Bug fixes and new features added to the 9 Jan 2009 version of LAMMPS. These are all part of the 7 Jul 2009 release, as discussed here.
6 Jul 2009
Reese Jones (Sandia), Philip Howell (Siemens), and Vikas Varsney (AFRL) have developed a new compute heat/flux command which can be used to calculate thermal conductivity via the Green-Kubo formalism. The doc page includes instructions on the methodology for doing this. This is a competing approach to the reverse-heat-flux method used by the fix thermal/conductivity command.
This patch file can be applied to the 5 Jul 2009 version. This is the list of changed files.
5 Jul 2009
Upgraded the degree-of-freedom detection done by the fix rigid command when tempterature is computed on atoms in rigid bodies. It should now work correctly with the finite-size particles which can now be part of rigid bodies (3Jul09 patch), and it should also detect when a rigid body consists of point particles in a straight line and thus has one less degree-of-freedom.
This patch file can be applied to the 4 Jul 2009 version. This is the list of changed files.
4 Jul 2009
Added a side option to the fix indent command to allow a spherical or cylindrical "indenter" to act as a constraining wall and push inward instead of outward. If the radius changes it can thus be used to squeeze a collection of particles.
This patch file can be applied to the 3 Jul 2009 version. This is the list of changed files.
3 Jul 2009
Enhanced the fix rigid command to work with constituent particles that are not just point particles (which is the default in LAMMPS), but can now also be finite-size particles. Thus a rigid body can be constructed from a combination of point-particles, spheroids, and ellipsoids. Finite-size particles alter the dynamics of a rigid body since they contribute differently to its moment of inertia. They can also contribute torque to the rigid body, e.g. due to tangential forces on a granular particle.
This patch file can be applied to the 2 Jul 2009 version. This is the list of changed files.
2 Jul 2009
Paul Crozier (Sandia) added a diagnostic output to the fix heat command.
This patch file can be applied to the 1 Jul 2009 version. This is the list of changed files.
Thanks to Ajit Vallabhaneni for the suggestion.
1 Jul 2009
Fixed an I/O bug in the new fix bond/reax command.
This patch file can be applied to the 30 Jun 2009 version. This is the list of changed files.
Thanks to Pablo Valentini for finding the issue.
30 Jun 2009
Changed the dump commmand to always output on the first timestep it is invoked, which it might not following a minimization which ends on an arbitrary timestep. This fixes a problem with the dump custom command not triggering the computation of virial or energy information on the next needed timestep.
This patch file can be applied to the 29 Jun 2009 version. This is the list of changed files.
Thanks to Minwoong Joe (KIST) for sending a script that illustrated this problem.
29 Jun 2009
Added an atom type option to the variable equal and variable atom commands.
This patch file can be applied to the 28 Jun 2009 version. This is the list of changed files.
28 Jun 2009
Made various small changes to pair styles, fixes, and computes that operate on finite-size particles like spheroids and aspherical particles (as opposed to the majority of LAMMPS that operates on point particles). The use of such particles is disussed here.
The goal here was to make LAMMPS more consistent about how these particles are treated, particularly if atom_style hybrid is used, which allows both a per-particle diameter and a per-type shape to be assigned. In this case, the per-particle diameter takes precedence.
This patch file can be applied to the 27 Jun 2009 version. This is the list of changed files.
27 Jun 2009
Andy Ballard (U Maryland) fixed two important bugs in the temper command used to do parallel replica exchange. The first was an incorrect normalization of the potential energy by atom count when thermodynamic output performs this normalization (which is the default for LJ units). The second was a failure to rescale the kinetic energy of two swapped ensembles which leads to incorrect sampling of the potential energy distribution by the set of replicas.
This patch file can be applied to the 26 Jun 2009 version. This is the list of changed files.
26 Jun 2009
Pim Schravendijk added a cone option to the region command, which is like a truncated cylinder with 2 different radii.
This patch file can be applied to the 25 Jun 2009 version. This is the list of changed files.
25 Jun 2009
One line bug fix in the restart2data tool to make it skip the MEAM potential correctly.
