Newest Features and Bug Fixes in LAMMPS

This page lists new features and bug fixes in the LAMMPS molecular dynamics package since the current version was released.

To add these features/fixes to your version of LAMMPS, you have 2 choices. You can download the upgrade tarball from the download page which includes all the new features/fixes listed below, and re-build LAMMPS from scratch. Or you can apply individual patch files to your copy of LAMMPS and do an incremental re-build, as described below. Note that for the latter, you must apply all patches in chronological order, starting from the date of your copy of LAMMPS (current version or upgrade-tarball), to stay up-to-date.

The current version of LAMMPS is 22 Jan 2008.

Applying patches:

• Download the patch file. You may have to shift-click in your browser to download the file instead of display it. Patch files have names like patch.12Dec04.
• Put the patch file in your top-level LAMMPS directory, where the LICENSE and README files are.
• Apply the patch by typing the following command from the top-level LAMMPS directory, where the redirected file is the name of the patch file.

  patch -bp1 < patch.12Dec04 
  

• A list of updated files print out to the screen. The -b switch creates backup files of your originals (e.g. src/force.cpp.orig), so you can manually undo the patch if something goes wrong.
• Type "make package-update" from the src directory to enforce consistency between the src and package directories. This is OK to do even if you don't use one or more packages. If you are applying several patches, you only need to type "make package-update" once at the end.
• Re-make LAMMPS and you have the bug-fix or new feature.

Additional notes:

• The link to a "list of changed files" will tell you what files the patch modifies in case you have edited those files yourself. Note that for source files in a package (a sub-directory of src), the master copy of the file is in the sub-directory. The copy in src will also be overwritten if ,you use the "make package-update" command as described above.

10 May 2008

Made some small changes to the output format for text files written out by various fixes, such as fix msd or fix gyration, so that non-numeric lines (e.g. header lines) have leading "#" characters. This should make the files easier to read in by various plotting programs.

This patch file can be applied to the 28 Apr 2008 version. This is the list of changed files.

Thanks to Ahmed Ismail (Sandia) for this suggestion.

28 Apr 2008

Added the keywords radius, omegax, omegay, and omegaz to the dump custom command. These are applicable to extended spherical and aspherical particles.

This patch file can be applied to the 21 Apr 2008 version. This is the list of changed files.

21 Apr 2008

Fixed a couple 1-character bugs in the angle_style class2 command, introduced before the 22Jan08 release, when per-atom energy and virials were coded.

This patch file can be applied to the 16 Apr 2008 version. This is the list of changed files.

Thanks to Gaurav Pranami (ISU) for sending some files that showed up the problem.

16 Apr 2008

Added a Langevin thermostatting term to the pair_style lubricate potential. Also cleaned up some of the units issues associated with the lubrication and thermostatting forces, as previously amended by the 12Apr08 patch. Hopefully all the units associated with this potential are now correct.

This patch file can be applied to the 15 Apr 2008 version. This is the list of changed files.

15 Apr 2008

Changed some attributes of the energy minimizer in LAMMPS as invoked by the minimize, min_style, and min_modify commands. The new version appears to be more robust and also do a better job at minimizing to the requested tolerance(s). Unfortunately, despite this patch's release date, it cannot be used to minimize your tax payment (US users only).

The main change is to replace the previous line-search algorithm options (secant, scan) with a backtracking routine that performs better and more robustly. "Better" means it is often more effective at reducing the energy and zeroing the forces. It is now the only line search option, so several of the keywords previously settable via the min_modify command have been removed.

The cg/fr minimize style has also been removed. The standard CG style (Polak-Ribieri) seems to do better on atomistic problems.

NOTE: The most visible change to users is the format of the minimize command, which now includes a force tolerance, in addition to the energy tolerance. See the doc page for details. The page also explains more about how the minimizer works, what the various stopping criteria are, and how to interpret the final output provided by the code when the minimization ends.

This patch file can be applied to the 14 Apr 2008 version. This is the list of changed files.

Thanks to Aidan Thompson and Denis Ridzal (Sandia) for help in formulating and testing the new minimizer algorithms.

14 Apr 2008

Axel Kohlmeyer (U Penn) sent an upgrade to the lmp2cfg tool to enable it handle dump files containing only a part of the system. See the README file for details.

This patch file can be applied to the 13 Apr 2008 version. This is the list of changed files.

13 Apr 2008

Gerolf Ziegenhain sent some code snippets that add a hcp lattice to the options available with the lattice command.

This patch file can be applied to the 12 Apr 2008 version. This is the list of changed files.

12 Apr 2008

Amended the units for viscosity, input as part of the pair_style lubricate command, to be accurate for all units choices in LAMMPS.

