Bug fixes and new features added to the 5 Oct 2007 version of LAMMPS. These are all part of the 22 Jan 2008 release, as discussed here.
21 Jan 2008
Changed the random number function that generated random values based on a particles position. We observed some unwanted correlations in the previous method. The new method uses a hash function, the Jenkins one-at-a-time method, that is claimed to be very random.
IMPORTANT NOTE: This will change the result of velocity initialization when using the velocity command with the "loop geom" option. It will also affect the results of the set and displace_atoms commands for their random options. Thus it can affect the initial state and subsequent dynamics of a LAMMPS simulation, though only in a statistical sense.
Changed the compile-time -DGZIP flag to -DLAMMPS_GZIP to be compatible with other compile flags.
Changed the ID of the presure compute created automatically by thermodynamics from "thermo_pressure" to "thermo_press" to be compatible with pressure computes created by other fixes like fix npt.
Added support for the pair_style lj/coul and pair_style buck/coul potentials to the restart2data tool. Changed the format of the dihedral OPLS potential as written to data files by the restart2data tool by a factor of 2 so that the data file written by the tool is now the same as the data file that created the restart file.
These changes will be part of the next LAMMPS release in the next couple days.
20 Jan 2008
Fixed a one-line bug in the fix ave/time command where it failed to check for an incompatible fix argument correctly.
This patch file can be applied to the 19 Jan 2008 version. This is the list of changed files.
Thanks to Ahmed Ismail (Sandia) for stumbling into this one.
19 Jan 2008
Axel Kohlmeyer (U Penn) provided some upgrades to the functionality of the dump dcd and dump xtc commands, for creating DCD and XTC formatted dump files, suitable for input into various visualization programs.
For DCD files, the dump_modify command can now specify an unwrap option to write out coordinates in "unwrapped" form as if they had not been wrapped back into a periodic simulation box.
For XTC files, the unwrap and precision options are now provided via dump modify. Also, for machines that do not have the required XDR include files, a compatability mode is available, provided thru extra functions and an associated header file. The compatability mode is activated by using a compile-time switch -DLAMMPS_XDR in your lo-level Makefile. This means you should now be able to write out XTC formatted dump files on any platform. See the Restrictions section of the dump doc page for more details.
This patch file can be applied to the 18 Jan 2008 version. This is the list of changed files.
18 Jan 2008
Mike Brown (Sandia) made some updates to his PyMol apherical viz tool to fix some link issues with gcc4, and also to skip output of spheres that are tagged as fully transparent.
He also added some speed enhancements to the GayBerne ellipsoidal particle potential for sphere-sphere and sphere-ellipse interactions.
This patch file can be applied to the 17 Jan 2008 version. This is the list of changed files.
17 Jan 2008
Added per-atom energy and virial (pressure) tabulation to the last remaining pair potentials and fix, namely pair_style meam, pair_style airebo, pair_style lj_cut_coul_long_tip4p, and fix poems. These quantities can be computed by the compute pe/atom and compute stress/atom commands.
This patch file can be applied to the 16 Jan 2008 version. This is the list of changed files.
Thanks to Greg Wagner and Aidan Thompson (Sandia) for informative discussions about virial calculations, particularly as it relates to the MEAM potential.
16 Jan 2008
Fixed a bug in the xmovie tool with its memory allocation when more than 256 snapshots are read in.
This patch file can be applied to the 12 Jan 2008 version. This is the list of changed files.
Thanks to Carolyn Phillips (U Michigan) for finding and debugging the problem.
12 Jan 2008
Added the bookkeeping to the fix shake and fix rigid commands to enable per-atom virial (stress) calculation via the compute stress/atom command. Now all that's left to complete the options for per-atom stress and energy is a few manybody pair styles and long-range forces.
This patch file can be applied to the 11 Jan 2008 version. This is the list of changed files.
11 Jan 2008
Fixed a bug with the neighbor lists construction for pair hybrid/overlay, that could cause a partial list not to be copied correctly.
This patch file can be applied to the 10 Jan 2008 version. This is the list of changed files.
Thanks to Dave Heine (Corning) for running into this problem.
10 Jan 2008
Fixed a bug with variable formulas scanning the numbers in the formula string in the input script. There was an error in how it looked for scientific notation that would cause a string like "10-2" to be evaluated as 10 instead of 8.
This patch file can be applied to the 9 Jan 2008 version. This is the list of changed files.
Thanks to James Palko (Aerospace Corp) for an email about this issue.
