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Giacomo Fiorin 3e89b270fd Update Colvars to version 2017-10-11 
Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics.  Also included are several small fixes.

Below is a list of relevant commits in the Colvars repository since the last update.

321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
2017-10-13 13:45:10 -04:00
..
ASPHERE
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
BODY
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
CLASS2
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
COLLOID
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
COMPRESS
propagate global package installation bugfix to explicit package scripts
2017-04-07 15:29:56 -04:00
CORESHELL
add C++ format identifiers to .h files
2017-06-20 16:18:34 -04:00
DEPEND
Fix more typos in src files
2017-03-07 00:55:01 -05:00
DIPOLE
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
GPU
Added references to GPU package citations
2017-08-09 10:09:40 -05:00
GRANULAR
Revert "avoid undesired negative forces for high particle velocities in granular models"
2017-06-15 11:01:36 -04:00
KIM
propagate global package installation bugfix to explicit package scripts
2017-04-07 15:29:56 -04:00
KOKKOS
Merge pull request #676 from stanmoore1/kokkos_reverse_comm
2017-10-05 17:08:49 -06:00
KSPACE
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
LATTE
update fix latte examples and virial
2017-09-21 10:40:54 -06:00
MAKE
Merge branch 'master' into user-intel-update
2017-10-06 10:18:38 -04:00
MANYBODY
Merge pull request #576 from akohlmey/sanitizer-changes
2017-07-20 12:03:40 -06:00
MC
white space cleanup
2017-07-10 17:21:20 -04:00
MEAM
make the deprecation warning nicer looking
2017-08-09 19:13:40 -04:00
MISC
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
MOLECULE
drop const qualifier to allow bracketing of lookup index
2017-10-13 10:29:49 -04:00
MPIIO
Updating from master to 19May17
2017-05-25 11:21:10 -06:00
MSCG
do not pollute global namespace by including mscg header in fix header
2017-08-08 13:20:25 -04:00
OPT
remove dead code and reduce trivial compiler warnings (clang++)
2017-03-27 14:28:50 -04:00
PERI
avoid division by zero in peri pair styles
2017-07-18 07:26:45 -04:00
POEMS
correctly initialize thermo_virial in fix poems and protect access to vflag_XXX by checking for evflag !=0
2017-09-17 20:49:41 -04:00
PYTHON
Fixes coverity issue CID 179426
2017-05-22 17:36:16 -04:00
QEQ
more cleanup, checks and generalization of QEQ parameter file parsing
2017-08-18 20:03:47 -04:00
REAX
make the deprecation warning nicer looking
2017-08-09 19:13:40 -04:00
REPLICA
need to re-init timers after initial setup
2017-09-25 23:20:42 -04:00
RIGID
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
SHOCK
restore lost KIM doc section in Section packages
2017-07-26 16:07:08 -06:00
SNAP
changes to SNAP virial from Aidan
2017-07-13 11:19:35 -06:00
SRD
Fix typos in src files
2017-03-05 21:03:40 -05:00
STUBS
add support for MPI_Request_free() to MPI STUBS library
2017-03-17 11:40:09 -04:00
USER-ATC
propagate global package installation bugfix to explicit package scripts
2017-04-07 15:29:56 -04:00
USER-AWPMD
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
USER-CGDNA
Added sequence-dependent stacking and base-pairing strength
2017-09-05 10:48:38 +01:00
USER-CGSDK
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
USER-COLVARS
Update Colvars to version 2017-10-11
2017-10-13 13:45:10 -04:00
USER-DIFFRACTION
add C++ format identifiers to .h files
2017-06-20 16:18:34 -04:00
USER-DPD
USER-DPD: finish renaming #ifdef DEBUG_PAIR_CT to DEBUG_SSA_PAIR_CT
2017-08-30 14:58:38 -05:00
USER-DRUDE
Mods for extra/special/per/atom and add toluene
2017-08-31 15:03:04 +02:00
USER-EFF
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
USER-FEP
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
USER-H5MD
propagate global package installation bugfix to explicit package scripts
2017-04-07 15:29:56 -04:00
USER-INTEL
Merge pull request #683 from wmbrownIntel/pppm_intel_fix
2017-10-09 08:29:52 -06:00
USER-LB
activate virial contribution in fix lb/rigid/pc/sphere by default and protect virial computation with evflag
2017-09-17 21:10:41 -04:00
USER-MANIFOLD
whitespace fixes, silence compiler warning about too few format specifiers
2017-09-25 16:31:39 -04:00
USER-MEAMC
remove some dead code and prune argument lists accordingly
2017-07-01 18:16:36 -04:00
USER-MESO
fix issues indicated by compiler warnings
2017-08-22 23:46:32 -04:00
USER-MGPT
new SNAP potential for W
2017-02-21 15:49:21 -07:00
USER-MISC
Authorize hybrid/overlay for fix srp
2017-09-25 16:18:08 +02:00
USER-MOLFILE
update VMD molfile plugin headers and move them to lib/molfile (where they belong)
2017-04-18 11:42:31 -04:00
USER-NETCDF
correct handling of "at" keyword for netcdf dumps as suggested by @pastewka in PR #681 review
2017-10-09 07:49:29 -04:00
USER-OMP
Remove hardcoded value in fix_qeq_reax
2017-10-05 11:23:31 -06:00
USER-PHONON
tweaked author syntax
2016-11-22 08:15:13 -07:00
USER-QMMM
propagate global package installation bugfix to explicit package scripts
2017-04-07 15:29:56 -04:00
USER-QTB
add C++ format identifiers to .h files
2017-06-20 16:18:34 -04:00
USER-QUIP
support QUIP wrapper API version query, relax hybrid restriction to allow hybrid/overlay, update docs
2017-07-19 13:17:35 -04:00
USER-REAXC
Remove hardcoded value in fix_qeq_reax
2017-10-05 11:23:31 -06:00
USER-SMD
add C++ format identifiers to .h files
2017-06-20 16:18:34 -04:00
USER-SMTBQ
add C++ format identifiers to .h files
2017-06-20 16:18:34 -04:00
USER-SPH
add error location propagation to force->bounds() and force->boundsbig()
2016-10-26 15:53:02 -04:00
USER-TALLY
avoid reporting negative memory allocation when memory_usage() is called before initialized
2017-07-22 23:14:17 -04:00
USER-VTK
add C++ format identifiers to .h files
2017-06-20 16:18:34 -04:00
VORONOI
propagate global package installation bugfix to explicit package scripts
2017-04-07 15:29:56 -04:00
.gitignore
update src/.gitignore for LATTE package
2017-09-25 19:37:55 -04:00
accelerator_kokkos.h
Fixing Kokkos execution space issue with regions
2017-07-25 13:37:01 -06:00
accelerator_omp.h
…
angle_hybrid.cpp
sync GHub with SVN
2017-01-26 14:06:43 -07:00
angle_hybrid.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
angle_zero.cpp
add error location propagation to force->bounds() and force->boundsbig()
2016-10-26 15:53:02 -04:00
angle_zero.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14868 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-22 17:54:49 +00:00
angle.cpp
Adding alloc flag to ev_setup
2017-03-08 12:36:23 -07:00
angle.h
Adding alloc flag to ev_setup
2017-03-08 12:36:23 -07:00
atom_map.cpp
add atom_modify map yes, also timers to create_atoms and replicate
2017-10-05 16:44:24 -06:00
atom_masks.h
Updates to Kokkos files
2016-12-15 11:18:50 -07:00
atom_vec_atomic.cpp
fix spring doc page update
2017-01-17 09:02:56 -07:00
atom_vec_atomic.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
atom_vec_body.cpp
fix spring doc page update
2017-01-17 09:02:56 -07:00
atom_vec_body.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 15:26:57 +00:00
atom_vec_charge.cpp
fix spring doc page update
2017-01-17 09:02:56 -07:00
atom_vec_charge.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
atom_vec_ellipsoid.cpp
fix spring doc page update
2017-01-17 09:02:56 -07:00
atom_vec_ellipsoid.h
remove executable permissions on non-executables and non-scripts
2016-09-08 14:45:07 -04:00
atom_vec_hybrid.cpp
Fix more typos in src files
2017-03-07 00:55:01 -05:00
atom_vec_hybrid.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
atom_vec_line.cpp
fix spring doc page update
2017-01-17 09:02:56 -07:00
atom_vec_line.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14480 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-01-23 00:49:16 +00:00
atom_vec_sphere.cpp
fix spring doc page update
2017-01-17 09:02:56 -07:00
atom_vec_sphere.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
atom_vec_tri.cpp
fix spring doc page update
2017-01-17 09:02:56 -07:00
atom_vec_tri.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
atom_vec.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15080 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-05-31 16:20:32 +00:00
atom_vec.h
changes to imbalance weight factors
2016-10-05 10:33:39 -06:00
atom.cpp
add atom_modify map yes, also timers to create_atoms and replicate
2017-10-05 16:44:24 -06:00
atom.h
Merge branch 'master' into USER-DPD_kokkos
2017-08-23 15:20:56 -06:00
balance.cpp
remove unused variable
2017-07-28 16:03:24 -04:00
balance.h
avoid integer overflow and remove unused function argument causing it
2017-07-26 11:55:50 -04:00
body.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
body.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14421 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-01-11 22:00:29 +00:00