This patch file can be applied to the 11 Apr 2008 version. This is the list of changed files.

11 Apr 2008

Enhanced the fix wall/gran command to allow the wall to impose a shear force on the granular particles via the shear keyword.

Also fixed 2 bugs with the command. The computed torques on particles by the wall for 2 of the pair_style granular options (no_history and hertzian) did not include a particle radius in the torque calculation. And the velocity of wiggling walls (via the wiggle keyword) was off by a factor of the timestep size.

This patch file can be applied to the 10 Apr 2008 version. This is the list of changed files.

Thanks to Jin Sun (Iowa State) and Justin Garvin (USAF AFRL) for pointing out these issues.

10 Apr 2008

Fixed a small bug with the fix addforce and fix aveforce commands, that wasn't allowing the total force before the constraint is applied to be accessed by thermodynamic output.

This patch file can be applied to the 9 Apr 2008 version. This is the list of changed files.

Thanks to Liang Wan for calling attention to this.

9 Apr 2008

Fixed a bug with the dump xyz and xtc commands that could occur in parallel if the number of atoms changed after the time the dump file was created, e.g. due to the delete_atoms command.

This patch file can be applied to the 8 Apr 2008 version. This is the list of changed files.

Thanks to Chengxiang Li for identifying there was a problem.

8 Apr 2008

Added a warning when any atoms are time integrated by more than one fix. This is probably an error and can happen when users define multiple time integration fixes in one input script. A typical mistake (which I've made a few times) is to run equilibration with NVT, followed by dynamics with NVE, and forget to unfix the fix nvt command.

This patch file can be applied to the 7 Apr 2008 version. This is the list of changed files.

7 Apr 2008

Added a howto section to the manaul on the topic of thermostatting, barostatting, and computation of temperature. It should provide a big-picture overview of different ways to do these operations in LAMMPS.

This patch file can be applied to the 6 Apr 2008 version. This is the list of changed files.

6 Apr 2008

This patch provides an updated version of the lmp2cfg tool, which does a better job of reading general box sizes from LAMMPS dump files.

This patch file can be applied to the 5 Apr 2008 version. This is the list of changed files.

Thanks to Axel Kohlmeyer (U Penn) for providing the fix.

5 Apr 2008

Fixed a bug in the recently upgraded fix viscosity command that could affect parallel execution.

This patch file can be applied to the 4 Apr 2008 version. This is the list of changed files.

Thanks to Dave Heine (Corning) for identifying the problem and providing an input script that showed it up.

4 Apr 2008

Axel Kohlmeyer (U Penn) provided some updates to the scripts in his lmp2vmd tool.

This patch file can be applied to the 3 Apr 2008 version. This is the list of changed files.

3 Apr 2008

The 1Apr08 patch introduced a round() function which turns out not to be in the standard C math library, though many compilers support it. This patch replaces the library call with a macro definition that does the same thing. So there should be no portablility problems.

This patch file can be applied to the 2 Apr 2008 version. This is the list of changed files.

2 Apr 2008

Wrote some simple Python scripts that wrap Pizza.py tools for performing common LAMMPS post-processing tasks:

• extract thermodynamic info from a log file as columns of numbers
• plot two columns of thermodynamic info from a log file using GnuPlot
• sort the snapshots in a dump file by atom ID
• convert dump files into XYZ, CFG, or PDB format for viz by other packages

These scripts are in lammps/tools/python along with the needed Pizza.py modules. Additional scripts can be added over time by developers or user contributions. See the README file in lammps/tools/python for details of how to use them.

This patch file can be applied to the 1 Apr 2008 version. This is the list of changed files.

1 Apr 2008

Gerolf Ziegenhain added 3 new math functions for formulas supported by the variable command, namely ceil(), floor(), and round(), as in the C math library. These allow you to convert floating points values to integers, rounding up, down, or in the usual way, which can be a useful conversion to perform in an input script.

This patch file can be applied to the 31 Mar 2008 version. This is the list of changed files.

31 Mar 2008

Enhanced the fix viscosity command with some options that allow more fine-grain control over how much momentum is exchanged between atoms if different layers of the simulation domain. This allows a wider range of effective shear rates and viscosities to be modeled.

This patch file can be applied to the 30 Mar 2008 version. This is the list of changed files.

Thanks to Matt Petersen (Sandia) for help in designing/testing these changes.

30 Mar 2008

Added a couple of scripts provided by Axel Kohlmeyer (U Penn) to the tools directory as part of a new lmp2vmd tool. These are for converting info in a LAMMPS data file to a format suitable for visualizing with VMD. Axel says more scripts are to come. Maybe others want to contribute LAMMPS -> VMD tools as well.

