31 Dec 2013
Added an option to apply SHAKE constraints to molecules inserted with the fix deposit or fix pour commands. The fix_deposit command also now has an option to insert rigid molecules via the fix rigid/small command.
BACKWARD COMPATIBILITY: This patch moved the fix shake command into the RIGID package, and the fix deposit command into the MISC pacakge.
30 Dec 2013
Enabled the fix pour command to work with the new molecule command and with fix rigid/small, so that granular rigid bodies can be poured into a simulation box.
17 Dec 2013
Added a new examples/deposit with input scripts that illustrate the use of the fix deposit command with atoms and molecules.
Added some options to the create_box command to allow empty molecular systems to be created without use of a data file and the read_data command. This is useful when commands like fix deposit will add molecules later.
16 Dec 2013
Added a molecule deposition capability to the fix deposit command. As part of this, a new molecule command was added to LAMMPS, to allow specification of template molecules. This will eventually be used by other commands as well.
7 Dec 2013
There were a couple of glitches in the 6Dec patch with restart file reading/writing that this patch fixes.
Thanks to various users who pointed these out.
6 Dec 2013
This patch adds enhanced parallel options for writing and reading binary restart files via the restart, write_restart, and read_restart commands. Similar to dump files and the dump modify nfile and fileper options, the restart and write_restart commands now accept the same nfile and fileper options. When running on large numbers of processors, this allows restart files to be written by a subset of the procs, which can be the fastest mode of output. The read_restart command detects how many files are in the restart and similarly reads the files in parallel efficiently.
Logic has also been added to detect when a specified file is an invalid restart file, and when the endian ordering of the restart file is incompatible with the machine that is reading it. Likewise some logic is added to detect when the restart file format has changed and the current version of LAMMPS is thus not capable of reading the restart file.
This patch also adds hooks that will be used by future enhancements I/that will use MPI-IO capabilties for more parallel high-performance I/O.
BACKWARD COMPATIBILITY: This patch changes the format of binary restart files. Versions dated 6Dec13 or later can thus NOT be used to read restart files from previous versions of LAMMPS.
5 Dec 2013
Ray Shan (Sandia) made some small changes to the COMB potential in pair_style comb.
Thanks to Teemu Hynninen (Aalto University) for sending a careful email regarding the COMB issues.
1 Dec 2013
Added a format-style variable to the variable command to allow printing of equal-style variables, e.g. via the print command in a desired format.
Also enabled the -r command line switch for creating data files from restart files to work for pair styles that don't store additional input script settings in the restart file.
Thanks to Dmitry Fedosov (Research Center Juelich, Germany) for an email about the restart file issue.
27 Nov 2013
Fixed a bug introduced with the 11Nov13 patch with one of the input file options for the neb final command.
Thanks to Charles Laybourne for pointing out the NEB issue.
25 Nov 2013
Added support for the new dump_modify buffer command to CFG-style dumps as well.
23 Nov 2013
The restart2data tool has been removed from LAMMPS. The write_data command now has all of its functionality. A -r command-line switch has been added to enable easy conversion of existing restart files to data files, e.g.
lmp_g++ -r restartfile datafile
which is the same as running a 2-line input script:
read_restart restartfile write_data datafile
BACKWARD COMPATIBILITY: This patch removes the restart2data tool.
22 Nov 2013
Made an optimization to the way in which text-based dump files are written via the dump command, for styles atom, custom, local, and xyz. Formatting of the output is now performed in parallel, and then written to disk by one or more processors as one big string. This takes about 2x as much memory per-processor, but is often faster for snapshots with large numbers of atoms.
This mode of output is now the default, but can be turned off (to be like the previous method) via the dump_modify buffer command.
This is a preliminary change necessary for supporting more parallel output via the MPI-IO library.
21 Nov 2013
Changed the format of the -h (help) output as a LAMMPS command-line switch, to be more readable and also list command-line options.
Also did some internal refactoring of the way 32-bit and 64-bit integers are stored in double-precision buffers, to avoid problems with some compiler optimizations.
11 Nov 2013
Made some enhancements and changes to the nudged elastic band energy barrier search, or neb command.
It now allows input of initial configuration atom coordinates via one file per replica, or no files. The latter means that the initial configs can be read by each replica thru data, restart, or dump files.
There is also added error checking on invalid atom IDs in the input files of atom coordinates.
BACKWARD COMPATIBILITY: This patch changes the syntax of the neb to enable different modes of initial configuration input. It also makes a slight change to the input file format for atomic coordinates, adding a line at the beginning which gives N = the number of lines to follow. This is to make the format compatible with other files read by LAMMPS.
10 Nov 2013
Francis Mackay and Colin Denniston (U Western Ontario) have added a Lattice Boltzmann capability that allows a background fluid to exert hydrodynamic forces on particles using a lattice superposed over the simulation domain. This patch releases it as USER-LB package with example files in examples/USER/lb. See the doc page for the fix lb/fluid command to get started.
9 Nov 2013
Added a velocity auto-correlation compute as a compute vacf command.
8 Nov 2013
Fixed a memory leak in neighbor lists that was triggered when multiple lists were requested and one could be a "copy" of another.