This patch file can be applied to the 24 Jun 2009 version. This is the list of changed files.
Thanks to Joerg Meyer (Max-Planck-Gesellschaft) for pointing this out.
24 Jun 2009
Aidan Thompson (Sandia) added a fix reax/bonds diagnostic command which outputs a file of bond information, as computed by the ReaxFF potential.
This patch file can be applied to the 23 Jun 2009 version. This is the list of changed files.
23 Jun 2009
Enabled the fix freeze command to keep track of total force on its group of atoms before it zeroes them, similar to fix setforce.
This patch file can be applied to the 22 Jun 2009 version. This is the list of changed files.
22 Jun 2009
Fixed a one-line bug in atom_style angle that would affect its use as one of the sub-styles in a atom_style hybrid model.
This patch file can be applied to the 6 Jun 2009 version. This is the list of changed files.
Thanks to Dmitry Fedosov (Brown Univ) for catching this.
6 Jun 2009
Paul Crozier (Sandia) fixed a bug in the fix dt/reset command when used with real or metal units. It was not applying a needed unit conversion, so the new timestep it computed was wrong.
We also made the timestep computation more accurate by including both velocity and force effects together. Also we insured the user-specified Xmax is now a hard limit on how far any atom moves. Before at atom could have moved up to twice as far (in rare cases).
I also changed the syntax for unspecified bounds from INF to NULL, to be more consistent with other LAMMPS commands.
This patch file can be applied to the 5 Jun 2009 version. This is the list of changed files.
5 Jun 2009
Aidan Thompson (Sandia) discovered a bug in the minimizer when it's used with the new fix box/relax command that sometimes caused it to exit before full convergence. This patch fixes it.
This patch file can be applied to the 4 Jun 2009 version. This is the list of changed files.
4 Jun 2009
Ahmed Ismail (Sandia) added a Born-Mayer-Huggins pair potential.
This patch file can be applied to the 3 Jun 2009 version. This is the list of changed files.
3 Jun 2009
The restart2data tool was missing a few lines that enable processing of dihedral_style helix.
This patch file can be applied to the 2 Jun 2009 version. This is the list of changed files.
Thanks to Axel Kohlmeyer (U Penn) for sending a patch for this.
2 Jun 2009
Paul Crozier (Sandia) and Carolyn Phillips (U Michigan) made some upgrades to the two-temperature model they've been working on.
This patch file can be applied to the 1 Jun 2009 version. This is the list of changed files.
1 Jun 2009
Aidan Thompson (Sandia) has made some enhancements to the Fortran options for building the REAX package and the associated documentation.
This patch file can be applied to the 19 May 2009 version. This is the list of changed files.
19 May 2009
The patch on 16Apr09 to have the restart2data tool skip the new pair_style reax setting was incomplete. Needed another line added.
This patch file can be applied to the 18 May 2009 version. This is the list of changed files.
Thanks to Dundar Yilmaz (Bilkent U) for finding this.
18 May 2009
Fixed a bug in the fix ave/spatial command that could affect the layer width when using the "units lattice" option.
This patch file can be applied to the 12 May 2009 version. This is the list of changed files.
Thanks to Marco Kalwelt (Cranfield, UK) for sending this bug fix.
12 May 2009
Changed the energy tabulation in the fix temp/rescale command so that it is cummulative energy added/subtracted by the velocity rescaling, so that it can be monitored during a run.
This patch file can be applied to the 6 May 2009 version. This is the list of changed files.
Thanks to Zhun-yong Ong for calling attention to this.
6 May 2009
Fixed a one character bug in the 28Apr09 patch that affected variables with region options using 3 arguments, vcm().
This patch file can be applied to the 2 May 2009 version. This is the list of changed files.
Thanks to Ming Ma for flagging this.
2 May 2009
Fixed a logic bug in the new 30Apr09 compute temp/profile command.
This patch file can be applied to the 1 May 2009 version. This is the list of changed files.
Thanks to Randy Schunk (Sandia) for exposing this.
