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04248c2ccdf41f8e2977e72ce99f1a45715e3463
lammps/doc/src
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Axel Kohlmeyer 04248c2ccd finalize CMake build docs
2021-04-12 14:52:35 -04:00
..
_ext
make more compact
2020-09-06 06:10:39 -04:00
99
one more permission fix
2020-06-10 13:48:25 -04:00
2001
Fix typo
2020-03-14 13:57:48 +09:00
img
big update
2020-08-24 16:54:16 +02:00
JPG
Added the potential comparison with LJ
2021-01-27 21:39:52 -05:00
PDF
Fix some broken internal hyperlinks in Colvars PDF
2020-09-18 17:24:12 -04:00
.gitignore
start more detailed CMake howto document
2020-04-11 11:55:13 -04:00
accel_styles.rst
big update
2020-08-24 16:54:16 +02:00
angle_charmm.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_class2.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_coeff.rst
Undo lost headers
2020-09-02 12:54:08 -04:00
angle_cosine_buck6d.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
angle_cosine_delta.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_cosine_periodic.rst
fix a few minor issues with the docs
2021-03-30 11:45:47 -04:00
angle_cosine_shift_exp.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_cosine_shift.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_cosine_squared.rst
correct attribution of angle style cosine/squared with DREIDING
2021-03-22 11:28:22 -04:00
angle_cosine.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_cross.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_dipole.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_fourier_simple.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_fourier.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_gaussian.rst
address documentation link, spelling, and characterset issues
2020-11-25 15:57:18 -05:00
angle_harmonic.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_hybrid.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
angle_mm3.rst
big update
2020-08-24 16:54:16 +02:00
angle_none.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
angle_quartic.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_sdk.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_style.rst
Update angle_style.rst
2020-11-02 15:00:45 +01:00
angle_table.rst
Update headers in angle_*.rst files
2020-09-02 12:43:48 -04:00
angle_zero.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
angles.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
atc_add_molecule.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_add_species.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_atom_element_map.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_atom_weight.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_atomic_charge.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_boundary_dynamics.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_boundary_faceset.rst
fix rst formatting issues
2020-03-19 15:48:46 -04:00
atc_boundary_type.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_consistent_fe_initialization.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_control_localized_lambda.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_control_momentum.rst
big update
2020-08-24 16:54:16 +02:00
atc_control_thermal.rst
big update
2020-08-24 16:54:16 +02:00
atc_decomposition.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_electron_integration.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_equilibrium_start.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_extrinsic_exchange.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_fe_md_boundary.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_filter_scale.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_filter_type.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_fix_flux.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_fix.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_hardy_computes.rst
next chunk of converted atc doc files
2020-03-18 11:39:53 -04:00
atc_hardy_fields.rst
big update
2020-08-24 16:54:16 +02:00
atc_hardy_gradients.rst
big update
2020-08-24 16:54:16 +02:00
atc_hardy_kernel.rst
big update
2020-08-24 16:54:16 +02:00
atc_hardy_on_the_fly.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_hardy_rates.rst
big update
2020-08-24 16:54:16 +02:00
atc_initial.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_internal_element_set.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_internal_quadrature.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_kernel_bandwidth.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_lumped_lambda_solve.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_mask_direction.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_mass_matrix.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_material.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_mesh_add_to_nodeset.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_create_elementset.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_create_faceset_box.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_create_faceset_plane.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_create_nodeset.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_create.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_delete_elements.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_nodeset_to_elementset.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_output.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_mesh_quadrature.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_read.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_write.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_output_boundary_integral.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_output_contour_integral.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_output_nodeset.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_output_volume_integral.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_output.rst
Consistently use instead of
2020-11-10 14:04:49 +01:00
atc_pair_interactions.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_poisson_solver.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_read_restart.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_remove_molecule.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_remove_source.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_remove_species.rst
big update
2020-08-24 16:54:16 +02:00
atc_reset_atomic_reference.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_reset_time.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_sample_frequency.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_set_reference_pe.rst
big update
2020-08-24 16:54:16 +02:00
atc_source_integration.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_source.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_temperature_definition.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_time_filter.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_time_integration.rst
big update
2020-08-24 16:54:16 +02:00
atc_track_displacement.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_unfix_flux.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_unfix.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_write_atom_weights.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_write_restart.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atom_modify.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
atom_style.rst
small documentation update
2020-10-26 23:15:43 -04:00
balance.rst
fix spelling
2020-12-01 19:06:09 -05:00
Bibliography.rst
remove trailing whitespace
2020-09-25 16:32:54 -04:00
bond_class2.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_coeff.rst
big update
2020-08-24 16:54:16 +02:00
bond_fene_expand.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_fene.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_gaussian.rst
address documentation link, spelling, and characterset issues
2020-11-25 15:57:18 -05:00
bond_gromos.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_harmonic_shift_cut.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_harmonic_shift.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_harmonic.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_hybrid.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
bond_mm3.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
bond_morse.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_none.rst
big update
2020-08-24 16:54:16 +02:00
bond_nonlinear.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_oxdna.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_quartic.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_special.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_style.rst
Update bond_style.rst
2020-10-22 10:57:12 +02:00
bond_table.rst
Update headers in bond_*.rst files
2020-09-02 12:55:18 -04:00
bond_write.rst
big update
2020-08-24 16:54:16 +02:00
bond_zero.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
bonds.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
boundary.rst
big update
2020-08-24 16:54:16 +02:00
box.rst
big update
2020-08-24 16:54:16 +02:00
Build_basics.rst
fix a few minor issues with the docs
2021-03-30 11:45:47 -04:00
Build_cmake.rst
small tweaks
2020-10-12 23:51:00 -04:00
Build_development.rst
small updates.