Fixed a small bug in the just-released write_dump command.
Thanks to Andres Jaramillo-Botero (Caltech) for posting a simple script that illustrated the memory leak issue.
7 Nov 2013
Rodrigo Freitas (UC Berkeley) has contributed two thermodynamic integration fixes for computing free energies. They are now in the USER-MISC package, as the fix ti/rs and fix ti/spring commands.
6 Nov 2013
Ray Shan (Sandia), in collaboration with Tao Liang and Dundar Yilmaz (U Florida), and the U Florida groups of Simon Phillpot and Susan Sinnott, have released the 3rd-generation COMB potential in LAMMPS, as a pair_style comb3 command, with an option to include/exclude atomic polarization effects.
Andrew Jewett (UCSB) sent a new version 1.14 of his moltemplate tool, which is included in this patch.
5 Nov 2013
Lingti Kong (Shanghai Jiao Tong University) has upgraded his USER-PHONON package and its fix phonon command to allow for generation of the map file internally if one wants to calculate the phonons at the gamma point only.
Vikas Varshney also made an upgrade to the amber2lammps tool to support some current AMBER flags.
Ray Shan (Sandia) made a memory-usage improvement to the dump cfg command.
4 Nov 2013
Axel Kohlmeyer (ICTP, Italy) added a dump movie command, so that the movies can be written as a single file via the FFmpeg command available on many machines, including Windows boxes. The new capability works by leveraging the dump image command to create the individual image files.
Also removed a couple of ignored arguments from the just-released write_dump command.
1 Nov 2013
Axel Kohlmeyer (ICTP, Italy) added a write_dump command which can be used to write out an individual snapshot to a file, in any of the dump styles supported by LAMMPS.
30 Oct 2013
Axel Kohlmeyer (ICTP, Italy) added a variable getenv style and a shell putenv command.
He also made some upgrades to the following features:
29 Oct 2013
Axel Kohlmeyer (ICTP, Italy) added PNG image file support (lossless compression) to the dump image command.
This patch also fixes a few small bugs:
30 Sep 2013
Axel Kohlmeyer (ICTP, Italy) added an append option to the log command.
Ray Shan (Sandia) made the reported memory-usage per processor more accurate for the pair_style reax/c command. He and Oleg Sergeev (VNIIA) also fixed a bug with the fix reax/c/species command when using the position keyword to write center-of-mass position of identified molecules.
Stan Moore (Sandia) also fixed a bug with the energy keyword of the fix efield command and added a region keyword to it.
23 Sep 2013
Vikas Varshney created an xmgrace tool directory with several tools to assist in creating xmgrace plots of thermodynamic data in LAMMPS log files, including one that will make a plot from the current status of a running LAMMPS simulation.
This patch also contains several small bug fixes and upgrades to various commands.
19 Sep 2013
Added a q field to the read_dump command so that charge values can be read in from a dump file, which is useful for variable-charge potentials, like ReaxFF or COMB.
18 Sep 2013
Made a change to the read_dump command so that it assigns image flags for atoms with unwrapped coordinates more automatically.
17 Sep 2013
Aidan Thompson and Stephen Foiles (Sandia) have added a new pair style called zbl. It computes the Zeigler-Biersack-Littmark (ZBL) pairwise additive repulsive interaction for describing high-energy collisions between atoms.
13 Sep 2013
Released a VISCOSITY dir under the examples dir which contains various scripts for measuring the viscosity of a simple 2d LJ fluid system. The methods used are discussed in Section 6.21 of the manual.
12 Sep 2013
Released a KAPPA dir under the examples dir which contains various scripts for measuring the thermal conductivity of a simple LJ fluid system. The methods used are discussed in Section 6.20 of the manual.
10 Sep 2013
Released an ASPHERE dir under the examples dir which contains various scripts for modeling aspherical particles, either as point ellipsoids, rigid bodies, or line- and triangle-faceted bodies for generalized 2d and 3d shapes. Many of the models contain SRD solvent provided by the fix srd command. Most of the scripts produce dump or image files. Animations of the output have been added to the Movies page of the web site.
9 Sep 2013
Some adjustments were needed to the rigid fixes to prevent them from computing angular momentum explicitly when using bodies with overlapped particles and moments of inertia read in from a file. This was affecting the new velocity zero rigid option.
5 Sep 2013
Added compute ke/rigid and compute erotate/rigid commands to calculate the translationals and rotational energy of rigid bodies as defined by the fix rigid command variants.
This patch also fixes a few small bugs with some of the rigid-body options for reading/writing moments of inertia and zeroing linean/angular momenta that have recently been added.
4 Sep 2013
Added a rigid option to the velocity zero command to allow the linear and angular momentum of individual rigid bodies to be zeroed.
30 Aug 2013
Julian Devemy and collaborators at ICCF have implemented the N-M potential, available now as pair_styles nm/cut, nm/cut/coul/cut, and nm/cut/coul/long.
27 Aug 2013
Jonathan Lee (Sandia) added a fix wall/lj1043 potential as a new wall style.