This patch file can be applied to the 28 Mar 2008 version. This is the list of changed files.

28 Mar 2008

Updated the restart2data tool to skip pair_style airbebo. Potentials like this that read their data from a file are not stored in the restart file. They just need to be skipped appropriately.

This patch file can be applied to the 27 Mar 2008 version. This is the list of changed files.

27 Mar 2008

Fixed a one-line bug with pair_style yukawa, where it was missing a symmetrization of the pre-factor A for differing atom types.

This patch file can be applied to the 26 Mar 2008 version. This is the list of changed files.

Thanks to Stephanie Teich-McGoldrick (U Mich) and Ahmed Ismail (Sandia) for figuring this out.

26 Mar 2008

Updated the restart2data tool to support bond_style quartic and angle_style cosine/delta potentials.

This patch file can be applied to the 24 Mar 2008 version. This is the list of changed files.

Thanks to Vikas Varshney (WPAFB) and Axel Kohlmeyer (U Penn) for sending code snippets for these additions.

24 Mar 2008

Added a line to tools/restart2data.cpp to allow it to skip pair_style hybrid/overlay, as it should.

This patch file can be applied to the 23 Mar 2008 version. This is the list of changed files.

Thanks to Dongsheng Zhang for pointing this out.

23 Mar 2008

Forgot the files for the new fix nvt/sphere and fix npt/sphere commands in the 22Mar08 patch. This patch adds them.

This patch file can be applied to the 22 Mar 2008 version. This is the list of changed files.

22 Mar 2008

Enhanced the computes that calculate temperature, thermostatting fixes, and time integrators that use temperature control to be more flexible and consistent. This is for point particles, extended spherical particles, and aspherical particles. Also Added new compute ke and compute erotate/asphere commands.

These compute commands calculate temperature. All but the first 3 calculate velocity biases that are removed when computing a temperature. Temp/sphere and temp/asphere now allow computes that calculate such a biased temperature to be included as an additional argument, so that the translational velocity of extended spherical or aspherical particles can also be altered in prescribed ways.

• compute temp
• compute temp/sphere
• compute temp/asphere
• compute temp/com
• compute temp/deform
• compute temp/partial
• compute temp/ramp
• compute temp/region

Four thermostatting methods are available: Nose-Hoover, Berendsen, Langevin, and direct rescaling. Nose/Hoover works on rotational degrees-of-freedom for spherical and aspherical particles; the others only work on translational degrees of freedom. Any of these methods can use temperature computes that remove bias for the purpose of computing the current temperature and performing thermostatting only on the remaining thermal velocity. For non-equilibrium MD simulations., there is also a SLLOD fix which does NVT thermostatting in conjunction with the SLLOD equations of motion. These are the relevant fix commands:

• fix nvt
• fix nvt/sphere
• fix nvt/asphere
• fix nvt/sllod
• fix temp/berendsen
• fix langevin
• fix temp/rescale

Note that only the nvt fixes perform time integration. The others should be used with an NVE integration fix such as these:

• fix nve
• fix nve/sphere
• fix nve/asphere

Two barosttating methods are available: Nose-Hoover and Berendsen. The fix npt commands include Nose-Hoover thermostatting. Fix nph and fix press/bernendsen can be used in conjunction with any of the 4 thermostatting methods. These are the relevant fix commands:

• fix npt
• fix npt/sphere
• fix npt/asphere
• fix nph
• fix press/berendsen

This patch file can be applied to the 21 Mar 2008 version. This is the list of changed files.

21 Mar 2008

Fixed some problems with error checking in pair potentials that support the rRESPA integrator, when used with the rRESPA inner/middle/outer options. The issues occurred when mixing rules were also used with some of these potentials.

This patch file can be applied to the 20 Mar 2008 version. This is the list of changed files.

Thanks to Dave Heine (Corning) for catching this problem.

20 Mar 2008

Added a Berendsen barostat via the fix press/berendsen command, which can be used as an alternative to fix npt or fix nph which do barostatting via Nose/Hoover. To do constant NPT simulations, the Berendsen barostat can be used in conjunction with any LAMMPS thermostat, e.g. fix nvt, fix langevin, fix temp/berendsen, or fix temp/rescale.

This patch file can be applied to the 19 Mar 2008 version. This is the list of changed files.

Thanks to Manoj Warrier and Axel Kohlmeyer (U Penn) for help in understanding the details of Berendsen thermostats and barostats.

19 Mar 2008

Made the various commands that operate on extended spherical particles more consistent. Spherical particles are those with a radius, as opposed to point particles which is what most of LAMMPS operates on. Spherical particles have angular velocity, and can thus be acted on by torques, which cause them to rotate. The atom_style granular and dipole models within LAMMPS are examples of spherical particles.