9 Jan 2008
Altered and enriched the variable formula syntax for equal-style and atom-style variables, so that computes, fixes, and variables are all referenced in consistent ways. Any reference to a per-atom quantity is now done thru empty brackets, e.g. x[] or c_ID[] or c_ID[][2]. This also allows an equal-style variable to access a component of a per-atom quantity, e.g. c_ID[N], where N is a global atom ID. This is useful for debugging or cutomizing thermodynamic output.
This patch file can be applied to the 8 Jan 2008 version. This is the list of changed files.
8 Jan 2008
Fixed a bug in the way the hybrid potentials (pair_style hybrid, bond_style hybrid, etc) processed coefficients (pair_coeff, bond_coeff, etc) that could sometimes cause a problem if wild card coefficients were used.
This patch file can be applied to the 6 Jan 2008 version. This is the list of changed files.
Thanks to Zhang Junjie (Harbin Institute of Technology) for running into the bug.
7 Jan 2008
Gerolf Ziegenhain sent some add-on files for those who use the VIM editor which help in editing LAMMPS input scripts. This patch adds them to the tools directory.
Note: this patch got included with the 8Jan08 patch.
6 Jan 2008
Added a pair coul/debye potential, which is a like a cutoff Coulomb potential with an additional screening factor. Like the coul/cut and coul/long potentials, this can be combined via pair_style hybrid/overlay with other Lennard-Jones potentials, that don't have a debye option (only pair_style lj/cut/coul/debye does) to enable a wider variety of simulations using screened Coulombic interactions.
This patch file can be applied to the 5 Jan 2008 version. This is the list of changed files.
Thanks to Dongsheng Zhang for suggesting this option.
5 Jan 2008
Added fix coord/original and compute displace/atom commands to allow the displacement of each atom to be calculated and used with various output options such as being written to a dump file.
This patch file can be applied to the 4 Jan 2008 version. This is the list of changed files.
Thanks to Greg Wagner (Sandia) for suggesting these new features.
4 Jan 2008
This patch adds an uncompute command to delete previously defined computes. The functionality for this was implemented in the code, but without a hook for it in the input script parser.
This patch file can be applied to the 3 Jan 2008 version. This is the list of changed files.
Thanks to Vikas Varshney (Wright-Patterson AFB) for pointing out the deficiency.
3 Jan 2008
Added a tabulation capability to the fix nve/limit command so that it tallies the number of atom velocity/position updates that are limited by the maximum distance criterion. The result can be printed with thermodynamic output or other forms of LAMMPS output.
This patch file can be applied to the 2 Jan 2008 version. This is the list of changed files.
2 Jan 2008
This patch makes some significant changes and improvements to the options for LAMMPS output. See this section of the documentation for a summary of output options and a table that lists the interrelationships between output commands.
The following commands have been deleted, since they are no longer needed: "compute variable/atom", "compute variable", "compute sum/atom", "compute attribute/atom".
The following commands have an enriched syntax that allows them to directly reference computes, fixes, or variables as part of their list of inputs: fix ave/time, fix ave/spatial, fix ave/atom, compute sum, and dump custom.
Formulas for equal-style and atom-style variables are now written in a more familiar format. The former format was easier for the code to parse, but harder for users to write. The equation parser in LAMMPS was made more robust, so formulas can be written more straightforwardly. For example, to calculate a per-atom kinetic energy, you can now write one of these lines
variable ke atom 0.5*mass*(vx*vx+vy*vy+vz*vz) variable ke atom "0.5*mass * (vx*vx + vy*vy + vz*vz)"
in the usual format, rather than the previous format
variable ke atom mult(mult(0.5,mass),add(add(mult(vx,vx),mult(vy,vy)),mult(vz,vz)))
Formulas for atom-style variables can now include references to other elements that calculate per-atom quantities: per-atom computes, per-atom fixes, or other atom-style variables. The details are given on the doc page for the variable command.
This patch file can be applied to the 20 Dec 2007 version. This is the list of changed files.
20 Dec 2007
Fixed a one-line bug with energy tabulation in the TIP4P pair style, introduced by the 1 Dec 2007 patch. Doesn't affect dynamics.
This patch file can be applied to the 19 Dec 2007 version. This is the list of changed files.
Thanks to Ahmed Ismail (Sandia) for pointing out the flaw.
19 Dec 2007
Fixed a small bug with the molecular atom_style when used as one of several atom styles via atom_style hybrid. Also fixed a bug with how the improper_style class2 command tallied virial information, introduced by the 1 Dec 07 patch.
