diff -Naur lammps-9Jan17/doc/html/.buildinfo lammps-17Jan17/doc/html/.buildinfo
--- lammps-9Jan17/doc/html/.buildinfo 2017-01-09 13:33:58.000000000 -0700
+++ lammps-17Jan17/doc/html/.buildinfo 2017-01-18 08:33:45.414433124 -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: 77e273bf55cdca4f3ac157243a46785b
+config: ad8be50116609dd15b1a9b9b50fe8610
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff -Naur lammps-9Jan17/doc/html/Manual.html lammps-17Jan17/doc/html/Manual.html
--- lammps-9Jan17/doc/html/Manual.html 2017-01-09 13:33:58.000000000 -0700
+++ lammps-17Jan17/doc/html/Manual.html 2017-01-18 08:33:45.445434041 -0700
@@ -148,7 +148,7 @@
LAMMPS Documentation
-
9 Jan 2017 version
+
17 Jan 2017 version
Version info:
diff -Naur lammps-9Jan17/doc/html/Section_errors.html lammps-17Jan17/doc/html/Section_errors.html
--- lammps-9Jan17/doc/html/Section_errors.html 2017-01-09 13:33:58.000000000 -0700
+++ lammps-17Jan17/doc/html/Section_errors.html 2017-01-18 08:33:45.419433272 -0700
@@ -194,12 +194,13 @@
LAMMPS errors are detected at setup time; others like a bond
stretching too far may not occur until the middle of a run.
LAMMPS tries to flag errors and print informative error messages so
-you can fix the problem. Of course, LAMMPS cannot figure out your
-physics or numerical mistakes, like choosing too big a timestep,
-specifying erroneous force field coefficients, or putting 2 atoms on
-top of each other! If you run into errors that LAMMPS doesn’t catch
-that you think it should flag, please send an email to the
-developers.
+you can fix the problem. For most errors it will also print the last
+input script command that it was processing. Of course, LAMMPS cannot
+figure out your physics or numerical mistakes, like choosing too big a
+timestep, specifying erroneous force field coefficients, or putting 2
+atoms on top of each other! If you run into errors that LAMMPS
+doesn’t catch that you think it should flag, please send an email to
+the developers.
If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by
looking in the log.lammps file or using the echo command
diff -Naur lammps-9Jan17/doc/html/Section_packages.html lammps-17Jan17/doc/html/Section_packages.html
--- lammps-9Jan17/doc/html/Section_packages.html 2017-01-09 13:33:58.000000000 -0700
+++ lammps-17Jan17/doc/html/Section_packages.html 2017-01-18 08:33:45.445434041 -0700
@@ -391,7 +391,7 @@
-
@@ -2318,21 +2287,13 @@
convention. This package implements a dump nc command
and a dump nc/mpiio command to output LAMMPS snapshots
in this format. See src/USER-NC-DUMP/README for more details.
-
-
NetCDF files can be directly visualized with the following tools:
-Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
+a NetCDF reader that is not present in the standard distribution of AtomEye
The person who created these files is Lars Pastewka at
Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
diff -Naur lammps-9Jan17/doc/html/Section_start.html lammps-17Jan17/doc/html/Section_start.html
--- lammps-9Jan17/doc/html/Section_start.html 2017-01-09 13:33:58.000000000 -0700
+++ lammps-17Jan17/doc/html/Section_start.html 2017-01-18 08:33:45.427433509 -0700
@@ -1813,8 +1813,9 @@
thermodynamic state and a total run time for the simulation. It then
appends statistics about the CPU time and storage requirements for the
simulation. An example set of statistics is shown here:
-
Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+
Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
97.0% CPU use with 4 MPI tasks x no OpenMP threads
@@ -1843,14 +1844,14 @@
Neighbor list builds = 26
Dangerous builds = 0
-
The first section provides a global loop timing summary. The loop time
+
The first section provides a global loop timing summary. The loop time
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
+continuations required and for comparing performance with other,
+similar MD codes. The CPU use line provides the CPU utilzation per
MPI task; it should be close to 100% times the number of OpenMP
-threads (or 1). Lower numbers correspond to delays due to file I/O or
-insufficient thread utilization.
+threads (or 1 of no OpenMP). Lower numbers correspond to delays due
+to file I/O or insufficient thread utilization.
The MPI task section gives the breakdown of the CPU run time (in
seconds) into major categories:
Kokkos support within LAMMPS must be built with a C++11 compatible
-compiler. If using gcc, version 4.8.1 or later is required.
+compiler. If using gcc, version 4.7.2 or later is required.
To build with Kokkos support for CPUs, your compiler must support the
OpenMP interface. You should have one or more multi-core CPUs so that
multiple threads can be launched by each MPI task running on a CPU.