26 Aug 2013
Mike Brown and Trung Nguyen (ORNL) have released an upgrade to their GPU package in LAMMPS, including the underlying lib/gpu.
The latter allows a single OpenCL build to be used on different accelerators (e.g. the Windows build).
25 Aug 2013
Axel Kohlmeyer (ICTP, Italy) has released an updated version of the msi2lmp tool.
This patch also fixes a bug when the change_box command is used with a triclinic geometry and shrink-wrapped boundaries, thanks to user Alban.
It also fixed a bug with the region cylinder command for using EDGE as an setting for the hi-end of the cylinder, thanks to Takaaki Aoki.
24 Aug 2013
Added support for writing out rigid body parameters (mass, center-of-mass, inertia tensor) to a file when writing restart files. This is so the file-based info can be read back in when restarting a run with rigid bodies, since LAMMPS cannot compute it and the user cannot easily generate it.
23 Aug 2013
Added support for reading rigid body parameters (mass, center-of-mass, inertia tensor) from a file to the fix rigid/small commmand, the same as the fix rigid command already allowed.
21 Aug 2013
Added support in the write_data command for outputting per-atom fields read and stored by the fix property/atom command.
BACKWARD COMPATIBILITY: This patch changes the output of the fix dt/reset command to only be a scalar value for the last timestep on which the timestep was changed. The current timestep size and cumulative simulation time (previous outputs) can now be obtained directly as thermo_style keywords dt and time.
20 Aug 2013
Stan Moore (Sandia) fixed some bugs and added support for the slab correction option with the KSpace solvers. Specifically:
19 Aug 2013
Release of a new version of the USER-ATC package by its developers Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia).
It adds significant new capabilities in two areas:
(1) Coarse graining
(2) Coupling
as well as the ability to use arbitrary hex & tet meshes, and a library of kernel estimators and time filters.
The syntax has changed slightly from the previous version. See the documentation (doc/USER/atc) and examples (examples/USER/atc) for details.
This patch also fixes a bug with the grmask() function for atom-style variables.
This patch also fixes a bug with the pair_style lj/charmm/coul/charmm/implicit command provided by Jens Pfeifer (Philipps-Universität Marburg).
This patch also adds some file printing options to the print command.
This patch adds a density keyword as an option with thermodynamic output.
16 Aug 2013
Small maintenance patch needed to fix a couple glitches introduced by recent patches that prevent some packages from compiling.
15 Aug 2013
Axel Kohlmeyer (ICTP, Italy) added support for the OPLS-AA force field to the msi2lmp tool as well as some USER-CUDA timer enhancements.
Added some error checking to union and intersection regions to insure their sub-regions have not been deleted by the time they are invoked.
14 Aug 2013
Added a CiteMe class from Axel Kohlmeyer (ICTP, Italy) to auto-generate BibTeX citations in a log.cite file when you use a specific feature in LAMMPS where someone wrote a paper about their implementation of it in LAMMPS, as listed on the citations page.
13 Aug 2013
Fixed some issues with the recent changes to shear history storage for granular potentials that affected restarting from restart files which also store that info.
12 Aug 2013
Added methods to the fix external command to allow an external driver program to set the potential energy associated with the forces it adds. This is to allow the fix to be used consistently in an energy minimization.
11 Aug 2013
Fixed a bug due to the recent changes to the fix langevin command when it is used with compute temp/region as a biasing temperature via fix_modify temp.
Thanks to Shengfeng Cheng (Sandia) for flagging the issue.
10 Aug 2013
Kudos to Rolf Isele-Holder (U Aachen) who fixed a long-standing bug with how the SHAKE contribution to pressure was calculated when using the rRESPA integrator.
9 Aug 2013
Rolf Isele-Holder (U Aachen) fixed a lingering bug when using pair_style hybrid with rRESPA and using the inner/middle/outer option for splitting the pair style.
8 Aug 2013
Fixed a logical bug in the FIRE and QuickMin minimizers when used with the nudged elastic band neb command that was slowing their convergence. This was due to some of their parameters being reset each time output was performed in the NEB procedure.
Thanks to Karl Hammond (U Tenn) for flagging this issue.
7 Aug 2013
Rezwan Rahman (U Texas San Antonio) added a visco-elastic model to the Peridynamics package in LAMMPS, now available as a pair_style peri/ves command.
6 Aug 2013
Vitaly Dozhdikov (JIHT of RAS) added a MOD variant of the Tersoff potential which is called pair_style tersoff/mod. There is a also a potential file for Si added to the potentials dir.
5 Aug 2013
Christopher Barrett and colleagues at Mississippi State added a compute basal/atom command which calculates the normal vector to the basal for each atom in an hcp lattice. It can be used to identiry twins and grains in hcp structures.
4 Aug 2013
Daniel Schwen (LANL) sent an update for his compute voronoi/atom command which adds several new features. See the doc page for details.
3 Aug 2013
Ryan Elliott (U Minn) sent an update to the pair_style kim command, to make it compatible with the latest version (v1.2.0) of their Knowledge Base for Interatomic Models (KIM) repository of interatomic potentials.