This patch file can be applied to the 18 Dec 2007 version. This is the list of changed files.
Thanks to Sefa Dag (LBL) for sending a script that caused the problem.
18 Dec 2007
The fix langevin command did not adjust its timestep-dependent white noise parameter when being used with an adaptive timestep via the fix dt/reset command. This patch fixes that.
This patch file can be applied to the 15 Dec 2007 version. This is the list of changed files.
Thanks to James Palko (Aerospace Corp) for noting the deficiency.
15 Dec 2007
Fixed a one-line bug with the virial tabulation in the dihedral_style class2 command. This was introduced by the 1 Dec 07 patch.
This patch file can be applied to the 14 Dec 2007 version. This is the list of changed files.
Thanks to Sezen Curgul (MIT) for finding the problem.
14 Dec 2007
Added the ability for the dump custom command to directly reference an atom-style variable in its list of per-atom quantities to output. This is one step in getting rid of the compute variable/atom command, which is an extra needless layer of complexity for LAMMPS output.
This patch file can be applied to the 13 Dec 2007 version. This is the list of changed files.
13 Dec 2007
Modified the syntax of the print and run every commands to be more consistent with their use of quoting. Also added an option to the fix print command to allow its output to be written to a file.
This patch file can be applied to the 9 Dec 2007 version. This is the list of changed files.
9 Dec 2007
The replicate command was not preserving the atom map setting from the atom_modify command, which could cause memory problems for huge runs (10s or 100s of millions of atoms). This patch fixes it.
This patch file can be applied to the 8 Dec 2007 version. This is the list of changed files.
8 Dec 2007
Added a binsize option to the neigh_modify command. This allows users to experiment with the size of bins used in neighbor list construction for optimization purposes.
This patch file can be applied to the 7 Dec 2007 version. This is the list of changed files.
7 Dec 2007
The fix msd command did not compute the correct atom displacement for non-orthogonal (triclinic) boxes when computing a mean-squared displacement. This patch fixes it.
This patch file can be applied to the 6 Dec 2007 version. This is the list of changed files.
Thanks to LingTi Kong (U Western Ontario) for pointing this out.
6 Dec 2007
Fixed a bug with the minimizer not computing the correct pressure on its final iteration. I think this was also introduced by the large 1 Dec 1007 patch.
This patch file can be applied to the 5 Dec 2007 version. This is the list of changed files.
Thanks to Zhenhai Xu for discovering there was a problem.
5 Dec 2007
Fixed a one-line bug with pair hybrid and pair airebo that computed pressure incorrectly as a result of the 1 Dec 2007 patch. A flag's value was checked incorrectly.
This patch file can be applied to the 4 Dec 2007 version. This is the list of changed files.
Thanks to Mike Brown (Sandia) for finding the issue.
4 Dec 2007
Pair_style meam lacked a couple of variable declarations in the 1 Dec 2007 patch. This patch fixes the problem.
This patch file can be applied to the 2 Dec 2007 version. This is the list of changed files.
Thanks to a couple of users for pointing out the deficiency.
2 Dec 2007
Tersoff energy was not tabulated correctly in the 1 Dec 2007 patch. This patch fixes it.
This patch file can be applied to the 1 Dec 2007 version. This is the list of changed files.
1 Dec 2007
Per-atom energy and stress (virial) tabulation has been enhanced in a way that makes it possible for any pairwise or bonded or manybody potential to generate the appropriate per-atom quantities with little overhead cost. Every potential in LAMMPS can now be used in this mode, with a few exceptions as noted below.
This is a significant patch that changes many files, though mostly in minor ways. To make all the various potentials consistent with the new tabulation routines, some variable rearrangement was necessary, which may have introduced bugs in the potentials themselves. Hopefully not, but it's a good idea to check if your results for this new version are consistent with the pre-patched version.
The following changes have been made:
See this section for details of how to use the global and per-atom computes for energy and stress (pressure) in conjunction with other computes and fixes.
Fix gran/diag was deleted because its functionality is available by using the compute stress/atom command in conjunction with fix ave/spatial.
There are 3 pair potentials that still need to be instrumented to work with the per-atom energy and stress computes: AIREBO, MEAM, and TIP4P. This will be implemented soon. Likewise, fixes that contribute to the virial (e.g. SHAKE, rigid), still need to be instrumented to extract their per-atom contributions.
This patch file can be applied to the 30 Nov 2007 version. This is the list of changed files.
Thanks to Aidan Thompson (Sandia) for very helpful discussions about the nitty-gritty details of virial computations.