1 May 2009
Added some more careful error checks for (pathological) simulations that exceed the one and page limits set by the neigh_modify command by large amounts. It is still possible to crash LAMMPS if you have a bazillion neighbors per atom and have not set one and page appropriately (which usually means your problem geometry is very wrong), but more likely now that you will get a nice error message.
This patch file can be applied to the 30 Apr 2009 version. This is the list of changed files.
30 Apr 2009
Added a compute temp/profile command to allow temperature to be computed on the thermal velocity that remains after subtracting out a spatially-averaged velocity field. Using this compute in conjunction with the various thermostatting fixes in LAMMPS (rescaling, Nose/Hoover, Berendsen, etc) enables a profile-unbiased thermostat (PUT), as advocated by Evans and Morriss in a 1986 PRL paper for systems undergoing complex flow.
This patch file can be applied to the 28 Apr 2009 version. This is the list of changed files.
Thanks to Matt Petersen (Sandia) for help in designing how this should work in LAMMPS.
28 Apr 2009
Added a compute reduce/region command and also region-based functions to the variable command. The former allows quantities to be summed (or "reduced") for atoms in a region. These allow quantities to be computed for just the atoms currently in a geometric region.
This patch file can be applied to the 17 Apr 2009 version. This is the list of changed files.
17 Apr 2009
Added some warnings to the read_restart command if the restart file and input script do not agree on the boundary or newton settings and the input script had changed the default values of these settings.
This patch file can be applied to the 16 Apr 2009 version. This is the list of changed files.
Thanks to David Olmsted for this suggestion.
16 Apr 2009
Added one line to the restart2data tool to have it skip the new ReaxFF setting in restart files, as it does for all potentials setup from tabulated files.
This patch file can be applied to the 15 Apr 2009 version. This is the list of changed files.
Thanks to Pablo Valentini for running into this.
15 Apr 2009
Enabled the following commands to work with rRESPA: fix gravity, fix wall/gran, and fix freeze.
This patch file can be applied to the 13 Apr 2009 version. This is the list of changed files.
Thanks to Brian Novak (LSU) for calling attention to this.
13 Apr 2009
This patch adds a few header files to the POEMS library, invoked by the fix poems command, so that it compiles without issue with the latest g++ 4.3.
This patch file can be applied to the 10 Apr 2009 version. This is the list of changed files.
Thanks to Prashant Kumar (U Pitt) for these changes.
10 Apr 2009
Added a warning message to help users avoid a common input script mistake: using the thermo_modify command before a thermo_style command. The latter wipes out settings made by the former.
This patch file can be applied to the 6 Apr 2009 version. This is the list of changed files.
6 Apr 2009
Paul Crozier (Sandia) has added a two-temperature model for coupling electronic and atomic degrees of freedom which involves solving for the electronic temperature on a spatial grid and using a Langevin thermostat to do the thermostatting between the two temperatures. This is implemented as a new fix ttm which gives the details and citations to the literature on this method.
This patch file can be applied to the 3 Apr 2009 version. This is the list of changed files.
3 Apr 2009
Fixed a couple small bugs with the energy minimizer. The first caused problems if one or more processors had no atoms, and the second was a memory issue if a 2nd minimization was performed after unfixing the fix box/relax command.
Also reduced the number of force evaluations and re-neighborings required by the minimizer. The latter issue was also causing the minimizer to potentially mess up the images flags of atoms that crossed periodic boundaries during minimization steps.
This patch file can be applied to the 1 Apr 2009 version. This is the list of changed files.
Thanks to Jervis Chu, Liang Wan, and Pablo Vanentini for input on these issues.
1 Apr 2009
Liang Wan (Chinese Academy of Sciences) found another memory issue in the new fix box/relax command. This patch fixes it.
This patch file can be applied to the 27 Mar 2009 version. This is the list of changed files.
27 Mar 2009
Fixed a bug in the new fix box/relax command, with the logic of the dilate keyword. Also added the ability to reset its computation of pressure and temperature via the fix_modify command, which the doc page claimed (erroneously) should be possible.