bond_hybrid.cpp
sync GHub with SVN
2017-01-26 14:06:43 -07:00
bond_hybrid.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
bond_zero.cpp
add error location propagation to force->bounds() and force->boundsbig()
2016-10-26 15:53:02 -04:00
bond_zero.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14868 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-22 17:54:49 +00:00
bond.cpp
Made fix adapt work with bond_harmonic.
2017-04-04 12:35:26 -04:00
bond.h
Made fix adapt work with bond_harmonic.
2017-04-04 12:35:26 -04:00
change_box.cpp
add rigid body overlap warnings to change_box and delete_atoms
2017-06-13 16:26:49 -04:00
change_box.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
citeme.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
citeme.h
Spelling fixes in source files
2017-03-05 18:30:39 -05:00
comm_brick.cpp
Add Kokkos threaded reverse comm option
2017-10-03 10:14:24 -06:00
comm_brick.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15187 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 17:39:55 +00:00
comm_tiled.cpp
remove dead code and reduce trivial compiler warnings (clang++)
2017-03-27 14:28:50 -04:00
comm_tiled.h
changes to imbalance weight factors
2016-10-05 10:33:39 -06:00
comm.cpp
change ring communication API to no longer require a static variable pointing to 'this' of the caller
2017-06-14 17:01:06 -04:00
comm.h
change ring communication API to no longer require a static variable pointing to 'this' of the caller
2017-06-14 17:01:06 -04:00
compute_aggregate_atom.cpp
add a compute aggregate/atom, that combines the rules for compute cluster/atom and fragment/atom
2017-08-21 13:12:43 -04:00
compute_aggregate_atom.h
add a compute aggregate/atom, that combines the rules for compute cluster/atom and fragment/atom
2017-08-21 13:12:43 -04:00
compute_angle_local.cpp
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_angle_local.h
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_angle.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:02 -04:00
compute_angle.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_angmom_chunk.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:02 -04:00
compute_angmom_chunk.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13286 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-25 15:50:57 +00:00
compute_bond_local.cpp
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_bond_local.h
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_bond.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:02 -04:00
compute_bond.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_centro_atom.cpp
whitespace cleanup
2017-09-20 11:13:13 -04:00
compute_centro_atom.h
Added axes keyword
2016-07-27 23:06:18 +00:00
compute_chunk_atom.cpp
Bugfix for the limit keyword
2017-09-14 11:00:55 +02:00
compute_chunk_atom.h
change ring communication API to no longer require a static variable pointing to 'this' of the caller
2017-06-14 17:01:06 -04:00
compute_cluster_atom.cpp
fix typo
2017-08-21 13:12:48 -04:00
compute_cluster_atom.h
add new compute fragment/atom
2017-08-18 19:07:32 -04:00
compute_cna_atom.cpp
make certain class member list is initialized to NULL before assigned to a neighbor list
2017-06-20 16:09:11 -04:00
compute_cna_atom.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_com_chunk.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:02 -04:00
compute_com_chunk.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15170 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-14 22:14:34 +00:00
compute_com.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15100 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-02 14:08:20 +00:00
compute_com.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
compute_contact_atom.cpp
new SNAP potential for W
2017-02-21 15:49:21 -07:00
compute_contact_atom.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_coord_atom.cpp
remove unused variable
2017-01-25 15:40:52 -07:00
compute_coord_atom.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_dihedral_local.cpp
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_dihedral_local.h
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_dihedral.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
compute_dihedral.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_dipole_chunk.cpp
new Section package and start doc pages and build scripts
2017-05-04 11:22:20 -06:00
compute_dipole_chunk.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14860 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-22 15:55:54 +00:00
compute_displace_atom.cpp
individual computes do not need to set vector/array to NULL. reordering fixes to silence compiler warnings
2016-08-30 06:41:02 -04:00
compute_displace_atom.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12996 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-01-28 15:55:56 +00:00
compute_erotate_sphere_atom.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
compute_erotate_sphere_atom.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
compute_erotate_sphere.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
compute_erotate_sphere.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
compute_fragment_atom.cpp
skip over disabled bonds
2017-08-20 09:49:01 -04:00
compute_fragment_atom.h
add new compute fragment/atom
2017-08-18 19:07:32 -04:00
compute_global_atom.cpp
new compute global/atom command, also bug fix for descending dump sorts
2016-11-30 14:01:27 -07:00
compute_global_atom.h
new compute global/atom command, also bug fix for descending dump sorts
2016-11-30 14:01:27 -07:00
compute_group_group.cpp
patch 12Feb17 - change int to tagint for compute group/group
2017-02-13 08:40:54 -07:00
compute_group_group.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_gyration_chunk.cpp
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_gyration_chunk.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13278 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-23 23:30:50 +00:00
compute_gyration.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-06 23:21:39 +00:00
compute_gyration.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
compute_heat_flux.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
compute_heat_flux.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
compute_hexorder_atom.cpp
Using correct ndegree instead of nnn
2017-05-28 15:44:12 -07:00
compute_hexorder_atom.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_improper_local.cpp
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_improper_local.h
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_improper.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
compute_improper.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_inertia_chunk.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
compute_inertia_chunk.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13278 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-23 23:30:50 +00:00
compute_ke_atom.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
compute_ke_atom.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
compute_ke.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
compute_ke.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
compute_msd_chunk.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
compute_msd_chunk.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 15:26:57 +00:00
compute_msd.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
compute_msd.h
Added average keyword
2015-12-02 05:06:52 +00:00
compute_omega_chunk.cpp
sync with 7Sep16 patch
2016-09-06 17:00:32 -06:00
compute_omega_chunk.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13286 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-25 15:50:57 +00:00
compute_orientorder_atom.cpp
fix bug in compute orientorder/atom argument parsing
2017-06-10 04:35:11 -04:00
compute_orientorder_atom.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_pair_local.cpp
insure compute pair/property local will use a copy of granular neigh list
2017-06-21 12:44:35 -06:00
compute_pair_local.h
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_pair.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
compute_pair.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_pe_atom.cpp
remove executable permissions on non-executables and non-scripts
2016-09-08 14:45:07 -04:00
compute_pe_atom.h
remove executable permissions on non-executables and non-scripts
2016-09-08 14:45:07 -04:00
compute_pe.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15291 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-12 22:59:27 +00:00
compute_pe.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15291 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-12 22:59:27 +00:00
compute_pressure.cpp
whether virial contributions from fixes are included depend on thermo_virial, not virial_flag.
