evaluted and the result is TRUE or +script. A Boolean expression is evaluated and the result is TRUE or FALSE. Note that as in the examples above, the expression can contain variables, as defined by the "variable"_variable.html command, which will be evaluated as part of the expression. Thus a user-defined @@ -93,7 +93,7 @@ of the loop to finish the run. Note that any variable could be checked, so long as it is current on the timestep when the run completes. As explained on the "variable"_variable.html doc page, -this can be insured by includig the variable in thermodynamic output. +this can be insured by including the variable in thermodynamic output. variable myTemp equal temp label loop diff -Naur lammps-21Feb17/doc/src/improper_hybrid.txt lammps-7Mar17/doc/src/improper_hybrid.txt --- lammps-21Feb17/doc/src/improper_hybrid.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/improper_hybrid.txt 2017-03-07 09:48:20.062786000 -0700 @@ -60,7 +60,7 @@ Unlike other improper styles, the hybrid improper style does not store improper coefficient info for individual sub-styles in a "binary -restart files"_restart.html. Thus when retarting a simulation from a +restart files"_restart.html. Thus when restarting a simulation from a restart file, you need to re-specify improper_coeff commands. [Related commands:] diff -Naur lammps-21Feb17/doc/src/improper_ring.txt lammps-7Mar17/doc/src/improper_ring.txt --- lammps-21Feb17/doc/src/improper_ring.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/improper_ring.txt 2017-03-07 09:48:20.062786000 -0700 @@ -36,7 +36,7 @@ The "ring" improper style implements the improper potential introduced by Destree et al., in Equation (9) of "(Destree)"_#Destree. This potential does not affect small amplitude vibrations but is used in an -ad-hoc way to prevent the onset of accidentially large amplitude +ad-hoc way to prevent the onset of accidentally large amplitude fluctuations leading to the occurrence of a planar conformation of the three bonds i-j, j-k and j-l, an intermediate conformation toward the chiral inversion of a methine carbon. In the "Impropers" section of diff -Naur lammps-21Feb17/doc/src/info.txt lammps-7Mar17/doc/src/info.txt --- lammps-21Feb17/doc/src/info.txt 2016-11-17 09:06:01.000000000 -0700 +++ lammps-7Mar17/doc/src/info.txt 2017-03-07 09:48:20.062786000 -0700 @@ -94,7 +94,7 @@ process that writes output (usually MPI rank 0). The {configuration} command prints some information about the LAMMPS -version and architection and OS it is run on. Where supported, also +version and architecture and OS it is run on. Where supported, also information about the memory consumption provided by the OS is reported. diff -Naur lammps-21Feb17/doc/src/jump.txt lammps-7Mar17/doc/src/jump.txt --- lammps-21Feb17/doc/src/jump.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/jump.txt 2017-03-07 09:48:20.062786000 -0700 @@ -87,7 +87,7 @@ of the loop to finish the run. Note that any variable could be checked, so long as it is current on the timestep when the run completes. As explained on the "variable"_variable.html doc page, -this can be insured by includig the variable in thermodynamic output. +this can be insured by including the variable in thermodynamic output. variable myTemp equal temp label loop diff -Naur lammps-21Feb17/doc/src/kspace_modify.txt lammps-7Mar17/doc/src/kspace_modify.txt --- lammps-21Feb17/doc/src/kspace_modify.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/kspace_modify.txt 2017-03-07 09:48:20.062786000 -0700 @@ -98,7 +98,7 @@ The {overlap} keyword can be used in conjunction with the {minorder} keyword with the PPPM styles to adjust the amount of communication -that occurs when values on the FFT grid are exchangeed between +that occurs when values on the FFT grid are exchanged between processors. This communication is distinct from the communication inherent in the parallel FFTs themselves, and is required because processors interpolate charge and field values using grid point values @@ -122,7 +122,7 @@ {order} setting can become. The minimum allowed value for PPPM is 2, which is the default. If {minorder} is set to the same value as {order} then no reduction is allowed, and LAMMPS will generate an -error if the grid communcation is non-nearest-neighbor and {overlap} +error if the grid communication is non-nearest-neighbor and {overlap} is set to {no}. The {minorder} keyword is not currently supported in MSM. @@ -284,7 +284,7 @@ performance and accuracy in the results is obtained when these values are different. -The {disp/auto} option controlls whether the pppm/disp is allowed to +The {disp/auto} option controls whether the pppm/disp is allowed to generate PPPM parameters automatically. If set to {no}, parameters have to be specified using the {gewald/disp}, {mesh/disp}, {force/disp/real} or {force/disp/kspace} keywords, or diff -Naur lammps-21Feb17/doc/src/kspace_style.txt lammps-7Mar17/doc/src/kspace_style.txt --- lammps-21Feb17/doc/src/kspace_style.txt 2017-01-20 13:23:11.000000000 -0700 +++ lammps-7Mar17/doc/src/kspace_style.txt 2017-03-07 09:48:20.062786000 -0700 @@ -131,7 +131,7 @@ for a given mesh size. Or a coarser mesh can be used for the same target accuracy, which saves CPU time. However, there is a trade-off since FFTs on two meshes are now performed which increases the -compuation required. See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov, +computation required. See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov, and "(Hockney)"_#Hockney for details of the method. For high relative accuracy, using staggered PPPM allows the mesh size @@ -174,7 +174,7 @@ lo-level Makefile. This setting also changes some of the PPPM operations (e.g. mapping charge to mesh and interpolating electric fields to particles) to be performed in single precision. This option -can speed-up long-range calulations, particularly in parallel or on +can speed-up long-range calculations, particularly in parallel or on GPUs. The use of the -DFFT_SINGLE flag is discussed in "this section"_Section_start.html#start_2_4 of the manual. MSM does not currently support the -DFFT_SINGLE compiler switch. @@ -233,7 +233,7 @@ simulation where the box size changes dramatically, is to break it into shorter simulations (multiple "run"_run.html commands). This works because the grid size is re-computed at the beginning of each -run. Another way to ensure the descired accuracy requirement is met +run. Another way to ensure the described accuracy requirement is met is to run a short simulation at the maximum expected tilt or length, note the required grid size, and then use the "kspace_modify"_kspace_modify.html {mesh} command to manually set the @@ -255,7 +255,7 @@ See the "kspace_modify"_kspace_modify.html command for additional options of the K-space solvers that can be set, including a {force} -option for setting an absoulte RMS error in forces, as opposed to a +option for setting an absolute RMS error in forces, as opposed to a relative RMS error. :line @@ -341,7 +341,7 @@ Adam Hilger, NY (1989). :link(Kolafa) -[(Kolafa)] Kolafa and Perram, Molecular Simualtion, 9, 351 (1992). +[(Kolafa)] Kolafa and Perram, Molecular Simulation, 9, 351 (1992). :link(Petersen) [(Petersen)] Petersen, J Chem Phys, 103, 3668 (1995). diff -Naur lammps-21Feb17/doc/src/lammps.book lammps-7Mar17/doc/src/lammps.book --- lammps-21Feb17/doc/src/lammps.book 2017-01-18 11:33:29.000000000 -0700 +++ lammps-7Mar17/doc/src/lammps.book 2017-03-07 09:48:20.062786000 -0700 @@ -194,6 +194,7 @@ fix_meso_stationary.html fix_momentum.html fix_move.html +fix_mscg.html fix_msst.html fix_neb.html fix_nh.html @@ -218,6 +219,7 @@ fix_nve_noforce.html fix_nve_sphere.html fix_nve_tri.html +fix_nvk.html fix_nvt_asphere.html fix_nvt_body.html fix_nvt_manifold_rattle.html @@ -432,6 +434,7 @@ pair_hbond_dreiding.html pair_hybrid.html pair_kim.html +pair_kolmogorov_crespi_z.html pair_lcbop.html pair_line_lj.html pair_list.html @@ -458,7 +461,7 @@ pair_nb3b_harmonic.html pair_nm.html pair_none.html -pair_oxdna_excv.html +pair_oxdna.html pair_peri.html pair_polymorphic.html pair_quip.html @@ -497,7 +500,7 @@ bond_class2.html bond_fene.html bond_fene_expand.html -bond_oxdna_fene.html +bond_oxdna.html bond_harmonic.html bond_harmonic_shift.html bond_harmonic_shift_cut.html diff -Naur lammps-21Feb17/doc/src/minimize.txt lammps-7Mar17/doc/src/minimize.txt --- lammps-21Feb17/doc/src/minimize.txt 2016-10-18 11:10:29.000000000 -0600 +++ lammps-7Mar17/doc/src/minimize.txt 2017-03-07 09:48:20.062786000 -0700 @@ -48,7 +48,7 @@ running dynamics. Note that you can minimize some atoms in the system while holding the -coordiates of other atoms fixed by applying "fix +coordinates of other atoms fixed by applying "fix setforce"_fix_setforce.html to the other atoms. See a fuller discussion of using fixes while minimizing below. @@ -58,7 +58,7 @@ performed using a line search algorithm. The line search typically evaluates forces and energies several times to set new coordinates. Currently, a backtracking algorithm is used which may not be optimal -in terms of the number of force evaulations performed, but appears to +in terms of the number of force evaluations performed, but appears to be more robust than previous line searches we've tried. The backtracking method is described in Nocedal and Wright's Numerical Optimization (Procedure 3.1 on p 41). @@ -201,7 +201,7 @@ Note that a cutoff Lennard-Jones potential (and others) can be shifted so that its energy is 0.0 at the cutoff via the "pair_modify"_pair_modify.html command. See the doc pages for -inidividual "pair styles"_pair_style.html for details. Note that +individual "pair styles"_pair_style.html for details. Note that Coulombic potentials always have a cutoff, unless versions with a long-range component are used (e.g. "pair_style lj/cut/coul/long"_pair_lj.html). The CHARMM potentials go to 0.0 at diff -Naur lammps-21Feb17/doc/src/molecule.txt lammps-7Mar17/doc/src/molecule.txt --- lammps-21Feb17/doc/src/molecule.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/molecule.txt 2017-03-07 09:48:20.062786000 -0700 @@ -155,7 +155,7 @@ self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body around its center of mass. The values are with respect to -the simulation box XYZ axes, not with respect to the prinicpal axes of +the simulation box XYZ axes, not with respect to the principal axes of the rigid body itself. LAMMPS performs the latter calculation internally. diff -Naur lammps-21Feb17/doc/src/neb.txt lammps-7Mar17/doc/src/neb.txt --- lammps-21Feb17/doc/src/neb.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/neb.txt 2017-03-07 09:48:20.062786000 -0700 @@ -58,7 +58,7 @@ discussion. NOTE: As explained below, a NEB calculation perfoms a damped dynamics -minimization across all the replicas. The mimimizer uses whatever +minimization across all the replicas. The minimizer uses whatever timestep you have defined in your input script, via the "timestep"_timestep.html command. Often NEB will converge more quickly if you use a timestep about 10x larger than you would normally @@ -81,7 +81,7 @@ computed in the usual way due only to other atoms within their replica. Conceptually, the non-NEB atoms provide a background force field for the NEB atoms. They can be allowed to move during the NEB -minimiation procedure (which will typically induce different +minimization procedure (which will typically induce different coordinates for non-NEB atoms in different replicas), or held fixed using other LAMMPS commands such as "fix setforce"_fix_setforce.html. Note that the "partition"_partition.html command can be used to invoke @@ -97,7 +97,7 @@ be a state with all the atoms (NEB and non-NEB) having coordinates on one side of the energy barrier. A perfect energy minimum is not required, since atoms in the first replica experience no spring forces -from the 2nd replica. Thus the damped dynamics minimizaiton will +from the 2nd replica. Thus the damped dynamics minimization will drive the first replica to an energy minimum if it is not already there. However, you will typically get better convergence if the initial state is already at a minimum. For example, for a system with @@ -366,7 +366,7 @@ There are 2 Python scripts provided in the tools/python directory, neb_combine.py and neb_final.py, which are useful in analyzing output from a NEB calculation. Assume a NEB simulation with M replicas, and -the NEB atoms labelled with a specific atom type. +the NEB atoms labeled with a specific atom type. The neb_combine.py script extracts atom coords for the NEB atoms from all M dump files and creates a single dump file where each snapshot diff -Naur lammps-21Feb17/doc/src/neigh_modify.txt lammps-7Mar17/doc/src/neigh_modify.txt --- lammps-21Feb17/doc/src/neigh_modify.txt 2016-09-08 14:20:32.000000000 -0600 +++ lammps-7Mar17/doc/src/neigh_modify.txt 2017-03-07 09:17:45.819464000 -0700 @@ -34,8 +34,10 @@ M,N = exclude if one atom in pair is type M, other is type N group group1-ID group2-ID group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd - molecule group-ID - groupname = exclude if both atoms are in the same molecule and in the same group + molecule/intra group-ID + group-ID = exclude if both atoms are in the same molecule and in group + molecule/inter group-ID + group-ID = exclude if both atoms are in different molecules and in group none delete all exclude settings {page} value = N @@ -52,7 +54,7 @@ neigh_modify exclude type 2 3 neigh_modify exclude group frozen frozen check no neigh_modify exclude group residue1 chain3 -neigh_modify exclude molecule rigid :pre +neigh_modify exclude molecule/intra rigid :pre [Description:] @@ -130,9 +132,11 @@ atom is of type M and the other of type N. M can equal N. The {exclude group} option turns off the interaction if one atom is in the first group and the other is the second. Group1-ID can equal -group2-ID. The {exclude molecule} option turns off the interaction if -both atoms are in the specified group and in the same molecule, as -determined by their molecule ID. +group2-ID. The {exclude molecule/intra} option turns off the +interaction if both atoms are in the specified group and in the same +molecule, as determined by their molecule ID. The {exclude +molecule/inter} turns off the interaction between pairs of atoms that +have different molecule IDs and are both in the specified group. Each of the exclude options can be specified multiple times. The {exclude type} option is the most efficient option to use; it requires @@ -195,8 +199,8 @@ If the "delay" setting is non-zero, then it must be a multiple of the "every" setting. -The exclude molecule option can only be used with atom styles that -define molecule IDs. +The molecule/intra and molecule/inter exclude options can only be used +with atom styles that define molecule IDs. The value of the {page} setting must be at least 10x larger than the {one} setting. This insures neighbor pages are not mostly empty diff -Naur lammps-21Feb17/doc/src/package.txt lammps-7Mar17/doc/src/package.txt --- lammps-21Feb17/doc/src/package.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/package.txt 2017-03-07 09:48:20.062786000 -0700 @@ -110,7 +110,7 @@ If this command is specified in an input script, it must be near the top of the script, before the simulation box has been defined. This is because it specifies settings that the accelerator packages use in -their intialization, before a simultion is defined. +their initialization, before a simulation is defined. This command can also be specified from the command-line when launching LAMMPS, using the "-pk" "command-line @@ -166,7 +166,7 @@ building currently cannot be used with a triclinic box. GPU neighbor list calculation currently cannot be used with "hybrid"_pair_hybrid.html pair styles. GPU neighbor lists are not -compatible with comannds that are not GPU-enabled. When a non-GPU +compatible with commands that are not GPU-enabled. When a non-GPU enabled command requires a neighbor list, it will also be built on the CPU. In these cases, it will typically be more efficient to only use CPU neighbor list builds. @@ -199,7 +199,7 @@ The {split} keyword can be used for load balancing force calculations between CPU and GPU cores in GPU-enabled pair styles. If 0 < {split} < 1.0, a fixed fraction of particles is offloaded to the GPU while force -calculation for the other particles occurs simulataneously on the CPU. +calculation for the other particles occurs simultaneously on the CPU. If {split} < 0.0, the optimal fraction (based on CPU and GPU timings) is calculated every 25 timesteps, i.e. dynamic load-balancing across the CPU and GPU is performed. If {split} = 1.0, all force @@ -295,7 +295,7 @@ environment variable, see the discussion of the {Nthreads} setting on this doc page for the "package omp" command. Nthreads is a required argument for the USER-OMP package. Its meaning is exactly the same -for the USER-INTEL pacakge. +for the USER-INTEL package. NOTE: If you build LAMMPS with both the USER-INTEL and USER-OMP packages, be aware that both packages allow setting of the {Nthreads} @@ -347,7 +347,7 @@ within 5 to 10 percent of the optimal fixed fraction. The {ghost} keyword determines whether or not ghost atoms, i.e. atoms -at the boundaries of proessor sub-domains, are offloaded for neighbor +at the boundaries of processor sub-domains, are offloaded for neighbor and force calculations. When the value = "no", ghost atoms are not offloaded. This option can reduce the amount of data transfer with the coprocessor and can also overlap MPI communication of forces with @@ -516,7 +516,7 @@ What combination of threads and MPI tasks gives the best performance is difficult to predict and can depend on many components of your input. Not all features of LAMMPS support OpenMP threading via the -USER-OMP packaage and the parallel efficiency can be very different, +USER-OMP package and the parallel efficiency can be very different, too. Optional keyword/value pairs can also be specified. Each has a @@ -527,7 +527,7 @@ to {no} then neighbor list calculation is performed only by MPI tasks with no OpenMP threading. If {mode} is {yes} (the default), a multi-threaded neighbor list build is used. Using {neigh} = {yes} is -almost always faster and should produce idential neighbor lists at the +almost always faster and should produce identical neighbor lists at the expense of using more memory. Specifically, neighbor list pages are allocated for all threads at the same time and each thread works within its own pages. diff -Naur lammps-21Feb17/doc/src/pair_adp.txt lammps-7Mar17/doc/src/pair_adp.txt --- lammps-21Feb17/doc/src/pair_adp.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_adp.txt 2017-03-07 09:48:20.062786000 -0700 @@ -68,7 +68,7 @@ specify the path for the potential file. As an example, the potentials/AlCu.adp file, included in the -potentials directory of the LAMMPS distrbution, is an extended {setfl} +potentials directory of the LAMMPS distribution, is an extended {setfl} file which has tabulated ADP values for w elements and their alloy interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Al, and the 4th to be Cu, you would use diff -Naur lammps-21Feb17/doc/src/pair_agni.txt lammps-7Mar17/doc/src/pair_agni.txt --- lammps-21Feb17/doc/src/pair_agni.txt 2016-11-17 09:06:01.000000000 -0700 +++ lammps-7Mar17/doc/src/pair_agni.txt 2017-03-07 09:48:20.062786000 -0700 @@ -34,7 +34,7 @@ The method implements the recently proposed machine learning access to atomic forces as discussed extensively in the following publications - "(Botu1)"_#Botu2015adaptive and "(Botu2)"_#Botu2015learning. The premise -of the method is to map the atomic enviornment numerically into a +of the method is to map the atomic environment numerically into a fingerprint, and use machine learning methods to create a mapping to the vectorial atomic forces. diff -Naur lammps-21Feb17/doc/src/pair_airebo.txt lammps-7Mar17/doc/src/pair_airebo.txt --- lammps-21Feb17/doc/src/pair_airebo.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_airebo.txt 2017-03-07 09:48:20.062786000 -0700 @@ -53,7 +53,7 @@ Potential of "(Brenner)"_#Brenner. Note that this is the so-called 2nd generation REBO from 2002, not the original REBO from 1990. As discussed below, 2nd generation REBO is closely related to the -intial AIREBO; it is just a subset of the potential energy terms. +initial AIREBO; it is just a subset of the potential energy terms. The AIREBO potential consists of three terms: diff -Naur lammps-21Feb17/doc/src/pair_beck.txt lammps-7Mar17/doc/src/pair_beck.txt --- lammps-21Feb17/doc/src/pair_beck.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_beck.txt 2017-03-07 09:48:20.062786000 -0700 @@ -73,7 +73,7 @@ [Mixing, shift, table, tail correction, restart, rRESPA info]: -For atom type pairs I,J and I != J, coeffiecients must be specified. +For atom type pairs I,J and I != J, coefficients must be specified. No default mixing rules are used. This pair style does not support the "pair_modify"_pair_modify.html shift diff -Naur lammps-21Feb17/doc/src/pair_body.txt lammps-7Mar17/doc/src/pair_body.txt --- lammps-21Feb17/doc/src/pair_body.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_body.txt 2017-03-07 09:48:20.062786000 -0700 @@ -59,7 +59,7 @@ interactions between the body and point particle are computed. The interaction between two sub-particles, or a sub-particle and point -particle, or betwee two point particles is computed as a Lennard-Jones +particle, or between two point particles is computed as a Lennard-Jones interaction, using the standard formula :c,image(Eqs/pair_lj.jpg) diff -Naur lammps-21Feb17/doc/src/pair_bop.txt lammps-7Mar17/doc/src/pair_bop.txt --- lammps-21Feb17/doc/src/pair_bop.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_bop.txt 2017-03-07 09:48:20.062786000 -0700 @@ -36,11 +36,11 @@ "Pettifor_2"_#Pettifor_2, "Pettifor_3"_#Pettifor_3) and later updated by Murdick, Zhou, and Ward ("Murdick"_#Murdick, "Ward"_#Ward). Currently, BOP potential files for these systems are provided with -LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A sysstem with +LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A system with only a subset of these elements, including a single element (e.g. C or Cu or Al or Ga or Zn or CdZn), can also be modeled by using the appropriate alloy file and assigning all atom types to the -singleelement or subset of elements via the pair_coeff command, as +single element or subset of elements via the pair_coeff command, as discussed below. The BOP potential consists of three terms: @@ -49,7 +49,7 @@ where phi_ij(r_ij) is a short-range two-body function representing the repulsion between a pair of ion cores, beta_(sigma,ij)(r_ij) and -beta_(sigma,ij)(r_ij) are respectively sigma and pi bond ingtegrals, +beta_(sigma,ij)(r_ij) are respectively sigma and pi bond integrals, THETA_(sigma,ij) and THETA_(pi,ij) are sigma and pi bond-orders, and U_prom is the promotion energy for sp-valent systems. @@ -78,8 +78,8 @@ bond-orders. Bond-order terms can be understood in terms of molecular orbital hopping paths based upon the Cyrot-Lackmann theorem ("Pettifor_1"_#Pettifor_1). The sigma bond-order with a half-full -valence shell is used to interpolate the bond-order expressiont that -incorporated explicite valance band filling. This pi bond-order +valence shell is used to interpolate the bond-order expression that +incorporated explicit valance band filling. This pi bond-order expression also contains also contains a three-member ring term that allows implementation of an asymmetric density of states, which helps to either stabilize or destabilize close-packed structures. The pi @@ -299,7 +299,7 @@ function can contain up to 10 term thus 10 constants. The first line can contain up to five constants. If the spline has more than five terms the second line will contain the remaining constants The -following lines will then contain the constants for the remainaing g0, +following lines will then contain the constants for the remaining g0, g1, g2... (for e_1-e_1-e_2) and the other three body interactions :l :ule diff -Naur lammps-21Feb17/doc/src/pair_comb.txt lammps-7Mar17/doc/src/pair_comb.txt --- lammps-21Feb17/doc/src/pair_comb.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_comb.txt 2017-03-07 09:48:20.062786000 -0700 @@ -86,7 +86,7 @@ all currently-available 2nd generation COMB parameterizations: for Si, Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style {comb3}, the potential file {ffield.comb3} contains all -currently-available 3rd generation COMB paramterizations: O, Cu, N, C, +currently-available 3rd generation COMB parameterizations: O, Cu, N, C, H, Ti, Zn and Zr. The status of the optimization of the compounds, for example Cu2O, TiN and hydrocarbons, are given in the following table: diff -Naur lammps-21Feb17/doc/src/pair_coul.txt lammps-7Mar17/doc/src/pair_coul.txt --- lammps-21Feb17/doc/src/pair_coul.