This patch file can be applied to the 26 Mar 2009 version. This is the list of changed files.
Thanks to Liang Wan (Chinese Academy of Sciences) for pointing out these problems.
26 Mar 2009
Fixed a small bug introduced in the fix viscosity command due to a previous patch, probably 13Feb09. It has to do with how particle mass is accessed in one of two ways, on a per-particle or per-type basis.
This patch file can be applied to the 25 Mar 2009 version. This is the list of changed files.
Thanks to Matt Petersen (Sandia) for stumbling into this.
25 Mar 2009
Fixed a one-line bug in the dump custom command for doing threshholding on the iz keyword via the dump_modify thresh command.
Aidan Thompson (Sandia) made some small improvements to the quadratic line search in the energy minimizer.
This patch file can be applied to the 24 Mar 2009 version. This is the list of changed files.
Thanks to Liang Wan (Chinese Academy of Sciences) for identifying the dump custom issue.
24 Mar 2009
Added a fix evaporate command to allow solvent (or other) particles to be removed periodically from the simulation. This enables a simple model of evaporation or drying of a mixture system.
This patch file can be applied to the 23 Mar 2009 version. This is the list of changed files.
23 Mar 2009
Just realized the group delete command causes the restart file format to change due to the way deleted groups are written out, which I normally don't like to do except at major releases. So this patch makes the restart file format backward compatible with the previous format.
This patch file can be applied to the 22 Mar 2009 version. This is the list of changed files.
22 Mar 2009
The 19Mar09 patch of a group delete command requires the restart2data tool to read the restart file in a slightly different way. This patch updates that tool.
This patch file can be applied to the 21 Mar 2009 version. This is the list of changed files.
Thanks to Kelly Anderson (PNG) for pointing this out.
21 Mar 2009
Added a wiggle option to the fix deform command to allow the box dimensions or tilt factor (for triclinic boxes) to be oscillated in time.
This patch file can be applied to the 20 Mar 2009 version. This is the list of changed files.
20 Mar 2009
Added xu, yu, zu options to the fix ave/atom command to allow atom coordinates to be time averaged without worrying whether the atoms cross periodic boundaries.
This patch file can be applied to the 19 Mar 2009 version. This is the list of changed files.
19 Mar 2009
Added a delete option to the group command to allow a group definition no longer in use to be deleted. This can make it easier to live with the restriction that no more than 32 groups can be defined (at any one time). You cannot delete a group that is being used by a fix or compute or dump.
This patch file can be applied to the 18 Mar 2009 version. This is the list of changed files.
18 Mar 2009
Made some minor enhancements to the format of the files produced by the dump atom and dump custom commands in the header region of each snapshot, to make the files more self-describing. This is useful for post-processing programs that read LAMMPS dump files. Hopefully it won't break any tools you have, and will allow them to be more robust.
Specifically, if the simulation box is non-orthogonal, then the triclinic tilt factors are now included in the BOX BOUNDS portion of the header. And the ATOMS line in the header now lists the contents of the columns of the per-atom lines that follow. E.g.
ITEM: ATOMS
has become
ITEM: ATOMS id type x y z
Other LAMMPS tools that read dump files have been modified to read the extended format, namely xmovie, binary2txt, the Python scripts in the tools directory, and Pizza.py itself.
This patch file can be applied to the 17 Mar 2009 version. This is the list of changed files.
17 Mar 2009
Added an append option to the fix print command to allow it to append its file output to an already existing file if desired. This can be useful if your input script loops over multiple runs.
This patch file can be applied to the 16 Mar 2009 version. This is the list of changed files.
16 Mar 2009
Craig Maloney (CMU) sent a small bug fix for the pair_style lj/smooth command he originally authored. It only affects the calculation of energy, not forces or dynamics.
This patch file can be applied to the 12 Mar 2009 version. This is the list of changed files.