2 Aug 2013
Zachary Kraus (Georgia Tech) developed a tool for creating data files that bind polymer chains to nanoparticles. It's now in the tools/polybond directory, with a nice manual which explains how to use it.
1 Aug 2013
Stephen Bond and Andrew Baczewski (Sandia) have written a Generalized Langevin Dyanamics fix, called fix gld It models the effect of an implicit solvent with a temporally non-local dissipative force and a colored Gaussian random force, consistent with the Fluctuation-Dissipation Theorem. The functional form of the memory kernel associated with the temporally non-local force is constrained to be a Prony series. Details and a journal reference are given on the doc page.
31 Jul 2013
Andrew Jewett (UCSB) sent us a new version of his moltemplate builder tool, available in the tools dir of the LAMMPS distro.
30 Jul 2013
Added a fix property/atom command which allows molecule IDs to be added to atom styles that don't have them. It also allows addition of new custom per-atom attributes as named integer or floating-point vectors. These can be initialized by the read_data or set commands, and accessed for various purposes including output by the compute property/atom command.
This is a simple way 29 Jul 2013
Added a new kind of variable, namely atomfile
variables that read per-atom values from a specified file.
Also enhanced the set command to allow most
of the atom properties it sets to be specified as atom-style
variables, which means they can now be specified by a formula or
values read from a file.
26 Jul 2013
Changed the calculation performed by compute
temp/profile to use the center-of-mass
velocity for each spatial bin, rather than the average velocity. The
results will be the same if all particles have the same mass, but the
former is more consistent with how temperature is calculated if atoms
have different masses.
BACKWARD COMPATIBILITY: For systems with atoms with different masses,
the temperatures calculated by this compute will be now be different.
25 Jul 2013
Refactored the way fixes, computes, pair styles are created internally
within LAMMPS so that there is now no limit to the number there can
be. The previous method was using in-then-else logic that was
starting to exceed some compiler's limits.
Thanks to Richard Berger (JKU) for the suggestion on how to do this
efficiently.
24 Jul 2013
Removed a restriction on the fix
ave/spatial command that prevented its use
with the fix balance command.
23 Jul 2013
Stan Moore (Sandia) made some more optimizations to the kspace_style
msm solver based on recent scaling tests:
22 Jul 2013
Axel Kohlmeyer (ICTP, Italy) made some bug fixes to the USER-COLVARS
package.
He also re-factored the msi2lmp tool
and fixed some bugs in the process. This tool should now be better
supported by current LAMMPS developers, i.e. Axel.
11 Jul 2013
Fixed a logic bug in fix ave/correlate
with repsect to how the lower and auto/lower options looped over the
relevant pairings of input values.
Thanks to Niall Jackson (Imperial College) for catching this.
8 Jul 2013
Refactored one of the underlying data structures for storing neighbor
lists to streamline some of the code, and make it easier to use
with the USER-OMP threaded package.
2 Jul 2013
Removed a restriction in granular systems of having a hard-coded
maximum number of touching neighbors when storing shear history info.
This allows easier simulation of systems with a large polydispersity.
The history info is now stored similar to neighbor lists in a more
efficient paged data structure.
1 Jul 2013
Todd Zeitler (Sandia) contributed a new pair_style nb3b/harmonic,
which stands for nonbonded 3-body harmonic potential, which is a
many-body potential which enumerates and computes all 3-body
interactions.
30 Jun 2013
Andrew Jewett (UCSB) just released the 1.04 version of the
moltemplate builder tool, available in the tools dir of the
LAMMPS distro.
29 Jun 2013
This is a bug fix for the fix rigid/small command
when used with the granular pair styles.
Also, Axel Kohlmeyer (ICTP, Italy) added an option to use an environment
variable to specify the path for potentials files read-in by LAMMPS,
to make them easier to find. It is documented on the
pair_coeff doc page.
27 Jun 2013
Stan Moore (Sandia) has added a kspace_style
pppm/stagger command, which performs
calculations on two separate PPPM meshes, one shifted slightly with
respect to the other. This can reduce force aliasing errors and
increase accuracy of the method for the same-size mesh, or more
importantly it can reduce the mesh size needed for a specified target
accuracy. For high accuracy calculations it can be up to 4x faster
than regular PPPM. For low accuracy it can be up to 2x slower. See
Section accelerate of the manual for
more details.
25 Jun 2013
Rolf Isele-Holder (U Aachen) sent some bug fixes for the kspace_style
pppm/disp and pair_style
lj/long/tip4p/long commands.
Here are the details:
In pppm/disp, energies are computed incorrectly in large systems. The
problem here is that two integers are multiplied in calc_csum(). If
the system is too large, this leads to an integer overflow.
Furthermore, energies are not summed up correctly when using the
arithmetic mixing rule. Both of those bugs influenced only the energy
and not the dynamics.
In pair lj/long/tip4p/long there are two problems in the
compute_outer() function, used by run_style
respa. The first is, that the computed pressure
can be Nan because of a division by zero. The second is that the dummy
site has to be reset after the neighbor lists are build in the
compute_outer() function. The second error leads to a crash of the
simulation.