As part of these changes, extended spherical particles used in a 2d model are now treated as true spherical particles throughout LAMMPS, as opposed to circular disks. This means their moment of inertia is that of a sphere, as opposed to a disk.

New commands added by this patch are the following:

• fix nve/sphere
• compute temp/sphere
• compute erotate/sphere

The following commands and styles are deleted by this patch:

• fix nve/gran
• fix nve/dipole
• compute rotate/dipole
• compute rotate/gran
• compute temp/dipole
• thermo_style granular
• thermo_style dipole

All the options of the deleted commands can be invoked via the new commands.

This patch file can be applied to the 18 Mar 2008 version. This is the list of changed files.

18 Mar 2008

Enhanced the fix addforce and fix aveforce commands to store the forces on the group of atoms before modification, so those values can be accessed as part of thermodynamic or other output.

This patch file can be applied to the 17 Mar 2008 version. This is the list of changed files.

17 Mar 2008

Fixed a bug with atom-style variables when using a unary minus sign operator.

This patch file can be applied to the 12 Mar 2008 version. This is the list of changed files.

Thanks to June Zhong (Ames Lab) for identifying there was a problem.

12 Mar 2008

Forgot to add the two files for the Berendsen thermostat fix to the 11Mar08 patch. This patch remedies that.

This patch file can be applied to the 11 Mar 2008 version. This is the list of changed files.

11 Mar 2008

Added some flexibility to the various fixes that perform thermostatting and to the various compute commands that calculate temperature. The idea is to formulate the temperature computations as first removing a "bias" from atom velocities before the thermal temperature is calculatd. The thermostatting fix uses this temperature, and performs its thermostatting on atoms that have this bias removed from their velocities, before restoring the bias afterwards.

The 4 thermostatting fixes that now work in this manner are as follows: fix nvt, fix temp/rescale, fix langevin, and fix temp/berendsen. The Berendsen thermostat is new.

The temperature computes that include a bias term are as follows: compute temp/com, compute temp/partial, compute temp/region, compute temp/deform, and compute temp/ramp.

Basically, any of these temperature computes can be used with any of these thermostatting fixes. As before, the assignment of a temperature compute to a thermostatting fix is done via the fix_modify command. A standard temperature with no bias is the default; see the compute temp command.

Note that previously, the fix langevin and fix temp/rescale commands had options like region or partial to enable specific kinds of bias to be removed. This new capability is more general, so those command options have been removed.

This patch file can be applied to the 10 Mar 2008 version. This is the list of changed files.

10 Mar 2008

Fixed a bug that affected thermodynamic print-out of pressure when both total pressure and pressure tensor components were being printed, and the thermo_modify command was used to specify a user-defined pressure compute.

This patch file can be applied to the 5 Mar 2008 version. This is the list of changed files.

Thanks to LT Kong who showed up the bug.

5 Mar 2008

Added a compute temp/com command to allow temperature of a group of atoms to be compute, after subtracting out the center-of-mass velocity of the group. Useful if the group has a net velocity for some reason.

This patch file can be applied to the 4 Mar 2008 version. This is the list of changed files.

4 Mar 2008

Added a start option to the fix ave/time command to allow a delay in when it starts doing its final averaging. This is useful if you want to discard early non-equilibrium values from the output averages.

This patch file can be applied to the 29 Feb 2008 version. This is the list of changed files.

29 Feb 2008

Amended many typos in the doc pages as well as changed some files with DOS-style end-of-lines to the Unix standard.

Also undid the 14Feb08 IBM-specific patch since it's possible to use a compiler switch to fix this rather than a source code change.

This patch file can be applied to the 21 Feb 2008 version. This is the list of changed files.

Thanks to Tom Oppe who identified all these issues.

21 Feb 2008

Fixed a one-line bug in the pair_style hybrid command that was preventing in from working correctly with the compute group/group diagnostic.

This patch file can be applied to the 20 Feb 2008 version. This is the list of changed files.

Thanks to user Ganesh for sending a script with the problem.

20 Feb 2008

Enhanced the compute sum command to become the compute reduce command with a mode option to either sum, take a min, or take a max of per-atom values to produce a single global result.

This patch file can be applied to the 19 Feb 2008 version. This is the list of changed files.

19 Feb 2008

Fixed a one-line bug in the fix wall/lj126 command, where the wall force needed an additional 1/r factor.

This patch file can be applied to the 15 Feb 2008 version. This is the list of changed files.

Thanks to user Wende from the Soft Condensed Matter Physics Lab for pointing out the problem.