30 Nov 2007
Paul Crozier has made the grid size selection code in the PPPM kspace_style solver more robust, so it can more often select a good grid size without user intervention via the kspace_modify mesh command.
This patch file can be applied to the 29 Nov 2007 version. This is the list of changed files.
29 Nov 2007
Made a change to the Lennard-Jones pressure tail correction option specified by the pair_modify command. Now it is only applied to the 3 diagonal components of the pressure tensor, not to the off-diagonal components.
This patch file can be applied to the 27 Nov 2007 version. This is the list of changed files.
Thanks to LT Kong (University of Western Ontario) for calling attention to this issue.
27 Nov 2007
Fixed a bug with the virial (and hence pressure) computation for the GayBerne and RE-squared pair potentials.
Also changed an error condition with fix ave/time and fix ave/spatial so that the timestep to compute the first average is incremented rather than generating an error.
This patch file can be applied to the 26 Nov 2007 version. This is the list of changed files.
26 Nov 2007
Changed Make.csh in the src dir because the "make makelib" and "make makelist" were failing due to too many source files. The shell was complaining about too long a word, as generated by the script.
This patch file can be applied to the 16 Nov 2007 version. This is the list of changed files.
Thanks to Wende Tian for pointing out the problem.
16 Nov 2007
Added support for the pair_style lj/smooth potential to the restart2data tool.
This patch file can be applied to the 15 Nov 2007 version. This is the list of changed files.
Thanks to Javier Ramos (Instituto de Estructura de la Materia, Spain) for noting the omission.
15 Nov 2007
Fixed a bug with the pressure contribution computed by pair style lj/cut/coul/long/tip4p. This bug was introduced recently when neighbor lists and the way pair styles use them was changed. It doesn't effect dynamics, only the thermodynamic reporting of pressure (unless you're running an NPT or NPH ensemble).
This patch file can be applied to the 13 Nov 2007 version. This is the list of changed files.
Thanks to Ahmed Ismail (Sandia) for helping with this.
13 Nov 2007
Added a diagnostic to sum the applied forces due to the fix spring and fix drag commands. The vector of applied force can be accessed by various output commands. This is useful for thermodynamic integration when umbrella sampling is performed.
Also fixed a couple small bugs with the indexing of applied forces accessible from other fixes: fix indent, fix wall/lj93, and fix wall/lj126.
This patch file can be applied to the 12 Nov 2007 version. This is the list of changed files.
Thanks to Kelly Anderson (Procter & Gamble) for suggesting this feature.
12 Nov 2007
Fixed a one-line bug in the compute ebond/atom command for computing bond energies on a per-atoms basis.
This patch file can be applied to the 8 Nov 2007 version. This is the list of changed files.
Thanks to Naida Lacevic (LLNL) for finding the problem.
8 Nov 2007
Fixed a dumb bug in the new compute sum command where it failed to sum the result across processors.
This patch file can be applied to the 7 Nov 2007 version. This is the list of changed files.
Thanks to Ishraq Shabib (Carleton U, Canada) for showing up the problem.
7 Nov 2007
Fixed a small bug in pair_style sw that prevented it from working correctly with the new pair_style hybrid options recently released.
This patch file can be applied to the 6 Nov 2007 version. This is the list of changed files.
Thanks to Limel Xu (U Utah) for running into the bug.
6 Nov 2007
Fixed a one-line bug in a neighboring routine that is invoked when newton pair is off and both half and full neighbor lists are used in the same simulation.
This patch file can be applied to the 5 Nov 2007 version. This is the list of changed files.
Thanks to Kim Sangrak (Kyonggi U, Korea) for finding the bug.
5 Nov 2007
Added a compute pe command to allow potential energy to be calculated and used by fix ave/time, variables, etc in the various ways outlined in this section of the manual.
This patch file can be applied to the 4 Nov 2007 version. This is the list of changed files.
4 Nov 2007
Fixed a bug with how a half neighbor list was built from a full neighbor list in a pair hybrid simulation.
This patch file can be applied to the 2 Nov 2007 version. This is the list of changed files.
Thanks to Yonggang Zheng (Dalian University of Technology) for providing a script that identified the issue.
2 Nov 2007
Fixed a dumb bug in the Yukawa potential where the force had a pre-factor that didn't match the energy. Would not affect a simulation if the pre-factor A = 1.
This patch file can be applied to the 1 Nov 2007 version. This is the list of changed files.
Thanks to Dave Heine (Corning) for noticing this.