Axel Kohlmeyer (ICTP, Italy) also sent an update for the USER-COLVARS
pacakge. Here are the highlights:
24 Jun 2013
This patch fixes a bug in the switching function of the pair_style
hbond/dreiding commands.
The patch also contains small code maintenance changes to many files,
most of them due to Axel Kohlmeyer (ICTP, Italy).
Thanks to Karteek Kumar (JNCASR, Bangalore) and Andrew Jewett (UCSB)
for sending these fixes.
17 Jun 2013
Stan Moore (Sandia) added logic to the fix
efield command for the applied E-field to operate
on point dipoles, in addition to charges.
13 Jun 2013
Paul Crozier (Sandia) added a fix
tune/kspace command to allow on-the-fly
adjustement of various KSpace options, with the goal of determining
what are the fastest options for a particular simulation. The best
choice is often a function of system size, number of processors,
accuracy tolerance, and other factors that can be hard to predict.
Hence this fix auto-tunes.
7 Jun 2013
Aidan Thompson (Sandia) has added the new Gronbech-Jensen/Farago
formulation of the Langevin thermostat to LAMMPS as a gjf option on
the fix langevin command. It allows the use
of much larger timesteps (e.g. 3 fs) for systems containing bonds with
light atoms. See the fix langevin doc page
for more info.
Also, Orestis Alexiadis found a problem with the dihedral_style
nharmonic command, which Loukas
Peristeras has now fixed.
6 Jun 2013
Stan Moore (Sandia) has done some nice work to clean up and fix bugs
in some code for both short- and long-range dipole/dipole and
charge/dipole interactions. Two new pair_styles were also added:
pair_style lj/cut/dipole/long and
lj/long/coul/long. Long-range dipole
interactions can now be computed by kspace_style
ewald/disp. All of the options are described
in the pertinent pair_style and
kspace_style doc pages.
BACKWARD COMPATIBILITY: The names of two of the previous dipole pair
styles were changed to be more compatible with the LAMMPS naming
conventions. Specifically, dipole/cut was changed to
lj/cut/dipole/cut, and dipole/sf was changed to lj/cut/dipole/sf.
5 Jun 2013
Fixed a bug with neighbor list building when using pair
hybrid and rRESPA
inner/middle/outer options in pair styles.
Fixed a bug when reading multi-file restart
files on a different number of processors than
they were written on.
Thanks to Rolf Isele-Holder (U Aachen) for identifying where in the
code the rRESPA issue was. Thanks to Paul Coffman (IBM) for likewise
flagging the issue with restart file reading.
4 Jun 2013
Fixed a memory deallocation bug in the PPPM
solver when it was used with per-atom values
and commands that re-initialized the system were invoked between runs.
Rolf Isele-Holder (U Aachen) sent some patches for small
bugs in the long-range LJ PPPM solver.
One was for errors in the computed energies if either only a pppm for
Coulomb or only a pppm for dispersion interactions is used. The
second was for errors in computed forces when using the arithmetic
mixing rule. This bug was introduced when I send you the file that
solved the problems with massive parallelization.
He also fixed an issue with tallying per-atom long-range energies and
virial in the PPPM/TIP4P solver when running
with TIP4P.
Thanks to Alexandre Barthelemy (Soitec) for sending a script for the
memory bug.
31 May 2013
Axel Kohlmeyer (ICTP, Italy) added a pair_style
list command which allows explicit tabulation of
interaction pairs of atoms, e.g. as restraints.
Rob Hoy added a compute msd/nongauss
command which calculates non-Gaussian mean-squared-displacement
effects.
30 May 2013
Made some maintenance changes to the build system and associated
documentation, to make it easier to build LAMMPS with packages
that require auxiliary libraries. Also simplified the underlying
scripts for package management.
Thanks to Axel Kohlmeyer (ICTP, Italy) and Jeff Hammond (Argonne) for
good suggestions.
26 May 2013
Fixed a bug with the probability calculation for creating/deleting a
bond in the fix bond/create and fix
bond/break commands. It came about by trying
to be too clever with assuring bonds were created/deleted consistently
when 2 processors own the atoms in the bond.
Thanks to Scott Grindy for identifying the issue.
25 May 2013
Added a new polydispersity option to the fix pour
command for granular particles. The diam keyword now has 3 options:
one or range or poly, where the latter can be used to specify a
series of particle diameters with relative probabilities.
BACKWARD COMPATIBILITY: The syntax of the fix pour diam keyword
arguments has now changed. What before was simply "diam lo hi" is now
"diam range lo hi" and there are other options besides range. The use
of the diam keyword was optional, so you only need to change your old
scripts if they used the diam keyword.
24 May 2013
Added a mol option to the delete_atoms
command, so that entire molecules can be deleted wheverer one or more
of the atoms in the molecule are selected for deletion. This should
help prevent deletion of only a subset of atoms in a bond, angle, or
dihedral interaction.
Also added a time keyword to the thermo_style
custom command to allow simulation time to be
output. The output value accounts for changes in timestep size or
restting of the timestep.