15 Feb 2008

Changed the way the 11Feb08 patch was implemented to work with a new atom_modify first group command. This is a cleaner and slightly faster implementation and also allows fixes, like time integration fixes, to take advantage of the atom ordering it induces, if appropriate.

This patch file can be applied to the 14 Feb 2008 version. This is the list of changed files.

14 Feb 2008

Added a one-line kludge to a LAMMPS source file to get around a problem caused by the IBM AIX compiler and a #define of a common variable name it uses in one of its system header files.

This patch file can be applied to the 13 Feb 2008 version. This is the list of changed files.

13 Feb 2008

Made a small correction to the way the virial (pressure) is compute in the TIP4P pair potential. This turned up when we implemented per-atom energy and virial tabulation for all LAMMPS potentials. Thanks to Ahmed Ismail (Sandia) for helping me work thru the intracacies of the force interactions generated by this potential.

This patch file can be applied to the 12 Feb 2008 version. This is the list of changed files.

12 Feb 2008

Added a compute group/group command to allow the total energy and force bewteen two groups of atoms (or the same group) to be calculated. These quantities can then be used in the usual ways by other output commands in LAMMPS.

Naveen Michaud-Agrawal (JHU) wrote an early version of this as a fix. This version is a compute which is compatible with current LAMMPS design.

This patch file can be applied to the 11 Feb 2008 version. This is the list of changed files.

11 Feb 2008

Added communicate group and neigh_modify include group commands to limit communication and pairwise neighbor list construction to atoms in a group. This is useful for models of lightweight background solvent we're developing, since they don't interact with solute particles via the usual pairwise style of interactions.

This patch file can be applied to the 10 Feb 2008 version. This is the list of changed files.

10 Feb 2008

Axel Kohlmeyer (U Penn) has written a user package for coarse-graining called USER-CG-CMM. From the README file in src/USER-CG-CMM:

The current version of this package should be considered beta quality. The CG potentials work correctly and well, but there will be optimizations, cleanups and additional tools to aid in setting up and analyzing simulations with this package added in the next months.

This package implements 4 commands which can be used in a LAMMPS input script:

• pair_style cg/cmm
• pair_style cg/cmm/coul/cut
• pair_style cg/cmm/coul/long
• angle_style cg/cmm

See the documentation files for these commands for details.

There is also an cg-cmm example directory under examples/USER with sample inputs and outputs.

These styles allow coarse grained MD simulations with the parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007) (cg/cmm), with extensions to simulate ionic liquids, electrolytes, lipids and charged amino acids (to be published soon).

Thanks for contributions, support and testing goes to

• Wataru Shinoda (AIST, Tsukuba)
• Russell DeVane (CMM / U Penn, Philadelphia)
• Balasubramanian Sundaram (JNCASR, Bangalore)
• Michael L. Klein (CMM / U Penn, Philadelphia)

This patch file can be applied to the 9 Feb 2008 version. This is the list of changed files.

9 Feb 2008

Small bug fix for the dump xtc command provided by Axel Kohlmeyer (U Penn) that cleans up a memory allocation issue when a dump file is opened and closed multiple times.

This patch file can be applied to the 8 Feb 2008 version. This is the list of changed files.

8 Feb 2008

Added an option to the fix langevin command to allow the second term in the thermostat (random force) to be weighted differently than the first term (viscous force). This is useful is some thermostatting models where a different coupling constant to the background solvent is desired.

This patch file can be applied to the 5 Feb 2008 version. This is the list of changed files.

5 Feb 2008

Added the keywords xy, xz, yz as options to the thermo_style custom command, so the tilt factors of a triclinic (non-orthogonal) box can be monitored.

This patch file can be applied to the 31 Jan 2008 version. This is the list of changed files.

31 Jan 2008

Xiaowang Zhou (Sandia) has contributed two improvements to the Stillinger-Weber potential invoked by the pair_style sw command.

(1) A new parameter tol must be added on each line of the potential file. It specifies a tolerance value specifying the accuracy required for a virtual cut-off distance. The virtual cut-off is always less than the theoretical SW cut-off. Setting tol to zero forces LAMMPS to use the theoretical SW cut-off, reproducing the behavior of the old code. With a tolerance, less interactions are computed, speeding up the potential calculation.

(2) The treatment of the three-body energy for alloys has been enhanced to allow common literature alloy parametrizations. See the upgraded documentation page and the file potentials/GaN.sw for details.

This patch file can be applied to the 29 Jan 2008 version. This is the list of changed files.

29 Jan 2008

Fixed a bug in the delete_atoms overlap command with parallel execution.

This patch file can be applied to the 26 Jan 2008 version. This is the list of changed files.