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_coul.txt 2017-03-07 09:48:20.062786000 -0700 @@ -127,15 +127,15 @@ :c,image(Eqs/pair_coul_wolf.jpg) where {alpha} is the damping parameter, and erc() and erfc() are -error-fuction and complementary error-function terms. This potential +error-function and complementary error-function terms. This potential is essentially a short-range, spherically-truncated, charge-neutralized, shifted, pairwise {1/r} summation. With a -manipulation of adding and substracting a self term (for i = j) to the +manipulation of adding and subtracting a self term (for i = j) to the first and second term on the right-hand-side, respectively, and a small enough {alpha} damping parameter, the second term shrinks and the potential becomes a rapidly-converging real-space summation. With a long enough cutoff and small enough alpha parameter, the energy and -forces calcluated by the Wolf summation method approach those of the +forces calculated by the Wolf summation method approach those of the Ewald sum. So it is a means of getting effective long-range interactions with a short-range potential. @@ -188,7 +188,7 @@ carbides (such as SiC, TiN). Pair coul/strietz used by itself or with any other pair style such as EAM, MEAM, Tersoff, or LJ in hybrid/overlay mode. To do this, you would need to provide a -Streitz-Mintmire parameterizaion for the material being modeled. +Streitz-Mintmire parameterization for the material being modeled. :line @@ -222,7 +222,7 @@ See the "howto section"_Section_howto.html#howto_8 for more information on how to use the TIP4P pair styles and lists of -parameters to set. Note that the neighobr list cutoff for Coulomb +parameters to set. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for the offset distance of the fictitious charges on O atoms in water molecules. Thus it is diff -Naur lammps-21Feb17/doc/src/pair_coul_diel.txt lammps-7Mar17/doc/src/pair_coul_diel.txt --- lammps-21Feb17/doc/src/pair_coul_diel.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_coul_diel.txt 2017-03-07 09:48:20.062786000 -0700 @@ -23,11 +23,11 @@ [Description:] -Style {coul/diel} computes a Coulomb correction for implict solvent -ion interactions in which the dielectric perimittivity is distance dependent. +Style {coul/diel} computes a Coulomb correction for implicit solvent +ion interactions in which the dielectric permittivity is distance dependent. The dielectric permittivity epsilon_D(r) connects to limiting regimes: One limit is defined by a small dielectric permittivity (close to vacuum) -at or close to contact seperation between the ions. At larger separations +at or close to contact separation between the ions. At larger separations the dielectric permittivity reaches a bulk value used in the regular Coulomb interaction coul/long or coul/cut. The transition is modeled by a hyperbolic function which is incorporated @@ -48,7 +48,7 @@ solvent simulations of salt ions "(Lenart)"_#Lenart and of ionic surfactants "(Jusufi)"_#Jusufi. Note that this potential is only reasonable for implicit solvent simulations -and in combiantion with coul/cut or coul/long. It is also usually combined +and in combination with coul/cut or coul/long. It is also usually combined with gauss/cut, see "(Lenart)"_#Lenart or "(Jusufi)"_#Jusufi. The following coefficients must be defined for each pair of atom diff -Naur lammps-21Feb17/doc/src/pair_dpd.txt lammps-7Mar17/doc/src/pair_dpd.txt --- lammps-21Feb17/doc/src/pair_dpd.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_dpd.txt 2017-03-07 09:48:20.062786000 -0700 @@ -88,7 +88,7 @@ where T is the temperature set by the "pair_style"_pair_style.html command so it does not need to be specified. -For style {dpd/tstat}, the coefficiencts defined for each pair of +For style {dpd/tstat}, the coefficients defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command is the same, except that A is not included. diff -Naur lammps-21Feb17/doc/src/pair_eam.txt lammps-7Mar17/doc/src/pair_eam.txt --- lammps-21Feb17/doc/src/pair_eam.txt 2017-01-09 13:29:27.000000000 -0700 +++ lammps-7Mar17/doc/src/pair_eam.txt 2017-03-07 09:48:20.062786000 -0700 @@ -273,7 +273,7 @@ lines added to it, at the end of the file: line 1: Comment line (ignored) -line 2: N Coefficient0 Coefficient1 ... CoeffincientN :ul +line 2: N Coefficient0 Coefficient1 ... CoefficientN :ul The last line begins with the degree {N} of the polynomial function {h(x)} that modifies the cross interaction between A and B elements. diff -Naur lammps-21Feb17/doc/src/pair_edip.txt lammps-7Mar17/doc/src/pair_edip.txt --- lammps-21Feb17/doc/src/pair_edip.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_edip.txt 2017-03-07 09:48:20.062786000 -0700 @@ -95,7 +95,7 @@ At the moment, only a single element parametrization is implemented. However, the author is not aware of other -multi-element EDIP parametrizations. If you know any and +multi-element EDIP parameterization. If you know any and you are interest in that, please contact the author of the EDIP package. diff -Naur lammps-21Feb17/doc/src/pair_eff.txt lammps-7Mar17/doc/src/pair_eff.txt --- lammps-21Feb17/doc/src/pair_eff.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_eff.txt 2017-03-07 09:48:20.062786000 -0700 @@ -149,7 +149,7 @@ :line -The {limit/eradius} and {pressure/evirials} keywrods are optional. +The {limit/eradius} and {pressure/evirials} keywords are optional. Neither or both must be specified. If not specified they are unset. The {limit/eradius} keyword is used to restrain electron size from @@ -197,7 +197,7 @@ :line -NOTE: This implemention of eFF gives a reasonably accurate description +NOTE: This implementation of eFF gives a reasonably accurate description for systems containing nuclei from Z = 1-6 in "all electron" representations. For systems with increasingly non-spherical electrons, Users should use the ECP representations. ECPs are now @@ -284,7 +284,7 @@ section for more info. These pair styles require that particles store electron attributes -such as radius, radial velocity, and radital force, as defined by the +such as radius, radial velocity, and radial force, as defined by the "atom_style"_atom_style.html. The {electron} atom style does all of this. diff -Naur lammps-21Feb17/doc/src/pair_eim.txt lammps-7Mar17/doc/src/pair_eim.txt --- lammps-21Feb17/doc/src/pair_eim.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_eim.txt 2017-03-07 09:48:20.062786000 -0700 @@ -97,7 +97,7 @@ The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The filename is the EIM potential file. The Na and Cl arguments (before the file name) are the two elements for which info will be -extracted from the potentail file. The first three trailing Na +extracted from the potential file. The first three trailing Na arguments map LAMMPS atom types 1,2,3 to the EIM Na element. The final Cl argument maps LAMMPS atom type 4 to the EIM Cl element. @@ -107,7 +107,7 @@ that will be used with other potentials. The ffield.eim file in the {potentials} directory of the LAMMPS -distribution is formated as follows: +distribution is formatted as follows: Lines starting with # are comments and are ignored by LAMMPS. Lines starting with "global:" include three global values. The first value diff -Naur lammps-21Feb17/doc/src/pair_exp6_rx.txt lammps-7Mar17/doc/src/pair_exp6_rx.txt --- lammps-21Feb17/doc/src/pair_exp6_rx.txt 2017-01-06 10:16:03.000000000 -0700 +++ lammps-7Mar17/doc/src/pair_exp6_rx.txt 2017-03-07 09:48:20.062786000 -0700 @@ -63,7 +63,7 @@ to be the internal chemical energy (uChem). The fourth argument specifies the type of scaling that will be used -to scale the EXP-6 paramters as reactions occur. Currently, there +to scale the EXP-6 parameters as reactions occur. Currently, there are three scaling options: {exponent}, {polynomial} and {none}. Exponent scaling requires two additional arguments for scaling @@ -72,7 +72,7 @@ represented by the coarse-grain particle and exponent is specified as a pair coefficient argument for {Rm} and {epsilon}, respectively. The {Rm} and {epsilon} parameters are multiplied by the scaling -factor to give the scaled interaction paramters for the CG particle. +factor to give the scaled interaction parameters for the CG particle. Polynomial scaling requires a filename to be specified as a pair coeff argument. The file contains the coefficients to a fifth order diff -Naur lammps-21Feb17/doc/src/pair_gran.txt lammps-7Mar17/doc/src/pair_gran.txt --- lammps-21Feb17/doc/src/pair_gran.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_gran.txt 2017-03-07 09:48:20.062786000 -0700 @@ -224,7 +224,7 @@ last 3 (8-10) the components of the relative velocity in the tangential direction. -These extra quantites can be accessed by the "compute +These extra quantities can be accessed by the "compute pair/local"_compute_pair_local.html command, as {p1}, {p2}, ..., {p10}. diff -Naur lammps-21Feb17/doc/src/pair_hbond_dreiding.txt lammps-7Mar17/doc/src/pair_hbond_dreiding.txt --- lammps-21Feb17/doc/src/pair_hbond_dreiding.txt 2016-10-24 08:19:10.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_hbond_dreiding.txt 2017-03-07 09:48:20.062786000 -0700 @@ -101,13 +101,13 @@ pairs for atoms which act as joint donors/acceptors need to be specified; all other type pairs are assumed to be inactive. -NOTE: A "pair_coeff"_pair_coeff.html command can be speficied multiple +NOTE: A "pair_coeff"_pair_coeff.html command can be specified multiple times for the same donor/acceptor type pair. This enables multiple hydrogen types to be assigned to the same donor/acceptor type pair. For other pair_styles, if the pair_coeff command is re-used for the same I.J type pair, the settings for that type pair are overwritten. For the hydrogen bond potentials this is not the case; the settings -are cummulative. This means the only way to turn off a previous +are cumulative. This means the only way to turn off a previous setting, is to re-use the pair_style command and start over. For the {hbond/dreiding/lj} style the list of coefficients is as diff -Naur lammps-21Feb17/doc/src/pair_hybrid.txt lammps-7Mar17/doc/src/pair_hybrid.txt --- lammps-21Feb17/doc/src/pair_hybrid.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_hybrid.txt 2017-03-07 09:48:20.062786000 -0700 @@ -63,7 +63,7 @@ sub-style. For efficiency this should only be done if your model requires it. E.g. if you have different regions of Si and C atoms and wish to use a Tersoff potential for pure Si for one set of atoms, and -a Tersoff potetnial for pure C for the other set (presumably with some +a Tersoff potential for pure C for the other set (presumably with some 3rd potential for Si-C interactions), then the sub-style {tersoff} could be listed twice. But if you just want to use a Lennard-Jones or other pairwise potential for several different atom type pairs in your @@ -189,7 +189,7 @@ Different force fields (e.g. CHARMM vs AMBER) may have different rules for applying weightings that change the strength of pairwise -interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4 +interactions between pairs of atoms that are also 1-2, 1-3, and 1-4 neighbors in the molecular bond topology, as normally set by the "special_bonds"_special_bonds.html command. Different weights can be assigned to different pair hybrid sub-styles via the "pair_modify diff -Naur lammps-21Feb17/doc/src/pair_kim.txt lammps-7Mar17/doc/src/pair_kim.txt --- lammps-21Feb17/doc/src/pair_kim.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_kim.txt 2017-03-07 09:48:20.062786000 -0700 @@ -46,7 +46,7 @@ or KIM if there is an incompatibility. The argument {printflag} is optional. If it is set to a non-zero -value then a KIM dsecriptor file is printed when KIM is invoked. This +value then a KIM descriptor file is printed when KIM is invoked. This can be useful for debugging. The default is to not print this file. Only a single pair_coeff command is used with the {kim} style which diff -Naur lammps-21Feb17/doc/src/pair_kolmogorov_crespi_z.txt lammps-7Mar17/doc/src/pair_kolmogorov_crespi_z.txt --- lammps-21Feb17/doc/src/pair_kolmogorov_crespi_z.txt 1969-12-31 17:00:00.000000000 -0700 +++ lammps-7Mar17/doc/src/pair_kolmogorov_crespi_z.txt 2017-03-07 09:48:20.062786000 -0700 @@ -0,0 +1,72 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style kolmogorov/crespi/z command :h3 + +[Syntax:] + +pair_style hybrid/overlay kolmogorov/crespi/z cutoff :pre + +[Examples:] + +pair_style hybrid/overlay kolmogorov/crespi/z 20.0 +pair_coeff * * none +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre + +pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 +pair_coeff * * rebo CH.airebo C C +pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre + +[Description:] + +The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction +potential as described in "(KC05)"_#KC05. An important simplification is made, +which is to take all normals along the z-axis. + +:c,image(Eqs/pair_kolmogorov_crespi_z.jpg) + +It is important to have a suffiently large cutoff to ensure smooth forces. +Energies are shifted so that they go continously to zero at the cutoff assuming +that the exponential part of {Vij} (first term) decays sufficiently fast. +This shift is achieved by the last term in the equation for {Vij} above. + +This potential is intended for interactions between two layers of graphene. +Therefore, to avoid interaction between layers in multi-layered materials, +each layer should have a separate atom type and interactions should only +be computed between atom types of neighbouring layers. + +The parameter file (e.g. CC.KC), is intended for use with metal +"units"_units.html, with energies in meV. An additional parameter, {S}, +is available to facilitate scaling of energies in accordance with +"(vanWijk)"_#vanWijk. + +This potential must be used in combination with hybrid/overlay. +Other interactions can be set to zero using pair_style {none}. + +[Restrictions:] + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html +"pair_none"_pair_none.html +"pair_style hybrid/overlay"_pair_hybrid.html + +[Default:] none + +:line + +:link(KC05) +[(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) + +:link(vanWijk) +[(vanWijk)] M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, +Physical Review Letters, 113, 135504 (2014) diff -Naur lammps-21Feb17/doc/src/pair_line_lj.txt lammps-7Mar17/doc/src/pair_line_lj.txt --- lammps-21Feb17/doc/src/pair_line_lj.txt 2016-10-24 08:19:10.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_line_lj.txt 2017-03-07 09:48:20.062786000 -0700 @@ -39,7 +39,7 @@ size for that particle type. If a line segment has a length L and is of type I, then the number of spheres N that represent the segment is calculated as N = L/sizeI, rounded up to an integer value. Thus if L -is not evenly divisibly by sizeI, N is incremented to include one +is not evenly divisible by sizeI, N is incremented to include one extra sphere. The centers of the spheres are spaced equally along the line segment. Imagine N+1 equally-space points, which include the 2 end points of the segment. The sphere centers are halfway between @@ -48,7 +48,7 @@ The LJ interaction between 2 spheres on different line segments (or a sphere on a line segment and a point particles) is computed with sub-particle epsilon, sigma, and cutoff values that are set by the -pair_coeff command, as described below. If the distance bewteen the 2 +pair_coeff command, as described below. If the distance between the 2 spheres is greater than the sub-particle cutoff, there is no interaction. This means that some pairs of sub-particles on 2 line segments may interact, but others may not. @@ -90,7 +90,7 @@ line particles of type I and type J. They are used to define the N sub-particles per segment as described above. These coefficients are actually stored on a per-type basis. Thus if there are multiple -pair_coeff commmands that involve type I, as either the first or +pair_coeff commands that involve type I, as either the first or second atom type, you should use consistent values for sizeI or sizeJ in all of them. If you do not do this, the last value specified for sizeI will apply to all segments of type I. If typeI or typeJ refers @@ -112,7 +112,7 @@ [Mixing, shift, table, tail correction, restart, rRESPA info]: -For atom type pairs I,J and I != J, coeffiecients must be specified. +For atom type pairs I,J and I != J, coefficients must be specified. No default mixing rules are used. This pair style does not support the "pair_modify"_pair_modify.html diff -Naur lammps-21Feb17/doc/src/pair_lj.txt lammps-7Mar17/doc/src/pair_lj.txt --- lammps-21Feb17/doc/src/pair_lj.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_lj.txt 2017-03-07 09:48:20.062786000 -0700 @@ -197,7 +197,7 @@ See the "howto section"_Section_howto.html#howto_8 for more information on how to use the TIP4P pair styles and lists of -parameters to set. Note that the neighobr list cutoff for Coulomb +parameters to set. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for the offset distance of the fictitious charges on O atoms in water molecules. Thus it is diff -Naur lammps-21Feb17/doc/src/pair_lj_long.txt lammps-7Mar17/doc/src/pair_lj_long.txt --- lammps-21Feb17/doc/src/pair_lj_long.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_lj_long.txt 2017-03-07 09:48:20.062786000 -0700 @@ -91,7 +91,7 @@ See the "howto section"_Section_howto.html#howto_8 for more information on how to use the TIP4P pair style. Note that the -neighobr list cutoff for Coulomb interactions is effectively extended +neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for the offset distance of the fictitious charges on O atoms in water molecules. Thus it is typically best in an efficiency sense to use a diff -Naur lammps-21Feb17/doc/src/pair_lj_smooth.txt lammps-7Mar17/doc/src/pair_lj_smooth.txt --- lammps-21Feb17/doc/src/pair_lj_smooth.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_lj_smooth.txt 2017-03-07 09:48:20.062786000 -0700 @@ -51,7 +51,7 @@ epsilon (energy units) sigma (distance units) -innner (distance units) +inner (distance units) outer (distance units) :ul The last 2 coefficients are optional inner and outer cutoffs. If not diff -Naur lammps-21Feb17/doc/src/pair_lj_soft.txt lammps-7Mar17/doc/src/pair_lj_soft.txt --- lammps-21Feb17/doc/src/pair_lj_soft.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_lj_soft.txt 2017-03-07 09:48:20.062786000 -0700 @@ -106,7 +106,7 @@ The {lj/cut/soft} style and substyles compute the 12/6 Lennard-Jones and Coulomb potential modified by a soft core, in order to avoid singularities during free energy calculations when sites are created -or anihilated "(Beutler)"_#Beutler, +or annihilated "(Beutler)"_#Beutler, :c,image(Eqs/pair_lj_soft.jpg) @@ -120,14 +120,14 @@ which can be set by the "dielectric"_dielectric.html command. The coefficient lambda is an activation parameter. When lambda = 1 the -pair potentiel is identical to a Lennard-Jones term or a Coulomb term +pair potential is identical to a Lennard-Jones term or a Coulomb term or a combination of both. When lambda = 0 the interactions are deactivated. The transition between these two extrema is smoothed by a soft repulsive core in order to avoid singularities in potential -energy and forces when sites are created or anihilated and can overlap +energy and forces when sites are created or annihilated and can overlap "(Beutler)"_#Beutler. -The paratemers n, alpha_LJ and alpha_C are set in the +The parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the cutoffs. Usual choices for the exponent are n = 2 or n = 1. For the remaining coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are @@ -164,7 +164,7 @@ TIP4P water model. The usage of this pair style is documented in the "pair_lj"_pair_lj.html styles. The soft-core version introduces the lambda parameter to the list of arguments, after epsilon and sigma in -the "pair_coeff"_pair_coeff.html command. The paratemers n, alpha_LJ +the "pair_coeff"_pair_coeff.html command. The parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the cutoffs. @@ -175,7 +175,7 @@ in the "pair_charmm"_pair_charmm.html styles. The soft-core version introduces the lambda parameter to the list of arguments, after epsilon and sigma in the "pair_coeff"_pair_coeff.html command (and -before the optional eps14 and sigma14). The paratemers n, +before the optional eps14 and sigma14). The parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the cutoffs. @@ -192,7 +192,7 @@ NOTES: When using the core-softed Coulomb potentials with long-range solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.) in a free energy calculation in which sites holding electrostatic charges are -being created or anihilated (using "fix adapt/fep"_fix_adapt_fep.html +being created or annihilated (using "fix adapt/fep"_fix_adapt_fep.html and "compute fep"_compute_fep.html) it is important to adapt both the lambda activation parameter (from 0 to 1, or the reverse) and the value of the charge (from 0 to its final value, or the reverse). This diff -Naur lammps-21Feb17/doc/src/pair_lubricate.txt lammps-7Mar17/doc/src/pair_lubricate.txt --- lammps-21Feb17/doc/src/pair_lubricate.txt 2016-05-31 10:04:35.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_lubricate.txt 2017-03-07 09:48:20.062786000 -0700 @@ -94,7 +94,7 @@ {lubricate/poly} allows for polydisperse spherical particles. The viscosity {mu} can be varied in a time-dependent manner over the -course of a simluation, in which case in which case the pair_style +course of a simulation, in which case in which case the pair_style setting for {mu} will be overridden. See the "fix adapt"_fix_adapt.html command for details. diff -Naur lammps-21Feb17/doc/src/pair_meam_spline.txt lammps-7Mar17/doc/src/pair_meam_spline.txt --- lammps-21Feb17/doc/src/pair_meam_spline.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_meam_spline.txt 2017-03-07 09:48:20.062786000 -0700 @@ -140,5 +140,5 @@ :link(Lenosky) [(Lenosky)] Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, -Kress, Modelling Simulation Materials Science Enginerring, 8, 825 +Kress, Modelling Simulation Materials Science Engineering, 8, 825 (2000). diff -Naur lammps-21Feb17/doc/src/pair_mgpt.txt lammps-7Mar17/doc/src/pair_mgpt.txt --- lammps-21Feb17/doc/src/pair_mgpt.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_mgpt.txt 2017-03-07 09:48:20.062786000 -0700 @@ -75,7 +75,7 @@ by the code as Omega = V/N. In addition, the volume term E_vol and the potentials v_2, v_3 and v_4 have to be removed at the end of the time step, and then respecified at the new value of Omega. In all -smulations, Omega must remain within the defined volume range for +simulations, Omega must remain within the defined volume range for E_vol and the potentials for the given material. The default option volpress yes in the "pair_coeff"_pair_coeff.html diff -Naur lammps-21Feb17/doc/src/pair_mie.txt lammps-7Mar17/doc/src/pair_mie.txt --- lammps-21Feb17/doc/src/pair_mie.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_mie.txt 2017-03-07 09:48:20.062786000 -0700 @@ -57,7 +57,7 @@ For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of the mie/cut pair styles can be mixed. -If not explicity defined, both the repulsive and attractive gamma +If not explicitly defined, both the repulsive and attractive gamma exponents for different atoms will be calculated following the same mixing rule defined for distances. The default mix value is {geometric}. See the "pair_modify" command for details. diff -Naur lammps-21Feb17/doc/src/pair_morse.txt lammps-7Mar17/doc/src/pair_morse.txt --- lammps-21Feb17/doc/src/pair_morse.txt 2017-02-03 14:45:56.000000000 -0700 +++ lammps-7Mar17/doc/src/pair_morse.txt 2017-03-07 09:48:20.062786000 -0700 @@ -80,7 +80,7 @@ The {morse/soft} variant is similar to the {lj/cut/soft} pair style in that it modifies the potential at short range to have a soft core. This helps to avoid singularities during free energy calculation in -which sites are created or anihilated. The formula differs from that +which sites are created or annihilated. The formula differs from that of {lj/cut/soft}, and is instead given by: :c,image(Eqs/pair_morse_soft.jpg) diff -Naur lammps-21Feb17/doc/src/pair_oxdna.txt lammps-7Mar17/doc/src/pair_oxdna.txt --- lammps-21Feb17/doc/src/pair_oxdna.txt 1969-12-31 17:00:00.000000000 -0700 +++ lammps-7Mar17/doc/src/pair_oxdna.txt 2017-03-07 09:48:20.062786000 -0700 @@ -0,0 +1,80 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style oxdna/excv command :h3 +pair_style oxdna/stk command :h3 +pair_style oxdna/hbond command :h3 +pair_style oxdna/xstk command :h3 +pair_style oxdna/coaxstk command :h3 + +[Syntax:] + +pair_style style :pre + +style = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul + +[Examples:] + +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre + +[Description:] + +The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field +for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the +excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk} +and coaxial stacking interaction {oxdna/coaxstk} as well +as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on +opposite strands. + +The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients +in the above example. The individual potentials consist of products of modulation factors, +which themselves are constructed from a number of more basic potentials +(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. +We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil and "(Ouldridge)"_#Ouldridge +for a detailed description of the oxDNA force field. + +NOTE: These pair styles have to be used together with the related oxDNA bond style +{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of +"bond_style oxdna/fene"_bond_oxdna.html). The coefficients +in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. + +Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/. +A simple python setup tool which creates single straight or helical DNA strands, +DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. +A technical report with more information on the model, the structure of the input file, +the setup tool and the performance of the LAMMPS-implementation of oxDNA +can be found "here"_PDF/USER-CGDNA-overview.pdf. + +:line + +[Restrictions:] + +These pair styles can only be used if LAMMPS was built with the +USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info on packages. + +[Related commands:] + +"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html + +[Default:] none + +:line + +:link(Ouldridge-DPhil) +[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). + +:link(Ouldridge) +[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). diff -Naur lammps-21Feb17/doc/src/pair_oxdna_excv.txt lammps-7Mar17/doc/src/pair_oxdna_excv.txt --- lammps-21Feb17/doc/src/pair_oxdna_excv.txt 2017-01-18 11:33:29.000000000 -0700 +++ lammps-7Mar17/doc/src/pair_oxdna_excv.txt 1969-12-31 17:00:00.000000000 -0700 @@ -1,80 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -pair_style oxdna_excv command :h3 -pair_style oxdna_stk command :h3 -pair_style oxdna_hbond command :h3 -pair_style oxdna_xstk command :h3 -pair_style oxdna_coaxstk command :h3 - -[Syntax:] - -pair_style style :pre - -style = {hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk} :ul - -[Examples:] - -pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk -pair_coeff * * oxdna_excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna_stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna_hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna_xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre - -[Description:] - -The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field -for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the -excluded volume interaction {oxdna_excv}, the stacking {oxdna_stk}, cross-stacking {oxdna_xstk} -and coaxial stacking interaction {oxdna_coaxstk} as well -as the hydrogen-bonding interaction {oxdna_hbond} between complementary pairs of nucleotides on -opposite strands. - -The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients -in the above example. The individual potentials consist of products of modulation factors, -which themselves are constructed from a number of more basic potentials -(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. -We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil and "(Ouldridge)"_#Ouldridge -for a detailed description of the oxDNA force field. - -NOTE: These pair styles have to be used together with the related oxDNA bond style -{oxdna_fene} for the connectivity of the phosphate backbone (see also documentation of -"bond_style oxdna_fene"_bond_oxdna_fene.html). The coefficients -in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. - -Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/. -A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/. -A technical report with more information on the model, the structure of the input file, -the setup tool and the performance of the LAMMPS-implementation of oxDNA -can be found "here"_PDF/USER-CGDNA-overview.pdf. - -:line - -[Restrictions:] - -These pair styles can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. - -[Related commands:] - -"bond_style oxdna_fene"_bond_oxdna_fene.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Ouldridge-DPhil) -[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). - -:link(Ouldridge) -[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). diff -Naur lammps-21Feb17/doc/src/pair_peri.txt lammps-7Mar17/doc/src/pair_peri.txt --- lammps-21Feb17/doc/src/pair_peri.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_peri.txt 2017-03-07 09:48:20.062786000 -0700 @@ -116,7 +116,7 @@ used as a bond breaking criteria. m_lambdai and m_taubi are the viscoelastic relaxation parameter and time constant, respectively. m_lambdai varies within zero to one. For very small -values of m_lambdai the viscoelsatic model responds very similar to a +values of m_lambdai the viscoelastic model responds very similar to a linear elastic model. For details please see the description in "(Mtchell2011)". diff -Naur lammps-21Feb17/doc/src/pair_quip.txt lammps-7Mar17/doc/src/pair_quip.txt --- lammps-21Feb17/doc/src/pair_quip.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_quip.txt 2017-03-07 09:48:20.062786000 -0700 @@ -45,12 +45,12 @@ to specify the path for the potential file. A QUIP potential is fully specified by the filename which contains the -parameters of the potential in XML format, the initialisation string, +parameters of the potential in XML format, the initialization string, and the map of atomic numbers. GAP potentials can be obtained from the Data repository section of "http://www.libatoms.org"_http://www.libatoms.org, where the -appropriate initialisation strings are also advised. The list of +appropriate initialization strings are also advised. The list of atomic numbers must be matched to the LAMMPS atom types specified in the LAMMPS data file or elsewhere. diff -Naur lammps-21Feb17/doc/src/pair_resquared.txt lammps-7Mar17/doc/src/pair_resquared.txt --- lammps-21Feb17/doc/src/pair_resquared.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_resquared.txt 2017-03-07 09:48:20.062786000 -0700 @@ -58,17 +58,17 @@ The parameters used depend on the type of the interacting particles, i.e. ellipsoids or LJ spheres. The type of a particle is determined -by the diameters specified for its 3 shape paramters. If all 3 shape +by the diameters specified for its 3 shape parameters. If all 3 shape parameters = 0.0, then the particle is treated as an LJ sphere. The epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If -the 3 shape paraemters are > 0.0, then the particle is treated as an +the 3 shape parameters are > 0.0, then the particle is treated as an ellipsoid (even if the 3 parameters are equal to each other). A12 specifies the energy prefactor which depends on the types of the two interacting particles. For ellipsoid/ellipsoid interactions, the interaction is computed by -the formulas in the supplementary docuement referenced above. A12 is +the formulas in the supplementary document referenced above. A12 is the Hamaker constant as described in "(Everaers)"_#Everaers. In LJ units: @@ -79,8 +79,8 @@ strength of the spherical particles. For ellipsoid/LJ sphere interactions, the interaction is also computed -by the formulas in the supplementary docuement referenced above. A12 -has a modifed form (see "here"_PDF/pair_resquared_extra.pdf for +by the formulas in the supplementary document referenced above. A12 +has a modified form (see "here"_PDF/pair_resquared_extra.pdf for details): :c,image(Eqs/pair_resquared2.jpg) diff -Naur lammps-21Feb17/doc/src/pair_smd_ulsph.txt lammps-7Mar17/doc/src/pair_smd_ulsph.txt --- lammps-21Feb17/doc/src/pair_smd_ulsph.txt 2016-11-30 14:03:35.000000000 -0700 +++ lammps-7Mar17/doc/src/pair_smd_ulsph.txt 2017-03-07 09:48:20.062786000 -0700 @@ -31,7 +31,7 @@ Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is defined. Note that {i} and {j} can be different, i.e., {ulsph} cross interactions -between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to preceed a cross interaction. +between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to precede a cross interaction. In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a number of floats and integers, the {ulsph} {pair coeff} definition is organised using keywords. These keywords mark the beginning of different sets of parameters for particle properties, diff -Naur lammps-21Feb17/doc/src/pair_smtbq.txt lammps-7Mar17/doc/src/pair_smtbq.txt --- lammps-21Feb17/doc/src/pair_smtbq.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_smtbq.txt 2017-03-07 09:48:20.062786000 -0700 @@ -36,7 +36,7 @@ The parameters appearing in the upper expressions are set in the ffield.SMTBQ.Syst file where Syst corresponds to the selected system -(e.g. field.SMTBQ.Al2O3). Exemples for TiO2, +(e.g. field.SMTBQ.Al2O3). Examples for TiO2, Al2O3 are provided. A single pair_coeff command is used with the SMTBQ styles which provides the path to the potential file with parameters for needed elements. These are mapped to LAMMPS diff -Naur lammps-21Feb17/doc/src/pair_soft.txt lammps-7Mar17/doc/src/pair_soft.txt --- lammps-21Feb17/doc/src/pair_soft.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_soft.txt 2017-03-07 09:48:20.062786000 -0700 @@ -60,7 +60,7 @@ through the "fix adapt"_fix_adapt.html command, as explained below. Note that if you use an old input script and specify Astart and Astop without a cutoff, then LAMMPS will interpret that as A and a cutoff, -which is probabably not what you want. +which is probably not what you want. The "fix adapt"_fix_adapt.html command can be used to vary A for one or more pair types over the course of a simulation, in which case diff -Naur lammps-21Feb17/doc/src/pair_sph_heatconduction.txt lammps-7Mar17/doc/src/pair_sph_heatconduction.txt --- lammps-21Feb17/doc/src/pair_sph_heatconduction.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_sph_heatconduction.txt 2017-03-07 09:48:20.062786000 -0700 @@ -20,7 +20,7 @@ [Description:] The sph/heatconduction style computes heat transport between SPH particles. -The transport model is the diffusion euqation for the internal energy. +The transport model is the diffusion equation for the internal energy. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff -Naur lammps-21Feb17/doc/src/pair_sph_idealgas.txt lammps-7Mar17/doc/src/pair_sph_idealgas.txt --- lammps-21Feb17/doc/src/pair_sph_idealgas.txt 2016-05-12 10:33:14.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_sph_idealgas.txt 2017-03-07 09:48:20.062786000 -0700 @@ -27,7 +27,7 @@ where gamma = 1.4 is the heat capacity ratio, rho is the local density, and e is the internal energy per unit mass. This pair style also computes Monaghan's artificial viscosity to prevent particles -from interpentrating "(Monaghan)"_#ideal-Monoghan. +from interpenetrating "(Monaghan)"_#ideal-Monoghan. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff -Naur lammps-21Feb17/doc/src/pair_sph_lj.txt lammps-7Mar17/doc/src/pair_sph_lj.txt --- lammps-21Feb17/doc/src/pair_sph_lj.txt 2016-05-09 11:22:38.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_sph_lj.txt 2017-03-07 09:48:20.062786000 -0700 @@ -24,7 +24,7 @@ Ree's 1980 polynomial fit "(Ree)"_#Ree. The Lennard-Jones parameters epsilon and sigma are set to unity. This pair style also computes Monaghan's artificial viscosity to prevent particles from -interpentrating "(Monaghan)"_#Monoghan. +interpenetrating "(Monaghan)"_#Monoghan. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff -Naur lammps-21Feb17/doc/src/pair_sph_taitwater.txt lammps-7Mar17/doc/src/pair_sph_taitwater.txt --- lammps-21Feb17/doc/src/pair_sph_taitwater.txt 2016-05-12 07:58:19.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_sph_taitwater.txt 2017-03-07 09:48:20.062786000 -0700 @@ -28,7 +28,7 @@ reference density and c_0 the reference speed of sound. This pair style also computes Monaghan's artificial viscosity to -prevent particles from interpentrating "(Monaghan)"_#Monaghan. +prevent particles from interpenetrating "(Monaghan)"_#Monaghan. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff -Naur lammps-21Feb17/doc/src/pair_srp.txt lammps-7Mar17/doc/src/pair_srp.txt --- lammps-21Feb17/doc/src/pair_srp.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_srp.txt 2017-03-07 09:48:20.062786000 -0700 @@ -86,7 +86,7 @@ types in your system accordingly; usually to be one larger than what would normally be the case, e.g. via the "create_box"_create_box.html or by changing the header in your "data file"_read_data.html. The -ficitious "bond particles" are inserted at the beginning of the run, +fictitious "bond particles" are inserted at the beginning of the run, and serve as placeholders that define the position of the bonds. This allows neighbor lists to be constructed and pairwise interactions to be computed in almost the same way as is done for actual particles. diff -Naur lammps-21Feb17/doc/src/pair_table.txt lammps-7Mar17/doc/src/pair_table.txt --- lammps-21Feb17/doc/src/pair_table.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_table.txt 2017-03-07 09:48:20.062786000 -0700 @@ -33,7 +33,7 @@ Style {table} creates interpolation tables from potential energy and force values listed in a file(s) as a function of distance. When -performing dynamics or minimation, the interpolation tables are used +performing dynamics or minimization, the interpolation tables are used to evaluate energy and forces for pairwise interactions between particles, similar to how analytic formulas are used for other pair styles. @@ -180,7 +180,7 @@ file are effectively ignored, and replaced by new values as described in the previous paragraph. If the distance value in the table is not very close to the new value (i.e. round-off difference), then you will -be assingning energy/force values to a different distance, which is +be assigning energy/force values to a different distance, which is probably not what you want. LAMMPS will warn if this is occurring. If used, the parameter "BITMAP" is also followed by 2 values {rlo} and diff -Naur lammps-21Feb17/doc/src/pair_tri_lj.txt lammps-7Mar17/doc/src/pair_tri_lj.txt --- lammps-21Feb17/doc/src/pair_tri_lj.txt 2016-09-06 16:56:36.000000000 -0600 +++ lammps-7Mar17/doc/src/pair_tri_lj.txt 2017-03-07 09:48:20.062786000 -0700 @@ -42,7 +42,7 @@ following manner. Assume the triangle is of type I, and sigma_II has been specified. We want a set of spheres with centers in the plane of the triangle, none of them larger in diameter than sigma_II, which -completely cover the triangle's area, but with minimial overlap and a +completely cover the triangle's area, but with minimal overlap and a minimal total number of spheres. This is done in a recursive manner. Place a sphere at the centroid of the original triangle. Calculate what diameter it must have to just cover all 3 corner points of the diff -Naur lammps-21Feb17/doc/src/pairs.txt lammps-7Mar17/doc/src/pairs.txt --- lammps-21Feb17/doc/src/pairs.txt 2017-01-18 11:33:29.000000000 -0700 +++ lammps-7Mar17/doc/src/pairs.txt 2017-03-07 09:48:20.062786000 -0700 @@ -39,6 +39,7 @@ pair_hbond_dreiding pair_hybrid pair_kim + pair_kolmogorov_crespi_z pair_lcbop pair_line_lj pair_list @@ -65,7 +66,7 @@ pair_nb3b_harmonic pair_nm pair_none - pair_oxdna_excv + pair_oxdna pair_peri pair_polymorphic pair_quip diff -Naur lammps-21Feb17/doc/src/partition.txt lammps-7Mar17/doc/src/partition.txt --- lammps-21Feb17/doc/src/partition.txt 2016-09-16 10:20:06.000000000 -0600 +++ lammps-7Mar17/doc/src/partition.txt 2017-03-07 09:48:20.062786000 -0700 @@ -39,7 +39,7 @@ The "partition" command is another mechanism for having as input script operate differently on different partitions. It is basically a -prefix on any LAMMPS command. The commmand will only be invoked on +prefix on any LAMMPS command. The command will only be invoked on the partition(s) specified by the {style} and {N} arguments. If the {style} is {yes}, the command will be invoked on any partition diff -Naur lammps-21Feb17/doc/src/prd.txt lammps-7Mar17/doc/src/prd.txt --- lammps-21Feb17/doc/src/prd.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/prd.txt 2017-03-07 09:48:20.062786000 -0700 @@ -133,7 +133,7 @@ The event check is performed by a compute with the specified {compute-ID}. Currently there is only one compute that works with the -PRD commmand, which is the "compute +PRD command, which is the "compute event/displace"_compute_event_displace.html command. Other event-checking computes may be added. "Compute event/displace"_compute_event_displace.html checks whether any atom in @@ -230,7 +230,7 @@ the PRD command, these contain the thermodynamic output for each replica. You will see short runs and minimizations corresponding to the dynamics and quench operations of the loop listed above. The -timestep will be reset aprpopriately depending on whether the +timestep will be reset appropriately depending on whether the operation advances time or not. After the PRD command completes, timing statistics for the PRD run are diff -Naur lammps-21Feb17/doc/src/processors.txt lammps-7Mar17/doc/src/processors.txt --- lammps-21Feb17/doc/src/processors.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/processors.txt 2017-03-07 09:48:20.062786000 -0700 @@ -27,7 +27,7 @@ {map} arg = {cart} or {cart/reorder} or {xyz} or {xzy} or {yxz} or {yzx} or {zxy} or {zyx} cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0 cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1 - xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering + xyz,xzy,yxz,yzx,zxy,zyx = map processors to 3d grid in IJK ordering {numa} arg = none {part} args = Psend Precv cstyle Psend = partition # (1 to Np) which will send its processor layout @@ -104,7 +104,7 @@ If load-balancing is never invoked via the "balance"_balance.html or "fix balance"_fix_balance.html commands, then the initial regular grid will persist for all simulations. If balancing is performed, some of -the methods invoked by those commands retain the logical toplogy of +the methods invoked by those commands retain the logical topology of the initial 3d grid, and the mapping of processors to the grid specified by the processors command. However the grid spacings in different dimensions may change, so that processors own sub-domains of @@ -179,7 +179,7 @@ Px Py Py :pre These must be compatible with the total number of processors -and the Px, Py, Pz settings of the processors commmand. +and the Px, Py, Pz settings of the processors command. This line should be immediately followed by P = Px*Py*Pz lines of the form: @@ -244,7 +244,7 @@ It can be useful when running in multi-partition mode, e.g. with the "run_style verlet/split"_run_style.html command. It specifies a -dependency bewteen a sending partition {Psend} and a receiving +dependency between a sending partition {Psend} and a receiving partition {Precv} which is enforced when each is setting up their own mapping of their processors to the simulation box. Each of {Psend} and {Precv} must be integers from 1 to Np, where Np is the number of @@ -271,7 +271,7 @@ 4. NOTE: If you use the "partition"_partition.html command to invoke -different "processsors" commands on different partitions, and you also +different "processors" commands on different partitions, and you also use the {part} keyword, then you must insure that both the sending and receiving partitions invoke the "processors" command that connects the 2 partitions via the {part} keyword. LAMMPS cannot easily check for diff -Naur lammps-21Feb17/doc/src/python.txt lammps-7Mar17/doc/src/python.txt --- lammps-21Feb17/doc/src/python.txt 2016-12-16 10:22:59.000000000 -0700 +++ lammps-7Mar17/doc/src/python.txt 2017-03-07 09:48:20.062786000 -0700 @@ -143,7 +143,7 @@ As explained on the "variable"_variable.html doc page, the definition of a python-style variable associates a Python function name with the variable. This must match the {func} setting for this command. For -exampe these two commands would be self-consistent: +example these two commands would be self-consistent: variable foo python myMultiply python myMultiply return v_foo format f file funcs.py :pre @@ -174,7 +174,7 @@ value set to a larger number (the code allocates space for Nlen+1 to include the string terminator). If the Python function generates a string longer than the default 63 or the specified {Nlen}, it will be -trunctated. +truncated. :line @@ -356,7 +356,7 @@ This has the effect of looping over a series of 10 short runs (10 timesteps each) where the pair style cutoff is increased from a value of 1.0 in distance units, in increments of 0.1. The looping stops -when the per-atom potential energy falls below a threshhold of -4.0 in +when the per-atom potential energy falls below a threshold of -4.0 in energy units. More generally, Python can be used to implement a loop with complex logic, much more so than can be created using the LAMMPS "jump"_jump.html and "if"_if.html commands. @@ -372,7 +372,7 @@ return statement. This cutoff value in the "cut" variable is then substituted (by LAMMPS) in the pair_style command that is executed next. Alternatively, the "LAMMPS command option" line could be used -in place of the 2 preceeding lines, to have Python insert the value +in place of the 2 preceding lines, to have Python insert the value into the LAMMPS command string. NOTE: When using the callback mechanism just described, recognize that @@ -384,7 +384,7 @@ executed in the LAMMPS input script directly at the same point. However, a Python function can also be invoked during a run, whenever -an associated LAMMPS variable it is assigned to is evaluted. If the +an associated LAMMPS variable it is assigned to is evaluated. If the variable is an input argument to another LAMMPS command (e.g. "fix setforce"_fix_setforce.html), then the Python function will be invoked inside the class for that command, in one of its methods that is diff -Naur lammps-21Feb17/doc/src/read_data.txt lammps-7Mar17/doc/src/read_data.txt --- lammps-21Feb17/doc/src/read_data.txt 2016-10-24 08:19:10.000000000 -0600 +++ lammps-7Mar17/doc/src/read_data.txt 2017-03-07 09:48:20.062786000 -0700 @@ -180,7 +180,7 @@ sections will be stored correctly in the larger data structures allocated by the use of the {extra} keywords. E.g. the substrate file can list mass and pair coefficients for type 1 silicon atoms. The -water file can list mass and pair coeffcients for type 1 and type 2 +water file can list mass and pair coefficients for type 1 and type 2 hydrogen and oxygen atoms. Use of the {extra} and {offset} keywords will store those mass and pair coefficient values appropriately in data structures that allow for 3 atom types (Si, H, O). Of course, @@ -574,7 +574,7 @@ template-atom = which atom within a template molecule the atom is template-index = which molecule within the molecule template the atom is part of theta = internal temperature of a DPD particle -triangleflag = 1 for triangular particles, 0 for point or sperhical particles +triangleflag = 1 for triangular particles, 0 for point or spherical particles volume = volume of Peridynamic particle (distance^3 units) x,y,z = coordinates of atom (distance units) :ul diff -Naur lammps-21Feb17/doc/src/read_dump.txt lammps-7Mar17/doc/src/read_dump.txt --- lammps-21Feb17/doc/src/read_dump.txt 2017-01-09 10:47:31.000000000 -0700 +++ lammps-7Mar17/doc/src/read_dump.txt 2017-03-07 09:48:20.062786000 -0700 @@ -58,7 +58,7 @@ Read atom information from a dump file to overwrite the current atom coordinates, and optionally the atom velocities and image flags and -the simluation box dimensions. This is useful for restarting a run +the simulation box dimensions. This is useful for restarting a run from a particular snapshot in a dump file. See the "read_restart"_read_restart.html and "read_data"_read_data.html commands for alternative methods to do this. Also see the @@ -214,7 +214,7 @@ If the {box} keyword is specified with a {yes} value, then the current simulation box dimensions are replaced by the dump snapshot box dimensions. If the {box} keyword is specified with a {no} value, the -current simulatoin box is unchanged. +current simulation box is unchanged. If the {purge} keyword is specified with a {yes} value, then all current atoms in the system are deleted before any of the operations diff -Naur lammps-21Feb17/doc/src/read_restart.txt lammps-7Mar17/doc/src/read_restart.txt --- lammps-21Feb17/doc/src/read_restart.txt 2016-10-24 08:19:10.000000000 -0600 +++ lammps-7Mar17/doc/src/read_restart.txt 2017-03-07 09:48:20.062786000 -0700 @@ -31,7 +31,7 @@ below. Basically this operation will re-create the simulation box with all its atoms and their attributes as well as some related global settings, at the point in time it was written to the restart file by a -previous simluation. The simulation box will be partitioned into a +previous simulation. The simulation box will be partitioned into a regular 3d grid of rectangular bricks, one per processor, based on the number of processors in the current simulation and the settings of the "processors"_processors.html command. The partitioning can later be diff -Naur lammps-21Feb17/doc/src/region.txt lammps-7Mar17/doc/src/region.txt --- lammps-21Feb17/doc/src/region.