BACKWARD COMPATIBILITY: Removed the elapsed time value stored by the
fix dt/reset command, since this new keyword
is a better way to keep track of simulation time.
14 May 2013
Reese Jones (Sandia) suggested we add a "sequence" option to the group
command, so that a large collection of atom IDs or molecule IDs can be
added to a group at once. The syntax is A:B:C, where for example
100:10000:10 would add atom IDs 100,110,120, ... 9990,10000 to a
group. C is optional and defaults to 1.
13 May 2013
A couple of changed files were left out of the 11May13 patch.
12 May 2013
Stan Moore (Sandia) added triclinic support to several of the
kspace_style long-range solvers in LAMMPS,
namely Ewald, PPPM, and MSM.
11 May 2013
Amended the write_data command to create data
files with high precision atomic coordinates and velocities (as well
as other floating point values), and box dimensions. This is so
restared simluations with these data files will agree better with the
original simulation.
Ray Shan (Sandia) fixed a couple initialization bugs in the fix
reax/c/bonds command, changed the fix
species command to fix reax/c/species,
and added a new position keyword to the fix
reax/c/species command, which writes
center-of-mass positions for each identified molecule.
BACKWARD COMPATIBILITY: The previous fix species command is
now fix reax/c/species.
9 May 2013
Albert Lu (LANL) found a logic bug with the prd
command, when multiple events happen simultaneously (in multiple
replicas) within the same time checking window.
NOTE: this turned out not to be a bug. The patch didn't create a new
bug; it just "fixed" something that was already working. So if you
were using PRD before this patch, don't worry - it should be
working the same before or after this patch.
8 May 2013
Bart Vorselaars (U Warwick, UK) fixed a bug with how atoms were
remapped by the fix move command in triclinic
(non-orthogonal) geometries.
Andrew Jewett (UCSB) released a new version of his moltemplate
tool, included in the LAMMPS tools
directory.
24 Apr 2013
Changed the format of the angmom keyword to the fix
langevin command to require input of a numeric
scale factor. This is so the user is made aware of the effect of the
scale factor on the rotational diffusivity of aspherical particles.
The details are now explained on the doc page.
Also added optional keywords to the pair_style
table command to allow it be used with specific
long-range solvers specified by the
kspace_style command.
Also added an optional keyword id to the fix
deposit command, so that users can choose
whether the atom IDs of newly deposited atoms increment consecutively
or are always assigned to the current maximum ID of atoms in the
system plus one.
BACKWARD COMPATIBILITY: The previous "angmom yes" syntax of the fix
langevin command is no longer allowed. You must choose a numeric
scale factor.
Thanks to Joakim Stenhammar (U Edinburgh) and Tomasz Panczyk (Polish
Academy of Sciences) for pointing out the subtle details in these
rotational diffusivity effects.
23 Apr 2013
Extended the read_data command to recognize a new
"PairIJ Coeffs" section of the data file, where pair coefficients for
all pairs I,J of atom types are listed, with I <= J. This section can
now be auto-generated by the write_data if the
new "pair ij" option is appended.
Axel Kohlmeyer (ICTP, Italy) sent another upgrade to the USER-COLVARS
package, invoked by the fix colvars command.
12 Apr 2013
Fixed a couple small bugs introduced recently into parallel file
writes via the dump cfg and
write_data commands.
6 Apr 2013
Maintenance patch with some internal refactoring and small bug fixes,
including a bug fix to the recent write_data
command.
3 Apr 2013
Added a write_data command to write out data
files from a LAMMPS input script. This will eventually replace the
restart2data tool.
2 Apr 2013
Using some code ideas sent by Christopher Knight, new nfile and
fileper keywords to the dump_modify command,
to allow dump files to be written out by a subset of processors, one
file per processor. This can be the most efficient way to write out
large dump files when running on many processors.
Also fixed a bug in the way the library interface opened successive
input files.
Also changed the low-level Makefiles to work with the gmake "vpath"
setting to find source files to compile. This avoids copying of files
into the object directories.
BACKWARD COMPATIBILITY: The change to the low-level Makefiles means
that if you maintain your own Makefile.foo you need to add two vpath
statements, the same as in now in all the other low-level Makefiles.
Thanks to Karl Hammond (Caltech) for sending an example that triggered
the problem with the library interface.
22 Mar 2013
Fixed an issue with the create_atoms random
command not always creating exactly the requested N atoms, due to
issues at periodic boundaries.
Also fixed a logic bug in the fix external
command.
Thanks to Paul Crozier (Sandia) for flagging the create_atoms issue
and Adrian Lange (Argonne) for flagging the fix external issue.
21 Mar 2013
Cem Sevik sent a Tersoff potential file for B,N,C and their "alloys",
developed by their group, that is now added to the potentials dir.
See the header of the file for literature citations on use of the
potential.
14 Mar 2013
Maintenance patch with some small changes to several files.
11 Mar 2013
Ling-Ti Kong (Shanghai Jiao Tong University) has contributed a fix
phonon command and associated post-processing
tools as part of a USER-PHONON package that is now part of the LAMMPS
distro. This allows phonon dispersions relations to be calculated
from dynamical matrices as part of a LAMMPS simulation. See the
src/USER-PHONON/README file and the doc page for the fix
phonon command for more details.