2020-11-25 16:51:41 -05:00
Build_extras.rst
finalize CMake build docs
2021-04-12 14:52:35 -04:00
Build_link.rst
update/correct documentation for changes to the STUBS library and its implications
2021-02-17 15:19:24 -05:00
Build_make.rst
more 'doc page' to 'page' changes
2020-10-08 08:32:15 -04:00
Build_manual.rst
update documentation for building the manual with PIP_OPTIONS settings
2021-02-16 12:32:37 -05:00
Build_package.rst
Eliminated doc build warnings
2021-04-08 14:09:19 -06:00
Build_settings.rst
more 'doc page' to 'page' changes
2020-10-08 08:32:15 -04:00
Build_windows.rst
tweak
2020-10-14 23:59:06 -04:00
Build.rst
small tweaks
2020-10-12 23:51:00 -04:00
change_box.rst
reformulate section about resetting image flags and add reference to change_box command
2020-11-11 17:01:56 -05:00
Classes_atom.rst
mass renaming of programmer guide files
2020-09-25 13:59:29 -04:00
Classes_input.rst
mass renaming of programmer guide files
2020-09-25 13:59:29 -04:00
Classes_lammps.rst
mass renaming of programmer guide files
2020-09-25 13:59:29 -04:00
Classes.rst
update header texts
2020-10-14 23:28:28 -04:00
clear.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
comm_modify.rst
spelling
2020-12-18 23:02:28 -05:00
comm_style.rst
big update
2020-08-24 16:54:16 +02:00
Commands_all.rst
add preliminary documentation for plugin command and about how to write plugins
2021-03-11 19:33:07 -05:00
Commands_bond.rst
consolidate documentation for dihedral styles table and table/cut into one file
2021-03-23 13:49:37 -04:00
Commands_category.rst
convert lists to tables for more compact presentation
2020-02-28 18:52:13 +01:00
Commands_compute.rst
big update
2020-08-24 16:54:16 +02:00
Commands_fix.rst
Feb2021 GPU Package Update - Documentation Files
2021-02-15 11:07:43 -08:00
Commands_input.rst
big update
2020-08-24 16:54:16 +02:00
Commands_kspace.rst
remove backslash escapes for underscore in doc references
2020-01-23 16:52:38 -05:00
commands_list.rst
add preliminary documentation for plugin command and about how to write plugins
2021-03-11 19:33:07 -05:00
Commands_pair.rst
Move A.Thomson's modifications on doc and examples in:
2021-04-07 12:43:28 +02:00
Commands_parse.rst
add not input parsing section about handling of UFT-8 characters
2021-01-25 21:44:02 -05:00
Commands_removed.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Commands_structure.rst
remove trailing whitespace from documentation sources
2020-03-10 15:51:06 -04:00
Commands.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
compute_ackland_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_adf.rst
big update
2020-08-24 16:54:16 +02:00
compute_angle_local.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_angle.rst
fix broken internal links in the manual
2020-10-21 10:56:52 -04:00
compute_angmom_chunk.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_basal_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_body_local.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_bond_local.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_bond.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_centro_atom.rst
small format tweak
2020-09-28 14:09:03 -04:00
compute_chunk_atom.rst
big update
2020-08-24 16:54:16 +02:00
compute_chunk_spread_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_cluster_atom.rst
Update headers in compute_*.rst files
2020-09-02 12:56:24 -04:00
compute_cna_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_cnp_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_com_chunk.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_com.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_contact_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_coord_atom.rst
Update headers in compute_*.rst files
2020-09-02 12:56:24 -04:00
compute_damage_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_dihedral_local.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_dihedral.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_dilatation_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_dipole_chunk.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_displace_atom.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
compute_dpd_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_dpd.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_edpd_temp_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_entropy_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_erotate_asphere.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_erotate_rigid.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_erotate_sphere_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_erotate_sphere.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_event_displace.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_fep.rst
Update compute_fep.rst
2021-02-28 11:39:02 +01:00
compute_global_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_group_group.rst
big update
2020-08-24 16:54:16 +02:00
compute_gyration_chunk.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_gyration_shape_chunk.rst
big update
2020-08-24 16:54:16 +02:00
compute_gyration_shape.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_gyration.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_heat_flux.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_hexorder_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_hma.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_improper_local.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_improper.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_inertia_chunk.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_ke_atom_eff.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_ke_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_ke_eff.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_ke_rigid.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_ke.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_mesont.rst
Update headers in compute_*.rst files
2020-09-02 12:56:24 -04:00
compute_mliap.rst
doc updates
2020-12-07 18:08:13 -05:00
compute_modify.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
compute_momentum.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_msd_chunk.rst
big update
2020-08-24 16:54:16 +02:00
compute_msd_nongauss.rst
big update
2020-08-24 16:54:16 +02:00
compute_msd.rst
big update
2020-08-24 16:54:16 +02:00
compute_omega_chunk.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_orientorder_atom.rst
Update chunksize
2021-01-05 08:29:47 -07:00
compute_pair_local.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_pair.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_pe_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_pe.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_plasticity_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_pressure_cylinder.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_pressure_uef.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_pressure.rst
clarified Voigt ordering and non-Voigt ordering for virial[6]
2021-02-10 09:55:28 -07:00
compute_property_atom.rst
final steps
2020-08-24 17:04:35 +02:00
compute_property_chunk.rst
big update
2020-08-24 16:54:16 +02:00
compute_property_local.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_ptm_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_rdf.rst
big update
2020-08-24 16:54:16 +02:00
compute_reduce_chunk.rst
fix typo
2021-02-07 09:39:07 -05:00
compute_reduce.rst
correct formatting of examples
2020-09-14 17:15:53 -04:00
compute_rigid_local.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_saed.rst
big update
2020-08-24 16:54:16 +02:00
compute_slice.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_contact_radius.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_damage.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_hourglass_error.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_internal_energy.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_plastic_strain_rate.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_plastic_strain.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_rho.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_tlsph_defgrad.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_tlsph_dt.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_tlsph_num_neighs.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_tlsph_shape.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_tlsph_strain_rate.rst
convert remaining style doc sections to be a logical header
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compute_smd_tlsph_strain.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_tlsph_stress.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_triangle_vertices.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_ulsph_effm.rst
