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lammps/doc/src
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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
..
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
removed leftover tex files
2016-11-16 15:39:02 -05:00
Eqs
tweak an eq in USER-MESO, also allow neigh to be built w/out styles
2017-08-25 17:04:36 -06:00
JPG
Adding pair style dpd/intel and dihedral style fourier/intel
2017-10-02 04:53:17 -07:00
PDF
Update Colvars to version 2017-10-11
2017-10-13 13:45:10 -04:00
USER/atc
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
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
Minor adjustments to intel makefiles and documentation based on the reversed
2017-10-02 23:41:14 -07:00
accelerate_kokkos.txt
update docs for changes to makefiles
2017-09-06 14:20:24 -04:00
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
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
angle_coeff.txt
…
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
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
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
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
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_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
correct broken link in html bond doc overview
2017-04-21 14:02:17 -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
fully integrate temper/npt command into manual
2017-08-31 13:53:40 -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
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_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
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_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
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
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
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
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
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_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.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
SNAP changes by Aidan
2017-05-30 10:21:07 -06:00
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.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
make links unique, fix doc format warnings and add entries to administrative files
2017-08-23 00:39:52 -04:00
create_atoms.txt
change to RCB cuts in load-balancing commands, also a new option for fix halt
2017-03-10 15:55:07 -07:00
create_bonds.txt
spell-check new additions to create_bonds doc page
2017-06-30 14:59:08 -04:00
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
…
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_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
remove dependence of dump modify 'at' and 'append'
2017-10-06 09:44:29 -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
new Section package and start doc pages and build scripts
2017-05-04 11:22:20 -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
clean up doc src
2016-10-06 13:00:46 -06:00
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
correct cut-n-paste errors in the documentation of fix_modify virial
2017-09-15 01:20:56 -04:00
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
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_deform.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
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
mention restriction for use with fix shake or fix rigid in fix gcmc docs
2017-07-10 17:34:00 -04:00
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
Correct a typo in the fix_halt.txt documentation.
2017-03-10 21:30:03 -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
make links unique, fix doc format warnings and add entries to administrative files
2017-08-23 00:39:52 -04:00
fix_neb.txt
fix typo in formatting
2017-09-26 16:52:24 -04:00
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.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
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
fix_python.txt
fixup docs after last change
2017-05-12 00:34:47 -04:00
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_rigid.txt
correct cut-n-paste errors in the documentation of fix_modify virial
2017-09-15 01:20:56 -04:00
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
correct cut-n-paste errors in the documentation of fix_modify virial
2017-09-15 01:20:56 -04:00
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
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -05:00
fix_smd_integrate_ulsph.txt
correct broken link to USER-SMD docs PDF
2016-11-28 11:34:22 -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_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
update fix ti/spring docs to reflect it is part of USER-MISC
2017-06-21 09:36:30 -04:00
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
correct formatting and broken/colliding link issues with LATTE package related documentation
2017-09-26 16:52:10 -04:00
group2ndx.txt
clean up doc src
2016-10-06 13:00:46 -06:00
group.txt
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
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_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
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
include.txt
…
info.txt
improve memory usage reporting in info and output class
2017-03-16 18:35:04 -04:00
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.book
add missing entry for pdf version of manual
2017-09-26 16:53:36 -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
Added Gaussian bump. Updated e-mail address.
2017-06-06 16:03:09 -04:00
Manual.txt
patch 22Sep17
2017-09-22 15:46:34 -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
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
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.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 manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_brownian.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_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.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_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
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_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_kim.txt
correct a link and a name for OpenKIM
2017-08-04 11:19:09 -04:00
pair_kolmogorov_crespi_z.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -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
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
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
update documentation for USER-MEAMC package and pair style meam/c
2017-06-11 21:54:18 -04:00
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
clean up doc src
2016-10-06 13:00:46 -06:00
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
clean up doc src
2016-10-06 13:00:46 -06:00
pair_smd_ulsph.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -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
make links unique, fix doc format warnings and add entries to administrative files
2017-08-23 00:39:52 -04:00
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_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
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_zbl.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
pair_zero.txt
small documentation fixes to fix typos and formatting issues
2017-05-21 11:13:47 -04:00
pairs.txt
make links unique, fix doc format warnings and add entries to administrative files
2017-08-23 00:39:52 -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
clean up doc src
2016-10-06 13:00:46 -06:00
processors.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
python.txt
whitespace cleanup in docs
2017-06-21 09:38:10 -04:00
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
make links unique, fix doc format warnings and add entries to administrative files
2017-08-23 00:39:52 -04:00
read_dump.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
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
Second batch of spelling fixes in manual
2017-03-05 21:02:51 -05:00
rerun.txt
fix typo in rerun docs. closes #486
2017-05-16 04:27:15 -04:00
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
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
Section_commands.txt
remove dependence of dump modify 'at' and 'append'
2017-10-06 09:44:29 -06:00
Section_errors.txt
remove special_bonds extra keyword and refer to read_data and create_box instead
2017-08-10 15:12:56 -04:00
Section_example.txt
better Install.py script for KIM from Ryan Elliott
2017-07-14 16:25:16 -06:00
Section_history.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
Section_howto.txt
Mods for extra/special/per/atom and add toluene
2017-08-31 15:03:04 +02:00
Section_intro.txt
new Section package and start doc pages and build scripts
2017-05-04 11:22:20 -06:00
Section_modify.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
Section_packages.txt
avoid merge conflict
2017-10-06 14:41:38 -04:00
Section_perf.txt
Third batch of spelling fixes in manual
2017-03-07 00:51:31 -05:00
Section_python.txt
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
Section_start.txt
update docs for changes to makefiles
2017-09-06 14:20:24 -04:00
Section_tools.txt
refactor msi2lmp documentation to emphasize lack of active development
2017-04-17 17:40:21 -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
Add missing link flag
2017-07-31 15:52:44 -06:00
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
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
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
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
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