9 Mar 2013
Pavel Elkind (Gothenburg University) added a pair_style
lj/cut/tip4p/cut command, which is part of this
patch.
Also fixed a bug with performing consecutive runs with the new fix
rigid/small command.
7 Mar 2013
Stan Moore (Sandia) made some further optimizations to kspace_style
msm, including improving the single-core performance
and increasing parallel scalability. A bug in MSM for mixed periodic
and non-periodic boundary conditions was also fixed.
Some issues with the run_style repsa command were also
addressed, to enable it to be indentical to Verlet when running rRESPA
with one level.
5 Mar 2013
Upgraded the memory management strategy for atom_style
body to not use many tiny mallocs and frees as
body-style particles migrate between processors.
4 Mar 2013
Ray Shan and Aidan Thompson (Sandia) made some changes to the
USER-REAXC package. The pair_style reax/c
command and its pair coeff command now reads
chemical symbols instead of integers, like other many-body pair
styles. The time averaging capability for the fix
reax/c/bonds command was also removed, since
it is now available in the fix species command.
22 Feb 2013
Ray Shan (Sandia) upgraded the fix qeq/comb
command which does charge equilibration for the COMB
potential, so that it also works during energy
minimization. Thus charges can be adjusted when performing a
minimization.
Also fixed an indexing bug in the read_dump
command that could affect certain fields for atoms being added from a
snapshot.
21 Feb 2013
Added output of a scalar temperature and some diagnostic output for
the extent of rigid bodies needed to determine the cutoff for ghost
atom communication, to the new fix rigid/small
command.
20 Feb 2013
Daniel Moller (Autonomous University of Barcelona) added syntax for
immediate evaluation of variables to
input script lines, without having to assign the formula string to a
variable. For example this
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
is now equivalent to
variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
19 Feb 2013
Ray Shan (Sandia) added a new on-the-fly chemical species analysis fix
to the USER-REAXC package. It is the fix
species command and eliminates the need to
perform post-processing on the large files generated by fix
reax/c/bond. It also performs
time-averaging of bond-order.
18 Feb 2013
Another small change to the new fix rigid/small command to work
with the temperature computes cleanly.
17 Feb 2013
Fixed a bug with the fix ave/histo command
when it was accessing a column of an array stored by a per-atom
compute. The offset if was using into the array
was sometimes incorrect, so it could grab the wrong values.
Thanks to Luis Goncalves for flagging the problem.
17 Feb 2013
The 14Feb patch introduced a bug in thermostatting via the Nose/Hoover
commands like fix nvt with respect to how degrees
of freedom are computed. This patch should fix it.
16 Feb 2013
Daniel Schwen added a modulo operator "%" to the formula options in
the variable command.
This patch also includes several small changes/upgrades/optimizations
to some of the KSPACE and USER_OMP and USER-CUDA pacakage files to
make them consistent and fix some minor bugs.
15 Feb 2013
Made some logic changes to the creation of pairwise exclusion lists to
handle small ring topologies more accurately. Previously if both the
angle yes and dihedral yes options were used with the
special_bonds command, and an atom was both a
1-3 and 1-4 neighbor, it could be removed from the exclusion list for
not being in an angle but not included for also being part of a
dihedral. This is now not the case.
14 Feb 2013
Release of a new fix rigid/small command,
suitable for modeling large numbers of small rigid bodies in more
scalable way than the original fix rigid command.
13 Feb 2013
Axel Kohlmeyer (ICTP, Italy) upgraded the various USER-OMP kspace
styles to be fully compatible with the most recent refactoring of the
kspace styles in main LAMMPS.
12 Feb 2013
Rolf Isele-Holder (U Aachen) sent a couple upgrades to the
kspace_style pppm/disp and kspace/style
pppm/tip4p/omp command. The former had a small
bug in the energies and pressures (not forces, hence not dynamics).
The latter needed to be upgraded to match the latest TIP4P version in
LAMMPS.
11 Feb 2013
Several small bug fixes and a couple new features. Thanks to various
folks who flagged the bugs.
3 Feb 2013
Fixed a bug with yesterday's patch that could affect parallel
runs with body particles. Also updated one of the Makefile shell
scripts to work with the new BODY package from a default build
when no body styles exist.
1 Feb 2013
Released a new BODY package that defines a new atom_style body with
takes a body style as an argument. Bodies are a new kind of particle
in LAMMPS where a single body particle can represent complex entities,
such as surface meshes of discrete points, collections of
sub-particles, deformable objects, etc. A simple body style that
treats a body particles as a rigid body with a variable number N of
sub-particles is provided as an example.
The body page has more details.
These are the new commands that are part of the package:
27 Jan 2013
Joakim Stenhammar (U Edinburgh) found a problem with the rotational
thermostatting option in the fix langevin
command. The drag term needs to be increased by a factor of 10/3 and
the random noise term by sqrt(10/3) to produce the correct variance in
the rotation which affects the rotational diffusivity (but not the
rotational temperature/energy itself).