2017-09-17 20:50:22 -04:00
compute_pressure.h
initial import of adapted gREM code by David Stelter and Edyta Malolepsza
2016-11-13 18:44:10 -05:00
compute_property_atom.cpp
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_property_atom.h
remove vector/array class members shadowing the base class
2016-08-30 07:04:54 -04:00
compute_property_chunk.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
compute_property_chunk.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_property_local.cpp
insure compute pair/property local will use a copy of granular neigh list
2017-06-21 12:44:35 -06:00
compute_property_local.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
compute_rdf.cpp
whitespace cleanup
2017-07-07 15:50:19 -04:00
compute_rdf.h
add support for recomputing normalization factors and finite size correction during
2017-07-07 15:39:25 -04:00
compute_reduce_region.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15083 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-05-31 16:33:07 +00:00
compute_reduce_region.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
compute_reduce.cpp
Kokkos updates by Stan
2016-11-17 08:58:22 -07:00
compute_reduce.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13278 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-23 23:30:50 +00:00
compute_slice.cpp
added functionity to lib interface
2016-12-13 16:22:17 -07:00
compute_slice.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
compute_stress_atom.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:04 -04:00
compute_stress_atom.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13278 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-23 23:30:50 +00:00
compute_temp_chunk.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:04 -04:00
compute_temp_chunk.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 15:26:57 +00:00
compute_temp_com.cpp
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_com.h
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_deform.cpp
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_deform.h
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_partial.cpp
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_partial.h
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_profile.cpp
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_profile.h
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_ramp.cpp
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_ramp.h
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_region.cpp
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_region.h
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_sphere.cpp
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp_sphere.h
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
compute_temp.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
compute_temp.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 15:26:57 +00:00
compute_torque_chunk.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:04 -04:00
compute_torque_chunk.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13278 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-23 23:30:50 +00:00
compute_vacf.cpp
remove executable permissions on non-executables and non-scripts
2016-09-08 14:45:07 -04:00
compute_vacf.h
remove executable permissions on non-executables and non-scripts
2016-09-08 14:45:07 -04:00
compute_vcm_chunk.cpp
Fixed initialization of arrays in computes
2016-08-24 17:26:04 -04:00
compute_vcm_chunk.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13278 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-23 23:30:50 +00:00
compute.cpp
fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof
2017-03-23 15:31:27 -06:00
compute.h
Merge pull request #510 from akohlmey/collected-small-changes
2017-06-15 11:12:14 -06:00
create_atoms.cpp
rename misleading "CPU time" into "Time spent"
2017-10-06 14:34:10 -04:00
create_atoms.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
create_bonds.cpp
add single options to create_bonds command
2017-06-30 11:30:43 -06:00
create_bonds.h
add single options to create_bonds command
2017-06-30 11:30:43 -06:00
create_box.cpp
make certain, that atom->maxspecial is incremented with extra special space
2016-10-21 11:55:36 -04:00
create_box.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
delete_atoms.cpp
Merge pull request #528 from akohlmey/no_static_in_ring_comm
2017-06-15 11:13:07 -06:00
delete_atoms.h
Merge pull request #528 from akohlmey/no_static_in_ring_comm
2017-06-15 11:13:07 -06:00
delete_bonds.cpp
add error location propagation to force->bounds() and force->boundsbig()
2016-10-26 15:53:02 -04:00
delete_bonds.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
Depend.sh
USER-OMP package depends on USER-DRUDE
2017-09-25 23:15:49 -04:00
dihedral_hybrid.cpp
sync GHub with SVN
2017-01-26 14:06:43 -07:00
dihedral_hybrid.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
dihedral_zero.cpp
add error location propagation to force->bounds() and force->boundsbig()
2016-10-26 15:53:02 -04:00
dihedral_zero.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14868 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-22 17:54:49 +00:00
dihedral.cpp
Adding alloc flag to ev_setup
2017-03-08 12:36:23 -07:00
dihedral.h
Adding alloc flag to ev_setup
2017-03-08 12:36:23 -07:00
displace_atoms.cpp
add rigid body overlap warnings to change_box and delete_atoms
2017-06-13 16:26:49 -04:00
displace_atoms.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 15:26:57 +00:00
domain.cpp
Bugfix for checking image flags
2017-10-09 21:29:07 +09:00
domain.h
new Section package and start doc pages and build scripts
2017-05-04 11:22:20 -06:00
dump_atom.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15428 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-03 16:29:35 +00:00
dump_atom.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
dump_cfg.cpp
NULLing ptrs in comm_brick and dump*.cpp
2016-11-07 15:50:18 +01:00
dump_cfg.h
remove executable permissions on non-executables and non-scripts
2016-09-08 14:45:07 -04:00
dump_custom.cpp
Merge pull request #476 from akohlmey/dump_custom_bugfix
2017-05-11 09:27:08 -06:00
dump_custom.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
dump_dcd.cpp
NULLing ptrs in comm_brick and dump*.cpp
2016-11-07 15:50:18 +01:00
dump_dcd.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14602 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 16:10:43 +00:00
dump_image.cpp
NULL ptrs in dump_custom and dump_image
2016-11-07 15:56:47 +01:00
dump_image.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15309 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-14 19:42:39 +00:00
dump_local.cpp
disallow binary output with dump style local. fixes #596
2017-07-22 10:35:16 -04:00
dump_local.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
dump_movie.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
dump_movie.h
…
dump_xyz.cpp
NULLing ptrs in comm_brick and dump*.cpp
2016-11-07 15:50:18 +01:00
dump_xyz.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
dump.cpp
whitespace cleanup
2017-10-02 15:03:48 -04:00
dump.h
make pre-processor defines for using libc's qsort() consistent
2017-06-20 17:13:42 -04:00
error.cpp
print the last input line, when error->all() is called
2017-01-09 17:03:06 -05:00
error.h
Make exceptions control flow and functions optional
2016-09-16 18:57:37 -04:00
exceptions.h
Make exceptions control flow and functions optional
2016-09-16 18:57:37 -04:00
finish.cpp
whitespace fixes, silence compiler warning about too few format specifiers
2017-09-25 16:31:39 -04:00
finish.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_adapt.cpp
patch 11Apr17
2017-04-11 09:00:37 -06:00
fix_adapt.h
Made fix adapt work with bond_harmonic.