Update headers in compute_*.rst files
2020-09-02 12:56:24 -04:00
compute_smd_ulsph_num_neighs.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_ulsph_strain_rate.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_ulsph_strain.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_ulsph_stress.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_smd_vol.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_sna_atom.rst
Update headers in compute_*.rst files
2020-09-02 12:56:24 -04:00
compute_sph_e_atom.rst
Update headers in compute_*.rst files
2020-09-02 12:56:24 -04:00
compute_sph_rho_atom.rst
Update headers in compute_*.rst files
2020-09-02 12:56:24 -04:00
compute_sph_t_atom.rst
Update headers in compute_*.rst files
2020-09-02 12:56:24 -04:00
compute_spin.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_stress_atom.rst
clarified Voigt ordering and non-Voigt ordering for virial[6]
2021-02-10 09:55:28 -07:00
compute_stress_mop.rst
correct formatting of examples
2020-09-14 17:15:53 -04:00
compute_tally.rst
Fix broken page
2020-10-05 18:04:30 -04:00
compute_tdpd_cc_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_asphere.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_body.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_chunk.rst
need to use column 1 in fix ave/time example
2021-02-22 07:10:35 -05:00
compute_temp_com.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_cs.rst
big update
2020-08-24 16:54:16 +02:00
compute_temp_deform_eff.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_deform.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_drude.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_eff.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_partial.rst
big update
2020-08-24 16:54:16 +02:00
compute_temp_profile.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_ramp.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_region_eff.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_region.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_rotate.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_sphere.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp_uef.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_temp.rst
Update headers in compute_*.rst files
2020-09-02 12:56:24 -04:00
compute_ti.rst
big update
2020-08-24 16:54:16 +02:00
compute_torque_chunk.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_vacf.rst
big update
2020-08-24 16:54:16 +02:00
compute_vcm_chunk.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_viscosity_cos.rst
big update
2020-08-24 16:54:16 +02:00
compute_voronoi_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
compute_xrd.rst
big update
2020-08-24 16:54:16 +02:00
compute.rst
big update
2020-08-24 16:54:16 +02:00
computes.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
Cplusplus.rst
mass renaming of programmer guide files
2020-09-25 13:59:29 -04:00
create_atoms.rst
Revert "support choosing the molecule index from the set of molecules in a template"
2020-10-26 15:46:58 -04:00
create_bonds.rst
fix issues with multiple uses of create_bonds command
2021-02-12 06:15:05 -06:00
create_box.rst
add missing keyword to list
2021-03-03 05:37:41 -05:00
delete_atoms.rst
big update
2020-08-24 16:54:16 +02:00
delete_bonds.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
Developer_flow.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Developer_notes.rst
address a whole bunch of spelling issues that suddenly popped up.
2021-02-09 12:38:46 -05:00
Developer_org.rst
update docs about the organization of sources and relation between classes
2021-01-31 21:06:35 -05:00
Developer_plugins.rst
update docs
2021-03-18 18:20:32 -04:00
Developer_unittest.rst
update information about adding unit tests to reflect recent changes
2021-04-04 20:51:58 -04:00
Developer_utils.rst
include new split_lines() function in Developer docs
2021-04-01 09:35:52 -04:00
Developer_write.rst
update header texts
2020-10-14 23:28:28 -04:00
Developer.rst
add preliminary documentation for plugin command and about how to write plugins
2021-03-11 19:33:07 -05:00
dielectric.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
dihedral_charmm.rst
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
dihedral_class2.rst
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
dihedral_coeff.rst
big update
2020-08-24 16:54:16 +02:00
dihedral_cosine_shift_exp.rst
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
dihedral_fourier.rst
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
dihedral_harmonic.rst
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
dihedral_helix.rst
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
dihedral_hybrid.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
dihedral_multi_harmonic.rst
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
dihedral_nharmonic.rst
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
dihedral_none.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
dihedral_opls.rst
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
dihedral_quadratic.rst
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
dihedral_spherical.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
dihedral_style.rst
consolidate documentation for dihedral styles table and table/cut into one file
2021-03-23 13:49:37 -04:00
dihedral_table.rst
fix a few minor issues with the docs
2021-03-30 11:45:47 -04:00
dihedral_zero.rst
Update headers in dihedral_*.rst files
2020-09-02 12:57:44 -04:00
dihedrals.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
dimension.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
displace_atoms.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dump_adios.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dump_cfg_uef.rst
remove unneeded escapes from input examples
2020-09-28 07:52:38 -04:00
dump_h5md.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dump_image.rst
remove inactive code and documentation for dump image persp option
2020-09-28 08:19:26 -04:00
dump_modify.rst
Update docs for COMPRESS styles
2020-09-01 12:17:08 -04:00
dump_molfile.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
dump_netcdf.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
dump_vtk.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dump.rst
correct URL to XTC file format docs on the gromacs homepage
2021-04-02 16:48:13 -04:00
dynamical_matrix.rst
big update
2020-08-24 16:54:16 +02:00
echo.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
Errors_bugs.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Errors_common.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Errors_debug.rst
big update
2020-08-24 16:54:16 +02:00
Errors_messages.rst
remove inactive code and documentation for dump image persp option
2020-09-28 08:19:26 -04:00
Errors_warnings.rst
Fix inconsistent formatting in Error & Warning doc
2020-11-12 13:35:04 +01:00
Errors.rst
provide info about including debug support in executable and a stack trace debug tutorial
2020-04-12 15:34:00 -04:00
Examples.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
fix_accelerate_cos.rst
big update
2020-08-24 16:54:16 +02:00
fix_adapt_fep.rst
Update fix_adapt_fep.rst
2021-02-28 11:41:28 +01:00
fix_adapt.rst
Update fix_adapt.rst
2021-02-28 11:40:43 +01:00
fix_addforce.rst
doc pages for virial contributions of fixes
2021-01-26 09:26:31 -07:00
fix_addtorque.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_append_atoms.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_atc.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_atom_swap.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_ave_atom.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_ave_chunk.rst
Updated documentation to clarify the treatment of temperature using norm all
2021-03-17 09:01:35 +10:00
fix_ave_correlate_long.rst
big update
2020-08-24 16:54:16 +02:00
fix_ave_correlate.rst
remove extra word
2020-12-30 08:55:32 -05:00
fix_ave_histo.rst
fix errors/typos in manual
2021-04-02 21:00:42 -04:00
fix_ave_time.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_aveforce.rst
big update
2020-08-24 16:54:16 +02:00
fix_balance.rst
big update
2020-08-24 16:54:16 +02:00
fix_bocs.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_bond_break.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_bond_create.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_bond_react.rst
Merge pull request #2545 from akohlmey/citation-refactor
2021-02-10 18:19:21 -05:00
fix_bond_swap.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_box_relax.rst
big update
2020-08-24 16:54:16 +02:00
fix_client_md.rst
doc pages for virial contributions of fixes
2021-01-26 09:26:31 -07:00
fix_cmap.rst
add proper r-RESPA support for fix cmap
2021-03-30 07:36:53 -04:00
fix_colvars.rst
address a whole bunch of spelling issues that suddenly popped up.