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/region.txt 2017-03-07 09:48:20.062786000 -0700 @@ -212,7 +212,7 @@ The {units} keyword determines the meaning of the distance units used to define the region for any argument above listed as having distance -units. It also affects the scaling of the velocity vector specfied +units. It also affects the scaling of the velocity vector specified with the {vel} keyword, the amplitude vector specified with the {wiggle} keyword, and the rotation point specified with the {rotate} keyword, since they each involve a distance metric. @@ -283,9 +283,9 @@ variable dx equal ramp(0,10) region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL :pre -Note that the initial displacemet is 0.0, though that is not required. +Note that the initial displacement is 0.0, though that is not required. -Either of these varaibles would "wiggle" the region back and forth in +Either of these variables would "wiggle" the region back and forth in the y direction: variable dy equal swiggle(0,5,100) @@ -352,7 +352,7 @@ In the last example above, a {cone} region is defined along the z-axis that is open at the zlo value (e.g. for use as a funnel). -For all other styles, the {open} keyword is ignored. As inidcated +For all other styles, the {open} keyword is ignored. As indicated above, this includes the {intersect} and {union} regions, though their sub-regions can be defined with the {open} keyword. diff -Naur lammps-21Feb17/doc/src/replicate.txt lammps-7Mar17/doc/src/replicate.txt --- lammps-21Feb17/doc/src/replicate.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/replicate.txt 2017-03-07 09:48:20.062786000 -0700 @@ -53,7 +53,7 @@ NOTE: You cannot use the replicate command on a system which has a molecule that spans the box and is bonded to itself across a periodic -boundary, so that the molecule is efffectively a loop. A simple +boundary, so that the molecule is effectively a loop. A simple example would be a linear polymer chain that spans the simulation box and bonds back to itself across the periodic boundary. More realistic examples would be a CNT (meant to be an infinitely long CNT) or a diff -Naur lammps-21Feb17/doc/src/rerun.txt lammps-7Mar17/doc/src/rerun.txt --- lammps-21Feb17/doc/src/rerun.txt 2016-09-08 14:20:32.000000000 -0600 +++ lammps-7Mar17/doc/src/rerun.txt 2017-03-07 09:48:20.062786000 -0700 @@ -40,7 +40,7 @@ [Description:] -Perform a psuedo simulation run where atom information is read one +Perform a pseudo simulation run where atom information is read one snapshot at a time from a dump file(s), and energies and forces are computed on the shapshot to produce thermodynamic or other output. @@ -121,7 +121,7 @@ the {start}/{stop} or {first}/{last} keywords, then LAMMPS treats the pseudo run as going from 0 to a huge value (effectively infinity). This means that any quantity that a fix scales as a fraction of -elapsed time in the run, will essentially remain at its intiial value. +elapsed time in the run, will essentially remain at its initial value. Also note that an error will occur if you read a snapshot from the dump file with a timestep value larger than the {stop} setting you have specified. @@ -178,7 +178,7 @@ The various forms of LAMMPS output, as defined by the "thermo_style"_thermo_style.html, "thermo"_thermo.html, "dump"_dump.html, and "restart"_restart.html commands occur on -specific timesteps. If successvive dump snapshots skip those +specific timesteps. If successive dump snapshots skip those timesteps, then no output will be produced. E.g. if you request thermodynamic output every 100 steps, but the dump file snapshots are every 1000 steps, then you will only see thermodynamic output every diff -Naur lammps-21Feb17/doc/src/restart.txt lammps-7Mar17/doc/src/restart.txt --- lammps-21Feb17/doc/src/restart.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/restart.txt 2017-03-07 09:48:20.062786000 -0700 @@ -97,7 +97,7 @@ written on the last timestep of a minimization if N > 0 and the minimization converges. -Instead of a numeric value, N can be specifed as an "equal-style +Instead of a numeric value, N can be specified as an "equal-style variable"_variable.html, which should be specified as v_name, where name is the variable name. In this case, the variable is evaluated at the beginning of a run to determine the next timestep at which a diff -Naur lammps-21Feb17/doc/src/run_style.txt lammps-7Mar17/doc/src/run_style.txt --- lammps-21Feb17/doc/src/run_style.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/run_style.txt 2017-03-07 09:48:20.062786000 -0700 @@ -76,7 +76,7 @@ "kspace_style"_kspace_style.html portion of the force field on the 1st partition. This include the "pair style"_pair_style.html, "bond style"_bond_style.html, "neighbor list building"_neighbor.html, -"fixes"_fix.html including time intergration, and output. The +"fixes"_fix.html including time integration, and output. The "kspace_style"_kspace_style.html portion of the calculation is performed on the 2nd partition. @@ -105,23 +105,23 @@ procssors * * * part 1 2 multiple :pre You can also use the "partition"_partition.html command to explicitly -specity the processor layout on each partition. E.g. for 2 partitions +specify the processor layout on each partition. E.g. for 2 partitions of 60 and 15 processors each: partition yes 1 processors 3 4 5 partition yes 2 processors 3 1 5 :pre When you run in 2-partition mode with the {verlet/split} style, the -thermodyanmic data for the entire simulation will be output to the log +thermodynamic data for the entire simulation will be output to the log and screen file of the 1st partition, which are log.lammps.0 and screen.0 by default; see the "-plog and -pscreen command-line switches"_Section_start.html#start_7 to change this. The log and screen file for the 2nd partition will not contain thermodynamic -output beyone the 1st timestep of the run. +output beyond the 1st timestep of the run. See "Section 5"_Section_accelerate.html of the manual for performance details of the speed-up offered by the {verlet/split} -style. One important performance consideration is the assignemnt of +style. One important performance consideration is the assignment of logical processors in the 2 partitions to the physical cores of a parallel machine. The "processors"_processors.html command has options to support this, and strategies are discussed in @@ -182,7 +182,7 @@ requires as many level assignments as there are hybrid substyles, which assigns each sub-style to a rRESPA level, following their order of definition in the pair_style command. Since the {hybrid} keyword -operates on pair style computations, it is mututally exclusive with +operates on pair style computations, it is mutually exclusive with either the {pair} or the {inner}/{middle}/{outer} keywords. When using rRESPA (or for any MD simulation) care must be taken to diff -Naur lammps-21Feb17/doc/src/set.txt lammps-7Mar17/doc/src/set.txt --- lammps-21Feb17/doc/src/set.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/set.txt 2017-03-07 09:48:20.062786000 -0700 @@ -374,7 +374,7 @@ command. These keywords do not allow use of an atom-style variable. Keywords {meso/e}, {meso/cv}, and {meso/rho} set the energy, heat -capacity, and density of smmothed particle hydrodynamics (SPH) +capacity, and density of smoothed particle hydrodynamics (SPH) particles. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff -Naur lammps-21Feb17/doc/src/suffix.txt lammps-7Mar17/doc/src/suffix.txt --- lammps-21Feb17/doc/src/suffix.txt 2016-11-01 09:22:44.000000000 -0600 +++ lammps-7Mar17/doc/src/suffix.txt 2017-03-07 09:48:20.062786000 -0700 @@ -91,7 +91,7 @@ your input script use a standard LAMMPS style (i.e. a non-accelerated variant), which can be useful for testing or benchmarking purposes. Of course this is also possible by not using any suffix commands, and -explictly appending or not appending the suffix to the relevant +explicitly appending or not appending the suffix to the relevant commands in your input script. NOTE: The default "run_style"_run_style.html verlet is invoked prior to diff -Naur lammps-21Feb17/doc/src/tad.txt lammps-7Mar17/doc/src/tad.txt --- lammps-21Feb17/doc/src/tad.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/tad.txt 2017-03-07 09:48:20.062786000 -0700 @@ -130,7 +130,7 @@ The event check is performed by a compute with the specified {compute-ID}. Currently there is only one compute that works with the -TAD commmand, which is the "compute +TAD command, which is the "compute event/displace"_compute_event_displace.html command. Other event-checking computes may be added. "Compute event/displace"_compute_event_displace.html checks whether any atom in @@ -144,7 +144,7 @@ dynamics minimizer. The tolerances and limits for each NEB calculation can be set by the {neb} keyword. As discussed on the "neb"_neb.html, it is often advantageous to use a larger timestep for -NEB than for normal dyanmics. Since the size of the timestep set by +NEB than for normal dynamics. Since the size of the timestep set by the "timestep"_timestep.html command is used by TAD for performing dynamics, there is a {neb_step} keyword which can be used to set a larger timestep for each NEB calculation if desired. @@ -258,7 +258,7 @@ Note that within a single state, the dynamics will typically temporarily continue beyond the event that is ultimately chosen, until -the stopping criterionis satisfied. When the event is eventually +the stopping criterion is satisfied. When the event is eventually executed, the timestep counter is reset to the value when the event was detected. Similarly, after each quench and NEB minimization, the timestep counter is reset to the value at the start of the diff -Naur lammps-21Feb17/doc/src/thermo.txt lammps-7Mar17/doc/src/thermo.txt --- lammps-21Feb17/doc/src/thermo.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/thermo.txt 2017-03-07 09:48:20.062786000 -0700 @@ -30,7 +30,7 @@ "thermo_style"_thermo_style.html and "thermo_modify"_thermo_modify.html commands. -Instead of a numeric value, N can be specifed as an "equal-style +Instead of a numeric value, N can be specified as an "equal-style variable"_variable.html, which should be specified as v_name, where name is the variable name. In this case, the variable is evaluated at the beginning of a run to determine the next timestep at which diff -Naur lammps-21Feb17/doc/src/thermo_style.txt lammps-7Mar17/doc/src/thermo_style.txt --- lammps-21Feb17/doc/src/thermo_style.txt 2016-10-24 08:19:10.000000000 -0600 +++ lammps-7Mar17/doc/src/thermo_style.txt 2017-03-07 09:48:20.062786000 -0700 @@ -226,7 +226,7 @@ not been reset. If the timestep has changed (e.g. via "fix dt/reset"_fix_dt_reset.html) or the timestep has been reset (e.g. via the "reset_timestep" command), then the simulation time is effectively -a cummulative value up to the current point. +a cumulative value up to the current point. The {cpu} keyword is elapsed CPU seconds since the beginning of this run. The {tpcpu} and {spcpu} keywords are measures of how fast your @@ -236,7 +236,7 @@ picoseconds per CPU second. The {spcpu} keyword is the number of timesteps per CPU second. Both quantities are on-the-fly metrics, measured relative to the last time they were invoked. Thus if you are -printing out thermodyamic output every 100 timesteps, the two keywords +printing out thermodynamic output every 100 timesteps, the two keywords will continually output the time and timestep rate for the last 100 steps. The {tpcpu} keyword does not attempt to track any changes in timestep size, e.g. due to using the "fix dt/reset"_fix_dt_reset.html @@ -289,7 +289,7 @@ {cellgamma}, correspond to the usual crystallographic quantities that define the periodic unit cell of a crystal. See "this section"_Section_howto.html#howto_12 of the doc pages for a geometric -description of triclinic periodic cells, including a precise defintion +description of triclinic periodic cells, including a precise definition of these quantities in terms of the internal LAMMPS cell dimensions {lx}, {ly}, {lz}, {yz}, {xz}, {xy}. diff -Naur lammps-21Feb17/doc/src/timer.txt lammps-7Mar17/doc/src/timer.txt --- lammps-21Feb17/doc/src/timer.txt 2017-01-17 09:44:40.000000000 -0700 +++ lammps-7Mar17/doc/src/timer.txt 2017-03-07 09:48:20.062786000 -0700 @@ -16,7 +16,7 @@ {off} = do not collect or print any timing information {loop} = collect only the total time for the simulation loop {normal} = collect timer information broken down by sections (default) - {full} = like {normal} but also include CPU and thread utilzation + {full} = like {normal} but also include CPU and thread utilization {sync} = explicitly synchronize MPI tasks between sections {nosync} = do not synchronize MPI tasks between sections (default) {timeout} elapse = set walltime limit to {elapse} @@ -48,11 +48,11 @@ information for portions of the timestep (pairwise calculations, neighbor list construction, output, etc) are collected as well as information about load imbalances for those sections across -procsessors. The {full} setting adds information about CPU +processors. The {full} setting adds information about CPU utilization and thread utilization, when multi-threading is enabled. With the {sync} setting, all MPI tasks are synchronized at each timer -call which measures load imbalance for each section more accuractly, +call which measures load imbalance for each section more accurately, though it can also slow down the simulation by prohibiting overlapping independent computations on different MPI ranks Using the {nosync} setting (which is the default) turns this synchronization off. diff -Naur lammps-21Feb17/doc/src/tutorial_drude.txt lammps-7Mar17/doc/src/tutorial_drude.txt --- lammps-21Feb17/doc/src/tutorial_drude.txt 2016-11-04 11:01:14.000000000 -0600 +++ lammps-7Mar17/doc/src/tutorial_drude.txt 2017-03-07 09:48:20.062786000 -0700 @@ -72,17 +72,17 @@ The motion of of the Drude particles can be calculated by minimizing -the energy of the induced dipoles at each timestep, by an interative, +the energy of the induced dipoles at each timestep, by an iterative, self-consistent procedure. The Drude particles can be massless and therefore do not contribute to the kinetic energy. However, the -relaxed method is computationall slow. An extended-lagrangian method +relaxed method is computational slow. An extended-lagrangian method can be used to calculate the positions of the Drude particles, but this requires them to have mass. It is important in this case to decouple the degrees of freedom associated with the Drude oscillators from those of the normal atoms. Thermalizing the Drude dipoles at temperatures comparable to the rest of the simulation leads to several problems (kinetic energy transfer, very short timestep, etc.), which -can be remediated by the "cold Drude" technique ("Lamoureux and +can be remediate by the "cold Drude" technique ("Lamoureux and Roux"_#Lamoureux). Two closely related models are used to represent polarization through @@ -270,7 +270,7 @@ instance, a DP can escape from its DC and be captured by another DC, which makes the force and energy diverge and the simulation crash. Even without reaching this extreme case, the correlation -between nearby dipoles on the same molecule may be exagerated. Often, +between nearby dipoles on the same molecule may be exaggerated. Often, special bond relations prevent bonded neighboring atoms to see the charge of each other's DP, so that the problem does not always appear. It is possible to use screened dipole dipole interactions by using the diff -Naur lammps-21Feb17/doc/src/tutorial_pylammps.txt lammps-7Mar17/doc/src/tutorial_pylammps.txt --- lammps-21Feb17/doc/src/tutorial_pylammps.txt 2016-11-22 08:52:42.000000000 -0700 +++ lammps-7Mar17/doc/src/tutorial_pylammps.txt 2017-03-07 09:48:20.062786000 -0700 @@ -328,7 +328,7 @@ Examples of IPython notebooks can be found in the python/examples/pylammps subdirectory. To open these notebooks launch {jupyter notebook} inside this directory and navigate to one of them. If you compiled and installed -a LAMMPS shared library with execeptions, PNG, JPEG and FFMPEG support +a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support you should be able to rerun all of these notebooks. Validating a dihedral potential :h3 diff -Naur lammps-21Feb17/doc/src/units.txt lammps-7Mar17/doc/src/units.txt --- lammps-21Feb17/doc/src/units.txt 2016-10-06 12:59:16.000000000 -0600 +++ lammps-7Mar17/doc/src/units.txt 2017-03-07 09:48:20.062786000 -0700 @@ -73,7 +73,7 @@ electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon density = mass/volume, where rho* = rho sigma^dim :ul -Note that for LJ units, the default mode of thermodyamic output via +Note that for LJ units, the default mode of thermodynamic output via the "thermo_style"_thermo_style.html command is to normalize all extensive quantities by the number of atoms. E.g. potential energy is extensive because it is summed over atoms, so it is output as diff -Naur lammps-21Feb17/doc/src/variable.txt lammps-7Mar17/doc/src/variable.txt --- lammps-21Feb17/doc/src/variable.txt 2016-10-06 15:50:57.000000000 -0600 +++ lammps-7Mar17/doc/src/variable.txt 2017-03-07 09:48:20.062786000 -0700 @@ -501,7 +501,7 @@ :line -Numers, constants, and thermo keywords :h4 +Numbers, constants, and thermo keywords :h4 Numbers can contain digits, scientific notation (3.0e20,3.0e-20,3.0E20,3.0E-20), and leading minus signs. @@ -576,7 +576,7 @@ These relational and logical operators can be used as a masking or selection operation in a formula. For example, the number of atoms -whose properties satifsy one or more criteria could be calculated by +whose properties satisfy one or more criteria could be calculated by taking the returned per-atom vector of ones and zeroes and passing it to the "compute reduce"_compute_reduce.html command. @@ -623,7 +623,7 @@ is the nearest integer to its argument. The ramp(x,y) function uses the current timestep to generate a value -linearly intepolated between the specified x,y values over the course +linearly interpolated between the specified x,y values over the course of a run, according to this formula: value = x + (y-x) * (timestep-startstep) / (stopstep-startstep) :pre @@ -669,7 +669,7 @@ The stride(x,y,z) function uses the current timestep to generate a new timestep. X,y >= 0 and z > 0 and x <= y are required. The generated timesteps increase in increments of z, from x to y, i.e. it generates -the sequece x,x+z,x+2z,...,y. If y-x is not a multiple of z, then +the sequence x,x+z,x+2z,...,y. If y-x is not a multiple of z, then similar to the way a for loop operates, the last value will be one that does not exceed y. For any current timestep, the next timestep in the sequence is returned. Thus if stride(1000,2000,100) is used @@ -781,7 +781,7 @@ the variable. These functions operate on a global vector of inputs and reduce it to -a single scalar value. This is analagous to the operation of the +a single scalar value. This is analogous to the operation of the "compute reduce"_compute_reduce.html command, which performs similar operations on per-atom and local vectors. @@ -1068,7 +1068,7 @@ elsewhere in the input script. As discussed on this doc page, equal-style variables generate a single -global numeric value, vector-style variables gerarate a vector of +global numeric value, vector-style variables generate a vector of global numeric values, and atom-style and atomfile-style variables generate a per-atom vector of numeric values. All other variables store one or more strings. @@ -1169,7 +1169,7 @@ during the run. Note that it is a mistake to enclose a variable formula in double -quotes if it contains variables preceeded by $ signs. For example, +quotes if it contains variables preceded by $ signs. For example, variable vratio equal "$\{vfinal\}/$\{v0\}" :pre @@ -1214,7 +1214,7 @@ (1) The variable may be evaluated accurately. If it contains references to a compute or fix, and these values were calculated on -the last timestep of a preceeding run, then they will be accessed and +the last timestep of a preceding run, then they will be accessed and used by the variable and the result will be accurate. (2) LAMMPS may not be able to evaluate the variable and will generate diff -Naur lammps-21Feb17/doc/src/write_dump.txt lammps-7Mar17/doc/src/write_dump.txt --- lammps-21Feb17/doc/src/write_dump.txt 2016-10-24 08:19:10.000000000 -0600 +++ lammps-7Mar17/doc/src/write_dump.txt 2017-03-07 09:48:20.062786000 -0700 @@ -53,7 +53,7 @@ separate the two sets of args. Note that if the specified filename uses wildcard characters "*" or -"%", as supported by the "dump"_dump.html commmand, they will operate +"%", as supported by the "dump"_dump.html command, they will operate in the same fashion to create the new filename(s). Normally, "dump image"_dump_image.html files require a filename with a "*" character for the timestep. That is not the case for the write_dump command; no @@ -78,7 +78,7 @@ For example, it is not possible to dump per-atom energy with this command before a run has been performed, since no energies and forces have yet been calculated. See the "variable"_variable.html doc page -sectinn on Variable Accuracy for more information on this topic. +section on Variable Accuracy for more information on this topic. [Related commands:] diff -Naur lammps-21Feb17/doc/utils/sphinx-config/conf.py lammps-7Mar17/doc/utils/sphinx-config/conf.py --- lammps-21Feb17/doc/utils/sphinx-config/conf.py 2016-10-24 08:16:13.000000000 -0600 +++ lammps-7Mar17/doc/utils/sphinx-config/conf.py 2017-03-07 09:48:20.062786000 -0700 @@ -299,4 +299,11 @@ epub_author = 'The LAMMPS Developers' +# configure spelling extension if present +import importlib.util +spelling_spec = importlib.util.find_spec("sphinxcontrib.spelling") +if spelling_spec: + extensions.append('sphinxcontrib.spelling') + spelling_lang='en_US' + spelling_word_list_filename='false_positives.txt' diff -Naur lammps-21Feb17/doc/utils/sphinx-config/false_positives.txt lammps-7Mar17/doc/utils/sphinx-config/false_positives.txt --- lammps-21Feb17/doc/utils/sphinx-config/false_positives.txt 1969-12-31 17:00:00.000000000 -0700 +++ lammps-7Mar17/doc/utils/sphinx-config/false_positives.txt 2017-03-07 09:48:20.062786000 -0700 @@ -0,0 +1,2667 @@ +aa +aat +abc +abf 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+walltime +warmup +wavefunction +wavepacket +wavepackets +wavevector +wB +Wbody +Weckner +Wennberg +Westview +Whelan +whenthe +whitesmoke +whitespace +Wi +Wicaksono +wih +Wirnsberger +wirtes +witin +wn +Wolde +Worley +Wriggers +Wurtzite +www +wx +Wx +wy +Wy +wz +Wz +xa +xAVX +xb +Xc +xcm +Xcm +xCORE +Xeon +xflag +xhi +xHost +Xiaowang +xk +xlat +xlo +xmax +Xmax +xmgrace +xMIC +xmovie +Xmovie +xmu +Xmu +XP +XPlor +xrd +xs +xstk +xsu +xtc +xu +Xu +xy +xyz +xz +xzhou +Yamada +Ybar +ybox +Yc +ycm +Yeh +yellowgreen +yflag +yhi +yi +ylat +ylo +Yoshida +ys +ysu +yu +Yu +yukawa +Yukawa +yx +yy +yz +Zannoni +zbl +ZBL +Zc +zcm +Zepeda +zflag +Zhang +zhi +Zhou +Zhu +zi +Zi +ziegenhain +Ziegenhain +Zj +zlim +zlo +zN +zs +zsu +zu +zx +zy +Zybin +zz diff -Naur lammps-21Feb17/doc/utils/txt2html/README.html lammps-7Mar17/doc/utils/txt2html/README.html --- lammps-21Feb17/doc/utils/txt2html/README.html 2016-05-10 08:05:06.000000000 -0600 +++ lammps-7Mar17/doc/utils/txt2html/README.html 2017-03-07 09:48:20.062786000 -0700 @@ -205,7 +205,7 @@
  • "}" (right bracket) --> turn-off italics by inserting a </I> -

    If a backspace '\' preceeds any of the bold/italic mark-up characters, +

    If a backspace '\' precedes any of the bold/italic mark-up characters, then mark-up is not performed; the mark-up character is simply left in the text.