2017-04-04 12:35:26 -04:00
fix_addforce.cpp
correct cut-n-paste error, add docs
2017-09-15 00:54:19 -04:00
fix_addforce.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
fix_ave_atom.cpp
fix argument indexing bug in fix ave/atom
2016-09-19 23:24:37 -04:00
fix_ave_atom.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
fix_ave_chunk.cpp
changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution
2017-03-21 08:56:37 -06:00
fix_ave_chunk.h
changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution
2017-03-21 08:56:37 -06:00
fix_ave_correlate.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_ave_correlate.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 15:26:57 +00:00
fix_ave_histo_weight.cpp
Fix typos in src files
2017-03-05 21:03:40 -05:00
fix_ave_histo_weight.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 15:26:57 +00:00
fix_ave_histo.cpp
protect fix ave/histo from segfaulting on non-existing computes, fixes or variables
2017-04-03 18:08:15 -04:00
fix_ave_histo.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15463 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-09 14:10:55 +00:00
fix_ave_time.cpp
new compute global/atom command, also bug fix for descending dump sorts
2016-11-30 14:01:27 -07:00
fix_ave_time.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
fix_aveforce.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_aveforce.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_balance.cpp
Fix typos in src files
2017-03-05 21:03:40 -05:00
fix_balance.h
adjustments to balancing weights and factors, also XOR op for formulas, if, dump_modify thresh
2016-10-05 15:46:20 -06:00
fix_box_relax.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_box_relax.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_controller.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_controller.h
remove executable permissions on non-executables and non-scripts
2016-09-08 14:45:07 -04:00
fix_deform.cpp
add restart support to fix deform. only "initial" data is restored and some consistency check performed
2017-06-10 17:28:17 -04:00
fix_deform.h
add restart support to fix deform. only "initial" data is restored and some consistency check performed
2017-06-10 17:28:17 -04:00
fix_deprecated.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-06 23:21:39 +00:00
fix_deprecated.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15104 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-02 14:14:17 +00:00
fix_drag.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_drag.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_dt_reset.cpp
enable dynamic groups for fix dt/reset
2016-09-30 09:09:44 -04:00
fix_dt_reset.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_enforce2d.cpp
fix enforce2d has to be defined after fixes with enforce2d_flag set
2017-07-12 11:26:16 -04:00
fix_enforce2d.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15189 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 20:54:47 +00:00
fix_external.cpp
fix external only needs to collect virial in case it is requested
2017-09-17 23:59:34 -04:00
fix_external.h
additional fix external hooks for calling programs
2017-07-05 10:01:19 -06:00
fix_gravity.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_gravity.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_group.cpp
support dynamic groups with run style respa
2016-09-29 15:13:46 -04:00
fix_group.h
Fix more typos in src files
2017-03-07 00:55:01 -05:00
fix_halt.cpp
patch 31Mar17 for stable release
2017-03-30 10:07:27 -06:00
fix_halt.h
change to RCB cuts in load-balancing commands, also a new option for fix halt
2017-03-10 15:55:07 -07:00
fix_heat.cpp
apply the rigid body checks to some more example codes
2017-06-05 16:30:30 -04:00
fix_heat.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_indent.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_indent.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_langevin.cpp
added functionity to lib interface
2016-12-13 16:22:17 -07:00
fix_langevin.h
Spelling fixes in source files
2017-03-05 18:30:39 -05:00
fix_lineforce.cpp
enable support for dynamic groups in fix planeforce and fix lineforce
2017-06-02 08:45:15 -04:00
fix_lineforce.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_minimize.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_minimize.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_momentum.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15089 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-05-31 16:50:28 +00:00
fix_momentum.h
fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof
2017-03-23 15:31:27 -06:00
fix_move.cpp
doc page sync with SVN
2016-09-21 20:54:20 -06:00
fix_move.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 15:26:57 +00:00
fix_nh_sphere.cpp
changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution
2017-03-21 08:56:37 -06:00
fix_nh_sphere.h
changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution
2017-03-21 08:56:37 -06:00
fix_nh.cpp
Changed the check on initial and final temperature to <= 0 for both.
2017-03-28 11:22:10 -04:00
fix_nh.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15369 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-27 14:04:56 +00:00
fix_nph_sphere.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-06 23:21:39 +00:00
fix_nph_sphere.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_nph.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-06 23:21:39 +00:00
fix_nph.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_npt_sphere.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-06 23:21:39 +00:00
fix_npt_sphere.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_npt.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-06 23:21:39 +00:00
fix_npt.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_nve_limit.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
fix_nve_limit.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 15:26:57 +00:00
fix_nve_noforce.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
fix_nve_noforce.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_nve_sphere.cpp
changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution
2017-03-21 08:56:37 -06:00
fix_nve_sphere.h
changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution
2017-03-21 08:56:37 -06:00
fix_nve.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
fix_nve.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_nvt_sllod.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-06 23:21:39 +00:00
fix_nvt_sllod.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_nvt_sphere.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-06 23:21:39 +00:00
fix_nvt_sphere.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_nvt.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-06 23:21:39 +00:00
fix_nvt.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_planeforce.cpp
enable support for dynamic groups in fix planeforce and fix lineforce
2017-06-02 08:45:15 -04:00
fix_planeforce.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_press_berendsen.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_press_berendsen.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_print.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_print.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
fix_property_atom.cpp
Change to fix_property_atom to allow virtual override of grow_arrays() function
2016-12-15 15:48:09 -07:00
fix_property_atom.h
Change to fix_property_atom to allow virtual override of grow_arrays() function
2016-12-15 15:48:09 -07:00
fix_read_restart.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_read_restart.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_recenter.cpp
bug fix for fix GCMC w/ fix shake, enhance of fix wall/gran/region with restarting
2016-10-13 16:55:53 -06:00
fix_recenter.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12814 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-12-02 02:15:39 +00:00
fix_respa.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_respa.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13757 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-28 16:04:10 +00:00
fix_restrain.cpp
pair TIP4P bug fix for cutoffs >> box size
2017-01-06 09:57:27 -07:00
fix_restrain.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_setforce.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_setforce.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_shear_history.cpp
fix bug in fix shear/history reported by kevin hanley. see #500
2017-05-25 10:11:24 -04:00
fix_shear_history.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15333 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-16 20:00:36 +00:00
fix_spring_chunk.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_spring_chunk.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_spring_rg.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_spring_rg.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_spring_self.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_spring_self.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_spring.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_spring.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_store_force.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_store_force.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_store_state.cpp
patch 17Mar17
2017-03-17 11:29:23 -06:00
fix_store_state.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14423 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-01-11 23:38:16 +00:00
fix_store.cpp
added LAST option to dump_modify thresh, more restart info printed out to screen
2016-10-11 12:39:52 -06:00
fix_store.h
sync with SVN
2016-09-23 14:52:45 -06:00
fix_temp_berendsen.cpp
apply the rigid body checks to some more example codes
2017-06-05 16:30:30 -04:00
fix_temp_berendsen.h
…
fix_temp_csld.cpp
apply the rigid body checks to some more example codes
2017-06-05 16:30:30 -04:00
fix_temp_csld.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13320 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-27 20:39:27 +00:00
fix_temp_csvr.cpp
make certain, that -log() doesn't overflow and assign a suitable maximum number instead.
2016-09-15 14:55:32 -04:00
fix_temp_csvr.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14582 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-08 16:18:20 +00:00
fix_temp_rescale.cpp
patch to add DPD-VV
2016-10-12 07:35:47 -06:00
fix_temp_rescale.h
…
fix_tmd.cpp
correct logic bug in bufix for fix tmd
2016-10-01 06:26:52 -04:00
fix_tmd.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
fix_vector.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_vector.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13278 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-23 23:30:50 +00:00
fix_viscous.cpp
allow fix viscous to be used with dynamic groups
2017-09-18 18:08:57 -04:00
fix_viscous.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix_wall_harmonic.cpp
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
fix_wall_harmonic.h
…
fix_wall_lj93.cpp
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
fix_wall_lj93.h
Adding fix_wall_lj93_kokkos
2017-03-02 14:02:49 -07:00
fix_wall_lj126.cpp
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
fix_wall_lj126.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_wall_lj1043.cpp
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
fix_wall_lj1043.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
fix_wall_reflect.cpp
Fixed initialization of arrays in fixes
2016-08-28 22:23:22 -04:00
fix_wall_reflect.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
fix_wall_region.cpp
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
fix_wall_region.h
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
fix_wall.cpp
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
fix_wall.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
fix.cpp
add infrastructure for enabling fixes to contribute to the virial by aidan
2017-09-11 11:09:59 -04:00
fix.h
add infrastructure for enabling fixes to contribute to the virial by aidan
2017-09-11 11:09:59 -04:00
force.cpp
remove special_bonds extra keyword and refer to read_data and create_box instead
2017-08-10 15:12:56 -04:00
force.h
use CHARMM energy conversion factor with new CHARMM pair styles
2017-06-22 09:15:15 -06:00
group.cpp
change ring communication API to no longer require a static variable pointing to 'this' of the caller
2017-06-14 17:01:06 -04:00
group.h
change ring communication API to no longer require a static variable pointing to 'this' of the caller
2017-06-14 17:01:06 -04:00
image.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
image.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
imbalance_group.cpp
changes to imbalance weight factors
2016-10-05 10:33:39 -06:00
imbalance_group.h
new verion of balance weighting
2016-09-23 14:37:53 -06:00
imbalance_neigh.cpp
new SNAP potential for W
2017-02-21 15:49:21 -07:00
imbalance_neigh.h
new verion of balance weighting
2016-09-23 14:37:53 -06:00
imbalance_store.cpp
new verion of balance weighting
2016-09-23 14:37:53 -06:00
imbalance_store.h
new verion of balance weighting
2016-09-23 14:37:53 -06:00
imbalance_time.cpp
adjustments to balancing weights and factors, also XOR op for formulas, if, dump_modify thresh
2016-10-05 15:46:20 -06:00
imbalance_time.h
adjustments to balancing weights and factors, also XOR op for formulas, if, dump_modify thresh
2016-10-05 15:46:20 -06:00
imbalance_var.cpp
adjustments to balancing weights and factors, also XOR op for formulas, if, dump_modify thresh
2016-10-05 15:46:20 -06:00
imbalance_var.h
adjustments to balancing weights and factors, also XOR op for formulas, if, dump_modify thresh
2016-10-05 15:46:20 -06:00
imbalance.cpp
new verion of balance weighting
2016-09-23 14:37:53 -06:00
imbalance.h
adjustments to balancing weights and factors, also XOR op for formulas, if, dump_modify thresh
2016-10-05 15:46:20 -06:00
improper_hybrid.cpp
sync GHub with SVN
2017-01-26 14:06:43 -07:00
improper_hybrid.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
improper_zero.cpp
add error location propagation to force->bounds() and force->boundsbig()
2016-10-26 15:53:02 -04:00
improper_zero.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14868 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-22 17:54:49 +00:00
improper.cpp
Adding alloc flag to ev_setup
2017-03-08 12:36:23 -07:00
improper.h
Adding alloc flag to ev_setup
2017-03-08 12:36:23 -07:00
info.cpp
fix incorrect preprocessor define for windows
2017-08-12 00:35:50 -04:00
info.h
provide an accessor for names of LAMMPS variables
2016-10-17 19:56:18 -04:00
input.cpp
use <> for system includes not ""
2017-09-29 09:19:38 -04:00
input.h
print the last input line, when error->all() is called
2017-01-09 17:03:06 -05:00
Install.sh
address issue where uninstalling an empty package will erase all code in src
2017-04-06 11:08:57 -04:00
integrate.cpp
added functionity to lib interface
2016-12-13 16:22:17 -07:00
integrate.h
fix gcmc updates from Aidan, trimming of output for replica commands
2017-04-11 08:35:09 -06:00
irregular.cpp
minor changes to NEB doc pages and examples
2017-06-20 08:19:23 -06:00
irregular.h
make pre-processor defines for using libc's qsort() consistent
2017-06-20 17:13:42 -04:00
kspace.cpp
Adding alloc flag to ev_setup
2017-03-08 12:36:23 -07:00
kspace.h
Adding alloc flag to ev_setup
2017-03-08 12:36:23 -07:00
lammps.cpp
Refactor PYTHON package and wrapper classes
2017-04-11 21:22:30 -04:00
lammps.h
Refactor PYTHON package and wrapper classes
2017-04-11 21:22:30 -04:00
lattice.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15157 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-08 15:41:04 +00:00
lattice.h
…
library.cpp
Add missing globals in library interface
2017-09-04 19:57:02 -04:00
library.h
added functionity to lib interface
2016-12-13 16:22:17 -07:00
lmptype.h
Fix more typos in src files
2017-03-07 00:55:01 -05:00
lmpwindows.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
main.cpp
add call to fftw_cleanup() before exiting to avoid bogus leak reports when compiling with FFTW v3.x
2017-10-04 00:22:56 -04:00
Make.sh
restore locale and enforce grep option squashing
2016-09-09 15:42:14 -04:00
Makefile
Merge pull request #652 from junghans/latte
2017-09-22 10:32:19 -06:00
Makefile.list
remove pair_zhou from Makefile.list
2017-03-18 20:48:49 -04:00
Makefile.package.empty
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13579 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-14 17:39:05 +00:00
Makefile.package.settings.empty
…
math_complex.h
…
math_const.h
comm tiled bug fix
2016-09-16 10:31:52 -06:00
math_extra.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15369 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-27 14:04:56 +00:00
math_extra.h
fix spring doc page update
2017-01-17 09:02:56 -07:00
math_special.cpp
Improve C++-ness, eliminate some macros
2017-06-11 16:55:41 +02:00
math_special.h
Improve C++-ness, eliminate some macros
2017-06-11 16:55:41 +02:00
math_vector.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
memory.cpp
restore change to make -DLAMMPS_MEMALIGN=64 default when USER-INTEL package is installed (which requires it)
2016-12-14 15:24:55 -05:00
memory.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
mergesort.h
remove ifdefs for selecting between plain and hybrid merge sort. use hybrid only.
2017-06-17 09:30:41 -04:00
min_cg.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
min_cg.h
…
min_fire.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
min_fire.h
…
min_hftn.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15468 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-10 14:59:04 +00:00
min_hftn.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15393 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-29 14:28:58 +00:00
min_linesearch.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
min_linesearch.h
…
min_quickmin.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
min_quickmin.h
…
min_sd.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
min_sd.h
…
min.cpp
make neighbor list reset message for minimization more explicit
2017-06-22 19:07:57 -04:00
min.h
print warning about minimization energy with fix box/relax
2017-05-03 15:33:22 -04:00
minimize.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
minimize.h
Adding error checks for Kokkos-incompatible features
2016-01-28 23:32:16 +00:00
modify.cpp
remove dependence of dump modify 'at' and 'append'
2017-10-06 09:44:29 -06:00
modify.h
Fixed proper deletion of fixes if fix is NULL
2017-09-27 16:20:07 +02:00
molecule.cpp
Merge pull request #622 from akohlmey/collected-small-fixes
2017-08-23 14:12:45 -06:00
molecule.h
Fix more typos in src files
2017-03-07 00:55:01 -05:00
mpiio.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14655 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-17 15:56:48 +00:00
my_page.h
fixed bug with pair hybrid/overaly and manybody potentials finding the right skip neighbor method
2016-12-21 09:50:29 -07:00
my_pool_chunk.h
extra python_wrapper change needed for last patch
2016-12-16 11:35:42 -07:00
nbin_standard.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
nbin_standard.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nbin.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
nbin.h
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
neigh_list.cpp
Fixing memory leak in Kokkos neighborlist
2017-06-26 10:51:26 -06:00
neigh_list.h
Fixing memory leak in Kokkos neighborlist
2017-06-26 10:51:26 -06:00
neigh_request.cpp
Remove unused code detected by coverity CID 177700
2017-05-22 17:51:40 -04:00
neigh_request.h
new SNAP potential for W
2017-02-21 15:49:21 -07:00
neighbor.cpp
Merge branch 'master' (21893539cb Aug 25) into USER-DPD_kokkos_merge
2017-08-28 14:46:50 -05:00
neighbor.h
insure compute pair/property local will use a copy of granular neigh list
2017-06-21 12:44:35 -06:00
npair_copy.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_copy.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_full_bin_atomonly.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_full_bin_atomonly.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_full_bin_ghost.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_full_bin_ghost.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_full_bin.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_full_bin.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_full_multi.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_full_multi.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_full_nsq_ghost.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_full_nsq_ghost.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_full_nsq.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_full_nsq.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_bin_atomonly_newton.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_half_bin_atomonly_newton.h
new SNAP potential for W
2017-02-21 15:49:21 -07:00
npair_half_bin_newtoff_ghost.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_half_bin_newtoff_ghost.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_bin_newtoff.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_half_bin_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_bin_newton_tri.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_half_bin_newton_tri.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_bin_newton.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_half_bin_newton.h
new SNAP potential for W
2017-02-21 15:49:21 -07:00
npair_half_multi_newtoff.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_half_multi_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_multi_newton_tri.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_half_multi_newton_tri.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_multi_newton.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_half_multi_newton.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_nsq_newtoff_ghost.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_nsq_newtoff_ghost.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_nsq_newtoff.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_nsq_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_nsq_newton.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_nsq_newton.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_respa_bin_newtoff.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_half_respa_bin_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_respa_bin_newton_tri.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_half_respa_bin_newton_tri.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_respa_bin_newton.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_half_respa_bin_newton.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_respa_nsq_newtoff.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_respa_nsq_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_respa_nsq_newton.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_respa_nsq_newton.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_size_bin_newtoff.cpp
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
npair_half_size_bin_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_size_bin_newton_tri.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_half_size_bin_newton_tri.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_size_bin_newton.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_half_size_bin_newton.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_size_nsq_newtoff.cpp
new SNAP potential for W
2017-02-21 15:49:21 -07:00
npair_half_size_nsq_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_half_size_nsq_newton.cpp
new SNAP potential for W
2017-02-21 15:49:21 -07:00
npair_half_size_nsq_newton.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_halffull_newtoff.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_halffull_newtoff.h
new SNAP potential for W
2017-02-21 15:49:21 -07:00
npair_halffull_newton.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_halffull_newton.h
new SNAP potential for W
2017-02-21 15:49:21 -07:00
npair_skip_respa.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
npair_skip_respa.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_skip_size_off2on_oneside.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_skip_size_off2on_oneside.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_skip_size_off2on.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_skip_size_off2on.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_skip_size.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_skip_size.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair_skip.cpp
new SNAP potential for W
2017-02-21 15:49:21 -07:00
npair_skip.h
new SNAP potential for W
2017-02-21 15:49:21 -07:00
npair.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
npair.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_full_bin_2d.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_full_bin_2d.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_full_bin_3d.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_full_bin_3d.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_full_ghost_bin_2d.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_full_ghost_bin_2d.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_full_ghost_bin_3d.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_full_ghost_bin_3d.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_full_multi_2d.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_full_multi_2d.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_full_multi_3d.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_full_multi_3d.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_bin_2d_newtoff.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_half_bin_2d_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_bin_2d_newton_tri.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_half_bin_2d_newton_tri.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_bin_2d_newton.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_bin_2d_newton.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_bin_3d_newtoff.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_half_bin_3d_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_bin_3d_newton_tri.cpp
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_half_bin_3d_newton_tri.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_bin_3d_newton.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_bin_3d_newton.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_ghost_bin_2d_newtoff.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_ghost_bin_2d_newtoff.h
major neighbor list style whitespace cleanup
2017-05-30 17:04:48 -04:00
nstencil_half_ghost_bin_3d_newtoff.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_ghost_bin_3d_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_2d_newtoff.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_2d_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_2d_newton_tri.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_2d_newton_tri.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_2d_newton.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_2d_newton.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_3d_newtoff.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_3d_newtoff.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_3d_newton_tri.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_3d_newton_tri.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_3d_newton.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil_half_multi_3d_newton.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
nstencil.cpp
new SNAP potential for W
2017-02-21 15:49:21 -07:00
nstencil.h
USER-DPD: SSA with Kokkos: make stencil's sx, sy, sz variables public
2017-02-22 15:08:21 -05:00
ntopo_angle_all.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_angle_all.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_angle_partial.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_angle_partial.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_angle_template.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_angle_template.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_bond_all.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_bond_all.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_bond_partial.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_bond_partial.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_bond_template.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_bond_template.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_dihedral_all.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_dihedral_all.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_dihedral_partial.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_dihedral_partial.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_dihedral_template.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_dihedral_template.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_improper_all.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_improper_all.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_improper_partial.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_improper_partial.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_improper_template.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo_improper_template.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo.cpp
new neighbor list changes
2016-09-07 13:42:58 -06:00
ntopo.h
new neighbor list changes
2016-09-07 13:42:58 -06:00
output.cpp
bugfix. avoiding operating on uninitialize data. closes #690
2017-10-13 00:15:15 -04:00
output.h
fix gcmc updates from Aidan, trimming of output for replica commands
2017-04-11 08:35:09 -06:00
pack.h
…
Package.sh
enforce C or POSIX locale in all shell scripts and turn of enforced global grep options
2016-08-27 01:57:45 -04:00
pair_beck.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_beck.h
…
pair_born_coul_dsf.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_born_coul_dsf.h
pair style born/coul/dsf added with its coreshell version
2016-11-08 11:32:38 +01:00
pair_born_coul_wolf.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_born_coul_wolf.h
…
pair_born.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_born.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_buck_coul_cut.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_buck_coul_cut.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13303 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-27 13:41:29 +00:00
pair_buck.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_buck.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13058 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-02-04 22:14:27 +00:00
pair_coul_cut.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_coul_cut.h
Fixing a few bugs in Kokkos
2015-02-23 23:45:29 +00:00
pair_coul_debye.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_coul_debye.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_coul_dsf.cpp
add error location propagation to force->bounds() and force->boundsbig()
2016-10-26 15:53:02 -04:00
pair_coul_dsf.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
pair_coul_streitz.cpp
new SNAP potential for W
2017-02-21 15:49:21 -07:00
pair_coul_streitz.h
add C++ format identifiers to .h files
2017-06-20 16:18:34 -04:00
pair_coul_wolf.cpp
add error location propagation to force->bounds() and force->boundsbig()
2016-10-26 15:53:02 -04:00
pair_coul_wolf.h
…
pair_dpd_tstat.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_dpd_tstat.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_dpd.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_dpd.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_gauss.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_gauss.h
add mixing for pair styles gauss and gauss/cut contributed by andrew jewett. also add support for write_data.
2016-10-18 22:26:47 -04:00
pair_hybrid_overlay.cpp
new SNAP potential for W
2017-02-21 15:49:21 -07:00
pair_hybrid_overlay.h
Merge branch 'master' into USER-DPD_kokkos as of patch 21Feb17
2017-02-22 11:29:01 -05:00
pair_hybrid.cpp
Error out if using pair hybrid with Kokkos, but not pair hybrid/overlay
2017-08-25 15:16:19 -06:00
pair_hybrid.h
Error out if using pair hybrid with Kokkos, but not pair hybrid/overlay
2017-08-25 15:16:19 -06:00
pair_lj96_cut.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_lj96_cut.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_lj_cubic.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_lj_cubic.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_lj_cut_coul_cut.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_lj_cut_coul_cut.h
Fixing a few bugs in Kokkos
2015-02-23 23:45:29 +00:00
pair_lj_cut_coul_debye.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
pair_lj_cut_coul_debye.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_lj_cut_coul_dsf.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_lj_cut_coul_dsf.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
pair_lj_cut.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_lj_cut.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_lj_expand.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_lj_expand.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13303 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-27 13:41:29 +00:00
pair_lj_gromacs_coul_gromacs.cpp
add error location propagation to force->bounds() and force->boundsbig()
2016-10-26 15:53:02 -04:00
pair_lj_gromacs_coul_gromacs.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13303 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-27 13:41:29 +00:00
pair_lj_gromacs.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_lj_gromacs.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13303 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-27 13:41:29 +00:00
pair_lj_smooth_linear.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_lj_smooth_linear.h
alias pair style lj/sf to lj/smooth/linear and remove/update related files
2017-06-06 17:26:06 -04:00
pair_lj_smooth.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_lj_smooth.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_mie_cut.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_mie_cut.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_morse.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_morse.h
Ported Morse to KOKKOS
2017-02-01 17:45:21 +01:00
pair_soft.cpp
correct the inner loop range for resetting cutoffs when redefining a pair style
2017-05-16 00:26:18 -04:00
pair_soft.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_table.cpp
skip table consistency check for bitmapped tables
2017-07-17 18:18:21 -04:00
pair_table.h
lots of work towards compiling
2017-01-11 13:15:01 -07:00
pair_yukawa.cpp
avoid division by zero when using cutoff 0.0 with pair_modify shift yes
2017-07-14 23:33:00 -04:00
pair_yukawa.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
pair_zbl.cpp
add error location propagation to force->bounds() and force->boundsbig()
2016-10-26 15:53:02 -04:00
pair_zbl.h
Modifed ZBL to accomodate mixing
2015-09-23 00:30:30 +00:00
pair_zero.cpp
add error location propagation to force->bounds() and force->boundsbig()
2016-10-26 15:53:02 -04:00
pair_zero.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14926 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-05-03 16:01:16 +00:00
pair.cpp
fix bug with pair_modify <style> compute not triggering the correct global change
2017-08-11 08:28:37 -04:00
pair.h
Updating to master
2017-06-19 10:56:24 -06:00
pointers.h
Refactor PYTHON package and wrapper classes
2017-04-11 21:22:30 -04:00
procmap.cpp
Spelling fixes in source files
2017-03-05 18:30:39 -05:00
procmap.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
Purge.list
remove another couple of purge items from long ago
2017-09-17 19:22:43 -04:00
python.cpp
implement functions to execute arbitrary python code from strings or files and recast the python source keyword through using them.