2021-02-09 12:38:46 -05:00
fix_controller.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_deform.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_deposit.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_dpd_energy.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_dpd_source.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_drag.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_drude_transform.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_drude.rst
Minor fix for molecular DOF calculation. Update doc.
2020-11-16 17:23:53 +01:00
fix_dt_reset.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_efield.rst
fix some typos
2021-01-26 09:30:28 -07:00
fix_ehex.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_electron_stopping.rst
whitespace
2020-11-30 13:33:09 -05:00
fix_enforce2d.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_eos_cv.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_eos_table_rx.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_eos_table.rst
big update
2020-08-24 16:54:16 +02:00
fix_evaporate.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_external.rst
fix some typos
2021-01-26 09:30:28 -07:00
fix_ffl.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_filter_corotate.rst
Consistently use instead of
2020-11-10 14:04:49 +01:00
fix_flow_gauss.rst
document __version__ module member and version check
2021-02-09 12:29:14 -05:00
fix_freeze.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_gcmc.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_gld.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_gle.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_gravity.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_grem.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_halt.rst
add stop on file example to fix halt docs
2021-04-02 12:31:46 -04:00
fix_heat.rst
big update
2020-08-24 16:54:16 +02:00
fix_hyper_global.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_hyper_local.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_imd.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_indent.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_ipi.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_langevin_drude.rst
big update
2020-08-24 16:54:16 +02:00
fix_langevin_eff.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_langevin_spin.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_langevin.rst
added Developer doc info for this refactoring
2021-01-26 10:54:02 -07:00
fix_latte.rst
doc pages for virial contributions of fixes
2021-01-26 09:26:31 -07:00
fix_lb_fluid.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_lb_momentum.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_lb_pc.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_lb_rigid_pc_sphere.rst
doc pages for virial contributions of fixes
2021-01-26 09:26:31 -07:00
fix_lb_viscous.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_lineforce.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_manifoldforce.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_meso_move.rst
big update
2020-08-24 16:54:16 +02:00
fix_modify_atc_commands.rst
Convert a first set of AtC documentation html files to rst and add infrastructure files and links
2020-03-12 14:26:04 -04:00
fix_modify.rst
address a whole bunch of spelling issues that suddenly popped up.
2021-02-09 12:38:46 -05:00
fix_momentum.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_move.rst
big update
2020-08-24 16:54:16 +02:00
fix_mscg.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_msst.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_mvv_dpd.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_neb_spin.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_neb.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nh_eff.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_nh_uef.rst
fix broken internal links in the manual
2020-10-21 10:56:52 -04:00
fix_nh.rst
Feb2021 GPU Package Update - Documentation Files
2021-02-15 11:07:43 -08:00
fix_nph_asphere.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_nph_body.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_nph_sphere.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_nphug.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_npt_asphere.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_npt_body.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_npt_cauchy.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_npt_sphere.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_numdiff.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_nve_asphere_noforce.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nve_asphere.rst
Feb2021 GPU Package Update - Documentation Files
2021-02-15 11:07:43 -08:00
fix_nve_awpmd.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nve_body.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nve_dot.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nve_dotc_langevin.rst
big update
2020-08-24 16:54:16 +02:00
fix_nve_eff.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nve_limit.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nve_line.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nve_manifold_rattle.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nve_noforce.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nve_sphere.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_nve_spin.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_nve_tri.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nve.rst
Feb2021 GPU Package Update - Documentation Files
2021-02-15 11:07:43 -08:00
fix_nvk.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nvt_asphere.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_nvt_body.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_nvt_manifold_rattle.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_nvt_sllod_eff.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_nvt_sllod.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_nvt_sphere.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_oneway.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_orient_eco.rst
address a whole bunch of spelling issues that suddenly popped up.
2021-02-09 12:38:46 -05:00
fix_orient.rst
address a whole bunch of spelling issues that suddenly popped up.
2021-02-09 12:38:46 -05:00
fix_pafi.rst
citation update
2020-05-01 16:19:03 +02:00
fix_phonon.rst
fix typos and remove false false positive
2020-11-27 15:16:32 -05:00
fix_pimd.rst
finish updating docs for fixes using code-block plus a few other improvements
2020-03-11 12:58:57 -04:00
fix_planeforce.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_plumed.rst
doc pages for virial contributions of fixes
2021-01-26 09:26:31 -07:00
fix_poems.rst
doc pages for virial contributions of fixes
2021-01-26 09:26:31 -07:00
fix_pour.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_precession_spin.rst
address a whole bunch of spelling issues that suddenly popped up.
2021-02-09 12:38:46 -05:00
fix_press_berendsen.rst
big update
2020-08-24 16:54:16 +02:00
fix_print.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_propel_self.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_property_atom.rst
add ":class: note" to admonitions where it was missing for consistent formatting
2020-10-07 20:24:56 -04:00
fix_python_invoke.rst
Revert "Add missing index entries"
2020-09-02 14:02:53 -04:00
fix_python_move.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_qbmsst.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_qeq_comb.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_qeq_reax.rst
update formatting of keyword summary
2020-09-12 19:06:30 -04:00
fix_qeq.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_qmmm.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_qtb.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_reaxc_bonds.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_reaxc_species.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_recenter.rst
big update
2020-08-24 16:54:16 +02:00
fix_restrain.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_rhok.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_rigid_meso.rst
Fix unhandled cases in docs LAMMPS syntax highlighting
2021-03-19 18:51:21 -04:00
fix_rigid.rst
extra files that were not checked in
2021-01-26 11:02:27 -07:00
fix_rx.rst
Consistently use instead of
2020-11-10 14:04:49 +01:00
fix_saed_vtk.rst
big update
2020-08-24 16:54:16 +02:00
fix_setforce.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_shake.rst
doc pages for virial contributions of fixes
2021-01-26 09:26:31 -07:00
fix_shardlow.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_smd_adjust_dt.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_smd_integrate_tlsph.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_smd_integrate_ulsph.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_smd_move_triangulated_surface.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_smd_setvel.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_smd_wall_surface.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_smd.rst
doc pages for virial contributions of fixes
2021-01-26 09:26:31 -07:00
fix_sph_stationary.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_sph.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_spring_chunk.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_spring_rg.rst
big update
2020-08-24 16:54:16 +02:00
fix_spring_self.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_spring.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_srd.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_store_force.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_store_state.rst
add comments/warnings to docs of fix property/atom and fix store/state about restarting
2020-09-04 00:14:01 -04:00
fix_temp_berendsen.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_temp_csvr.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_temp_rescale_eff.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_temp_rescale.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix_tfmc.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_tgnh_drude.rst
address a whole bunch of spelling issues that suddenly popped up.
2021-02-09 12:38:46 -05:00
fix_thermal_conductivity.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_ti_spring.rst
Merge branch 'master' into collected-small-changes
2021-02-08 22:46:21 -05:00
fix_tmd.rst
big update
2020-08-24 16:54:16 +02:00
fix_ttm.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_tune_kspace.rst
big update
2020-08-24 16:54:16 +02:00
fix_vector.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_viscosity.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_viscous.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_wall_body_polygon.rst
correct docs
2021-02-26 15:54:20 -05:00
fix_wall_body_polyhedron.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_wall_ees.rst
address a whole bunch of spelling issues that suddenly popped up.
2021-02-09 12:38:46 -05:00
fix_wall_gran_region.rst
whitespace fixes
2021-04-07 14:59:33 -04:00
fix_wall_gran.rst
whitespace fixes
2021-04-07 14:59:33 -04:00
fix_wall_piston.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_wall_reflect_stochastic.rst
replace parsed-literal with code-block where appropriate. typeset keywords in cursive
2020-03-10 16:54:04 -04:00
fix_wall_reflect.rst
Apply header fix to all remaining fix styles docs
2020-09-02 11:05:33 -04:00
fix_wall_region.rst
fix some typos
2021-01-26 09:30:28 -07:00
fix_wall_srd.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
fix_wall.rst
fix some typos
2021-01-26 09:30:28 -07:00
fix_widom.rst
doc page updates for energy contributions of thermostat and non-thermostat fixes
2021-01-26 08:51:47 -07:00
fix.rst
Merge branch 'master' into tgnh
2020-12-20 14:48:49 -05:00
fixes.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
Fortran.rst
mention example using the new Fortran module in examples/COUPLE/simple
2020-10-14 23:29:03 -04:00
group2ndx.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
group.rst
Fix unhandled cases in docs LAMMPS syntax highlighting
2021-03-19 18:51:21 -04:00
Howto_2d.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Howto_barostat.rst
delete empty lines at the end of files
2020-01-31 14:03:52 -05:00
Howto_bioFF.rst
correct attribution of angle style cosine/squared with DREIDING
2021-03-22 11:28:22 -04:00
Howto_body.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Howto_chunk.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Howto_client_server.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Howto_cmake.rst
add preset for Intel's new oneAPI LLVM based compiler
2021-03-13 13:07:25 -05:00
Howto_coreshell.rst
big update
2020-08-24 16:54:16 +02:00
Howto_couple.rst
fix up a few internal references
2020-09-25 14:04:44 -04:00
Howto_diffusion.rst
delete superfluous horizontal line plus preceding empty lines at the end of doc files
2020-01-31 14:06:14 -05:00
Howto_dispersion.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Howto_drude2.rst
Merge branch 'master' into tgnh
2020-12-20 14:48:49 -05:00
Howto_drude.rst
Update docs for TGNH
2020-11-14 17:08:26 +01:00
Howto_elastic.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Howto_github.rst
Fix casing of the word GitHub
2020-11-10 14:20:52 +01:00
Howto_granular.rst
update granular howto
2021-03-29 23:44:38 -04:00
Howto_kappa.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Howto_library.rst
rename sections to User Guide and Programmer Guide
2020-10-15 12:00:36 -04:00
Howto_manifold.rst
some more fixups
2020-03-13 17:02:59 -04:00
Howto_multiple.rst
big update
2020-08-24 16:54:16 +02:00
Howto_nemd.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
Howto_output.rst
big update
2020-08-24 16:54:16 +02:00
Howto_polarizable.rst
delete empty lines at the end of files
2020-01-31 14:03:52 -05:00
Howto_pylammps.rst
Update docs
2020-12-17 11:57:40 -05:00
Howto_replica.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
Howto_restart.rst
big update
2020-08-24 16:54:16 +02:00
Howto_spc.rst
typeset symbols in water model howtos
2020-03-10 16:20:52 -04:00
Howto_spherical.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Howto_spins.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