26 Jan 2008

Enhanced the delete_atoms overlap command to work with two groups of atoms instead of atom types. This allows more flexibility in choosing what atoms get deleted, e.g. when deleting solvent that overlaps with macro-particles. Also fixed a bug that was preventing delete_atoms overlap from working with pair_style hybrid and hybrid_overlay due to the latest changes to neighbor list formats.

This patch file can be applied to the 25 Jan 2008 version. This is the list of changed files.

25 Jan 2008

Axel Kohlmeyer (U Penn) provided a new angle_style cosine/delta potential, similar to the angle_style cosine/squared potential except the interaction is proporational to the difference in cosines, rather than the difference squared.

This patch file can be applied to the 24 Jan 2008 version. This is the list of changed files.

24 Jan 2008

Fixed a bug in atom styles ellipsoid, granular, and dipole that prevented them from working correctly when used as part of the atom_style hybrid command.

This patch file can be applied to the 23 Jan 2008 version. This is the list of changed files.

Thanks to Georg Ganzenmueller for identifying there was a problem and posting an input script.

23 Jan 2008

Updated the doc pages for the various pair styles to reflect that all of them can now tally per-atom energy and stress so that they can be used with the compute pe/atom and compute stress/atom commands.

This patch file can be applied to the 22 Jan 2008 version. This is the list of changed files.

New release of LAMMPS (C++ version). 125,009 lines of code in src dir with all packages included (but no library source files).

IMPORTANT: Velocity initialization via the velocity command using the loop geom option now uses a new random number generation scheme, as do certain options of the set and displace_atoms commands. Hence an input script using these commands will initialize a system differently (i.e. statistically the same, but with a different set of random velocities). The following commands are deleted in this version, since they have been replaced by more general output options: "fix gran/diag", "compute epair/atom", "compute ebond/atom", "compute variable/atom", "compute variable", "compute sum/atom", and "compute attribute/atom".

These are the most significant features added or enhanced since the 5 Oct 2007 version. People who contributed to the features are listed in parentheses:

• LAMMPS output options for thermodynamic and dump output
• thermo_style custom and dump custom
• fix ave/time, fix ave/spatial, and fix ave/atom
• per-atom energy and virial tabulation for all potentials and internal constraint fixes
• easier-to-use variable formula syntax
• fix dt/reset
• pair_style lubricate (Randy Schunk, Sandia)
• pair coul/debye
• fix coord/original
• compute pe/atom
• compute stress/atom
• compute sum
• pair_style resquared (Mike Brown, Sandia)
• fix viscosity
• compute displace/atom

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

New release of LAMMPS (C++ version). 118,521 lines of code in src dir with all packages included (but no library source files).

IMPORTANT: The syntax of the fix ave/spatial, fix ave/time, and fix gravity commands has changed. The "compute etotal/atom" command was deleted and replaced by the more general compute sum/atom command. Some keywords for the dump custom command have been removed: epair, ke, etotal, centro, stress. These are now invoked by creating a compute of the appropriate style and referencing it in the dump custom command.

These are the most significant features added since the 22 Jun 2007 version. People who contributed to the features are listed in parentheses:

• displace_box
• change_box
• compute ebond/atom
• changes to 2d pressure computation
• rigid bodies with fix deform
• pair_style airebo (Ase Henry, MIT)
• fix nve/limit
• fix ave/atom
• compute attribute/atom
• compute sum/atom
• user-contributed packages
• pair_style hybrid/overlay for superposing pairwise potentials
• kspace_style ewald/n for long-range dispersion contributions from 1/r^6 LJ terms (Pieter in 't Veld, SNL)
• pair_style lj/coul (Pieter in 't Veld, SNL)
• pair_style buck/coul (Pieter in 't Veld, SNL)
• compute ackland/atom (Gerolf Ziegenhain)

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

New release of LAMMPS (C++ version). 106,005 lines of code in src dir (with all packages included).

IMPORTANT: The format of restart files was changed to make it easier to add new atom info in the future. Thus this version will not read restart files created by older versions. For hybrid atom styles, the format of atom lines in input data files was changed. The syntax of the create_atoms command was changed. The fix volume/rescale and fix uniaxial commands were deleted since their functionality is now present in the fix deform command.