12 Mar 2009
Turned off the action of the bond-order scaling parameter bom, the 12th parameter in the list for each bond in ffield.reax. bom is normally set to 1, in which case the change will have no effect. This change makes the LAMMPS implementation of ReaxFF consistent with more recent versions of Adri van Duin's code, and eliminates unexpected behavior when using ffield.reax files in which bom has been set to zero.
This patch file can be applied to the 7 Mar 2009 version. This is the list of changed files.
Thanks to Mike Russo and Adri van Duin for tracking down this problem.
7 Mar 2009
rRESPA neighbor lists, used when pair interactions are spread across multiple rRESPA levels, were broken by an earlier change to neighbor lists. This patch fixes what was broken.
This patch file can be applied to the 6 Mar 2009 version. This is the list of changed files.
Thanks to Brian Novak (LSU) for pointing out the problem.
6 Mar 2009
The pair_write command, when used with pair_style hybrid, wasn't nsuring the values written to the tabulated file repspected the cutoff distances of individual sub-styles. This one-line patch fixes that problem.
This patch file can be applied to the 5 Mar 2009 version. This is the list of changed files.
Thanks to Dave Heine (Corning) for noticing this.
5 Mar 2009
With help from Aidan Thompson and David Olmsted (Sandia), this patch adds a fix box/relax command that can be used to apply pressure to a simulation box during energy minimization to allow the box size to change as atoms relax. This is analagous to performing NPT dynamics, e.g. via the fix npt command.
This patch also makes some additional tweaks to the minimizer itself.
This patch file can be applied to the 25 Feb 2009 version. This is the list of changed files.
25 Feb 2009
Aidan Thompson (Sandia) worked on improving the energy minimizer in LAMMPS. There are now 2 options for the linesearch algorithm used, accessible by the min_modify command, The default is backtrack (as before), but the algorithm has been improved in several ways as has the conjugate gradient driver that calls it. Overall this option should perform better than before and require less energy/force evaluations. If you want to drive forces close to 0.0, then try the quadratic linesearch option, which performs a quadratic projection of the line search distance and can sometimes do a better job, though it may be less robust.
This patch file can be applied to the 19 Feb 2009 version. This is the list of changed files.
19 Feb 2009
Aidan Thompson (Sandia) added a once option to the neigh_modify command. This allows you to turn off reneighboring when you know neighbor lists do not need to be recomputed. E.g. when running a crystalline structure at cold temperatures.
This patch file can be applied to the 13 Feb 2009 version. This is the list of changed files.
13 Feb 2009
Various bookkeeping changes to distinguish more carefully between the two ways LAMMPS allows particle mass to be specified, either on a per-type or per-atom basis. Hybrid simulations using the atom_style hybrid command can actually use both. These changes make it so particle mass is referenced in the correct way, whichever way mass is defined.
This is in preparation for an enhanced fix rigid which will soon be released, allowing for more general rigid bodies composed of different types of particles.
This patch file can be applied to the 12 Feb 2009 version. This is the list of changed files.
12 Feb 2009
Aidan Thompson (Sandia) and Hansohl Cho (MIT) have added ReaxFF potentials to LAMMPS. This force field was originally developed by Adri van Duin in Bill Goddard's group at CalTech. This was added as a new "reax" package which links to a Fortran library, which is now distributed with LAMMPS. See the making LAMMPS section of the documentation for instructions on how to build LAMMPS with packages and libraries. See the pair_style reax doc page for details of how to use the ReaxFF in LAMMPS.
This patch file can be applied to the 29 Jan 2009 version. This is the list of changed files.
29 Jan 2009
Fixed a small bug in the restart2data tool to make it work on restart files written from simulations with optimized pair potentials like pair_style lj/cut/opt.
This patch file can be applied to the 27 Jan 2009 version. This is the list of changed files.
Thanks to Vladamir Stegailov for flagging this.
27 Jan 2009
Mike Brown (Sandia) has added a more accurate distance-of-closest- approach calculation to the pair_style resquared potential. This is for the mixture case when a large ellipsoid interacts with a small spherical solvent particle and results in a more accurate "size" for the ellipsoid as seen by the solvent particles.