Howto_temperature.rst
delete empty lines at the end of files
2020-01-31 14:03:52 -05:00
Howto_thermostat.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Howto_tip3p.rst
typeset symbols in water model howtos
2020-03-10 16:20:52 -04:00
Howto_tip4p.rst
big update
2020-08-24 16:54:16 +02:00
Howto_triclinic.rst
big update
2020-08-24 16:54:16 +02:00
Howto_viscosity.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Howto_viz.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
Howto_walls.rst
Fix typo in Howto Walls
2020-11-10 14:03:16 +01:00
Howto_wsl.rst
big update
2020-08-24 16:54:16 +02:00
Howto.rst
move Tutorials to bottom of Howto section
2020-09-25 15:12:31 -04:00
hyper.rst
big update
2020-08-24 16:54:16 +02:00
if.rst
allow forward slash in strings for if statements
2020-10-06 18:44:26 -04:00
improper_class2.rst
Update headers in improper_*.rst files
2020-09-02 13:03:03 -04:00
improper_coeff.rst
big update
2020-08-24 16:54:16 +02:00
improper_cossq.rst
Update headers in improper_*.rst files
2020-09-02 13:03:03 -04:00
improper_cvff.rst
Update headers in improper_*.rst files
2020-09-02 13:03:03 -04:00
improper_distance.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
improper_distharm.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
improper_fourier.rst
Update headers in improper_*.rst files
2020-09-02 13:03:03 -04:00
improper_harmonic.rst
Update headers in improper_*.rst files
2020-09-02 13:03:03 -04:00
improper_hybrid.rst
big update
2020-08-24 16:54:16 +02:00
improper_inversion_harmonic.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
improper_none.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
improper_ring.rst
Update headers in improper_*.rst files
2020-09-02 13:03:03 -04:00
improper_sqdistharm.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
improper_style.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
improper_umbrella.rst
Update headers in improper_*.rst files
2020-09-02 13:03:03 -04:00
improper_zero.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
impropers.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
include.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
info.rst
add documentation for added keyword and library interface functions
2021-01-12 20:11:38 -05:00
Install_conda.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Install_git.rst
update install instructions for updates via patch and git for CMake/GNU make
2021-03-30 11:43:56 -04:00
Install_linux.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Install_mac.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Install_patch.rst
update install instructions for updates via patch and git for CMake/GNU make
2021-03-30 11:43:56 -04:00
Install_tarball.rst
Point users to the LAMMPS GitHub Releases page for downloading archives
2021-02-16 06:51:50 -05:00
Install_windows.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Install.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Intro_authors.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Intro_citing.rst
document updated citation reminder
2021-01-08 18:29:15 -05:00
Intro_features.rst
update the intro for the kim command
2021-02-23 06:12:07 -06:00
Intro_nonfeatures.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Intro_opensource.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Intro_overview.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Intro_website.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Intro.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
jump.rst
big update
2020-08-24 16:54:16 +02:00
kim_commands.rst
Fix unhandled cases in docs LAMMPS syntax highlighting
2021-03-19 18:51:21 -04:00
kspace_modify.rst
big update
2020-08-24 16:54:16 +02:00
kspace_style.rst
Update index for kspace_style commands
2020-09-02 13:40:24 -04:00
label.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
lattice.rst
whitespace
2020-12-13 00:07:48 -05:00
Library_add.rst
update section headlines
2020-10-08 10:32:02 -04:00
Library_atoms.rst
update titles as suggested by steve and move a few entries around
2020-10-07 20:07:30 -04:00
Library_config.rst
add documentation for added keyword and library interface functions
2021-01-12 20:11:38 -05:00
Library_create.rst
reorder functions in library.h and library.cpp to match order in manual
2020-10-22 12:11:42 -04:00
Library_execute.rst
add comment to explain using the LAMMPS_LIB_MPI define in example
2020-10-09 11:50:53 -04:00
Library_neighbor.rst
update titles as suggested by steve and move a few entries around
2020-10-07 20:07:30 -04:00
Library_objects.rst
update section headlines
2020-10-08 10:32:02 -04:00
Library_properties.rst
update titles as suggested by steve and move a few entries around
2020-10-07 20:07:30 -04:00
Library_scatter.rst
address spelling and manual processing issues
2021-04-03 11:11:18 -04:00
Library_utility.rst
reorder functions in library.h and library.cpp to match order in manual
2020-10-22 12:11:42 -04:00
Library.rst
add comment to explain using the LAMMPS_LIB_MPI define in example
2020-10-09 11:50:53 -04:00
log.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
Manual_version.rst
Use User's Guide and Programmer's Guide. Normalize header level formatting
2020-10-12 23:31:03 -04:00
Manual.rst
rephrase paragraph about availability of the manual and add note about browser compatibility
2020-10-28 04:49:09 -04:00
mass.rst
big update
2020-08-24 16:54:16 +02:00
message.rst
fix small render issue
2020-11-25 16:51:41 -05:00
min_modify.rst
add missing option
2020-09-14 09:27:49 -04:00
min_spin.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
min_style.rst
big update
2020-08-24 16:54:16 +02:00
minimize.rst
big update
2020-08-24 16:54:16 +02:00
Modify_atom.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Modify_body.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Modify_bond.rst
clarify tasks for single() for Bond and Angle classes
2020-10-16 10:48:00 -04:00
Modify_command.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Modify_compute.rst
fix broken internal links in the manual
2020-10-21 10:56:52 -04:00
Modify_contribute.rst
update formulations in docs to incorporate suggestions by @sjplimp
2021-01-12 20:44:43 -05:00
Modify_dump.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Modify_fix.rst
big update
2020-08-24 16:54:16 +02:00
Modify_kspace.rst
big update
2020-08-24 16:54:16 +02:00
Modify_min.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Modify_overview.rst
fix incorrectly formatted "notes"
2020-10-07 18:35:05 -04:00
Modify_pair.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Modify_region.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Modify_thermo.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Modify_variable.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
Modify.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
molecule.rst
clairfy docs
2020-11-16 15:09:17 -05:00
neb_spin.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
neb.rst
big update
2020-08-24 16:54:16 +02:00
neigh_modify.rst
replace "xxxn't" with "xxx not"
2020-03-18 07:02:34 -04:00
neighbor.rst
spelling
2020-12-18 23:02:28 -05:00
newton.rst
big update
2020-08-24 16:54:16 +02:00
next.rst
big update
2020-08-24 16:54:16 +02:00
package.rst
Adding some notes about KOKKOS thread settings to the package doc.