These are the most significant features added since the 12 Feb 2007 version. People who contributed to the features are listed in parentheses:

• static and dynamic non-orthogonal simulation boxes (Pieter in 't Veld, SNL)
• fix heat (Paul Crozier, SNL)
• input script if command
• new Finnis/Sinclair EAM potentials (Mikhail Mendelev, Ames Lab)
• displace_atoms random
• new set command options
• create_atoms single
• compute coord/atom
• fix ave/time (Pieter in 't Veld, SNL)
• fix ave/spatial (Pieter in 't Veld, SNL)
• variable atom
• COLLOID package with pair colloid potential (Pieter in 't Veld, SNL)
• neighbor multi option (Pieter in 't Veld, SNL)
• communicate multi option (Pieter in 't Veld, SNL)
• DIPOLE package for point-dipole particles with pair dipole/cut
• ASPHERE package for ellipsoidal particles with a GayBerne potential (Mike Brown, SNL)
• aspherical particle integrators (Mike Brown, SNL)
• NEMD simulations via fix deform and fix nvt/sllod and compute temp/deform (Pieter in 't Veld, SNL)
• PyMol viz converter pymol_asphere for ellipsoidal particles (Mike Brown, SNL)

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

New release of LAMMPS (C++ version). 95,029 lines of code in src dir (with all packages included).

IMPORTANT: The temperature command was replaced by the compute command in this release, which is now a more flexible way to define global calculations (temp, pressure, etc) and per-atom calculations (energy, stress, etc) which can be output as thermodynamic and dump info or be accessed by input script variables.

There were also minor changes in the hi-level code structure to make LAMMPS more library-friendly.

These are the most significant features added since the 1 Oct 2006 version. People who contributed to the features are listed in parentheses:

• Tersoff potential (Aidan Thompson, SNL)
• Stillinger-Weber potential (Aidan Thompson, SNL)
• MEAM (modified EAM) potential (Greg Wagner, SNL)
• non-orthogonal lattices
• fix wall/lj126 (Mark Stevens, SNL)
• fix deposit
• uloop variables
• removal of global variables so LAMMPS can be instantiated multiple times (Ben FrantzDale, RPI)
• optimized versions of lj/cut, eam, morse, and lj/charmm/coul/long pair potentials (James Fischer; High Performance Technologies), David Richie and Vincent Natoli (Stone Ridge Technologies)
• compute command
• new options for thermo_style custom
• new options for dump custom
• new options for variable equal
• higher-precision real/metal units (Paul Crozier, SNL)

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

New release of LAMMPS (C++ version). 85,559 lines of code in src dir (with all packages included).

IMPORTANT: The storage of periodic box image flags in restart files changed with this release. The current version will still read old restart files, but the values of the image flags will be wrong if you use them in a computation or subsequently output them (e.g. in a dump file).

There were also changes in the hi-level code structure and in pair style routines. These were for the purpose of making LAMMPS more library friendly and in anticipation of new many-body potentials we hope to release soon (Stillinger-Weber, Tersoff, REBO, etc).

These are the most significant features added since the 17 Jul 2006 version. People who contributed to the features are listed in parentheses:

• dihedral_style opls (Mark Stevens, SNL)
• allow 2d granular simulations
• allow per-processor restart files to be written
• shell command for using cd, mkdir, mv, rm, rmdir in input scripts
• lattice diamond style
• several new options for run command
• fix gyration (Naveen Michaud-Agrawal, JHU)
• fix recenter (Naveen Michaud-Agrawal, JHU)
• fix momentum (Naveen Michaud-Agrawal, JHU)
• new set command options for atom attributes
• multi-letter variables in input scripts (Naveen Michaud-Agrawal, JHU)
• equal style variables can compute group properties (Naveen Michaud-Agrawal, JHU)
• read_restart can read latest restart file
• LJ tail corrections via pair_modify option (Paul Crozier, SNL)

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

New release of LAMMPS (C++ version). 82,729 lines of code in src dir (with all packages included).

These are the most significant features added since the 12 Apr 2006 version. People who contributed to the features are listed in parentheses:

• fix wall/reflect command
• fix spring/self, and fix spring/rg commands (Naveen Michaud-Agrawal, Johns Hopkins U and Paul Crozier, SNL)
• enhanced fix langevin command to include a region option
• pair_style lj/smooth potential (Craig Maloney, UCSB)
• fix orient/fcc command for driving grain boundary motion (Koenraad Janssens and David Olmsted, SNL)
• dump dcd and dump xtc styles (Naveen Michaud-Agrawal, Johns Hopkins U)
• temperature region style for computing temperatures on geometric regions of atoms
• thermo_style custom t_ID option for printing one or more user-defined temperatures as thermodynamic output
• bond_style quartic (Mark Stevens and Chris Lorenz, SNL)
• faster pair_style hybrid potential (James Fischer, High Performance Technologies, Inc; Vincent Natoli and David Richie, Stone Ridge Technology)
• angle_style hybrid, dihedral_style hybrid, improper_style hybrid potentials
• delete_atoms overlap option for deleting created atoms that are too close
• TIP4P water potential (Ahmed Ismail and Amalie Frischknecht, SNL)
• dumping of per atom energy, stress, centro parameters during energy minimization
• fix poems command which hooks to the POEMS library from RPI to simulate the motion of coupled rigid bodies (Rudranarayan Mukherjee, RPI)

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

New release of LAMMPS (C++ version). 74,353 lines of code in src dir (with all packages included).