1 Nov 2007
The 31 Oct 2007 patch didn't include two new files for the compute sum command. This patch adds them.
This patch file can be applied to the 31 Oct 2007 version. This is the list of changed files.
31 Oct 2007
Added a compute sum command, which generates a global scalar or vector of values by summing over the per-atom quantities calculated by one or more other computes. The results can be accessed by the thermo_style custom or fix ave/time commands or by a user-defined variable.
An example of using compute sum would be to sum the total force on atoms in a group.
This patch file can be applied to the 30 Oct 2007 version. This is the list of changed files.
30 Oct 2007
Fixed a bug with the volume option in the fix deform that was due to a couple quantities being initialized incorrectly. This worked at one point, so not sure when this bug crept in!
This patch file can be applied to the 29 Oct 2007 version. This is the list of changed files.
Thanks to Vikas Varshney (Wright-Patterson AFB) and Rob Hoy (UC Santa Barbara) for calling attention to the problem.
29 Oct 2007
Aidan Thompson and Xiaowang Zhou (Sandia) have extended the Tersoff potential in LAMMPS to enable both the original Tersoff and more recent variants to be used. As part of this effort, several new Tersoff potential files were added to the potential directory for alloy modeling:
The SiCGe.tersoff file includes several Si variants, which can be used in single-element or alloy simulations. Other Tersoff potential files were modified to match the new format. Note that potential files in the old format no longer work with this patch, though modifying them to satisfy the new format is not difficult.
The doc page for the Tersoff potential has details of the new format and parameters.
This patch file can be applied to the 28 Oct 2007 version. This is the list of changed files.
28 Oct 2007
One-line bug fix in the restart2data tool for GayBerne ellipsoidal potentials. The format for printing the pair coefficients was wrong.
This patch file can be applied to the 27 Oct 2007 version. This is the list of changed files.
Thanks to Jiwu Liu for flagging this.
27 Oct 2007
Added a check for the reset_timestep command to insure dump files and restart files have not been already been written out based on the old timestep. This can mess up the determination of the next timestep on which file output should be performed.
This patch file can be applied to the 26 Oct 2007 version. This is the list of changed files.
26 Oct 2007
Mike Brown (Sandia) has implemented a new RE-squared interaction potential for aspherical particles, which can be invoked via the pair_style resquared command. This anisotropic interaction potential for ellipsoids is an alternative to the Gay-Berne potential. The RE-squared potential treats ellipsoids as composites of smaller spherical particles and therefore may be more accurate than Gay-Berne for large ellipsoids where the scaling of interaction energy does not follow simple power rules. An additional difference is that the RE-squared potential does become isotropic in the large distance limit.
He also upgraded the pymol_asphere tool for converting LAMMPS output to PyMol input for aspherical particles. This fixed a bug to force normal output for ellipsoids (this will fix shading problems on some graphics cards). The tool no longer attempts to read LAMMPS input files and will work on general LAMMPS dump files in the usual "tag type x y z" format (see tool documentation). The number of particles per timestep is no longer fixed.
This patch file can be applied to the 25 Oct 2007 version. This is the list of changed files.
25 Oct 2007
Fixed a bug with pair_style airebo that was created by changes in the format of neighbor lists in the most recent major release (5Oct07).
This patch file can be applied to the 24 Oct 2007 version. This is the list of changed files.
Thanks to Liang Wan (Chinese Academy of Science) for catching this.
24 Oct 2007
Fixed a memory issue with neighbor lists that could appear when the delete_atoms command was used, before a simulation run.
This patch file can be applied to the 23 Oct 2007 version. This is the list of changed files.
Thanks to Liang Wan (Chinese Academy of Science) for identifying the problem.
23 Oct 2007
Fixed a one-line memory allocation bug in the fix ave/atom command.
This patch file can be applied to the 22 Oct 2007 version. This is the list of changed files.
22 Oct 2007
Added options to the fix ave/time and fix ave/spatial commands to allow their output to be averaged in two new ways. One is to calculate a running cummulative average from the point in time the fix was defined. The other is to compute an average within a moving time window, e.g. over the last 100 values. Adding these options changed the syntax of both commands.
These new options also make the thermo_style custom options for time-averaged thermodynamic output obsolete, since a richer variety of time-averaged output can now be calculated by fix ave/time and accessed by the f_ID keyword of thermo_style custom. As a result, the "tave", "pave", etc keywords of thermo_style custom have been deleted.
See this section of the manual for a summary of LAMMPS output options for thermodynamic and per-atom data.