2021-02-19 05:55:37 -08:00
Packages_details.rst
Added minimal info on downloading and building PACE library
2021-04-08 13:36:04 -06:00
Packages_standard.rst
add missing entry to standard packages list
2021-04-03 11:15:00 -04:00
Packages_user.rst
Eliminated doc build warnings
2021-04-08 14:09:19 -06:00
Packages.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
pair_adp.rst
update the kim command name
2021-02-23 06:12:09 -06:00
pair_agni.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_airebo.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_atm.rst
fix typo that has propagated to multiple pair style doc files
2020-11-10 05:00:56 -05:00
pair_awpmd.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_beck.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_body_nparticle.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_body_rounded_polygon.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_body_rounded_polyhedron.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_bop.rst
big update
2020-08-24 16:54:16 +02:00
pair_born.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_brownian.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_buck6d_coul_gauss.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_buck_long.rst
fix typo that has propagated to multiple pair style doc files
2020-11-10 05:00:56 -05:00
pair_buck.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_charmm.rst
Feb2021 GPU Package Update - Documentation Files
2021-02-15 11:07:43 -08:00
pair_class2.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_coeff.rst
Undo lost headers
2020-09-02 12:54:08 -04:00
pair_colloid.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_comb.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_cosine_squared.rst
use consistent style when referencing packages
2020-08-27 17:44:49 -04:00
pair_coul_diel.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_coul_shield.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_coul_slater.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_coul_tt.rst
dedup anchor
2020-10-09 17:29:31 -04:00
pair_coul.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_cs.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_dipole.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_dpd_fdt.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_dpd.rst
fix typo
2021-03-30 07:36:22 -04:00
pair_drip.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_dsmc.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_e3b.rst
big update
2020-08-24 16:54:16 +02:00
pair_eam.rst
update the kim command name
2021-02-23 06:12:09 -06:00
pair_edip.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_eff.rst
big update
2020-08-24 16:54:16 +02:00
pair_eim.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_exp6_rx.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_extep.rst
big update
2020-08-24 16:54:16 +02:00
pair_fep_soft.rst
fix typos
2021-03-30 07:49:15 -04:00
pair_gauss.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_gayberne.rst
fix typos
2021-03-30 07:49:15 -04:00
pair_gran.rst
whitespace fixes
2021-04-07 14:59:33 -04:00
pair_granular.rst
whitespace fixes
2021-04-07 14:59:33 -04:00
pair_gromacs.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_gw.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_hbond_dreiding.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_hybrid.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_ilp_graphene_hbn.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_kim.rst
naming update
2021-02-23 06:12:10 -06:00
pair_kolmogorov_crespi_full.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_kolmogorov_crespi_z.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_lcbop.rst
fix typo that has propagated to multiple pair style doc files
2020-11-10 05:00:56 -05:00
pair_lebedeva_z.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_line_lj.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_list.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_lj96.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_lj_cubic.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_lj_cut_coul.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_lj_cut_tip4p.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_lj_expand.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_lj_long.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_lj_relres.rst
final update with @sjplimp suggested change
2021-03-05 16:28:50 -05:00
pair_lj_smooth_linear.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_lj_smooth.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_lj_switch3_coulgauss_long.rst
consolidate the documentation for lj/switch3/coulgauss/long and mm3/switch3/coulgauss/long into a single file
2021-04-01 12:42:07 -04:00
pair_lj.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_local_density.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_lubricate.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_lubricateU.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_mdf.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_meam_spline.rst
update pair meam/spline docs to reflect limitations of the implementation
2020-12-01 19:06:54 -05:00
pair_meam_sw_spline.rst
big update
2020-08-24 16:54:16 +02:00
pair_meamc.rst
Revert "Add missing index entries"
2020-09-02 14:02:53 -04:00
pair_mesocnt.rst
discuss that USER-MESONT package potentials are not bundled and provide URL
2020-09-29 16:57:19 -04:00
pair_mesodpd.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_mesont_tpm.rst
discuss that USER-MESONT package potentials are not bundled and provide URL
2020-09-29 16:57:19 -04:00
pair_mgpt.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_mie.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_mliap.rst
whitespace fixes
2021-03-05 22:14:46 -05:00
pair_modify.rst
Undo lost headers
2020-09-02 12:54:08 -04:00
pair_momb.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_morse.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_multi_lucy_rx.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_multi_lucy.rst
big update
2020-08-24 16:54:16 +02:00
pair_nb3b_harmonic.rst
big update
2020-08-24 16:54:16 +02:00
pair_nm.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_none.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_oxdna2.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_oxdna.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_oxrna2.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_pace.rst
resolve whitespace issues
2021-04-07 18:05:00 -04:00
pair_peri.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_polymorphic.rst
fix typos
2021-03-26 23:12:29 -04:00
pair_python.rst
document changes to LAMMPS_POTENTIALS environment variable
2020-08-29 22:22:27 -04:00
pair_quip.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_reaxc.rst
reformat reax/c control file parameter descriptions
2020-10-07 22:28:34 -04:00
pair_resquared.rst
fix typo that has propagated to multiple pair style doc files
2020-11-10 05:00:56 -05:00
pair_sdk.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_sdpd_taitwater_isothermal.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_smd_hertz.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_smd_tlsph.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_smd_triangulated_surface.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_smd_ulsph.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_smtbq.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_snap.rst
whitespace fixes (no tabs, no trailing whitespace)
2021-03-10 04:58:57 -05:00