IMPORTANT: The syntax of these commands were changed. If you use these commands, you will need to modify your existing input scripts:

• Atom_style eam no longer exists; atom_style atomic can be used instead.
• Pair_style eam was split into 2 styles. Style eam is for EAM funcfl files (single element); style eam/alloy is for EAM setfl files (alloy).
• The arguments for fix temp/rescale command were reordered so the N value comes first, to be consistent with similar fixes.

These are the most significant features added since the 10 Nov 2005 version. People who contributed to the features are listed in parentheses:

• energy minimization via minimize, min_style, and min_modify commands
• dissipative particle dynamics (DPD) atom style and pair style potential (Kurt Smith, U Pitt and Frank van Swol, Sandia)
• time-averaged thermo output of several quantities
• Finnis/Sinclair variant of EAM pairwise potentials (Tim Lau, MIT)
• angle style cosine/squared and dihedral style helix (Naveen Michaud-Agrawal, JHU)
• dump options for creating per-snapshot, per-atom, and gzipped output files
• dump_modify options for outputting atoms within geometric regions and on threshhold criteria
• input script functionality: print command, fix print command, label command, jump command, more variable options, command-line argument -echo
• fix uniaxial command (Carsten Svaneborg, Max Planck Institute)
• more flexible thermo_style custom command; fixes can generate thermo output
• changes to fix npt to dilate around the box center more efficiently

Though previously advertised, TIP4P pairwise potentials and a bond_style restrain potential are not part of this release. They will be added as patches in the near future.

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

New release of LAMMPS (C++ version). 68,545 lines of code in src dir (with all packages included).

These are the most significant features added since the 3 Jun 2005 version:

• new or enhanced fix efield, fix indent, fix spring, fix nph, and fix gravity commands
• new option for fix nvt, fix npt, fix nph commands to damp oscillations
• new union and intersect region styles for creating complex geometric regions
• release of Pizza.py Toolkit, a Python-based collection of tools for setup, analysis, plotting, and visualization of LAMMPS data

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

New release of LAMMPS (C++ version). 66,806 lines of code in src dir (with all packages included).

The format of binary restart files changed with this version, due to hybrid atom and pair styles and the changes to enable very large simulations. Hence this version will NOT read older version's restart files.

Also, starting with this version, a build of LAMMPS will NOT include all optional packages by default. In particular the "granular" and "class2" packages will not be included unless you request them. See the Making LAMMPS section of the documentation for more details or type "make package" when building LAMMPS to see the options.

These are the most significant features added since the 17 Jan 2005 version:

• pair and intra-molecular potentials for class 2 interactions (the COMPASS force field of Accelrys) that were originally in LAMMPS 2001
• enable simulations with more than 2^31 (2 billion) atoms via memory and other changes
• simulation of mixed systems via a hybrid pair_style and hybrid atom_style
• read in pre-tabulated pair potential via the pair_style command
• Buckingham, Morse, Yukawa pair potentials for the pair_style command
• Morse bond potential for the bond_style command
• include command
• radial distribution functions (fix rdf)
• dump out tabulated pair potential file (pair_write)
• dump per-atom energy and stress (dump custom)

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

New release of LAMMPS (C++ version). 56,612 lines of code in src dir (with all packages included). These are the most significant features added since the 1 Sept 2004 version:

• better integrator for rigid bodies (fix rigid)
• centro-symmetry parameter via dump command (dump custom)
• targeted molecular dynamics option (fix tmd)
• code partitioned into optional packages (make)
• wild-carding enabled for several input script commands (mass, pair_coeff, bond_coeff, etc)
• pre-compute tables for pairwise portion of long-range Coulombic solvers (pair_modify)
• native FFT support for SGI machines via SCSL library
• new versions of post-processing tools for connecting LAMMPS to Accelrys Insight (tools)
• bond_style hybrid enables use of multiple bond styles (bond_style)
• generalized set_type command for atoms, bonds, etc (set)

Descriptions of all these enhancements and other bug fixes can be viewed on this page.

There is also a new release of LAMMPS 2001 (F90 version), which contains a few minor tweaks and bug fixes. These are included in the 2001 tar file now available from the download page.

1 Sept 2004

Initial public release of the C++ version of LAMMPS. 52,967 lines of code in src dir. This version supersedes earlier versions, including LAMMPS 2001 (F90) and LAMMPS 99 (F77).