This patch file can be applied to the 23 Jan 2009 version. This is the list of changed files.
23 Jan 2009
Somehow the doc files for fix bond/create and fix bond/break didn't make it into the 9Jan09 release, probably due to the derelict who manages our Subversion repository. This patch provides them.
This patch file can be applied to the 22 Jan 2009 version. This is the list of changed files.
Thanks to Dave Heini (Corning) for noticing the omission.
22 Jan 2009
Fixed a bug with temperature computation of systems with rigid bodies that could occur if the group used in a temperature compute did not include all the rigid bodies defined by the fix rigid command. The bug had to do with removing the appropriate number of degrees of freedom. LAMMPS now issues a warning if you try to compute temperature on only some of the atoms in a particular rigid body. See the fix rigid doc page for details on how degrees of freedom are now handled.
This patch file can be applied to the 21 Jan 2009 version. This is the list of changed files.
Thanks to Jiwu Liu (Michigan State Univ) for identifying the offending code.
21 Jan 2009
Fixed (yet another) bug with the fix spring command to do with summing forces in parallel for output by the fix. (Not a bug in the force applied to atoms.) Also added a 4th output field useful for computing the potential of mean force (PMF).
This patch file can be applied to the 19 Jan 2009 version. This is the list of changed files.
Thanks again to Xibing He (U Penn) for these suggestions.
19 Jan 2009
Liang Wan (Chinese Academy of Sciences) provided some code to use the common neighbor analysis (CNA) methodology to deduce a local crystal structure around each atom. This has become the compute cna/atom command.
This patch file can be applied to the 18 Jan 2009 version. This is the list of changed files.
18 Jan 2009
Fixed a sign error and a summation error (in parallel) in the spring force reported by the fix spring tether command. Also enabled this fix to store and use the energy of the spring, both for addition to the overall energy of the system (see the fix_modify energy command) and in energy minimization.
This patch file can be applied to the 17 Jan 2009 version. This is the list of changed files.
Thanks to Xibing He (U Penn) for catching the errors and making additional suggestions on how to enhance this command.
17 Jan 2009
Fixed another bug with how fixes trigger computes to be calculated on the correct timestep. Again something that got broken in the 9Jan09 release.
This patch file can be applied to the 16 Jan 2009 version. This is the list of changed files.
Thanks to LT Kong for posting commands that showed the problem.
16 Jan 2009
Fixed a bug in the "compute reduce" command and its interaction with other computes that calculate virial or energy quantities. This was broken by the 9Jan09 release.
This patch file can be applied to the 15 Jan 2009 version. This is the list of changed files.
Thanks to Yao Li for flagging this.
15 Jan 2009
Rudra Mukherjee (JPL) sent an update to the POEMS library used by LAMMPS via the fix poems command to insure compatibility on 32 and 64 bit machines.
This patch file can be applied to the 14 Jan 2009 version. This is the list of changed files.
14 Jan 2009
Removed the restriction on dump file output via the dump and dump_modify commands that output of scaled and unwrapped coordinates can only be done for orthogonal simulations boxes. It can now be done by either the dump atom or dump custom commands for triclinic (non-orthogonal boxes) as well.
This patch file can be applied to the 13 Jan 2009 version. This is the list of changed files.
Thanks to Liang Wan (Chinese Academy of Sciences) for suggesting how to do this.
13 Jan 2009
Enhanced the fix rigid command to allow for restricting the motion of rigid bodies, either translationally or rotationally, via the force and torque keywords. Also added some output options from this fix, so that the center-of-mass position, velocity, force, or torque can be tracked for one or more of the rigid bodies.
This patch file can be applied to the 12 Jan 2009 version. This is the list of changed files.
12 Jan 2009
Added some code to compute stress/atom command to enable it to work for granular systems which define mass on a per-particle basis instead of the usual way (per-type atom mass).
This patch file can be applied to the 9 Jan 2009 version. This is the list of changed files.
Thanks to Priscilla Fonseca (Northwestern) for sending a script that illustrated the problem.