pair_soft.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_sph_heatconduction.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_sph_idealgas.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_sph_lj.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_sph_rhosum.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_sph_taitwater_morris.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_sph_taitwater.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_spin_dipole.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_spin_dmi.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_spin_exchange.rst
Fix pair_spin_exchange doc page title
2020-11-12 11:04:11 -05:00
pair_spin_magelec.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_spin_neel.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_srp.rst
fix typo that has propagated to multiple pair style doc files
2020-11-10 05:00:56 -05:00
pair_style.rst
Eliminated doc build warnings
2021-04-08 14:09:19 -06:00
pair_sw.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_table_rx.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_table.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_tersoff_mod.rst
update docs a bit more
2021-01-04 23:02:17 -05:00
pair_tersoff_zbl.rst
update docs a bit more
2021-01-04 23:02:17 -05:00
pair_tersoff.rst
update docs a bit more
2021-01-04 23:02:17 -05:00
pair_thole.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_tri_lj.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pair_ufm.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_vashishta.rst
fix typos
2021-03-30 07:49:15 -04:00
pair_wf_cut.rst
address spelling issues
2021-01-28 03:59:30 -05:00
pair_write.rst
Undo lost headers
2020-09-02 12:54:08 -04:00
pair_yukawa_colloid.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_yukawa.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_zbl.rst
Apply header fix to all remaining pair styles docs
2020-09-02 10:59:01 -04:00
pair_zero.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
pairs.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
partition.rst
big update
2020-08-24 16:54:16 +02:00
plugin.rst
update docs
2021-03-18 18:20:32 -04:00
prd.rst
big update
2020-08-24 16:54:16 +02:00
print.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
processors.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Python_atoms.rst
Fix docs after PR #2592
2021-02-15 13:19:25 -05:00
Python_call.rst
make headers more compact
2020-10-16 02:43:20 -04:00
Python_config.rst
add documentation for added keyword and library interface functions
2021-01-12 20:11:38 -05:00
Python_create.rst
Update Python docs
2020-10-15 18:19:57 -04:00
Python_error.rst
make headers more compact
2020-10-16 02:43:20 -04:00
Python_examples.rst
remove trailing whitespace
2020-10-20 21:24:02 -04:00
Python_execute.rst
Update Python_execute.rst
2020-10-16 18:22:29 -04:00
Python_ext.rst
Update docs
2020-12-17 11:57:40 -05:00
Python_formats.rst
Fix bug in AvgChunkReader and add docs
2021-02-25 16:56:19 -05:00
Python_head.rst
Fix bug in AvgChunkReader and add docs
2021-02-25 16:56:19 -05:00
Python_install.rst
reformat paragraph
2021-01-31 13:06:10 -05:00
Python_launch.rst
Add missing code-block language
2020-10-16 18:22:29 -04:00
Python_module.rst
fix errors/typos in manual
2021-04-02 21:00:42 -04:00
Python_neighbor.rst
address spelling and manual processing issues
2021-04-03 11:11:18 -04:00
Python_objects.rst
Fix docs after PR #2592
2021-02-15 13:19:25 -05:00
Python_overview.rst
Update docs
2020-12-17 11:57:40 -05:00
Python_properties.rst
Update Python docs
2020-10-15 18:19:57 -04:00
Python_run.rst
Add extra space in Python_run.rst
2020-10-16 17:20:38 -04:00
Python_scatter.rst
Update Python docs
2020-10-15 18:19:57 -04:00
Python_trouble.rst
Update docs
2020-12-17 11:57:40 -05:00
python.rst
Update docs
2020-12-17 11:57:40 -05:00
quit.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
read_data.rst
reformulate section about resetting image flags and add reference to change_box command
2020-11-11 17:01:56 -05:00
read_dump.rst
improve read_dump and rerun documentation. mention that native binary dumps are not supported
2020-11-06 17:30:08 -05:00
read_restart.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
region.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
replicate.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
rerun.rst
add post yes/no keyword to rerun commmand (with default to no)
2021-04-05 15:38:59 -04:00
reset_atom_ids.rst
big update
2020-08-24 16:54:16 +02:00
reset_mol_ids.rst
big update
2020-08-24 16:54:16 +02:00
reset_timestep.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
restart.rst
remove unneeded escapes from input examples
2020-09-28 07:52:38 -04:00
Run_basics.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Run_head.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
Run_options.rst
update formulations in docs to incorporate suggestions by @sjplimp
2021-01-12 20:44:43 -05:00
Run_output.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
run_style.rst
big update
2020-08-24 16:54:16 +02:00
Run_windows.rst
Some more code-blocks instead of parsed-literal
2020-03-13 18:38:47 -04:00
run.rst
big update
2020-08-24 16:54:16 +02:00
server_mc.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
server_md.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
server.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
set.rst
update keyword summary
2020-11-25 16:51:43 -05:00
shell.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
special_bonds.rst
big update
2020-08-24 16:54:16 +02:00
Speed_bench.rst
first chunk of revised updates to the manual addressing link issues.
2020-09-04 11:39:38 -04:00
Speed_compare.rst
use consistent capitalization with NVIDIA
2020-04-10 23:20:10 -04:00
Speed_gpu.rst
documentation corrections, spelling fixes and updates
2021-02-17 18:47:35 -05:00
Speed_intel.rst
merge error fix
2020-08-24 17:10:33 +02:00
Speed_kokkos.rst
Fix link
2021-01-25 14:04:26 -07:00
Speed_measure.rst
a few more cosmetic changes
2020-09-04 11:50:02 -04:00
Speed_omp.rst
a few more cosmetic changes
2020-09-04 11:50:02 -04:00
Speed_opt.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
Speed_packages.rst
Feb2021 GPU Package Update - Documentation Files
2021-02-15 11:07:43 -08:00
Speed_tips.rst
delete empty lines at the end of files
2020-01-31 14:03:52 -05:00
Speed.rst
update lammps.sandia.gov URLs to use https://
2020-03-12 00:28:28 -04:00
suffix.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
tad.rst
big update
2020-08-24 16:54:16 +02:00
temper_grem.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
temper_npt.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
temper.rst
big update
2020-08-24 16:54:16 +02:00
thermo_modify.rst
Merge branch 'master' into thermo-energy
2021-02-08 15:24:29 -05:00
thermo_style.rst
whitespace fixes
2021-02-08 21:45:58 -05:00
thermo.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
third_order.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
timer.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
timestep.rst
big update
2020-08-24 16:54:16 +02:00
Tools.rst
update docs for magic patterns
2021-03-14 06:39:59 -04:00
uncompute.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
undump.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
unfix.rst
convert remaining style doc sections to be a logical header
2020-08-21 23:33:41 -04:00
units.rst
Update units.rst
2021-03-31 06:44:52 +05:30
variable.rst
add is_file() special variable function and unit tests for it
2021-04-02 12:07:43 -04:00
velocity.rst
big update
2020-08-24 16:54:16 +02:00
write_coeff.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
write_data.rst
add ":class: note" to admonitions where it was missing for consistent formatting
2020-10-07 20:24:56 -04:00
write_dump.rst
Update docs for COMPRESS styles
2020-09-01 12:17:08 -04:00
write_restart.rst
document both, CMake and traditional procedure to enable MPIIO
2020-10-11 12:18:26 -04:00