26 Jan 2013
Fixed a bug with how the pair lubricate and
brownian styles interact sometimes with the
fix wall command.
Thanks to Luiz Zepeda (LLNL) for running into the problem and sending
an input script.
25 Jan 2013
Daniel Schwen added a compute
voronoi/atom command, which calculates
the Voronoi tesselation volume around atoms, using the Voro++
package.
24 Jan 2013
Update some USER-OMP pair styles to be compatible with recent changes.
21 Jan 2013
Extended the region command so that the radius of a
spherical or cylindrical region can be specified as an equal-style
variable.
20 Jan 2013
Added a variable option for the epsilon and sigma paramters of wall
interactions specified by the various fix wall
commmand options.
19 Jan 2013
Fixed an issue with pair_style hybrid not
getting some of its settings correct (e.g. KSpace compatibility flags)
when run from a restart file versus a data file.
Thanks to Andrew Jewett (UCSB) for sending a test case
that exposed the problem.
18 Jan 2013
With help from Dan Bolintineanu (Sandia), a velocity rescale option
was added to the fix srd command, to allow more
control over when the velocity of SRD particles are rescaled. This
can be important for simulations of pure SRD fluids when
thermostatting is not used, or when collisions with walls or big
particles is not sufficient to effectively thermostat the system.
17 Jan 2013
Axel Kohlmeyer (U Temple) fixed a bug with variable substitution in
the fix print command that was introduced by the
6 Jan patch.
Axel also added multi-threading (OpenMP) support to the kspace_style
msm command and corresponding MSM pair styles
in the USER-OMP package.
Jon Zimmerman (Sandia) made an addition to the ATC package to do
J-integral calculations via an eshelby stress field. This patch
includes some new examples in examples/USER/atc/hardy that demonstrate
the capability.
12 Jan 2013
Stan Moore and Paul Crozier (Sandia) have extended the kspace_style
msm to work for any combination of periodic,
non-periodic, or shrink-wrapped boundary conditions, which can be
specified using the boundary.
A bug in thermo output for the thermo_style
multi, due to the 6Jan13 line length patch was
fixed.
The use of atom-style variables for the fix
heat command was added.
11 Jan 2013
Enhanced the fix heat command so it can take a
time-dependent flux as an argument, but using an equal-style
variable.
10 Jan 2013
Oleg Sergeev (MIPT, Moscow) enhanced the fix
append/atoms command so that added atoms
can be of different types, corresponding to basis atoms in the defined
lattice.
Also added pair_style lj/expand to the list
of pair styles that can be modified on the fly via the fix
adapt command.
9 Jan 2013
Extended the fix external command so it can be
used in different ways by an external program that is invoking LAMMPS
thru its library interface.
BACKWARD COMPATIBILITY: The syntax of the fix external command
changed to become more general.
8 Jan 2013
Andrew Jewett (UCSB) made a small change to the dihedral_style
class2 command so that it handles negative
input angles in a consistent manner to produce an odd-function of
angle and not an even one.
7 Jan 2013
Yesterday's patch for input script parsing dropped a newline from
the per-line echoing to the log file. This fixes it.
6 Jan 2013
Changed the input script and thermo_style
custom command parsing to allow for arbitrary
length lines. Before, it was a large fixed value.
5 Jan 2013
Andrew Jewett (UCSB) fixed a numerical bug in the pair_style
hbond/dreiding/morse command as well as
a parsing error for the pair_coeff commands for both the LJ and Morse
variants of the Dreiding force field. He also made some careful
clarifications to the doc page for how to use this force field
properly in LAMMPS, that should be helpful to users.
4 Jan 2013
Andres Jaramillo-Botero (Caltech) has upgraded his USER-EFF package
with this patch. Details are as follows:
We have made very cool progress towards extending eFF to higher Zs by
using effective core potentials (ECPs). We now cover up to 2nd and
3rd row p-block elements of the periodic table. We are publishing new
results soon on SiC and SiO2 soon. The ECP captures the orbital
overlap between the core and valence electrons (i.e. Pauli repulsion)
with very simple functional forms (see pair_eff_cut.txt). We have
developed two different functional forms, one that approximates this
overlap assuming the core is an s-like orbital interacting with an
s-like valence electron (s-s) and another that assumes the interaction
is s-p. In principle one could use the s-s for all, albeit at reduced
accuracy for those systems that may have significant p-character
(e.g. C, N, O).
To support this, I have now modified some of the original USER-EFF
sources/docs/examples/tools as follows:
What changes for the user?
3 Jan 2013
Andrew Jewett (UCSB) released a new version 1.01 of his moltemplate
tool, included in the LAMMPS tools
directory.
2 Jan 2013
Mike Brown (ORNL) made some changes to the GPU PPPM solvers to
sync them with changes previously made to the non-GPU versions.
1 Jan 2013
Rolf Isele-Holder (Aachen University) fixed two small bugs with
specific KSpace solvers. The kspace_modify
order/disp command was not parsed correctly.
The pair_style lj/long/coul/long command was
expecting charge to be defined even when it was only used for
long-range LJ interactions.