To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
-version 6.5 or later must be installed on your system. See the
+version 7.5 or later must be installed on your system. See the
discussion for the GPU package for details of
how to check and do this.
cutoff = distance within which to count coordination neighbors (distance units)
-
typeN = atom type for Nth coordination count (see asterisk form below)
+
one cstyle must be appended
+
cstyle = cutoff or orientorder
+
+cutoff args = cutoff typeN
+ cutoff = distance within which to count coordination neighbors (distance units)
+ typeN = atom type for Nth coordination count (see asterisk form below)
+
+orientorder args = orientorderID threshold
+ orientorderID = ID of a previously defined orientorder/atom compute
+ threshold = minimum value of the scalar product between two 'connected' atoms (see text for explanation)
+
Examples
-compute 1 all coord/atom 2.0
-compute 1 all coord/atom 6.0 1 2
-compute 1 all coord/atom 6.0 2*4 5*8 *
+compute 1 all coord/atom cutoff 2.0
+compute 1 all coord/atom cutoff 6.0 1 2
+compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
+compute 1 all coord/atom orientorder 2 0.5
Description
-
Define a computation that calculates one or more coordination numbers
+
This compute performs generic calculations between neighboring atoms. So far,
+there are two cstyles implemented: cutoff and orientorder.
+The cutoff cstyle calculates one or more coordination numbers
for each atom in a group.
A coordination number is defined as the number of neighbor atoms with
specified atom type(s) that are within the specified cutoff distance
@@ -323,6 +336,13 @@
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
+
The orientorder cstyle calculates the number of ‘connected’ atoms j
+around each atom i. The atom j is connected to i if the scalar product
+(Ybar_lm(i),*Ybar_lm(j)*) is larger than threshold. Thus, this cstyle
+will work only if a compute orientorder/atom
+has been previously defined. This cstyle allows one to apply the
+ten Wolde’s criterion to identify cristal-like atoms in a system
+(see ten Wolde et al.).
The value of all coordination numbers will be 0.0 for atoms not in the
specified compute group.
The neighbor list needed to compute this quantity is constructed each
@@ -356,13 +376,17 @@
Restrictions
-
-
none
+
The cstyle orientorder can only be used if a
+compute orientorder/atom command
+was previously defined. Otherwise, an error message will be issued.
-keyword = cutoff or nnn or degrees
+keyword = cutoff or nnn or degrees or componentscutoff value = distance cutoff
nnn value = number of nearest neighbors
degrees values = nlvalues, l1, l2,...
+ components value = l
@@ -347,6 +350,12 @@
The numerical values of all order parameters up to Q12
for a range of commonly encountered high-symmetry structures are given
in Table I of Mickel et al..
+
The optional keyword components will output the components of
+the normalized complex vector Ybar_lm of degree l, which must be
+explicitly included in the keyword degrees. This option can be used
+in conjunction with compute coord_atom to
+calculate the ten Wolde’s criterion to identify crystal-like particles
+(see ten Wolde et al.).
The value of Ql is set to zero for atoms not in the
specified compute group, as well as for atoms that have less than
nnn neighbors within the distance cutoff.
@@ -372,6 +381,11 @@
Output info:
This compute calculates a per-atom array with nlvalues columns, giving the
Ql values for each atom, which are real numbers on the range 0 <= Ql <= 1.
+
If the keyword components is set, then the real and imaginary parts of each
+component of (normalized) Ybar_lm will be added to the output array in the
+following order:
+Re(Ybar_-m) Im(Ybar_-m) Re(Ybar_-m+1) Im(Ybar_-m+1) ... Re(Ybar_m) Im(Ybar_m).
+This way, the per-atom array will have a total of nlvalues+2*(2l+1) columns.
These values can be accessed by any command that uses
per-atom values from a compute as input. See Section 6.15 for an overview of LAMMPS output
options.
@@ -389,8 +403,9 @@
Default
The option defaults are cutoff = pair style cutoff, nnn = 12, degrees = 5 4 6 8 10 12 i.e. Q4, Q6, Q8, Q10, and Q12.
-
(Steinhardt) P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
-
(Mickel) W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
+
(Steinhardt) P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
+
(Mickel) W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
+
(tenWolde) P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
This fix implements the molecular dynamics version of the generalized
-replica exchange method (gREM) originally developed by (Kim),
+replica exchange method (gREM) originally developed by (Kim),
which uses non-Boltzmann ensembles to sample over first order phase
transitions. The is done by defining replicas with an enthalpy
dependent effective temperature
diff -Naur lammps-9Jan17/doc/html/fix_spring.html lammps-17Jan17/doc/html/fix_spring.html
--- lammps-9Jan17/doc/html/fix_spring.html 2017-01-09 13:33:58.000000000 -0700
+++ lammps-17Jan17/doc/html/fix_spring.html 2017-01-18 08:33:45.431433627 -0700
@@ -461,11 +461,7 @@
group can straddle a periodic boundary. See the dump doc
page for a discussion of unwrapped coordinates. It also means that a
spring connecting two groups or a group and the tether point can cross
-a periodic boundary and its length be calculated correctly. One
-exception is for rigid bodies, which should not be used with the fix
-spring command, if the rigid body will cross a periodic boundary.
-This is because image flags for rigid bodies are used in a different
-way, as explained on the fix rigid doc page.
+a periodic boundary and its length be calculated correctly.
Restart, fix_modify, output, run start/stop, minimize info: