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0c005f5cb0d9aecae9c5af910bbcc218fc72f996
lammps/doc/src
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Giacomo Fiorin 0c005f5cb0 Small fixes to Colvars library 
Primarily a list of small fixes, combined with cosmetic changes and cleanups
in several files.

6d0c917 2018-04-29 Fix missing deallocation of output stream object (reported by HanatoK) [Giacomo Fiorin]
c92d369 2018-04-17 Do not test for atom group size [Jérôme Hénin]
431e52a 2018-04-06 Allow scripted/custom colvars to be periodic [Jérôme Hénin]
81d391f 2018-04-05 Split colvarcomp constructor into POD constructor + init() function [Giacomo Fiorin]
9b85d5f 2018-03-13 Fix issue with out-of-order atom selections; clarify format for ref positions [Giacomo Fiorin]
0e0ed37 2018-03-07 Support triclinic unit cells in VMD, clean up PBC functions [Giacomo Fiorin]
eed97c9 2018-02-24 Obtain integer version number from version string [Giacomo Fiorin]
c17f3cd 2018-02-23 Write trajectory labels only when needed [Giacomo Fiorin]
2018-05-02 15:03:56 -04:00
..
99
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
2001
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
Developer
remove trailing whitespace
2018-04-13 11:38:02 -04:00
Eqs
minor cleanup in docs and updated log files for kolmogorov/crespi/full
2018-03-23 06:42:04 -04:00
JPG
Merge branch 'master' into HEAD
2017-10-07 12:35:51 -06:00
PDF
Small fixes to Colvars library
2018-05-02 15:03:56 -04:00
USER/atc
different style of AtC page headers that works well with html and pdf
2018-02-13 16:40:50 +01:00
accelerate_gpu.txt
correctly use the term CUDA (instead of Cuda) when not referring to the KOKKOS device flag (which is Cuda)
2017-08-09 19:08:23 -04:00
accelerate_intel.txt
fix speelink in documentation files
2017-12-07 16:01:02 -05:00
accelerate_kokkos.txt
replace non-ASCII quotation marks with ASCII equivalent
2018-01-12 11:30:27 -05:00
accelerate_omp.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
accelerate_opt.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_charmm.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_class2.txt
correct incorrect reference
2018-02-01 18:40:28 +01:00
angle_coeff.txt
…
angle_cosine_buck6d.txt
Added MOF-FF src, doc and example files
2018-01-21 11:40:48 +01:00
angle_cosine_delta.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_cosine_periodic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_cosine_shift_exp.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_cosine_shift.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_cosine_squared.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_cosine.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_dipole.txt
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
angle_fourier_simple.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_fourier.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_harmonic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_hybrid.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
angle_none.txt
…
angle_quartic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_sdk.txt
rename references to USER-CG-CMM to USER-CGSDK
2017-04-26 19:27:13 -04:00
angle_style.txt
…
angle_table.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_zero.txt
…
angles.txt
include added docpages in toctrees for sphinx
2018-02-01 18:50:25 +01:00
atom_modify.txt
add atom_modify map yes, also timers to create_atoms and replicate
2017-10-05 16:44:24 -06:00
atom_style.txt
new USER-MESO package
2017-08-18 17:33:42 -06:00
balance.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
body.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
bond_class2.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
bond_coeff.txt
…
bond_fene_expand.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
bond_fene.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
bond_gromos.txt
add gromos bond style
2017-10-16 14:57:12 -04:00
bond_harmonic_shift_cut.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
bond_harmonic_shift.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
bond_harmonic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
bond_hybrid.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
bond_morse.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
bond_none.txt
…
bond_nonlinear.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
bond_oxdna.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
bond_quartic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
bond_style.txt
…
bond_table.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
bond_write.txt
…
bond_zero.txt
…
bonds.txt
add gromos bond style
2017-10-16 14:57:12 -04:00
boundary.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
box.txt
…
change_box.txt
change to RCB cuts in load-balancing commands, also a new option for fix halt
2017-03-10 15:55:07 -07:00
clear.txt
…
comm_modify.txt
collected documentation updates and corrections from LAMMPS-ICMS
2016-10-06 15:48:18 -04:00
comm_style.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
commands.txt
complete integration of reset_ids into the documentation build system
2018-03-30 10:49:38 -04:00
compute_ackland_atom.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_angle_local.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15352 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-22 22:46:14 +00:00
compute_angle.txt
…
compute_angmom_chunk.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_basal_atom.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_body_local.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_bond_local.txt
Fixed small typos in doc
2016-12-07 19:37:51 -08:00
compute_bond.txt
…
compute_centro_atom.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
compute_chunk_atom.txt
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
compute_cluster_atom.txt
fix speelink in documentation files
2017-12-07 16:01:02 -05:00
compute_cna_atom.txt
integrate compute cnp/atom contributed by Paulo Branicio (USC)
2017-05-31 00:38:44 -04:00
compute_cnp_atom.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
compute_com_chunk.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_com.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_contact_atom.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_coord_atom.txt
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
compute_damage_atom.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_dihedral_local.txt
added missing "dihedral" in compute dihedral/local docs
2017-11-02 15:04:04 -04:00
compute_dihedral.txt
…
compute_dilatation_atom.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_dipole_chunk.txt
clean up doc src
2016-10-06 13:00:46 -06:00
compute_displace_atom.txt
Merge branch 'master' into resetids
2018-03-30 09:15:24 -06:00
compute_dpd_atom.txt
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
compute_dpd.txt
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
compute_edpd_temp_atom.txt
make links unique, fix doc format warnings and add entries to administrative files
2017-08-23 00:39:52 -04:00
compute_erotate_asphere.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_erotate_rigid.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_erotate_sphere_atom.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_erotate_sphere.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_event_displace.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_fep.txt
doc page changes
2016-10-25 09:45:55 -06:00
compute_global_atom.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
compute_group_group.txt
patch 12Feb17 - change int to tagint for compute group/group
2017-02-13 08:40:54 -07:00
compute_gyration_chunk.txt
clean up doc src
2016-10-06 13:00:46 -06:00
compute_gyration.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_heat_flux.txt
add info to compute heat/flux doc page
2018-04-13 08:57:24 -06:00
compute_hexorder_atom.txt
clean up doc src
2016-10-06 13:00:46 -06:00
compute_improper_local.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15352 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-22 22:46:14 +00:00
compute_improper.txt
…
compute_inertia_chunk.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
compute_ke_atom_eff.txt
clean up doc src
2016-10-06 13:00:46 -06:00
compute_ke_atom.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_ke_eff.txt
clean up doc src
2016-10-06 13:00:46 -06:00
compute_ke_rigid.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_ke.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_meso_e_atom.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_meso_rho_atom.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_meso_t_atom.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_modify.txt
fix problems with references
2017-03-27 15:01:32 -04:00
compute_msd_chunk.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_msd_nongauss.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_msd.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_omega_chunk.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_orientorder_atom.txt
address some formatting/markup issues reported by Nandor Tamaskovics
2018-01-12 12:50:02 -05:00
compute_pair_local.txt
fix issue with rRESPA inner/middle neighbor lists
2017-06-21 15:12:51 -06:00
compute_pair.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_pe_atom.txt
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
compute_pe.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_plasticity_atom.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_pressure_uef.txt
fix speelink in documentation files
2017-12-07 16:01:02 -05:00
compute_pressure.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
compute_property_atom.txt
collected documentation updates and corrections from LAMMPS-ICMS
2016-10-06 15:48:18 -04:00
compute_property_chunk.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
compute_property_local.txt
fix issue with rRESPA inner/middle neighbor lists
2017-06-21 15:12:51 -06:00
compute_rdf.txt
add support for recomputing normalization factors and finite size correction during
2017-07-07 15:39:25 -04:00
compute_reduce.txt
collected documentation updates and corrections from LAMMPS-ICMS
2016-10-06 15:48:18 -04:00
compute_rigid_local.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
compute_saed.txt
small documentation fixes to fix typos and formatting issues
2017-05-21 11:13:47 -04:00
compute_slice.txt
…
compute_smd_contact_radius.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_damage.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_hourglass_error.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_internal_energy.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_plastic_strain_rate.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_plastic_strain.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_rho.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_tlsph_defgrad.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_tlsph_dt.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_tlsph_num_neighs.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_tlsph_shape.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_tlsph_strain_rate.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_tlsph_strain.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_tlsph_stress.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_triangle_mesh_vertices.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_ulsph_num_neighs.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
compute_smd_ulsph_strain_rate.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_ulsph_strain.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_ulsph_stress.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_smd_vol.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
compute_sna_atom.txt
address some formatting/markup issues reported by Nandor Tamaskovics
2018-01-12 12:50:02 -05:00
compute_stress_atom.txt
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
compute_tally.txt
clean up doc src
2016-10-06 13:00:46 -06:00
compute_tdpd_cc_atom.txt
make links unique, fix doc format warnings and add entries to administrative files
2017-08-23 00:39:52 -04:00
compute_temp_asphere.txt
First batch of spelling fixes in manual
2017-03-05 18:27:38 -05:00
compute_temp_body.txt
First batch of spelling fixes in manual
2017-03-05 18:27:38 -05:00
compute_temp_chunk.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_temp_com.txt
…
compute_temp_cs.txt
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
compute_temp_deform_eff.txt
GH changes to doc pages
2016-09-06 22:56:36 +00:00
compute_temp_deform.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15069 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-05-31 14:48:46 +00:00
compute_temp_drude.txt
clean up doc src
2016-10-06 13:00:46 -06:00
compute_temp_eff.txt
clean up doc src
2016-10-06 13:00:46 -06:00
compute_temp_partial.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
compute_temp_profile.txt
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
compute_temp_ramp.txt
…
compute_temp_region_eff.txt
…
compute_temp_region.txt
clean up doc src
2016-10-06 13:00:46 -06:00
compute_temp_rotate.txt
…
compute_temp_sphere.txt
collected documentation updates and corrections from LAMMPS-ICMS
2016-10-06 15:48:18 -04:00
compute_temp_uef.txt
doc revisions
2017-09-29 15:36:41 -04:00
compute_temp.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
compute_ti.txt
clean up doc src
2016-10-06 13:00:46 -06:00
compute_torque_chunk.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_vacf.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
compute_vcm_chunk.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
compute_voronoi_atom.txt
Fixed typo in "compute_voronoi_atom.txt"
2017-08-04 17:48:27 -04:00
compute_xrd.txt
clean up doc src
2016-10-06 13:00:46 -06:00
compute.txt
fix another couple of typos
2017-09-05 12:48:28 -04:00
computes.txt
doc edits i missed in earlier commit
2017-09-28 17:46:39 -04:00
create_atoms.txt
shift files into doc/src
2018-03-28 13:35:13 -06:00
create_bonds.txt
fix cut-n-paste error in create_bond docs
2017-11-13 17:59:16 -05:00
create_box.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
delete_atoms.txt
shift files into doc/src
2018-03-28 13:35:13 -06:00
delete_bonds.txt
clean up doc src
2016-10-06 13:00:46 -06:00
dielectric.txt
clean up doc src
2016-10-06 13:00:46 -06:00
dihedral_charmm.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
dihedral_class2.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
dihedral_coeff.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
dihedral_cosine_shift_exp.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
dihedral_fourier.txt
Adding pair style dpd/intel and dihedral style fourier/intel
2017-10-02 04:53:17 -07:00
dihedral_harmonic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
dihedral_helix.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
dihedral_hybrid.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
dihedral_multi_harmonic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
dihedral_nharmonic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
dihedral_none.txt
…
dihedral_opls.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
dihedral_quadratic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
dihedral_spherical.txt
small documentation fixes to fix typos and formatting issues
2017-05-21 11:13:47 -04:00
dihedral_style.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15317 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-15 22:33:52 +00:00
dihedral_table.txt
remove work repetitions for 'the'
2016-11-01 11:40:07 -04:00
dihedral_zero.txt
…
dihedrals.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
dimension.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-16 16:20:06 +00:00
displace_atoms.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15169 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-14 21:25:00 +00:00
dump_cfg_uef.txt
doc edits i missed in earlier commit
2017-09-28 17:46:39 -04:00
dump_h5md.txt
new Section package and start doc pages and build scripts
2017-05-04 11:22:20 -06:00
dump_image.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
dump_modify.txt
shift files into doc/src
2018-03-28 13:35:13 -06:00
dump_molfile.txt
Revert "remove reference to removed section on VMD scripts"
2017-03-22 15:12:43 -04:00
dump_netcdf.txt
DOC: Added multi file example.
2017-10-01 14:28:20 +02:00
dump_vtk.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
dump.txt
Merge branch 'master' into resetids
2018-03-30 09:15:24 -06:00
echo.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_adapt_fep.txt
sync with GH
2016-09-08 20:20:32 +00:00
fix_adapt.txt
Added missing :pre to doc/src/fix_adapt.txt
2017-05-30 16:08:32 -04:00
fix_addforce.txt
correct cut-n-paste errors in the documentation of fix_modify virial
2017-09-15 01:20:56 -04:00
fix_addtorque.txt
sync with GH
2016-09-08 20:20:32 +00:00
fix_append_atoms.txt
…
fix_atc.txt
correct formatting in fix atc docs
2018-02-13 11:44:07 +01:00
fix_atom_swap.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_ave_atom.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_ave_chunk.txt
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_long.txt
collected documentation updates and corrections from LAMMPS-ICMS
2016-10-06 15:48:18 -04:00
fix_ave_correlate.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_ave_histo.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_ave_time.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_aveforce.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_balance.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_bond_break.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_bond_create.txt
remove special_bonds extra keyword and refer to read_data and create_box instead
2017-08-10 15:12:56 -04:00
fix_bond_swap.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_box_relax.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
fix_cmap.txt
explain position of fix cmap command in input for data and restart files
2018-01-28 06:20:03 -05:00
fix_colvars.txt
Backport typo fixes that were not previously pushed to the Colvars repository
2017-03-10 09:24:46 -05:00
fix_controller.txt
address some formatting/markup issues reported by Nandor Tamaskovics
2018-01-12 12:50:02 -05:00
fix_deform.txt
update to doc pages for new coreshell pair styles
2017-10-21 15:50:27 -06:00
fix_deposit.txt
fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof
2017-03-23 15:31:27 -06:00
fix_dpd_energy.txt
Update docs for Kokkos version of USER-DPD package
2017-08-25 16:20:42 -06:00
fix_dpd_source.txt
make links unique, fix doc format warnings and add entries to administrative files
2017-08-23 00:39:52 -04:00
fix_drag.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_drude_transform.txt
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_drude.txt
…
fix_dt_reset.txt
…
fix_efield.txt
correct cut-n-paste errors in the documentation of fix_modify virial
2017-09-15 01:20:56 -04:00
fix_ehex.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_enforce2d.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_eos_cv.txt
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_eos_table_rx.txt
Update docs for Kokkos version of USER-DPD package
2017-08-25 16:20:42 -06:00
fix_eos_table.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
fix_evaporate.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_external.txt
correct cut-n-paste errors in the documentation of fix_modify virial
2017-09-15 01:20:56 -04:00
fix_filter_corotate.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
fix_flow_gauss.txt
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_freeze.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_gcmc.txt
Added warning to discourage use of group all and fixed some segfault cases
2018-02-05 13:29:14 -07:00
fix_gld.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_gle.txt
small documentation fixes to fix typos and formatting issues
2017-05-21 11:13:47 -04:00
fix_gravity.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_grem.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
fix_halt.txt
fix speelink in documentation files
2017-12-07 16:01:02 -05:00
fix_heat.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_imd.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_indent.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_ipi.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
fix_langevin_drude.txt
small documentation fixes to fix typos and formatting issues
2017-05-21 11:13:47 -04:00
fix_langevin_eff.txt
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_langevin.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_latte.txt
correct bogus links in LATTE docs
2017-09-26 18:25:37 -04:00
fix_lb_fluid.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_lb_momentum.txt
collected documentation updates and corrections from LAMMPS-ICMS
2016-10-06 15:48:18 -04:00
fix_lb_pc.txt
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_lb_rigid_pc_sphere.txt
collected documentation updates and corrections from LAMMPS-ICMS
2016-10-06 15:48:18 -04:00
fix_lb_viscous.txt
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_lineforce.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_manifoldforce.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14997 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-05-10 20:05:38 +00:00
fix_meso_stationary.txt
…
fix_meso.txt
…
fix_modify.txt
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
fix_momentum.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_move.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_mscg.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
fix_msst.txt
make overlapping links to references unique to avoid anchor label errors
2017-08-04 11:11:41 -04:00
fix_mvv_dpd.txt
fix speelink in documentation files
2017-12-07 16:01:02 -05:00
fix_neb.txt
Merge pull request #749 from akohlmey/collected-bugfixes-and-updates
2018-01-08 09:20:18 -07:00
fix_nh_eff.txt
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_uef.txt
cross ref fix deform and new fix nvt/uef
2017-10-18 15:26:15 -06:00
fix_nh.txt
add atom_modify map yes, also timers to create_atoms and replicate
2017-10-05 16:44:24 -06:00
fix_nph_asphere.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_nph_body.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_nph_sphere.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_nphug.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_npt_asphere.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_npt_body.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_npt_sphere.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_nve_asphere_noforce.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
fix_nve_asphere.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_nve_body.txt
First batch of spelling fixes in manual
2017-03-05 18:27:38 -05:00
fix_nve_dot.txt
Included hyperlink to package
2017-09-05 11:45:32 +01:00
fix_nve_dotc_langevin.txt
Included hyperlink to package
2017-09-05 11:45:32 +01:00
fix_nve_eff.txt
…
fix_nve_limit.txt
First batch of spelling fixes in manual
2017-03-05 18:27:38 -05:00
fix_nve_line.txt
collected documentation updates and corrections from LAMMPS-ICMS
2016-10-06 15:48:18 -04:00
fix_nve_manifold_rattle.txt
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_noforce.txt
…
fix_nve_sphere.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_nve_tri.txt
collected documentation updates and corrections from LAMMPS-ICMS
2016-10-06 15:48:18 -04:00
fix_nve.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_nvk.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
fix_nvt_asphere.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_nvt_body.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_nvt_manifold_rattle.txt
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_nvt_sllod_eff.txt
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_nvt_sllod.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_nvt_sphere.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_oneway.txt
…
fix_orient.txt
First batch of spelling fixes in manual
2017-03-05 18:27:38 -05:00
fix_phonon.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_pimd.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_planeforce.txt
…
fix_poems.txt
…
fix_pour.txt
fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof
2017-03-23 15:31:27 -06:00
fix_press_berendsen.txt
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_print.txt
…
fix_property_atom.txt
Use bold font instead of underscores for emphasis.
2017-12-25 13:27:14 +01:00
fix_python_invoke.txt
Rename fix python to fix python/invoke
2017-12-15 13:53:04 -05:00
fix_python_move.txt
Rename fix python to fix python/invoke
2017-12-15 13:53:04 -05:00
fix_qbmsst.txt
make overlapping links to references unique to avoid anchor label errors
2017-08-04 11:11:41 -04:00
fix_qeq_comb.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_qeq_reax.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_qeq.txt
update fix qeq docs for the new, more flexible parameter file format
2017-08-23 11:22:09 -04:00
fix_qmmm.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_qtb.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_reax_bonds.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_reaxc_species.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_recenter.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15164 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-14 14:16:24 +00:00
fix_restrain.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_rhok.txt
small updates to recently added docs and rename of an example dir
2017-10-18 14:56:47 -06:00
fix_rigid.txt
correct listing of USER-OMP variants of fix rigid styles
2017-11-06 13:29:59 -05:00
fix_rx.txt
Update docs for Kokkos version of USER-DPD package
2017-08-25 16:20:42 -06:00
fix_saed_vtk.txt
fix syntax error in fix saed/vtk docs example
2017-09-05 17:45:56 -04:00
fix_setforce.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_shake.txt
address some formatting/markup issues reported by Nandor Tamaskovics
2018-01-12 12:50:02 -05:00
fix_shardlow.txt
Update docs for Kokkos version of USER-DPD package
2017-08-25 16:20:42 -06:00
fix_smd_adjust_dt.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
fix_smd_integrate_tlsph.txt
address some formatting/markup issues reported by Nandor Tamaskovics
2018-01-12 12:50:02 -05:00
fix_smd_integrate_ulsph.txt
address some formatting/markup issues reported by Nandor Tamaskovics
2018-01-12 12:50:02 -05:00
fix_smd_move_triangulated_surface.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
fix_smd_setvel.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_smd_wall_surface.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_smd.txt
add support for fix_modify virial yes to fix smd
2017-09-15 01:21:16 -04:00
fix_spring_chunk.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_spring_rg.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15201 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 23:13:02 +00:00
fix_spring_self.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_spring.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
fix_srd.txt
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_store_force.txt
…
fix_store_state.txt
collected documentation updates and corrections from LAMMPS-ICMS
2016-10-06 15:48:18 -04:00
fix_surface_global.txt
add dummy doc files for not-yet-implemented features
2018-01-12 12:29:03 -05:00
fix_temp_berendsen.txt
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_temp_csvr.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_temp_rescale_eff.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
fix_temp_rescale.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_tfmc.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_thermal_conductivity.txt
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_ti_spring.txt
make links to papers unique across files
2018-02-02 10:10:27 +01:00
fix_tmd.txt
…
fix_ttm.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_tune_kspace.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_vector.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_viscosity.txt
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_viscous.txt
clean up doc src
2016-10-06 13:00:46 -06:00
fix_wall_ees.txt
remove non-portable non-ascii blanks from fix wall/ees docs
2017-08-20 10:09:21 -04:00
fix_wall_gran_region.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_wall_gran.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_wall_piston.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_wall_reflect.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
fix_wall_region.txt
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
fix_wall_srd.txt
…
fix_wall.txt
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
fix.txt
add fix latte command to doc pages
2017-09-19 16:55:08 -06:00
fixes.txt
add dummy doc files for not-yet-implemented features
2018-01-12 12:29:03 -05:00
group2ndx.txt
clean up doc src
2016-10-06 13:00:46 -06:00
group.txt
Merge pull request #786 from jrgissing/per_atom_prop_group
2018-02-21 09:48:49 -07:00
if.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
improper_class2.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
improper_coeff.txt
…
improper_cossq.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
improper_cvff.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
improper_distance.txt
…
improper_fourier.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
improper_harmonic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
improper_hybrid.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
improper_inversion_harmonic.txt
Added MOF-FF src, doc and example files
2018-01-21 11:40:48 +01:00
improper_none.txt
…
improper_ring.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
improper_style.txt
remove work repetitions for 'the'
2016-11-01 11:40:07 -04:00
improper_umbrella.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
improper_zero.txt
…
impropers.txt
include added docpages in toctrees for sphinx
2018-02-01 18:50:25 +01:00
include.txt
…
info.txt
add a "coeffs" keyword to the info command for debugging "All XXX coeffs are not set" errors.
2018-01-09 12:47:33 -05:00
jump.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
kspace_modify.txt
reword the kspace_modify fftbench keyword docs to reflect the current state (i.e. off by default) of code
2017-06-22 19:17:41 -04:00
kspace_style.txt
USER-INTEL upgrade from M Brown
2017-06-16 16:56:28 -06:00
label.txt
…
lammps_commands_angle.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
lammps_commands_atc.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
lammps_commands_bond.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
lammps_commands_compute.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
lammps_commands_dihedral.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
lammps_commands_fix.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
lammps_commands_improper.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
lammps_commands_kspace.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
lammps_commands_pair.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
lammps_commands.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
lammps_support.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
lammps_tutorials.txt
fix up formatting of tutorials for PDF manual
2018-02-13 16:41:23 +01:00
lammps.book
complete integration of reset_ids into the documentation build system
2018-03-30 10:49:38 -04:00
lattice.txt
clean up doc src
2016-10-06 13:00:46 -06:00
log.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
manifolds.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
Manual.txt
patch 20Apr18
2018-04-20 17:22:38 -06:00
mass.txt
…
min_modify.txt
clean up doc src
2016-10-06 13:00:46 -06:00
min_style.txt
collected documentation updates and corrections from LAMMPS-ICMS
2016-10-06 15:48:18 -04:00
minimize.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
molecule.txt
First batch of spelling fixes in manual
2017-03-05 18:27:38 -05:00
neb.txt
fix speelink in documentation files
2017-12-07 16:01:02 -05:00
neigh_modify.txt
better Install.py script for KIM from Ryan Elliott
2017-07-14 16:25:16 -06:00
neighbor.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
newton.txt
…
next.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
package.txt
Add Kokkos threaded reverse comm option
2017-10-03 10:14:24 -06:00
pair_adp.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_agni.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_airebo.txt
USER-INTEL add-ons from Mike
2017-08-15 17:12:07 -06:00
pair_awpmd.txt
…
pair_beck.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_body_rounded_polygon.txt
add dummy doc files for not-yet-implemented features
2018-01-12 12:29:03 -05:00
pair_body.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
pair_bop.txt
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
pair_born.txt
update to doc pages for new coreshell pair styles
2017-10-21 15:50:27 -06:00
pair_brownian.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_buck6d_coul_gauss.txt
Added MOF-FF src, doc and example files
2018-01-21 11:40:48 +01:00
pair_buck_long.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_buck.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_charmm.txt
USER-INTEL add-ons from Mike
2017-08-15 17:12:07 -06:00
pair_class2.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_coeff.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15097 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-02 14:05:40 +00:00
pair_colloid.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_comb.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_coul_diel.txt
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
pair_coul_shield.txt
fix up and integrate documentation for contributed pair styles
2018-03-22 18:20:19 -04:00
pair_coul.txt
update to doc pages for new coreshell pair styles
2017-10-21 15:50:27 -06:00
pair_cs.txt
added some documentation and reference example
2017-10-20 12:03:22 +02:00
pair_dipole.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_dpd_fdt.txt
Update docs for Kokkos version of USER-DPD package
2017-08-25 16:20:42 -06:00
pair_dpd.txt
Adding pair style dpd/intel and dihedral style fourier/intel
2017-10-02 04:53:17 -07:00
pair_dsmc.txt
clean up doc src
2016-10-06 13:00:46 -06:00
pair_eam.txt
correct formatting and broken/colliding link issues with LATTE package related documentation
2017-09-26 16:52:10 -04:00
pair_edip.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_eff.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
pair_eim.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_exp6_rx.txt
Update docs for Kokkos version of USER-DPD package
2017-08-25 16:20:42 -06:00
pair_extep.txt
added ExTeP to USER-MISC
2017-11-27 21:16:51 +01:00
pair_gauss.txt
two small doc corrections from Andrew Jewett for pair style gauss and dihedral style spherical
2017-05-12 23:27:58 -04:00
pair_gayberne.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_gran.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_gromacs.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_gw.txt
update docs before patch release
2017-05-18 13:14:47 -06:00
pair_hbond_dreiding.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_hybrid.txt
Update docs for Kokkos version of USER-DPD package
2017-08-25 16:20:42 -06:00
pair_ilp_graphene_hbn.txt
refine the code and documentation
2018-03-23 13:26:40 +03:00
pair_kim.txt
correct a link and a name for OpenKIM
2017-08-04 11:19:09 -04:00
pair_kolmogorov_crespi_full.txt
fix up and integrate documentation for contributed pair styles
2018-03-22 18:20:19 -04:00
pair_kolmogorov_crespi_z.txt
fix up and integrate documentation for contributed pair styles
2018-03-22 18:20:19 -04:00
pair_lcbop.txt
remove the misleading "(which it is by default)" from several doc files
2016-11-04 12:20:17 -04:00
pair_line_lj.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
pair_list.txt
clean up doc src
2016-10-06 13:00:46 -06:00
pair_lj96.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_lj_cubic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_lj_expand.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_lj_long.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_lj_smooth_linear.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_lj_smooth.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_lj_soft.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_lj.txt
add USER-OMP versions of lj/cut/coul/wolf
2018-02-18 16:38:50 +01:00
pair_lubricate.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_lubricateU.txt
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
pair_mdf.txt
…
pair_meam_spline.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_meam_sw_spline.txt
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
pair_meam.txt
add restartinfo=0 to manbody file it was missing from
2018-03-06 12:45:40 -07:00
pair_meso.txt
new USER-MESO package
2017-08-18 17:33:42 -06:00
pair_mgpt.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
pair_mie.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
pair_modify.txt
add support to pair_modify to selectively disable compute/tally callbacks in sub-styles for pair hybrid and hybrid/overlay
2017-04-21 14:01:38 -04:00
pair_momb.txt
new CHARMM pair styles with force swithing/shifting
2017-03-24 13:53:07 -06:00
pair_morse.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_multi_lucy_rx.txt
Update docs for Kokkos version of USER-DPD package
2017-08-25 16:20:42 -06:00
pair_multi_lucy.txt
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
pair_nb3b_harmonic.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_nm.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_none.txt
…
pair_oxdna2.txt
Added sequence-dependent stacking and base-pairing strength
2017-09-05 10:48:38 +01:00
pair_oxdna.txt
Added sequence-dependent stacking and base-pairing strength
2017-09-05 10:48:38 +01:00
pair_peri.txt
Merge pull request #585 from akohlmey/make-py-manual-cleanup
2017-07-20 12:05:04 -06:00
pair_polymorphic.txt
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
pair_python.txt
small documentation fixes to fix typos and formatting issues
2017-05-21 11:13:47 -04:00
pair_quip.txt
support QUIP wrapper API version query, relax hybrid restriction to allow hybrid/overlay, update docs
2017-07-19 13:17:35 -04:00
pair_reax.txt
new Section package and start doc pages and build scripts
2017-05-04 11:22:20 -06:00
pair_reaxc.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_resquared.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_sdk.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_smd_hertz.txt
address some formatting/markup issues reported by Nandor Tamaskovics
2018-01-12 12:50:02 -05:00
pair_smd_tlsph.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
pair_smd_triangulated_surface.txt
address some formatting/markup issues reported by Nandor Tamaskovics
2018-01-12 12:50:02 -05:00
pair_smd_ulsph.txt
address some formatting/markup issues reported by Nandor Tamaskovics
2018-01-12 12:50:02 -05:00
pair_smtbq.txt
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
pair_snap.txt
Add Kokkos versions of pair_style snap and zbl
2018-01-09 17:03:49 -07:00
pair_soft.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_sph_heatconduction.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
pair_sph_idealgas.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
pair_sph_lj.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
pair_sph_rhosum.txt
…
pair_sph_taitwater_morris.txt
…
pair_sph_taitwater.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
pair_srp.txt
detect and refuse to run pair style srp together with fix rigid
2017-04-25 13:27:20 -04:00
pair_style.txt
clean up doc src
2016-10-06 13:00:46 -06:00
pair_sw.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_table_rx.txt
Update docs for Kokkos version of USER-DPD package
2017-08-25 16:20:42 -06:00
pair_table.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_tersoff_mod.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_tersoff_zbl.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_tersoff.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_thole.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_tri_lj.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
pair_ufm.txt
make links to papers unique across files
2018-02-02 10:10:27 +01:00
pair_vashishta.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_write.txt
…
pair_yukawa_colloid.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_yukawa.txt
Updated docs for pair_yukawa
2017-11-17 14:21:54 -05:00
pair_zbl.txt
Add Kokkos versions of pair_style snap and zbl
2018-01-09 17:03:49 -07:00
pair_zero.txt
small documentation fixes to fix typos and formatting issues
2017-05-21 11:13:47 -04:00
pairs.txt
fix up and integrate documentation for contributed pair styles
2018-03-22 18:20:19 -04:00
partition.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
prd.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
print.txt
add option to the print command to also print to the global universe screen and logfile
2017-11-07 10:00:57 -05:00
processors.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
python.txt
Rename fix python to fix python/invoke
2017-12-15 13:53:04 -05:00
quit.txt
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.txt
support offsets for molecule IDs (if available) in read_data similar to atomIDs
2018-02-23 18:02:05 -05:00
read_dump.txt
new option *add keep* added to read_dump
2018-03-27 10:08:58 -06:00
read_restart.txt
new SNAP potentials and examples
2017-09-20 08:54:30 -06:00
region.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
replicate.txt
Replicate bbox from Chris Knight
2017-11-06 11:31:43 -07:00
rerun.txt
fix typo in rerun docs. closes #486
2017-05-16 04:27:15 -04:00
reset_ids.txt
shift files into doc/src
2018-03-28 13:35:13 -06:00
reset_timestep.txt
…
restart.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
run_style.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
run.txt
new fix halt command, other sundry small bug fixes
2016-10-18 13:11:40 -06:00
Section_accelerate.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
Section_commands.txt
patch 30Mar18
2018-03-30 15:21:55 -06:00
Section_errors.txt
remove or reformulate references to USER-CUDA package, which no longer exists
2018-04-04 11:06:20 -04:00
Section_example.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
Section_history.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
Section_howto.txt
Merge pull request #850 from lammps/addlib
2018-03-27 14:39:16 -06:00
Section_intro.txt
remove or reformulate references to USER-CUDA package, which no longer exists
2018-04-04 11:06:20 -04:00
Section_modify.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
Section_packages.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
Section_perf.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
Section_python.txt
Merge pull request #850 from lammps/addlib
2018-03-27 14:39:16 -06:00
Section_start.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
Section_tools.txt
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
set.txt
new USER-MESO package
2017-08-18 17:33:42 -06:00
shell.txt
…
special_bonds.txt
remove special_bonds extra keyword and refer to read_data and create_box instead
2017-08-10 15:12:56 -04:00
suffix.txt
correctly use the term CUDA (instead of Cuda) when not referring to the KOKKOS device flag (which is Cuda)
2017-08-09 19:08:23 -04:00
tad.txt
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
temper_grem.txt
another workaround for duplicate labels (which sphinx does not like)
2017-01-09 17:51:19 -05:00
temper_npt.txt
fully integrate temper/npt command into manual
2017-08-31 13:53:40 -04:00
temper.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
thermo_modify.txt
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15439 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-05 15:14:30 +00:00
thermo_style.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
thermo.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
timer.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
timestep.txt
clean up doc src
2016-10-06 13:00:46 -06:00
tutorial_bash_on_windows.txt
update manual to point to packages.lammps.org instead of rpm.lammps.org
2017-08-15 16:19:09 -04:00
tutorial_drude.txt
remove special_bonds extra keyword and refer to read_data and create_box instead
2017-08-10 15:12:56 -04:00
tutorial_github.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
tutorial_pylammps.txt
fix up formatting of tutorials for PDF manual
2018-02-13 16:41:23 +01:00
tutorials.txt
update manual to point to packages.lammps.org instead of rpm.lammps.org
2017-08-15 16:19:09 -04:00
uncompute.txt
…
undump.txt
…
unfix.txt
…
units.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
variable.txt
fix typo in stride2() description in variable command docs reported by Jerome Guterl
2018-02-18 15:37:35 +01:00
velocity.txt
fix typo in docs
2017-05-17 09:59:30 -04:00
write_coeff.txt
clean up doc src
2016-10-06 13:00:46 -06:00
write_data.txt
rename noextra option to nofix
2018-03-04 09:49:50 -05:00
write_dump.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
write_restart.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00