    diff -Naur lammps-21Feb17/doc/utils/txt2html/txt2html.cpp lammps-7Mar17/doc/utils/txt2html/txt2html.cpp --- lammps-21Feb17/doc/utils/txt2html/txt2html.cpp 2016-05-10 08:05:06.000000000 -0600 +++ lammps-7Mar17/doc/utils/txt2html/txt2html.cpp 2017-03-07 09:48:20.062786000 -0700 @@ -561,7 +561,7 @@ string punctuation = ".,?!;:()"; // substitute for bold & italic markers - // if preceeded by \ char, then leave markers in text + // if preceded by \ char, then leave markers in text n = s.find_first_of("[]{}"); while (n != string::npos) { diff -Naur lammps-21Feb17/examples/KAPPA/README lammps-7Mar17/examples/KAPPA/README --- lammps-21Feb17/examples/KAPPA/README 2016-06-07 12:16:44.000000000 -0600 +++ lammps-7Mar17/examples/KAPPA/README 2017-03-07 09:48:20.062786000 -0700 @@ -85,7 +85,7 @@ (4) in.mp dQ = 15087 / 100 / 18.82^2 / 2 - 15087 = cummulative delta energy, tallied by fix thermal/conductivity + 15087 = cumulative delta energy, tallied by fix thermal/conductivity 100 = 20,000 steps at 0.005 tau timestep = run time in tau xy box area = 18.82^2 divide by 2 since energy flux goes in 2 directions due to periodic z diff -Naur lammps-21Feb17/examples/README lammps-7Mar17/examples/README --- lammps-21Feb17/examples/README 2017-01-09 11:15:00.000000000 -0700 +++ lammps-7Mar17/examples/README 2017-03-07 09:48:20.062786000 -0700 @@ -93,7 +93,7 @@ pour: pouring of granular particles into a 3d box, then chute flow prd: parallel replica dynamics of vacancy diffusion in bulk Si python: use of PYTHON package to invoke Python code from input script -qeq: use of QEQ pacakge for charge equilibration +qeq: use of QEQ package for charge equilibration reax: RDX and TATB models using the ReaxFF rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void diff -Naur lammps-21Feb17/examples/USER/atc/README lammps-7Mar17/examples/USER/atc/README --- lammps-21Feb17/examples/USER/atc/README 2013-08-21 18:22:23.000000000 -0600 +++ lammps-7Mar17/examples/USER/atc/README 2017-03-07 09:48:20.062786000 -0700 @@ -65,7 +65,7 @@ in.bar1d_ghost_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from ghost atoms in.bar1d_thermo_elastic - Quasi-1D finite temperature elastic wave propagation in.cnt_electrostatic - Mechanical response of CNT with fixed charge density in an electric field - in.cnt_electrostatic2 - Mechanical reponse of CNT with self-consistent charge density and electric field + in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field @@ -146,7 +146,7 @@ in.bar1d_ghost_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from ghost atoms in.bar1d_thermo_elastic - Quasi-1D finite temperature elastic wave propagation in.cnt_electrostatic - Mechanical response of CNT with fixed charge density in an electric field - in.cnt_electrostatic2 - Mechanical reponse of CNT with self-consistent charge density and electric field + in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field diff -Naur lammps-21Feb17/examples/USER/atc/fluids/in.bar1d_fluids lammps-7Mar17/examples/USER/atc/fluids/in.bar1d_fluids --- lammps-21Feb17/examples/USER/atc/fluids/in.bar1d_fluids 2013-08-07 15:29:05.000000000 -0600 +++ lammps-7Mar17/examples/USER/atc/fluids/in.bar1d_fluids 2017-03-07 09:48:20.062786000 -0700 @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff -Naur lammps-21Feb17/examples/USER/atc/thermal/in.bar1d lammps-7Mar17/examples/USER/atc/thermal/in.bar1d --- lammps-21Feb17/examples/USER/atc/thermal/in.bar1d 2013-08-22 18:14:37.000000000 -0600 +++ lammps-7Mar17/examples/USER/atc/thermal/in.bar1d 2017-03-07 09:48:20.062786000 -0700 @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at 40. +# temperature is initially 20 everywhere and the left boundary BC is fixed at 40. # The result should show heat diffusing through the FEM to the MD and back out # to the FEM on the right. Insufficient time is captured to reach the linear # steady state, but heat crossing both boundaries should be observed. diff -Naur lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_all_atoms lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_all_atoms --- lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_all_atoms 2013-08-07 15:29:05.000000000 -0600 +++ lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_all_atoms 2017-03-07 09:48:20.062786000 -0700 @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests thermostats applied in all atom simulations. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff -Naur lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_combined lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_combined --- lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_combined 2013-08-07 15:29:05.000000000 -0600 +++ lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_combined 2017-03-07 09:48:20.062786000 -0700 @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into an MD region at a fixed temperature at one end. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing the boundaries should be observed, diff -Naur lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_flux lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_flux --- lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_flux 2013-08-07 15:29:05.000000000 -0600 +++ lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_flux 2017-03-07 09:48:20.062786000 -0700 @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff -Naur lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_frac_step lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_frac_step --- lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_frac_step 2013-08-28 16:16:56.000000000 -0600 +++ lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_frac_step 2017-03-07 09:48:20.062786000 -0700 @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff -Naur lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_hoover lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_hoover --- lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_hoover 2013-08-07 15:29:05.000000000 -0600 +++ lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_hoover 2017-03-07 09:48:20.062786000 -0700 @@ -1,6 +1,6 @@ # AtC Thermal Coupling # This benchmark tests thermostats applied in all atom simulations. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff -Naur lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_interpolate lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_interpolate --- lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_interpolate 2013-08-07 15:29:05.000000000 -0600 +++ lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_interpolate 2017-03-07 09:48:20.062786000 -0700 @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff -Naur lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_lumped lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_lumped --- lammps-21Feb17/examples/USER/atc/thermal/in.bar1d_lumped 2013-08-07 15:29:05.000000000 -0600 +++ lammps-7Mar17/examples/USER/atc/thermal/in.bar1d_lumped 2017-03-07 09:48:20.062786000 -0700 @@ -1,6 +1,6 @@ #AtC Thermal Coupling # This benchmark tests heat conducting into and out of the MD region. The -# temperature is intially 20 everywhere and the left boundary BC is fixed at +# temperature is initially 20 everywhere and the left boundary BC is fixed at # 40.# The result should show heat diffusing through the FEM to the MD and back # out # to the FEM on the right. Insufficient time is captured to reach the # linear # steady state, but heat crossing both boundaries should be observed. diff -Naur lammps-21Feb17/examples/USER/lb/confined_colloid/in.confined_colloids lammps-7Mar17/examples/USER/lb/confined_colloid/in.confined_colloids --- lammps-21Feb17/examples/USER/lb/confined_colloid/in.confined_colloids 2013-11-07 13:05:59.000000000 -0700 +++ lammps-7Mar17/examples/USER/lb/confined_colloid/in.confined_colloids 2017-03-07 09:48:20.062786000 -0700 @@ -67,7 +67,7 @@ #--------------------------------------------------------------------------- # Create a lattice-Boltzmann fluid covering the simulation domain. # This fluid feels a force due to the particles specified through FluidAtoms -# (however, this fix does not explicity apply a force back on to these +# (however, this fix does not explicitly apply a force back on to these # particles...this is accomplished through the use of the viscous_lb fix). # Use the standard LB integration scheme, a fluid density = 1.0, # fluid viscosity = 1.0, lattice spacing dx=0.06, and mass unit, dm=0.00003. diff -Naur lammps-21Feb17/examples/USER/lb/microrheology/in.microrheology_default_gamma lammps-7Mar17/examples/USER/lb/microrheology/in.microrheology_default_gamma --- lammps-21Feb17/examples/USER/lb/microrheology/in.microrheology_default_gamma 2013-11-07 13:05:59.000000000 -0700 +++ lammps-7Mar17/examples/USER/lb/microrheology/in.microrheology_default_gamma 2017-03-07 09:48:20.062786000 -0700 @@ -61,7 +61,7 @@ #--------------------------------------------------------------------------- # Create a lattice-Boltzmann fluid covering the simulation domain. # This fluid feels a force due to the particles specified through FluidAtoms -# (however, this fix does not explicity apply a force back on to these +# (however, this fix does not explicitly apply a force back on to these # particles...this is accomplished through the use of the viscous_lb fix). # Use the standard LB integration scheme, a fluid viscosity = 1.0, fluid # density= 0.0009982071, lattice spacing dx=1.2, and mass unit, dm=0.003. diff -Naur lammps-21Feb17/examples/USER/lb/microrheology/in.microrheology_set_gamma lammps-7Mar17/examples/USER/lb/microrheology/in.microrheology_set_gamma --- lammps-21Feb17/examples/USER/lb/microrheology/in.microrheology_set_gamma 2013-11-07 13:05:59.000000000 -0700 +++ lammps-7Mar17/examples/USER/lb/microrheology/in.microrheology_set_gamma 2017-03-07 09:48:20.062786000 -0700 @@ -61,7 +61,7 @@ #--------------------------------------------------------------------------- # Create a lattice-Boltzmann fluid covering the simulation domain. # This fluid feels a force due to the particles specified through FluidAtoms -# (however, this fix does not explicity apply a force back on to these +# (however, this fix does not explicitly apply a force back on to these # particles...this is accomplished through the use of the rigid_pc_sphere # fix). # Use the LB integration scheme of Ollila et. al. (for stability reasons, diff -Naur lammps-21Feb17/examples/USER/lb/planewall/in.planewall_default_gamma lammps-7Mar17/examples/USER/lb/planewall/in.planewall_default_gamma --- lammps-21Feb17/examples/USER/lb/planewall/in.planewall_default_gamma 2013-11-07 13:05:59.000000000 -0700 +++ lammps-7Mar17/examples/USER/lb/planewall/in.planewall_default_gamma 2017-03-07 09:48:20.062786000 -0700 @@ -54,7 +54,7 @@ #---------------------------------------------------------------------------- # Create a lattice-Boltzmann fluid covering the simulation domain. # All of the particles in the simulation apply a force to the fluid. -# (however, this fix does not explicity apply a force back on to these +# (however, this fix does not explicitly apply a force back on to these # particles...this is accomplished through the use of the viscous_lb fix. # Use the standard LB integration scheme, a fluid density = 1.0, # fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0. diff -Naur lammps-21Feb17/examples/USER/lb/planewall/in.planewall_set_gamma lammps-7Mar17/examples/USER/lb/planewall/in.planewall_set_gamma --- lammps-21Feb17/examples/USER/lb/planewall/in.planewall_set_gamma 2013-11-07 13:05:59.000000000 -0700 +++ lammps-7Mar17/examples/USER/lb/planewall/in.planewall_set_gamma 2017-03-07 09:48:20.062786000 -0700 @@ -54,7 +54,7 @@ #---------------------------------------------------------------------------- # Create a lattice-Boltzmann fluid covering the simulation domain. # All of the particles in the simulation apply a force to the fluid. -# (however, this fix does not explicity apply a force back on to these +# (however, this fix does not explicitly apply a force back on to these # particles...this is accomplished through the use of the rigid_pc_sphere # fix). # Use the LB integration scheme of Ollila et. al. (for stability reasons, diff -Naur lammps-21Feb17/examples/USER/lb/polymer/data.polymer lammps-7Mar17/examples/USER/lb/polymer/data.polymer --- lammps-21Feb17/examples/USER/lb/polymer/data.polymer 2013-11-07 13:05:59.000000000 -0700 +++ lammps-7Mar17/examples/USER/lb/polymer/data.polymer 2017-03-07 09:48:20.062786000 -0700 @@ -1,1040 +1,1040 @@ -Position data for a 32-bead polymer consisting of 31-vertex extended spheres - -992 atoms -31 bonds - -2 atom types -1 bond types - -0 40 xlo xhi -0 40 ylo yhi -0 40 zlo zhi - -Atoms - -1 1 21.0439 24.2646 23.1337 1 -2 2 20.3839 24.2646 23.3669 1 -3 2 20.8557 23.6306 23.3629 1 -4 2 21.5866 23.883 23.3569 1 -5 2 21.5866 24.6463 23.3569 1 -6 2 20.8558 24.8987 23.3629 1 -7 2 20.3839 24.2646 22.9005 1 -8 2 20.8558 23.6306 22.9045 1 -9 2 21.5866 23.883 22.9105 1 -10 2 21.5866 24.6463 22.9105 1 -11 2 20.8557 24.8987 22.9045 1 -12 2 21.6158 24.2646 23.5374 1 -13 2 21.2339 24.8002 23.5425 1 -14 2 20.595 24.6026 23.5511 1 -15 2 20.595 23.9267 23.5511 1 -16 2 21.2339 23.7291 23.5425 1 -17 2 21.6158 24.2646 22.73 1 -18 2 21.2339 24.8002 22.7249 1 -19 2 20.595 24.6026 22.7163 1 -20 2 20.595 23.9267 22.7163 1 -21 2 21.2339 23.7291 22.7249 1 -22 2 21.3444 24.2646 23.7659 1 -23 2 21.1464 24.5394 23.7693 1 -24 2 20.8215 24.436 23.7749 1 -25 2 20.8215 24.0933 23.7749 1 -26 2 21.1464 23.9899 23.7693 1 -27 2 21.3444 24.2646 22.5015 1 -28 2 21.1464 24.5394 22.4981 1 -29 2 20.8214 24.436 22.4925 1 -30 2 20.8214 24.0933 22.4925 1 -31 2 21.1464 23.9899 22.4981 1 -32 1 21.5789 25.5745 23.3738 2 -33 2 20.9189 25.5745 23.6069 2 -34 2 21.3907 24.9404 23.603 2 -35 2 22.1216 25.1929 23.597 2 -36 2 22.1216 25.9562 23.597 2 -37 2 21.3907 26.2086 23.603 2 -38 2 20.9189 25.5745 23.1406 2 -39 2 21.3907 24.9404 23.1446 2 -40 2 22.1216 25.1929 23.1505 2 -41 2 22.1216 25.9562 23.1505 2 -42 2 21.3907 26.2086 23.1446 2 -43 2 22.1507 25.5745 23.7775 2 -44 2 21.7688 26.1101 23.7826 2 -45 2 21.13 25.9125 23.7912 2 -46 2 21.13 25.2365 23.7912 2 -47 2 21.7688 25.039 23.7826 2 -48 2 22.1507 25.5745 22.97 2 -49 2 21.7688 26.1101 22.965 2 -50 2 21.13 25.9125 22.9563 2 -51 2 21.13 25.2365 22.9563 2 -52 2 21.7688 25.039 22.965 2 -53 2 21.8794 25.5745 24.006 2 -54 2 21.6814 25.8493 24.0094 2 -55 2 21.3564 25.7458 24.015 2 -56 2 21.3564 25.4032 24.015 2 -57 2 21.6814 25.2997 24.0094 2 -58 2 21.8794 25.5745 22.7416 2 -59 2 21.6814 25.8493 22.7382 2 -60 2 21.3564 25.7458 22.7326 2 -61 2 21.3564 25.4032 22.7326 2 -62 2 21.6814 25.2997 22.7382 2 -63 1 22.5101 25.4302 22.2914 3 -64 2 21.8501 25.4302 22.5246 3 -65 2 22.322 24.7961 22.5206 3 -66 2 23.0528 25.0485 22.5146 3 -67 2 23.0528 25.8118 22.5146 3 -68 2 22.322 26.0643 22.5206 3 -69 2 21.8501 25.4302 22.0582 3 -70 2 22.322 24.7961 22.0622 3 -71 2 23.0528 25.0485 22.0682 3 -72 2 23.0528 25.8118 22.0682 3 -73 2 22.322 26.0643 22.0622 3 -74 2 23.082 25.4302 22.6951 3 -75 2 22.7001 25.9657 22.7002 3 -76 2 22.0612 25.7682 22.7088 3 -77 2 22.0612 25.0922 22.7088 3 -78 2 22.7001 24.8947 22.7002 3 -79 2 23.082 25.4302 21.8877 3 -80 2 22.7001 25.9657 21.8826 3 -81 2 22.0612 25.7682 21.874 3 -82 2 22.0612 25.0922 21.874 3 -83 2 22.7001 24.8947 21.8826 3 -84 2 22.8107 25.4302 22.9236 3 -85 2 22.6126 25.705 22.927 3 -86 2 22.2877 25.6015 22.9326 3 -87 2 22.2877 25.2589 22.9326 3 -88 2 22.6126 25.1554 22.927 3 -89 2 22.8107 25.4302 21.6592 3 -90 2 22.6126 25.705 21.6558 3 -91 2 22.2877 25.6015 21.6502 3 -92 2 22.2877 25.2589 21.6502 3 -93 2 22.6126 25.1554 21.6558 3 -94 1 23.895 25.0537 22.2951 4 -95 2 23.235 25.0537 22.5282 4 -96 2 23.7068 24.4196 22.5243 4 -97 2 24.4377 24.672 22.5183 4 -98 2 24.4377 25.4353 22.5183 4 -99 2 23.7068 25.6877 22.5243 4 -100 2 23.235 25.0537 22.0619 4 -101 2 23.7068 24.4196 22.0659 4 -102 2 24.4377 24.672 22.0718 4 -103 2 24.4377 25.4353 22.0718 4 -104 2 23.7068 25.6877 22.0659 4 -105 2 24.4668 25.0537 22.6988 4 -106 2 24.0849 25.5892 22.7039 4 -107 2 23.4461 25.3916 22.7125 4 -108 2 23.4461 24.7157 22.7125 4 -109 2 24.0849 24.5181 22.7039 4 -110 2 24.4668 25.0537 21.8913 4 -111 2 24.0849 25.5892 21.8863 4 -112 2 23.4461 25.3916 21.8776 4 -113 2 23.4461 24.7157 21.8776 4 -114 2 24.0849 24.5181 21.8863 4 -115 2 24.1955 25.0537 22.9273 4 -116 2 23.9975 25.3284 22.9307 4 -117 2 23.6725 25.225 22.9363 4 -118 2 23.6725 24.8823 22.9363 4 -119 2 23.9975 24.7789 22.9307 4 -120 2 24.1955 25.0537 21.6629 4 -121 2 23.9975 25.3284 21.6595 4 -122 2 23.6725 25.225 21.6538 4 -123 2 23.6725 24.8823 21.6538 4 -124 2 23.9975 24.7789 21.6595 4 -125 1 24.6582 26.0898 21.6598 5 -126 2 23.9982 26.0898 21.893 5 -127 2 24.4701 25.4557 21.889 5 -128 2 25.2009 25.7081 21.883 5 -129 2 25.2009 26.4714 21.883 5 -130 2 24.4701 26.7238 21.889 5 -131 2 23.9982 26.0898 21.4266 5 -132 2 24.4701 25.4557 21.4306 5 -133 2 25.2009 25.7081 21.4366 5 -134 2 25.2009 26.4714 21.4366 5 -135 2 24.4701 26.7238 21.4306 5 -136 2 25.2301 26.0898 22.0635 5 -137 2 24.8482 26.6253 22.0686 5 -138 2 24.2093 26.4277 22.0772 5 -139 2 24.2093 25.7518 22.0772 5 -140 2 24.8482 25.5542 22.0686 5 -141 2 25.2301 26.0898 21.2561 5 -142 2 24.8482 26.6253 21.251 5 -143 2 24.2093 26.4277 21.2424 5 -144 2 24.2093 25.7518 21.2424 5 -145 2 24.8482 25.5542 21.251 5 -146 2 24.9587 26.0898 22.292 5 -147 2 24.7607 26.3645 22.2954 5 -148 2 24.4358 26.2611 22.301 5 -149 2 24.4358 25.9185 22.301 5 -150 2 24.7607 25.815 22.2954 5 -151 2 24.9587 26.0898 21.0276 5 -152 2 24.7607 26.3645 21.0242 5 -153 2 24.4358 26.2611 21.0186 5 -154 2 24.4358 25.9184 21.0186 5 -155 2 24.7607 25.815 21.0242 5 -156 1 25.7401 26.9511 22.0433 6 -157 2 25.0801 26.9511 22.2765 6 -158 2 25.552 26.3171 22.2725 6 -159 2 26.2828 26.5695 22.2666 6 -160 2 26.2828 27.3328 22.2666 6 -161 2 25.552 27.5852 22.2725 6 -162 2 25.0801 26.9511 21.8102 6 -163 2 25.552 26.3171 21.8141 6 -164 2 26.2828 26.5695 21.8201 6 -165 2 26.2828 27.3328 21.8201 6 -166 2 25.552 27.5852 21.8141 6 -167 2 26.312 26.9511 22.4471 6 -168 2 25.9301 27.4867 22.4521 6 -169 2 25.2912 27.2891 22.4608 6 -170 2 25.2912 26.6132 22.4608 6 -171 2 25.9301 26.4156 22.4521 6 -172 2 26.312 26.9511 21.6396 6 -173 2 25.9301 27.4867 21.6345 6 -174 2 25.2912 27.2891 21.6259 6 -175 2 25.2912 26.6132 21.6259 6 -176 2 25.9301 26.4156 21.6345 6 -177 2 26.0406 26.9511 22.6755 6 -178 2 25.8426 27.2259 22.6789 6 -179 2 25.5177 27.1225 22.6845 6 -180 2 25.5177 26.7798 22.6845 6 -181 2 25.8426 26.6764 22.6789 6 -182 2 26.0406 26.9511 21.4111 6 -183 2 25.8426 27.2259 21.4077 6 -184 2 25.5177 27.1225 21.4021 6 -185 2 25.5177 26.7798 21.4021 6 -186 2 25.8426 26.6764 21.4077 6 -187 1 26.6309 26.6387 20.9623 7 -188 2 25.9709 26.6387 21.1955 7 -189 2 26.4427 26.0047 21.1916 7 -190 2 27.1736 26.2571 21.1856 7 -191 2 27.1736 27.0204 21.1856 7 -192 2 26.4427 27.2728 21.1916 7 -193 2 25.9709 26.6387 20.7292 7 -194 2 26.4427 26.0047 20.7331 7 -195 2 27.1736 26.2571 20.7391 7 -196 2 27.1736 27.0204 20.7391 7 -197 2 26.4427 27.2728 20.7331 7 -198 2 27.2028 26.6387 21.3661 7 -199 2 26.8208 27.1743 21.3712 7 -200 2 26.182 26.9767 21.3798 7 -201 2 26.182 26.3008 21.3798 7 -202 2 26.8208 26.1032 21.3712 7 -203 2 27.2027 26.6387 20.5586 7 -204 2 26.8209 27.1743 20.5535 7 -205 2 26.182 26.9767 20.5449 7 -206 2 26.182 26.3008 20.5449 7 -207 2 26.8208 26.1032 20.5535 7 -208 2 26.9314 26.6387 21.5946 7 -209 2 26.7334 26.9135 21.598 7 -210 2 26.4084 26.81 21.6036 7 -211 2 26.4084 26.4674 21.6036 7 -212 2 26.7334 26.364 21.598 7 -213 2 26.9314 26.6387 20.3301 7 -214 2 26.7334 26.9135 20.3267 7 -215 2 26.4084 26.8101 20.3211 7 -216 2 26.4084 26.4674 20.3211 7 -217 2 26.7334 26.364 20.3267 7 -218 1 27.7333 27.3399 21.5562 8 -219 2 27.0733 27.3399 21.7894 8 -220 2 27.5451 26.7058 21.7855 8 -221 2 28.276 26.9582 21.7795 8 -222 2 28.276 27.7215 21.7795 8 -223 2 27.5451 27.974 21.7855 8 -224 2 27.0733 27.3399 21.3231 8 -225 2 27.5451 26.7058 21.327 8 -226 2 28.276 26.9582 21.333 8 -227 2 28.276 27.7215 21.333 8 -228 2 27.5451 27.974 21.327 8 -229 2 28.3051 27.3399 21.96 8 -230 2 27.9232 27.8754 21.9651 8 -231 2 27.2844 27.6779 21.9737 8 -232 2 27.2844 27.0019 21.9737 8 -233 2 27.9232 26.8043 21.9651 8 -234 2 28.3051 27.3399 21.1525 8 -235 2 27.9232 27.8754 21.1474 8 -236 2 27.2844 27.6779 21.1388 8 -237 2 27.2844 27.0019 21.1388 8 -238 2 27.9232 26.8044 21.1474 8 -239 2 28.0338 27.3399 22.1885 8 -240 2 27.8358 27.6147 22.1919 8 -241 2 27.5108 27.5112 22.1975 8 -242 2 27.5108 27.1686 22.1975 8 -243 2 27.8358 27.0651 22.1919 8 -244 2 28.0338 27.3399 20.924 8 -245 2 27.8358 27.6147 20.9206 8 -246 2 27.5108 27.5112 20.915 8 -247 2 27.5108 27.1686 20.915 8 -248 2 27.8358 27.0651 20.9206 8 -249 1 28.2741 26.7179 22.7311 9 -250 2 27.6141 26.7179 22.9642 9 -251 2 28.086 26.0838 22.9603 9 -252 2 28.8168 26.3362 22.9543 9 -253 2 28.8168 27.0995 22.9543 9 -254 2 28.086 27.352 22.9603 9 -255 2 27.6141 26.7179 22.4979 9 -256 2 28.086 26.0838 22.5019 9 -257 2 28.8168 26.3362 22.5078 9 -258 2 28.8168 27.0995 22.5078 9 -259 2 28.086 27.352 22.5019 9 -260 2 28.846 26.7179 23.1348 9 -261 2 28.4641 27.2534 23.1399 9 -262 2 27.8252 27.0559 23.1485 9 -263 2 27.8252 26.3799 23.1485 9 -264 2 28.4641 26.1823 23.1399 9 -265 2 28.846 26.7179 22.3273 9 -266 2 28.4641 27.2534 22.3223 9 -267 2 27.8252 27.0559 22.3136 9 -268 2 27.8252 26.3799 22.3136 9 -269 2 28.4641 26.1823 22.3223 9 -270 2 28.5746 26.7179 23.3633 9 -271 2 28.3766 26.9927 23.3667 9 -272 2 28.0517 26.8892 23.3723 9 -273 2 28.0517 26.5466 23.3723 9 -274 2 28.3766 26.4431 23.3667 9 -275 2 28.5746 26.7179 22.0989 9 -276 2 28.3766 26.9927 22.0955 9 -277 2 28.0517 26.8892 22.0899 9 -278 2 28.0517 26.5466 22.0899 9 -279 2 28.3766 26.4431 22.0955 9 -280 1 26.9358 26.2738 22.9979 10 -281 2 26.2757 26.2738 23.2311 10 -282 2 26.7476 25.6397 23.2271 10 -283 2 27.4785 25.8921 23.2211 10 -284 2 27.4785 26.6554 23.2211 10 -285 2 26.7476 26.9079 23.2271 10 -286 2 26.2757 26.2738 22.7647 10 -287 2 26.7476 25.6397 22.7687 10 -288 2 27.4785 25.8921 22.7747 10 -289 2 27.4785 26.6554 22.7747 10 -290 2 26.7476 26.9079 22.7687 10 -291 2 27.5076 26.2738 23.4016 10 -292 2 27.1257 26.8093 23.4067 10 -293 2 26.4869 26.6118 23.4154 10 -294 2 26.4869 25.9358 23.4154 10 -295 2 27.1257 25.7382 23.4067 10 -296 2 27.5076 26.2738 22.5942 10 -297 2 27.1257 26.8093 22.5891 10 -298 2 26.4869 26.6118 22.5805 10 -299 2 26.4869 25.9358 22.5805 10 -300 2 27.1257 25.7382 22.5891 10 -301 2 27.2363 26.2738 23.6301 10 -302 2 27.0383 26.5486 23.6335 10 -303 2 26.7133 26.4451 23.6391 10 -304 2 26.7133 26.1025 23.6391 10 -305 2 27.0383 25.999 23.6335 10 -306 2 27.2363 26.2738 22.3657 10 -307 2 27.0383 26.5486 22.3623 10 -308 2 26.7133 26.4451 22.3567 10 -309 2 26.7133 26.1025 22.3567 10 -310 2 27.0383 25.999 22.3623 10 -311 1 27.733 25.5139 23.9181 11 -312 2 27.0729 25.5139 24.1512 11 -313 2 27.5448 24.8798 24.1473 11 -314 2 28.2756 25.1323 24.1413 11 -315 2 28.2756 25.8956 24.1413 11 -316 2 27.5448 26.148 24.1473 11 -317 2 27.0729 25.5139 23.6849 11 -318 2 27.5448 24.8798 23.6889 11 -319 2 28.2756 25.1323 23.6948 11 -320 2 28.2756 25.8956 23.6948 11 -321 2 27.5448 26.148 23.6889 11 -322 2 28.3048 25.5139 24.3218 11 -323 2 27.9229 26.0494 24.3269 11 -324 2 27.284 25.8519 24.3355 11 -325 2 27.284 25.1759 24.3355 11 -326 2 27.9229 24.9784 24.3269 11 -327 2 28.3048 25.5139 23.5143 11 -328 2 27.9229 26.0494 23.5093 11 -329 2 27.284 25.8519 23.5006 11 -330 2 27.284 25.1759 23.5006 11 -331 2 27.9229 24.9784 23.5093 11 -332 2 28.0335 25.5139 24.5503 11 -333 2 27.8354 25.7887 24.5537 11 -334 2 27.5105 25.6852 24.5593 11 -335 2 27.5105 25.3426 24.5593 11 -336 2 27.8354 25.2391 24.5537 11 -337 2 28.0335 25.5139 23.2859 11 -338 2 27.8354 25.7887 23.2825 11 -339 2 27.5105 25.6852 23.2769 11 -340 2 27.5105 25.3426 23.2769 11 -341 2 27.8354 25.2391 23.2825 11 -342 1 28.8712 25.1256 24.7012 12 -343 2 28.2111 25.1256 24.9344 12 -344 2 28.683 24.4916 24.9305 12 -345 2 29.4138 24.744 24.9245 12 -346 2 29.4138 25.5073 24.9245 12 -347 2 28.683 25.7597 24.9305 12 -348 2 28.2111 25.1256 24.4681 12 -349 2 28.683 24.4916 24.472 12 -350 2 29.4138 24.744 24.478 12 -351 2 29.4138 25.5073 24.478 12 -352 2 28.683 25.7597 24.472 12 -353 2 29.443 25.1256 25.105 12 -354 2 29.0611 25.6612 25.11 12 -355 2 28.4222 25.4636 25.1187 12 -356 2 28.4222 24.7877 25.1187 12 -357 2 29.0611 24.5901 25.11 12 -358 2 29.443 25.1256 24.2975 12 -359 2 29.0611 25.6612 24.2924 12 -360 2 28.4222 25.4636 24.2838 12 -361 2 28.4222 24.7877 24.2838 12 -362 2 29.0611 24.5901 24.2924 12 -363 2 29.1717 25.1256 25.3335 12 -364 2 28.9736 25.4004 25.3368 12 -365 2 28.6487 25.2969 25.3425 12 -366 2 28.6487 24.9543 25.3425 12 -367 2 28.9736 24.8509 25.3368 12 -368 2 29.1717 25.1256 24.069 12 -369 2 28.9736 25.4004 24.0656 12 -370 2 28.6487 25.297 24.06 12 -371 2 28.6487 24.9543 24.06 12 -372 2 28.9736 24.8509 24.0656 12 -373 1 30.0053 25.4778 25.507 13 -374 2 29.3453 25.4778 25.7401 13 -375 2 29.8172 24.8438 25.7362 13 -376 2 30.548 25.0962 25.7302 13 -377 2 30.548 25.8595 25.7302 13 -378 2 29.8172 26.1119 25.7362 13 -379 2 29.3453 25.4778 25.2738 13 -380 2 29.8172 24.8438 25.2777 13 -381 2 30.548 25.0962 25.2837 13 -382 2 30.548 25.8595 25.2837 13 -383 2 29.8172 26.1119 25.2777 13 -384 2 30.5772 25.4778 25.9107 13 -385 2 30.1953 26.0134 25.9158 13 -386 2 29.5564 25.8158 25.9244 13 -387 2 29.5564 25.1399 25.9244 13 -388 2 30.1953 24.9423 25.9158 13 -389 2 30.5772 25.4778 25.1032 13 -390 2 30.1953 26.0134 25.0982 13 -391 2 29.5564 25.8158 25.0895 13 -392 2 29.5564 25.1399 25.0895 13 -393 2 30.1953 24.9423 25.0982 13 -394 2 30.3058 25.4778 26.1392 13 -395 2 30.1078 25.7526 26.1426 13 -396 2 29.7829 25.6492 26.1482 13 -397 2 29.7829 25.3065 26.1482 13 -398 2 30.1078 25.2031 26.1426 13 -399 2 30.3058 25.4778 24.8747 13 -400 2 30.1078 25.7526 24.8714 13 -401 2 29.7829 25.6492 24.8657 13 -402 2 29.7829 25.3065 24.8657 13 -403 2 30.1078 25.2031 24.8714 13 -404 1 29.8427 26.8721 25.2081 14 -405 2 29.1827 26.8721 25.4413 14 -406 2 29.6545 26.238 25.4373 14 -407 2 30.3854 26.4904 25.4314 14 -408 2 30.3854 27.2537 25.4314 14 -409 2 29.6545 27.5061 25.4373 14 -410 2 29.1827 26.8721 24.975 14 -411 2 29.6545 26.238 24.9789 14 -412 2 30.3854 26.4904 24.9849 14 -413 2 30.3854 27.2537 24.9849 14 -414 2 29.6545 27.5061 24.9789 14 -415 2 30.4145 26.8721 25.6119 14 -416 2 30.0326 27.4076 25.6169 14 -417 2 29.3938 27.21 25.6256 14 -418 2 29.3938 26.5341 25.6256 14 -419 2 30.0326 26.3365 25.6169 14 -420 2 30.4145 26.8721 24.8044 14 -421 2 30.0326 27.4076 24.7993 14 -422 2 29.3938 27.21 24.7907 14 -423 2 29.3938 26.5341 24.7907 14 -424 2 30.0326 26.3365 24.7993 14 -425 2 30.1432 26.8721 25.8403 14 -426 2 29.9452 27.1468 25.8437 14 -427 2 29.6202 27.0434 25.8493 14 -428 2 29.6202 26.7007 25.8493 14 -429 2 29.9452 26.5973 25.8437 14 -430 2 30.1432 26.8721 24.5759 14 -431 2 29.9452 27.1468 24.5725 14 -432 2 29.6202 27.0434 24.5669 14 -433 2 29.6202 26.7007 24.5669 14 -434 2 29.9452 26.5973 24.5725 14 -435 1 29.3789 27.6387 26.3292 15 -436 2 28.7189 27.6387 26.5624 15 -437 2 29.1908 27.0046 26.5584 15 -438 2 29.9216 27.257 26.5524 15 -439 2 29.9216 28.0203 26.5524 15 -440 2 29.1908 28.2727 26.5584 15 -441 2 28.7189 27.6387 26.096 15 -442 2 29.1908 27.0046 26.1 15 -443 2 29.9216 27.257 26.106 15 -444 2 29.9216 28.0203 26.106 15 -445 2 29.1908 28.2727 26.1 15 -446 2 29.9508 27.6387 26.7329 15 -447 2 29.5689 28.1742 26.738 15 -448 2 28.93 27.9766 26.7467 15 -449 2 28.93 27.3007 26.7467 15 -450 2 29.5689 27.1031 26.738 15 -451 2 29.9508 27.6387 25.9255 15 -452 2 29.5689 28.1742 25.9204 15 -453 2 28.93 27.9766 25.9118 15 -454 2 28.93 27.3007 25.9118 15 -455 2 29.5689 27.1031 25.9204 15 -456 2 29.6794 27.6387 26.9614 15 -457 2 29.4814 27.9134 26.9648 15 -458 2 29.1565 27.81 26.9704 15 -459 2 29.1565 27.4674 26.9704 15 -460 2 29.4814 27.3639 26.9648 15 -461 2 29.6794 27.6387 25.697 15 -462 2 29.4814 27.9134 25.6936 15 -463 2 29.1565 27.81 25.688 15 -464 2 29.1565 27.4674 25.688 15 -465 2 29.4814 27.3639 25.6936 15 -466 1 28.587 28.4661 27.194 16 -467 2 27.927 28.4661 27.4272 16 -468 2 28.3989 27.832 27.4232 16 -469 2 29.1297 28.0844 27.4172 16 -470 2 29.1297 28.8477 27.4172 16 -471 2 28.3989 29.1002 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28.1562 28.3677 28.3561 17 -502 2 27.4254 28.6202 28.3621 17 -503 2 26.9535 27.9861 27.8997 17 -504 2 27.4254 27.352 27.9037 17 -505 2 28.1562 27.6044 27.9097 17 -506 2 28.1562 28.3677 27.9097 17 -507 2 27.4254 28.6202 27.9037 17 -508 2 28.1854 27.9861 28.5366 17 -509 2 27.8035 28.5216 28.5417 17 -510 2 27.1646 28.3241 28.5503 17 -511 2 27.1646 27.6481 28.5503 17 -512 2 27.8035 27.4506 28.5417 17 -513 2 28.1854 27.9861 27.7292 17 -514 2 27.8035 28.5216 27.7241 17 -515 2 27.1646 28.3241 27.7154 17 -516 2 27.1646 27.6481 27.7154 17 -517 2 27.8035 27.4506 27.7241 17 -518 2 27.914 27.9861 28.7651 17 -519 2 27.716 28.2609 28.7685 17 -520 2 27.3911 28.1574 28.7741 17 -521 2 27.3911 27.8148 28.7741 17 -522 2 27.716 27.7113 28.7685 17 -523 2 27.914 27.9861 27.5007 17 -524 2 27.716 28.2609 27.4973 17 -525 2 27.3911 28.1574 27.4917 17 -526 2 27.3911 27.8148 27.4917 17 -527 2 27.716 27.7113 27.4973 17 -528 1 28.7548 27.1277 28.2749 18 -529 2 28.0948 27.1277 28.508 18 -530 2 28.5666 26.4936 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28.7102 27.681 29.6805 19 -561 2 29.1821 27.0469 29.6765 19 -562 2 29.913 27.2993 29.6706 19 -563 2 29.913 28.0626 29.6706 19 -564 2 29.1821 28.3151 29.6765 19 -565 2 28.7102 27.681 29.2142 19 -566 2 29.1821 27.0469 29.2181 19 -567 2 29.913 27.2993 29.2241 19 -568 2 29.913 28.0626 29.2241 19 -569 2 29.1821 28.3151 29.2181 19 -570 2 29.9421 27.681 29.8511 19 -571 2 29.5602 28.2165 29.8561 19 -572 2 28.9214 28.019 29.8648 19 -573 2 28.9214 27.343 29.8648 19 -574 2 29.5602 27.1455 29.8561 19 -575 2 29.9421 27.681 29.0436 19 -576 2 29.5602 28.2165 29.0385 19 -577 2 28.9214 28.019 29.0299 19 -578 2 28.9214 27.343 29.0299 19 -579 2 29.5602 27.1455 29.0385 19 -580 2 29.6708 27.681 30.0795 19 -581 2 29.4728 27.9558 30.0829 19 -582 2 29.1478 27.8523 30.0885 19 -583 2 29.1478 27.5097 30.0885 19 -584 2 29.4728 27.4062 30.0829 19 -585 2 29.6708 27.681 28.8151 19 -586 2 29.4728 27.9558 28.8117 19 -587 2 29.1478 27.8523 28.8061 19 -588 2 29.1478 27.5097 28.8061 19 -589 2 29.4728 27.4062 28.8117 19 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29.6273 28.4641 21 -650 2 31.2034 29.2847 28.4641 21 -651 2 31.5284 29.1812 28.4697 21 -652 1 31.3008 28.2326 28.3655 22 -653 2 30.6408 28.2326 28.5987 22 -654 2 31.1126 27.5985 28.5947 22 -655 2 31.8435 27.851 28.5888 22 -656 2 31.8435 28.6143 28.5888 22 -657 2 31.1126 28.8667 28.5947 22 -658 2 30.6408 28.2326 28.1324 22 -659 2 31.1126 27.5985 28.1363 22 -660 2 31.8435 27.851 28.1423 22 -661 2 31.8435 28.6143 28.1423 22 -662 2 31.1126 28.8667 28.1363 22 -663 2 31.8726 28.2326 28.7693 22 -664 2 31.4907 28.7682 28.7743 22 -665 2 30.8519 28.5706 28.783 22 -666 2 30.8519 27.8946 28.783 22 -667 2 31.4907 27.6971 28.7743 22 -668 2 31.8726 28.2326 27.9618 22 -669 2 31.4907 28.7682 27.9567 22 -670 2 30.8519 28.5706 27.9481 22 -671 2 30.8519 27.8946 27.9481 22 -672 2 31.4907 27.6971 27.9567 22 -673 2 31.6013 28.2326 28.9977 22 -674 2 31.4033 28.5074 29.0011 22 -675 2 31.0783 28.4039 29.0067 22 -676 2 31.0783 28.0613 29.0067 22 -677 2 31.4033 27.9578 29.0011 22 -678 2 31.6013 28.2326 27.7333 22 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26.8623 28.7479 23 -709 2 32.4931 27.1371 27.4801 23 -710 2 32.2951 27.4119 27.4767 23 -711 2 31.9701 27.3084 27.4711 23 -712 2 31.9701 26.9658 27.4711 23 -713 2 32.2951 26.8623 27.4767 23 -714 1 33.0167 26.5192 29.1116 24 -715 2 32.3567 26.5192 29.3447 24 -716 2 32.8285 25.8851 29.3408 24 -717 2 33.5594 26.1375 29.3348 24 -718 2 33.5594 26.9008 29.3348 24 -719 2 32.8285 27.1532 29.3408 24 -720 2 32.3567 26.5192 28.8784 24 -721 2 32.8285 25.8851 28.8824 24 -722 2 33.5594 26.1375 28.8883 24 -723 2 33.5594 26.9008 28.8883 24 -724 2 32.8285 27.1532 28.8824 24 -725 2 33.5885 26.5192 29.5153 24 -726 2 33.2066 27.0547 29.5204 24 -727 2 32.5678 26.8571 29.529 24 -728 2 32.5678 26.1812 29.529 24 -729 2 33.2066 25.9836 29.5204 24 -730 2 33.5885 26.5192 28.7078 24 -731 2 33.2066 27.0547 28.7028 24 -732 2 32.5678 26.8571 28.6941 24 -733 2 32.5678 26.1812 28.6941 24 -734 2 33.2066 25.9836 28.7028 24 -735 2 33.3172 26.5192 29.7438 24 -736 2 33.1192 26.7939 29.7472 24 -737 2 32.7942 26.6905 29.7528 24 -738 2 32.7942 26.3478 29.7528 24 -739 2 33.1192 26.2444 29.7472 24 -740 2 33.3172 26.5192 28.4794 24 -741 2 33.1192 26.7939 28.476 24 -742 2 32.7942 26.6905 28.4704 24 -743 2 32.7942 26.3478 28.4704 24 -744 2 33.1192 26.2444 28.476 24 -745 1 33.3109 26.7605 30.4953 25 -746 2 32.6509 26.7605 30.7285 25 -747 2 33.1227 26.1264 30.7246 25 -748 2 33.8536 26.3789 30.7186 25 -749 2 33.8536 27.1422 30.7186 25 -750 2 33.1227 27.3946 30.7246 25 -751 2 32.6509 26.7605 30.2622 25 -752 2 33.1227 26.1264 30.2661 25 -753 2 33.8536 26.3789 30.2721 25 -754 2 33.8536 27.1422 30.2721 25 -755 2 33.1227 27.3946 30.2661 25 -756 2 33.8827 26.7605 30.8991 25 -757 2 33.5008 27.2961 30.9041 25 -758 2 32.862 27.0985 30.9128 25 -759 2 32.862 26.4226 30.9128 25 -760 2 33.5008 26.225 30.9041 25 -761 2 33.8827 26.7605 30.0916 25 -762 2 33.5008 27.2961 30.0865 25 -763 2 32.862 27.0985 30.0779 25 -764 2 32.862 26.4226 30.0779 25 -765 2 33.5008 26.225 30.0865 25 -766 2 33.6114 26.7605 31.1276 25 -767 2 33.4134 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31.1126 27.5985 28.1363 22 +660 2 31.8435 27.851 28.1423 22 +661 2 31.8435 28.6143 28.1423 22 +662 2 31.1126 28.8667 28.1363 22 +663 2 31.8726 28.2326 28.7693 22 +664 2 31.4907 28.7682 28.7743 22 +665 2 30.8519 28.5706 28.783 22 +666 2 30.8519 27.8946 28.783 22 +667 2 31.4907 27.6971 28.7743 22 +668 2 31.8726 28.2326 27.9618 22 +669 2 31.4907 28.7682 27.9567 22 +670 2 30.8519 28.5706 27.9481 22 +671 2 30.8519 27.8946 27.9481 22 +672 2 31.4907 27.6971 27.9567 22 +673 2 31.6013 28.2326 28.9977 22 +674 2 31.4033 28.5074 29.0011 22 +675 2 31.0783 28.4039 29.0067 22 +676 2 31.0783 28.0613 29.0067 22 +677 2 31.4033 27.9578 29.0011 22 +678 2 31.6013 28.2326 27.7333 22 +679 2 31.4033 28.5074 27.7299 22 +680 2 31.0783 28.4039 27.7243 22 +681 2 31.0783 28.0613 27.7243 22 +682 2 31.4033 27.9578 27.7299 22 +683 1 32.1926 27.1371 28.1123 23 +684 2 31.5325 27.1371 28.3454 23 +685 2 32.0044 26.503 28.3415 23 +686 2 32.7353 26.7554 28.3355 23 +687 2 32.7353 27.5187 28.3355 23 +688 2 32.0044 27.7712 28.3415 23 +689 2 31.5325 27.1371 27.8791 23 +690 2 32.0044 26.503 27.8831 23 +691 2 32.7353 26.7554 27.8891 23 +692 2 32.7353 27.5187 27.8891 23 +693 2 32.0044 27.7712 27.8831 23 +694 2 32.7644 27.1371 28.516 23 +695 2 32.3825 27.6726 28.5211 23 +696 2 31.7437 27.4751 28.5297 23 +697 2 31.7437 26.7991 28.5297 23 +698 2 32.3825 26.6015 28.5211 23 +699 2 32.7644 27.1371 27.7086 23 +700 2 32.3825 27.6726 27.7035 23 +701 2 31.7437 27.4751 27.6948 23 +702 2 31.7437 26.7991 27.6948 23 +703 2 32.3825 26.6015 27.7035 23 +704 2 32.4931 27.1371 28.7445 23 +705 2 32.2951 27.4119 28.7479 23 +706 2 31.9701 27.3084 28.7535 23 +707 2 31.9701 26.9658 28.7535 23 +708 2 32.2951 26.8623 28.7479 23 +709 2 32.4931 27.1371 27.4801 23 +710 2 32.2951 27.4119 27.4767 23 +711 2 31.9701 27.3084 27.4711 23 +712 2 31.9701 26.9658 27.4711 23 +713 2 32.2951 26.8623 27.4767 23 +714 1 33.0167 26.5192 29.1116 24 +715 2 32.3567 26.5192 29.3447 24 +716 2 32.8285 25.8851 29.3408 24 +717 2 33.5594 26.1375 29.3348 24 +718 2 33.5594 26.9008 29.3348 24 +719 2 32.8285 27.1532 29.3408 24 +720 2 32.3567 26.5192 28.8784 24 +721 2 32.8285 25.8851 28.8824 24 +722 2 33.5594 26.1375 28.8883 24 +723 2 33.5594 26.9008 28.8883 24 +724 2 32.8285 27.1532 28.8824 24 +725 2 33.5885 26.5192 29.5153 24 +726 2 33.2066 27.0547 29.5204 24 +727 2 32.5678 26.8571 29.529 24 +728 2 32.5678 26.1812 29.529 24 +729 2 33.2066 25.9836 29.5204 24 +730 2 33.5885 26.5192 28.7078 24 +731 2 33.2066 27.0547 28.7028 24 +732 2 32.5678 26.8571 28.6941 24 +733 2 32.5678 26.1812 28.6941 24 +734 2 33.2066 25.9836 28.7028 24 +735 2 33.3172 26.5192 29.7438 24 +736 2 33.1192 26.7939 29.7472 24 +737 2 32.7942 26.6905 29.7528 24 +738 2 32.7942 26.3478 29.7528 24 +739 2 33.1192 26.2444 29.7472 24 +740 2 33.3172 26.5192 28.4794 24 +741 2 33.1192 26.7939 28.476 24 +742 2 32.7942 26.6905 28.4704 24 +743 2 32.7942 26.3478 28.4704 24 +744 2 33.1192 26.2444 28.476 24 +745 1 33.3109 26.7605 30.4953 25 +746 2 32.6509 26.7605 30.7285 25 +747 2 33.1227 26.1264 30.7246 25 +748 2 33.8536 26.3789 30.7186 25 +749 2 33.8536 27.1422 30.7186 25 +750 2 33.1227 27.3946 30.7246 25 +751 2 32.6509 26.7605 30.2622 25 +752 2 33.1227 26.1264 30.2661 25 +753 2 33.8536 26.3789 30.2721 25 +754 2 33.8536 27.1422 30.2721 25 +755 2 33.1227 27.3946 30.2661 25 +756 2 33.8827 26.7605 30.8991 25 +757 2 33.5008 27.2961 30.9041 25 +758 2 32.862 27.0985 30.9128 25 +759 2 32.862 26.4226 30.9128 25 +760 2 33.5008 26.225 30.9041 25 +761 2 33.8827 26.7605 30.0916 25 +762 2 33.5008 27.2961 30.0865 25 +763 2 32.862 27.0985 30.0779 25 +764 2 32.862 26.4226 30.0779 25 +765 2 33.5008 26.225 30.0865 25 +766 2 33.6114 26.7605 31.1276 25 +767 2 33.4134 27.0353 31.1309 25 +768 2 33.0884 26.9318 31.1366 25 +769 2 33.0884 26.5892 31.1366 25 +770 2 33.4134 26.4857 31.1309 25 +771 2 33.6114 26.7605 29.8631 25 +772 2 33.4134 27.0353 29.8597 25 +773 2 33.0884 26.9318 29.8541 25 +774 2 33.0884 26.5892 29.8541 25 +775 2 33.4134 26.4857 29.8597 25 +776 1 32.6296 27.0741 31.7189 26 +777 2 31.9696 27.0741 31.952 26 +778 2 32.4414 26.4401 31.9481 26 +779 2 33.1723 26.6925 31.9421 26 +780 2 33.1723 27.4558 31.9421 26 +781 2 32.4414 27.7082 31.9481 26 +782 2 31.9696 27.0741 31.4857 26 +783 2 32.4414 26.4401 31.4897 26 +784 2 33.1723 26.6925 31.4956 26 +785 2 33.1723 27.4558 31.4956 26 +786 2 32.4414 27.7082 31.4897 26 +787 2 33.2014 27.0741 32.1226 26 +788 2 32.8195 27.6097 32.1277 26 +789 2 32.1807 27.4121 32.1363 26 +790 2 32.1807 26.7362 32.1363 26 +791 2 32.8195 26.5386 32.1277 26 +792 2 33.2014 27.0741 31.3151 26 +793 2 32.8195 27.6097 31.3101 26 +794 2 32.1807 27.4121 31.3014 26 +795 2 32.1807 26.7362 31.3014 26 +796 2 32.8195 26.5386 31.3101 26 +797 2 32.9301 27.0741 32.3511 26 +798 2 32.7321 27.3489 32.3545 26 +799 2 32.4071 27.2454 32.3601 26 +800 2 32.4071 26.9028 32.3601 26 +801 2 32.7321 26.7994 32.3545 26 +802 2 32.9301 27.0741 31.0867 26 +803 2 32.7321 27.3489 31.0833 26 +804 2 32.4071 27.2454 31.0777 26 +805 2 32.4071 26.9028 31.0777 26 +806 2 32.7321 26.7994 31.0833 26 +807 1 31.7049 27.9673 32.3567 27 +808 2 31.0449 27.9673 32.5899 27 +809 2 31.5167 27.3332 32.5859 27 +810 2 32.2476 27.5856 32.5799 27 +811 2 32.2476 28.3489 32.5799 27 +812 2 31.5167 28.6014 32.5859 27 +813 2 31.0449 27.9673 32.1235 27 +814 2 31.5167 27.3332 32.1275 27 +815 2 32.2476 27.5856 32.1335 27 +816 2 32.2476 28.3489 32.1335 27 +817 2 31.5167 28.6014 32.1275 27 +818 2 32.2767 27.9673 32.7604 27 +819 2 31.8948 28.5028 32.7655 27 +820 2 31.256 28.3053 32.7742 27 +821 2 31.256 27.6293 32.7742 27 +822 2 31.8948 27.4317 32.7655 27 +823 2 32.2767 27.9673 31.953 27 +824 2 31.8948 28.5028 31.9479 27 +825 2 31.256 28.3053 31.9393 27 +826 2 31.256 27.6293 31.9393 27 +827 2 31.8948 27.4317 31.9479 27 +828 2 32.0054 27.9673 32.9889 27 +829 2 31.8074 28.2421 32.9923 27 +830 2 31.4824 28.1386 32.9979 27 +831 2 31.4824 27.796 32.9979 27 +832 2 31.8074 27.6925 32.9923 27 +833 2 32.0054 27.9673 31.7245 27 +834 2 31.8074 28.2421 31.7211 27 +835 2 31.4824 28.1386 31.7155 27 +836 2 31.4824 27.796 31.7155 27 +837 2 31.8074 27.6925 31.7211 27 +838 1 30.3399 27.7351 32.7342 28 +839 2 29.6799 27.7351 32.9674 28 +840 2 30.1517 27.101 32.9634 28 +841 2 30.8826 27.3535 32.9574 28 +842 2 30.8826 28.1168 32.9574 28 +843 2 30.1517 28.3692 32.9634 28 +844 2 29.6799 27.7351 32.5011 28 +845 2 30.1517 27.101 32.505 28 +846 2 30.8826 27.3535 32.511 28 +847 2 30.8826 28.1168 32.511 28 +848 2 30.1517 28.3692 32.505 28 +849 2 30.9117 27.7351 33.138 28 +850 2 30.5298 28.2706 33.143 28 +851 2 29.891 28.0731 33.1517 28 +852 2 29.891 27.3971 33.1517 28 +853 2 30.5298 27.1996 33.143 28 +854 2 30.9117 27.7351 32.3305 28 +855 2 30.5298 28.2706 32.3254 28 +856 2 29.891 28.0731 32.3168 28 +857 2 29.891 27.3971 32.3168 28 +858 2 30.5298 27.1996 32.3254 28 +859 2 30.6404 27.7351 33.3664 28 +860 2 30.4424 28.0099 33.3698 28 +861 2 30.1174 27.9064 33.3754 28 +862 2 30.1174 27.5638 33.3754 28 +863 2 30.4424 27.4603 33.3698 28 +864 2 30.6404 27.7351 32.102 28 +865 2 30.4424 28.0099 32.0986 28 +866 2 30.1174 27.9064 32.093 28 +867 2 30.1174 27.5638 32.093 28 +868 2 30.4424 27.4603 32.0986 28 +869 1 29.8305 28.063 34.0352 29 +870 2 29.1705 28.063 34.2684 29 +871 2 29.6424 27.429 34.2644 29 +872 2 30.3732 27.6814 34.2584 29 +873 2 30.3732 28.4447 34.2584 29 +874 2 29.6424 28.6971 34.2644 29 +875 2 29.1705 28.063 33.8021 29 +876 2 29.6424 27.429 33.806 29 +877 2 30.3732 27.6814 33.812 29 +878 2 30.3732 28.4447 33.812 29 +879 2 29.6424 28.6971 33.806 29 +880 2 30.4024 28.063 34.439 29 +881 2 30.0205 28.5986 34.444 29 +882 2 29.3816 28.401 34.4527 29 +883 2 29.3816 27.7251 34.4527 29 +884 2 30.0205 27.5275 34.444 29 +885 2 30.4024 28.063 33.6315 29 +886 2 30.0205 28.5986 33.6264 29 +887 2 29.3816 28.401 33.6178 29 +888 2 29.3816 27.7251 33.6178 29 +889 2 30.0205 27.5275 33.6264 29 +890 2 30.1311 28.063 34.6674 29 +891 2 29.933 28.3378 34.6708 29 +892 2 29.6081 28.2344 34.6764 29 +893 2 29.6081 27.8917 34.6764 29 +894 2 29.933 27.7883 34.6708 29 +895 2 30.1311 28.063 33.403 29 +896 2 29.933 28.3378 33.3996 29 +897 2 29.6081 28.2344 33.394 29 +898 2 29.6081 27.8917 33.394 29 +899 2 29.933 27.7883 33.3996 29 +900 1 30.2349 27.8319 35.3927 30 +901 2 29.5749 27.8319 35.6258 30 +902 2 30.0468 27.1978 35.6219 30 +903 2 30.7776 27.4503 35.6159 30 +904 2 30.7776 28.2136 35.6159 30 +905 2 30.0468 28.466 35.6219 30 +906 2 29.5749 27.8319 35.1595 30 +907 2 30.0468 27.1978 35.1634 30 +908 2 30.7776 27.4503 35.1694 30 +909 2 30.7776 28.2136 35.1694 30 +910 2 30.0468 28.466 35.1634 30 +911 2 30.8068 27.8319 35.7964 30 +912 2 30.4249 28.3675 35.8015 30 +913 2 29.786 28.1699 35.8101 30 +914 2 29.786 27.4939 35.8101 30 +915 2 30.4249 27.2964 35.8015 30 +916 2 30.8068 27.8319 34.9889 30 +917 2 30.4249 28.3675 34.9839 30 +918 2 29.786 28.1699 34.9752 30 +919 2 29.786 27.4939 34.9752 30 +920 2 30.4249 27.2964 34.9839 30 +921 2 30.5354 27.8319 36.0249 30 +922 2 30.3374 28.1067 36.0283 30 +923 2 30.0125 28.0032 36.0339 30 +924 2 30.0125 27.6606 36.0339 30 +925 2 30.3374 27.5571 36.0283 30 +926 2 30.5354 27.8319 34.7604 30 +927 2 30.3374 28.1067 34.7571 30 +928 2 30.0125 28.0032 34.7514 30 +929 2 30.0125 27.6606 34.7514 30 +930 2 30.3374 27.5571 34.7571 30 +931 1 30.9967 26.7242 34.8903 31 +932 2 30.3366 26.7242 35.1234 31 +933 2 30.8085 26.0901 35.1195 31 +934 2 31.5393 26.3426 35.1135 31 +935 2 31.5393 27.1059 35.1135 31 +936 2 30.8085 27.3583 35.1195 31 +937 2 30.3366 26.7242 34.6571 31 +938 2 30.8085 26.0901 34.6611 31 +939 2 31.5393 26.3426 34.6671 31 +940 2 31.5393 27.1059 34.6671 31 +941 2 30.8085 27.3583 34.6611 31 +942 2 31.5685 26.7242 35.294 31 +943 2 31.1866 27.2598 35.2991 31 +944 2 30.5478 27.0622 35.3077 31 +945 2 30.5478 26.3862 35.3077 31 +946 2 31.1866 26.1887 35.2991 31 +947 2 31.5685 26.7242 34.4866 31 +948 2 31.1866 27.2598 34.4815 31 +949 2 30.5478 27.0622 34.4728 31 +950 2 30.5478 26.3862 34.4728 31 +951 2 31.1866 26.1887 34.4815 31 +952 2 31.2972 26.7242 35.5225 31 +953 2 31.0991 26.999 35.5259 31 +954 2 30.7742 26.8955 35.5315 31 +955 2 30.7742 26.5529 35.5315 31 +956 2 31.0991 26.4494 35.5259 31 +957 2 31.2972 26.7242 34.2581 31 +958 2 31.0991 26.999 34.2547 31 +959 2 30.7742 26.8955 34.2491 31 +960 2 30.7742 26.5529 34.2491 31 +961 2 31.0991 26.4494 34.2547 31 +962 1 29.9072 26.1623 34.144 32 +963 2 29.2472 26.1623 34.3772 32 +964 2 29.719 25.5283 34.3732 32 +965 2 30.4499 25.7807 34.3672 32 +966 2 30.4499 26.544 34.3672 32 +967 2 29.719 26.7964 34.3732 32 +968 2 29.2472 26.1623 33.9109 32 +969 2 29.719 25.5282 33.9148 32 +970 2 30.4499 25.7807 33.9208 32 +971 2 30.4499 26.544 33.9208 32 +972 2 29.719 26.7964 33.9148 32 +973 2 30.479 26.1623 34.5478 32 +974 2 30.0971 26.6979 34.5528 32 +975 2 29.4583 26.5003 34.5615 32 +976 2 29.4583 25.8244 34.5615 32 +977 2 30.0971 25.6268 34.5528 32 +978 2 30.479 26.1623 33.7403 32 +979 2 30.0971 26.6979 33.7352 32 +980 2 29.4583 26.5003 33.7266 32 +981 2 29.4583 25.8244 33.7266 32 +982 2 30.0971 25.6268 33.7352 32 +983 2 30.2077 26.1623 34.7762 32 +984 2 30.0097 26.4371 34.7796 32 +985 2 29.6847 26.3336 34.7852 32 +986 2 29.6847 25.991 34.7852 32 +987 2 30.0097 25.8876 34.7796 32 +988 2 30.2077 26.1623 33.5118 32 +989 2 30.0097 26.4371 33.5084 32 +990 2 29.6847 26.3336 33.5028 32 +991 2 29.6847 25.991 33.5028 32 +992 2 30.0097 25.8875 33.5084 32 + +Bonds + +1 1 1 32 +2 1 32 63 +3 1 63 94 +4 1 94 125 +5 1 125 156 +6 1 156 187 +7 1 187 218 +8 1 218 249 +9 1 249 280 +10 1 280 311 +11 1 311 342 +12 1 342 373 +13 1 373 404 +14 1 404 435 +15 1 435 466 +16 1 466 497 +17 1 497 528 +18 1 528 559 +19 1 559 590 +20 1 590 621 +21 1 621 652 +22 1 652 683 +23 1 683 714 +24 1 714 745 +25 1 745 776 +26 1 776 807 +27 1 807 838 +28 1 838 869 +29 1 869 900 +30 1 900 931 +31 1 931 962 diff -Naur lammps-21Feb17/examples/USER/lb/polymer/in.polymer_default_gamma lammps-7Mar17/examples/USER/lb/polymer/in.polymer_default_gamma --- lammps-21Feb17/examples/USER/lb/polymer/in.polymer_default_gamma 2015-10-21 12:16:47.000000000 -0600 +++ lammps-7Mar17/examples/USER/lb/polymer/in.polymer_default_gamma 2017-03-07 09:48:20.062786000 -0700 @@ -1,107 +1,107 @@ -#===========================================================================# -# polymer test # -# # -# Run consists of a lone 32-bead coarse-grained polymer # -# undergoing Brownian motion in thermal lattice-Boltzmann fluid. # -# # -# Here, gamma (used in the calculation of the monomer-fluid interaction # -# force) is set by the user (gamma = 0.03 for this simulation...this # -# value has been calibrated a priori through simulations of the drag # -# force acting on a single particle of the same radius). # -# Sample output from this run can be found in the file: # -# 'dump.polymer.lammpstrj' # -# and viewed using, e.g., the VMD software. # -# # -#===========================================================================# - -units nano -dimension 3 -boundary p p p -atom_style hybrid molecular -special_bonds fene -read_data data.polymer - -#---------------------------------------------------------------------------- -# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing -# to ensure that the particles belonging to a given processor remain inside -# that processors lattice-Boltzmann grid. -#---------------------------------------------------------------------------- -neighbor 0.5 bin -neigh_modify delay 0 every 1 check yes -neigh_modify exclude type 2 2 -neigh_modify exclude type 2 1 - -#---------------------------------------------------------------------------- -# Implement a hard-sphere interaction between the particles at the center of -# each monomer (use a truncated and shifted Lennard-Jones potential). -#---------------------------------------------------------------------------- -bond_style fene -bond_coeff 1 60.0 2.25 4.14195 1.5 -pair_style lj/cut 1.68369 -pair_coeff 1 1 4.14195 1.5 1.68369 -pair_coeff 1 2 4.14195 1.5 1.68369 -pair_coeff 2 2 0 1.0 - -mass * 0.000000771064 -timestep 0.00003 - -#---------------------------------------------------------------------------- -# ForceAtoms are the particles at the center of each monomer which -# do not interact with the fluid, but are used to implement the hard-sphere -# interactions. -# FluidAtoms are the particles representing the surface of the monomer -# which do interact with the fluid. Monomer surface is shell of radius 0.7 -#---------------------------------------------------------------------------- -group ForceAtoms type 1 -group FluidAtoms type 2 - -#--------------------------------------------------------------------------- -# Create a lattice-Boltzmann fluid covering the simulation domain. -# This fluid feels a force due to the particles specified through FluidAtoms -# (however, this fix does not explicity apply a force back on to these -# particles. This is accomplished through the use of the lb/viscous -# fix). -# Uses the standard LB integration scheme, fluid viscosity = 0.023333333, -# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit, -# dm=0.0000166368. -# Use the default method to calculate the interaction force between the -# particles and the fluid. This calculation requires the surface area -# of the composite object represented by each particle node. By default -# this area is assumed equal to dx*dx; however, since this is not the case -# here, it is input through the setArea keyword (i.e. particles of type 2 -# correspond to a surface area of 0.2025=4 Pi R^2/N ). -# Use the trilinear interpolation stencil to distribute the force from -# a given particle onto the fluid mesh (results in a smaller hydrodynamic -# radius than if the Peskin stencil is used). -# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number -# seed=15003). This enables the particles to undergo Brownian motion in -# the fluid. -#---------------------------------------------------------------------------- -fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003 - -#---------------------------------------------------------------------------- -# Apply the force from the fluid to the particles, and integrate their -# motion, constraining them to move and rotate together as a single rigid -# spherical object. -# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical -# shell) should move and rotate together, this fix is applied to all of -# the atoms in the system. However, since the central atoms should not -# feel a force due to the fluid, they are excluded from the fluid force -# calculation. -#---------------------------------------------------------------------------- -fix 2 FluidAtoms lb/viscous -fix 3 all rigid molecule - -#---------------------------------------------------------------------------- -# To ensure that numerical errors do not lead to a buildup of momentum in the -# system, the momentum_lb fix is used every 10000 timesteps to zero out the -# total (particle plus fluid) momentum in the system. -#---------------------------------------------------------------------------- -fix 4 all lb/momentum 10000 linear 1 1 1 - -#---------------------------------------------------------------------------- -# Write position and velocity coordinates into a file every 2000 time steps. -#---------------------------------------------------------------------------- - -dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz -run 2000001 +#===========================================================================# +# polymer test # +# # +# Run consists of a lone 32-bead coarse-grained polymer # +# undergoing Brownian motion in thermal lattice-Boltzmann fluid. # +# # +# Here, gamma (used in the calculation of the monomer-fluid interaction # +# force) is set by the user (gamma = 0.03 for this simulation...this # +# value has been calibrated a priori through simulations of the drag # +# force acting on a single particle of the same radius). # +# Sample output from this run can be found in the file: # +# 'dump.polymer.lammpstrj' # +# and viewed using, e.g., the VMD software. # +# # +#===========================================================================# + +units nano +dimension 3 +boundary p p p +atom_style hybrid molecular +special_bonds fene +read_data data.polymer + +#---------------------------------------------------------------------------- +# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing +# to ensure that the particles belonging to a given processor remain inside +# that processors lattice-Boltzmann grid. +#---------------------------------------------------------------------------- +neighbor 0.5 bin +neigh_modify delay 0 every 1 check yes +neigh_modify exclude type 2 2 +neigh_modify exclude type 2 1 + +#---------------------------------------------------------------------------- +# Implement a hard-sphere interaction between the particles at the center of +# each monomer (use a truncated and shifted Lennard-Jones potential). +#---------------------------------------------------------------------------- +bond_style fene +bond_coeff 1 60.0 2.25 4.14195 1.5 +pair_style lj/cut 1.68369 +pair_coeff 1 1 4.14195 1.5 1.68369 +pair_coeff 1 2 4.14195 1.5 1.68369 +pair_coeff 2 2 0 1.0 + +mass * 0.000000771064 +timestep 0.00003 + +#---------------------------------------------------------------------------- +# ForceAtoms are the particles at the center of each monomer which +# do not interact with the fluid, but are used to implement the hard-sphere +# interactions. +# FluidAtoms are the particles representing the surface of the monomer +# which do interact with the fluid. Monomer surface is shell of radius 0.7 +#---------------------------------------------------------------------------- +group ForceAtoms type 1 +group FluidAtoms type 2 + +#--------------------------------------------------------------------------- +# Create a lattice-Boltzmann fluid covering the simulation domain. +# This fluid feels a force due to the particles specified through FluidAtoms +# (however, this fix does not explicitly apply a force back on to these +# particles. This is accomplished through the use of the lb/viscous +# fix). +# Uses the standard LB integration scheme, fluid viscosity = 0.023333333, +# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit, +# dm=0.0000166368. +# Use the default method to calculate the interaction force between the +# particles and the fluid. This calculation requires the surface area +# of the composite object represented by each particle node. By default +# this area is assumed equal to dx*dx; however, since this is not the case +# here, it is input through the setArea keyword (i.e. particles of type 2 +# correspond to a surface area of 0.2025=4 Pi R^2/N ). +# Use the trilinear interpolation stencil to distribute the force from +# a given particle onto the fluid mesh (results in a smaller hydrodynamic +# radius than if the Peskin stencil is used). +# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number +# seed=15003). This enables the particles to undergo Brownian motion in +# the fluid. +#---------------------------------------------------------------------------- +fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003 + +#---------------------------------------------------------------------------- +# Apply the force from the fluid to the particles, and integrate their +# motion, constraining them to move and rotate together as a single rigid +# spherical object. +# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical +# shell) should move and rotate together, this fix is applied to all of +# the atoms in the system. However, since the central atoms should not +# feel a force due to the fluid, they are excluded from the fluid force +# calculation. +#---------------------------------------------------------------------------- +fix 2 FluidAtoms lb/viscous +fix 3 all rigid molecule + +#---------------------------------------------------------------------------- +# To ensure that numerical errors do not lead to a buildup of momentum in the +# system, the momentum_lb fix is used every 10000 timesteps to zero out the +# total (particle plus fluid) momentum in the system. +#---------------------------------------------------------------------------- +fix 4 all lb/momentum 10000 linear 1 1 1 + +#---------------------------------------------------------------------------- +# Write position and velocity coordinates into a file every 2000 time steps. +#---------------------------------------------------------------------------- + +dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz +run 2000001 diff -Naur lammps-21Feb17/examples/USER/lb/polymer/in.polymer_setgamma lammps-7Mar17/examples/USER/lb/polymer/in.polymer_setgamma --- lammps-21Feb17/examples/USER/lb/polymer/in.polymer_setgamma 2015-10-21 12:16:47.000000000 -0600 +++ lammps-7Mar17/examples/USER/lb/polymer/in.polymer_setgamma 2017-03-07 09:48:20.062786000 -0700 @@ -1,105 +1,105 @@ -#===========================================================================# -# polymer test # -# # -# Run consists of a lone 32-bead coarse-grained polymer # -# undergoing Brownian motion in thermal lattice-Boltzmann fluid. # -# # -# Here, gamma (used in the calculation of the monomer-fluid interaction # -# force) is set by the user (gamma = 0.03 for this simulation...this # -# value has been calibrated a priori through simulations of the drag # -# force acting on a single particle of the same radius). # -# Sample output from this run can be found in the file: # -# 'dump.polymer.lammpstrj' # -# and viewed using, e.g., the VMD software. # -# # -# Santtu Ollila # -# santtu.ollila@aalto.fi # -# Aalto University # -# August 14, 2013 # -#===========================================================================# - -units nano -dimension 3 -boundary p p p -atom_style hybrid molecular -special_bonds fene -read_data data.polymer - -#---------------------------------------------------------------------------- -# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing -# to ensure that the particles belonging to a given processor remain inside -# that processors lattice-Boltzmann grid. -#---------------------------------------------------------------------------- -neighbor 0.5 bin -neigh_modify delay 0 every 1 check yes -neigh_modify exclude type 2 2 -neigh_modify exclude type 2 1 - -#---------------------------------------------------------------------------- -# Implement a hard-sphere interaction between the particles at the center of -# each monomer (use a truncated and shifted Lennard-Jones potential). -#---------------------------------------------------------------------------- -bond_style fene -bond_coeff 1 60.0 2.25 4.14195 1.5 -pair_style lj/cut 1.68369 -pair_coeff 1 1 4.14195 1.5 1.68369 -pair_coeff 1 2 4.14195 1.5 1.68369 -pair_coeff 2 2 0 1.0 - -mass * 0.000000771064 -timestep 0.00003 - -#---------------------------------------------------------------------------- -# ForceAtoms are the particles at the center of each monomer which -# do not interact with the fluid, but are used to implement the hard-sphere -# interactions. -# FluidAtoms are the particles representing the surface of the monomer -# which do interact with the fluid. -#---------------------------------------------------------------------------- -group ForceAtoms type 1 -group FluidAtoms type 2 - -#--------------------------------------------------------------------------- -# Create a lattice-Boltzmann fluid covering the simulation domain. -# This fluid feels a force due to the particles specified through FluidAtoms -# (however, this fix does not explicity apply a force back on to these -# particles. This is accomplished through the use of the rigid_pc_sphere -# fix). -# Use the LB integration scheme of Ollila et. al. (for stability reasons, -# this integration scheme should be used when a large user set value for -# gamma is specified), a fluid viscosity = 0.023333333, -# fluid density= 0.0000166368, -# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368. -# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number -# seed=15003). This enables the particles to undergo Brownian motion in -# the fluid. -#---------------------------------------------------------------------------- -fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003 - -#---------------------------------------------------------------------------- -# Apply the force from the fluid to the particles, and integrate their -# motion, constraining them to move and rotate together as a single rigid -# spherical object. -# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical -# shell) should move and rotate together, this fix is applied to all of -# the atoms in the system. However, since the central atoms should not -# feel a force due to the fluid, they are excluded from the force -# calculation through the use of the 'innerNodes' keyword. -# NOTE: This fix should only be used when the user specifies a value for -# gamma (through the setGamma keyword) in the lb_fluid fix. -#---------------------------------------------------------------------------- -fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms - -#---------------------------------------------------------------------------- -# To ensure that numerical errors do not lead to a buildup of momentum in the -# system, the momentum_lb fix is used every 10000 timesteps to zero out the -# total (particle plus fluid) momentum in the system. -#---------------------------------------------------------------------------- -fix 3 all lb/momentum 10000 linear 1 1 1 - -#---------------------------------------------------------------------------- -# Write position and velocity coordinates into a file every 2000 time steps. -#---------------------------------------------------------------------------- - -dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz -run 2000001 +#===========================================================================# +# polymer test # +# # +# Run consists of a lone 32-bead coarse-grained polymer # +# undergoing Brownian motion in thermal lattice-Boltzmann fluid. # +# # +# Here, gamma (used in the calculation of the monomer-fluid interaction # +# force) is set by the user (gamma = 0.03 for this simulation...this # +# value has been calibrated a priori through simulations of the drag # +# force acting on a single particle of the same radius). # +# Sample output from this run can be found in the file: # +# 'dump.polymer.lammpstrj' # +# and viewed using, e.g., the VMD software. # +# # +# Santtu Ollila # +# santtu.ollila@aalto.fi # +# Aalto University # +# August 14, 2013 # +#===========================================================================# + +units nano +dimension 3 +boundary p p p +atom_style hybrid molecular +special_bonds fene +read_data data.polymer + +#---------------------------------------------------------------------------- +# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing +# to ensure that the particles belonging to a given processor remain inside +# that processors lattice-Boltzmann grid. +#---------------------------------------------------------------------------- +neighbor 0.5 bin +neigh_modify delay 0 every 1 check yes +neigh_modify exclude type 2 2 +neigh_modify exclude type 2 1 + +#---------------------------------------------------------------------------- +# Implement a hard-sphere interaction between the particles at the center of +# each monomer (use a truncated and shifted Lennard-Jones potential). +#---------------------------------------------------------------------------- +bond_style fene +bond_coeff 1 60.0 2.25 4.14195 1.5 +pair_style lj/cut 1.68369 +pair_coeff 1 1 4.14195 1.5 1.68369 +pair_coeff 1 2 4.14195 1.5 1.68369 +pair_coeff 2 2 0 1.0 + +mass * 0.000000771064 +timestep 0.00003 + +#---------------------------------------------------------------------------- +# ForceAtoms are the particles at the center of each monomer which +# do not interact with the fluid, but are used to implement the hard-sphere +# interactions. +# FluidAtoms are the particles representing the surface of the monomer +# which do interact with the fluid. +#---------------------------------------------------------------------------- +group ForceAtoms type 1 +group FluidAtoms type 2 + +#--------------------------------------------------------------------------- +# Create a lattice-Boltzmann fluid covering the simulation domain. +# This fluid feels a force due to the particles specified through FluidAtoms +# (however, this fix does not explicitly apply a force back on to these +# particles. This is accomplished through the use of the rigid_pc_sphere +# fix). +# Use the LB integration scheme of Ollila et. al. (for stability reasons, +# this integration scheme should be used when a large user set value for +# gamma is specified), a fluid viscosity = 0.023333333, +# fluid density= 0.0000166368, +# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368. +# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number +# seed=15003). This enables the particles to undergo Brownian motion in +# the fluid. +#---------------------------------------------------------------------------- +fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003 + +#---------------------------------------------------------------------------- +# Apply the force from the fluid to the particles, and integrate their +# motion, constraining them to move and rotate together as a single rigid +# spherical object. +# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical +# shell) should move and rotate together, this fix is applied to all of +# the atoms in the system. However, since the central atoms should not +# feel a force due to the fluid, they are excluded from the force +# calculation through the use of the 'innerNodes' keyword. +# NOTE: This fix should only be used when the user specifies a value for +# gamma (through the setGamma keyword) in the lb_fluid fix. +#---------------------------------------------------------------------------- +fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms + +#---------------------------------------------------------------------------- +# To ensure that numerical errors do not lead to a buildup of momentum in the +# system, the momentum_lb fix is used every 10000 timesteps to zero out the +# total (particle plus fluid) momentum in the system. +#---------------------------------------------------------------------------- +fix 3 all lb/momentum 10000 linear 1 1 1 + +#---------------------------------------------------------------------------- +# Write position and velocity coordinates into a file every 2000 time steps. +#---------------------------------------------------------------------------- + +dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz +run 2000001 diff -Naur lammps-21Feb17/examples/USER/misc/agni/Al_jpc.agni lammps-7Mar17/examples/USER/misc/agni/Al_jpc.agni --- lammps-21Feb17/examples/USER/misc/agni/Al_jpc.agni 1969-12-31 17:00:00.000000000 -0700 +++ lammps-7Mar17/examples/USER/misc/agni/Al_jpc.agni 2017-03-07 09:48:20.062786000 -0700 @@ -0,0 +1,3020 @@ +# DATE: 2017-02-24 CONTRIBUTOR: Venkatesh Botu CITATION: Botu, V., Batra, R., Chapman, J., and Ramprasad, R., J. Phys. Chem. C, 121 (1), 511 (2017). +# This potential is an updated version of Al_prb.agni, which is now deprecated. +# This potential file is parameterized for metal units + +generation 1 +n_elements 1 + +element Al + +interaction Al +Rc 8.0 +Rs 0.0 +neighbors 500 +eta 0.0036 0.0357 0.0715 0.1251 0.2144 0.3573 0.7147 1.4294 +sigma 13.8949549437 +lambda 1e-08 +b 102.870264493 +n_train 3000 +endVar + +0.000000000000000000e+00 -4.980622283254589000e+00 -2.662505672962482528e+00 -1.495155609938069619e+00 -7.333737039816567993e-01 -2.724952969791719082e-01 -6.613771156359619929e-02 -1.912092709590330940e-03 1.473705560509566359e-05 7.453680000000000305e-01 1.597331621434825659e+07 +1.000000000000000000e+00 -4.977152206916696464e+00 -2.661383130146552922e+00 -1.494564974611932495e+00 -7.326386664321046238e-01 -2.717745126429032543e-01 -6.595850089381591341e-02 -1.985476180073739681e-03 1.342170339121332597e-05 7.294220000000000148e-01 1.595073002517673187e+07 +2.000000000000000000e+00 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