2017-05-11 22:39:08 -04:00
python.h
implement functions to execute arbitrary python code from strings or files and recast the python source keyword through using them.
2017-05-11 22:39:08 -04:00
random_mars.cpp
NULLed ptrs in files
2016-11-07 16:07:37 +01:00
random_mars.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
random_park.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15203 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:48:15 +00:00
random_park.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14860 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-22 15:55:54 +00:00
rcb.cpp
avoid invalid calls to memcpy(): when ndot == 0, pointers may be NULL
2017-07-26 12:08:42 -04:00
rcb.h
change to RCB cuts in load-balancing commands, also a new option for fix halt
2017-03-10 15:55:07 -07:00
read_data.cpp
Revert change to read_data.cpp
2017-08-25 15:25:41 -06:00
read_data.h
consolidate and update error message and read_data documentation for the updated read_data command
2017-06-29 16:30:49 -04:00
read_dump.cpp
add fix mscg command, example, lib
2017-01-09 13:36:40 -07:00
read_dump.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
read_restart.cpp
Remove hardcoded map variables and debug output
2017-08-25 15:31:00 -06:00
read_restart.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 15:26:57 +00:00
reader_native.cpp
add fix mscg command, example, lib
2017-01-09 13:36:40 -07:00
reader_native.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
reader_xyz.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
reader_xyz.h
…
reader.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
reader.h
…
region_block.cpp
changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution
2017-03-21 08:56:37 -06:00
region_block.h
new fix wall/gran/region command, REBO bug fix, new example log files
2016-10-06 15:47:41 -06:00
region_cone.cpp
whitespace cleanup
2016-10-24 17:13:21 -04:00
region_cone.h
new fix wall/gran/region command, REBO bug fix, new example log files
2016-10-06 15:47:41 -06:00
region_cylinder.cpp
NULLed ptrs in files
2016-11-07 16:07:37 +01:00
region_cylinder.h
Spelling fixes in source files
2017-03-05 18:30:39 -05:00
region_intersect.cpp
NULLed ptrs in files
2016-11-07 16:07:37 +01:00
region_intersect.h
bug fix for fix GCMC w/ fix shake, enhance of fix wall/gran/region with restarting
2016-10-13 16:55:53 -06:00
region_plane.cpp
new fix wall/gran/region command, REBO bug fix, new example log files
2016-10-06 15:47:41 -06:00
region_plane.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
region_prism.cpp
new fix wall/gran/region command, REBO bug fix, new example log files
2016-10-06 15:47:41 -06:00
region_prism.h
new fix wall/gran/region command, REBO bug fix, new example log files
2016-10-06 15:47:41 -06:00
region_sphere.cpp
whitespace cleanup
2016-10-24 17:13:21 -04:00
region_sphere.h
Spelling fixes in source files
2017-03-05 18:30:39 -05:00
region_union.cpp
NULLed ptrs in files
2016-11-07 16:07:37 +01:00
region_union.h
bug fix for fix GCMC w/ fix shake, enhance of fix wall/gran/region with restarting
2016-10-13 16:55:53 -06:00
region.cpp
Fixing Kokkos execution space issue with regions
2017-07-25 13:37:01 -06:00
region.h
Fixing Kokkos execution space issue with regions
2017-07-25 13:37:01 -06:00
replicate.cpp
rename misleading "CPU time" into "Time spent"
2017-10-06 14:34:10 -04:00
replicate.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2014-10-21 17:09:24 +00:00
rerun.cpp
Fix more typos in src files
2017-03-07 00:55:01 -05:00
rerun.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13278 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-23 23:30:50 +00:00
respa.cpp
fix gcmc updates from Aidan, trimming of output for replica commands
2017-04-11 08:35:09 -06:00
respa.h
fix gcmc updates from Aidan, trimming of output for replica commands
2017-04-11 08:35:09 -06:00
run.cpp
pair TIP4P bug fix for cutoffs >> box size
2017-01-06 09:57:27 -07:00
run.h
Fix typos in src files
2017-03-05 21:03:40 -05:00
set.cpp
new USER-MESO package
2017-08-18 17:33:42 -06:00
set.h
new USER-MESO package
2017-08-18 17:33:42 -06:00
special.cpp
when recomputing special bonds, make certain we do not shrink atom->maxspecial and add force->special_extra only once
2017-08-10 06:47:26 -04:00
special.h
change ring communication API to no longer require a static variable pointing to 'this' of the caller
2017-06-14 17:01:06 -04:00
suffix.h
changes to imbalance weight factors
2016-10-05 10:33:39 -06:00
thermo.cpp
MAINT: DumpNetCDF and DumpNetCDFMPIIO need access to thermo output.
2017-06-08 23:18:54 +02:00
thermo.h
MAINT: DumpNetCDF and DumpNetCDFMPIIO need access to thermo output.
2017-06-08 23:18:54 +02:00
timer.cpp
reapply changes to the timer class that got lost somehow
2016-10-18 14:05:08 -04:00
timer.h
reapply changes to the timer class that got lost somehow
2016-10-18 14:05:08 -04:00
universe.cpp
initialize 'nper'
2016-11-11 07:47:42 -05:00
universe.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
update.cpp
use CHARMM energy conversion factor with new CHARMM pair styles
2017-06-22 09:15:15 -06:00
update.h
changes to imbalance weight factors
2016-10-05 10:33:39 -06:00
variable.cpp
fix bug in power operator in LAMMPS variable expressions
2017-07-27 15:51:45 -04:00
variable.h
Refactor PYTHON package and wrapper classes
2017-04-11 21:22:30 -04:00
velocity.cpp
apply test for overlap with rigid bodies to set and velocity command
2017-06-05 13:06:53 -04:00
velocity.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13278 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-03-23 23:30:50 +00:00
verlet.cpp
fix gcmc updates from Aidan, trimming of output for replica commands
2017-04-11 08:35:09 -06:00
verlet.h
fix gcmc updates from Aidan, trimming of output for replica commands
2017-04-11 08:35:09 -06:00
version.h
patch 22Sep17
2017-09-22 15:46:34 -06:00
write_coeff.cpp
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15387 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-28 13:51:40 +00:00
write_coeff.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14877 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-26 18:33:10 +00:00
write_data.cpp
Revert "added feature to write_data.cpp to support "extra bonds" (angles,dihedrals,impropers,special)."
2017-06-28 17:48:32 -07:00
write_data.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
write_dump.cpp
print write dump systen init warning only on MPI rank 0
2017-08-23 21:01:55 -04:00
write_dump.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13601 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-15 21:29:44 +00:00
write_restart.cpp
minor whitespace cleanup
2017-06-06 17:26:18 -04:00
write_restart.h
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14860 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-22 15:55:54 +00:00