This patch file can be applied to the 21 Oct 2007 version. This is the list of changed files.
21 Oct 2007
With help from Ed Maginn (U Notre Dame), a fix viscosity command has been added. This is to enable fluid viscosities to be calculated via the method of Florian Muller-Plathe described in Phys Rev E, 59, 4894-4898 (1999). The algorithm is explained briefly in the fix viscosity doc page; full details are in the paper. This is an alternative method to running a NEMD simulation to compute viscosity.
This patch file can be applied to the 20 Oct 2007 version. This is the list of changed files.
20 Oct 2007
Added the option to the fix ave/spatial command to generate a vector of values that can be accessed by other output commands such as thermo_style custom f_ID[N].
This patch file can be applied to the 19 Oct 2007 version. This is the list of changed files.
19 Oct 2007
Fixed a problem with the energy calculation in pair_style yukawa.
This patch file can be applied to the 18 Oct 2007 version. This is the list of changed files.
18 Oct 2007
Inadvertently left 2 needed files for the new fix dt/reset command out of the 10Oct07 patch. This patch adds them.
This patch file can be applied to the 17 Oct 2007 version. This is the list of changed files.
Thanks to Mike Brown (Sandia) for calling this to my attention.
17 Oct 2007
Added a restart capability to the fix deposit command so it will be easier to run long simulations of deposition onto a surface and restart them from an intermediate state.
This patch file can be applied to the 16 Oct 2007 version. This is the list of changed files.
16 Oct 2007
Gerolf Ziegenhain has provided some new EAM potentials for Cu, Al, and W as well as the source code for one-file programs that tabulate the potentials from an analytic formula. The latter have been added to the tools/eam_generate directory as a tool.
This patch file can be applied to the 15 Oct 2007 version. This is the list of changed files.
15 Oct 2007
Fixed a one-line bug with using the TIP4P pair potential with kspace_style pppm/tip4p that gave an error at start-up time.
This patch file can be applied to the 14 Oct 2007 version. This is the list of changed files.
Thanks to Jeetain Mittal (NIH) for identifying the issue.
14 Oct 2007
Randy Schunk (Sandia) has added hydrodynamic lubrication forces between particles due to an implicit solvent as a pair_style lubricate command. The pairwise lubrication forces have 4 components which can be turned on or off - squeeze, shear, pump, and twist - which produce force and torque on the particles.
This patch file can be applied to the 13 Oct 2007 version. This is the list of changed files.
13 Oct 2007
Fixed a memory bug with neighbor lists used by pair_style hybrid when doing multiple runs in the same input script.
This patch file can be applied to the 12 Oct 2007 version. This is the list of changed files.
Thanks to Mike Brown (Sandia) for stumbling into the bug.
12 Oct 2007
Fixed a one-line bug in the fix recenter command when using the shift option.
This patch file can be applied to the 11 Oct 2007 version. This is the list of changed files.
Thanks to Lukas Geyrhofer for identifying the bug.
11 Oct 2007
Enabled the fix ave/time command to produce global values that can be accessed by the thermo-style custom command. This means you can print out time averages of a variety of quantities as part of thermodynamic output. See this section for a discussion of output options.
This patch file can be applied to the 10 Oct 2007 version. This is the list of changed files.
10 Oct 2007
Added a fix dt/reset command which allows the timestep size to be reset continuously during a simulation, based on maximum velocities and accelerations experienced by the particles.
This can be useful when starting from a configuration with overlapping atoms, where forces will be large. Or it can be useful when running an impact simulation where one or more high-energy atoms collide with a solid, causing a damage cascade.
This patch file can be applied to the 9 Oct 2007 version. This is the list of changed files.
Thanks to Eduardo Bringa (LLNL) for suggesting this feature.
9 Oct 2007
Fixes can now compute global scalars and vector quantities which can be accessed by other LAMMPS output commands. An example of a scalar is the potential energy associated with the fix. An example of a vector is the aggregate force generated by the fix, e.g. by a wall or indenter or by fix setforce before it changes the forces. See the doc pages of individual fix commands for details of which fixes calculate these quantities.
The thermo_style custom command can access these fix quantities.
Variables can now access these fix quantities, like they can compute quantities.
The fix ave/time command was enhanced to allow access to these fix quantities, like compute quantities. Note that this changed the syntax of the fix ave/time command.
This howto section summarizes the various ways thermodyanmic and dump output can be produced and customized.
This patch file can be applied to the 5 Oct 2007 version. This is the list of changed files.