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lammps/doc/src
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Axel Kohlmeyer df08818fef refactor handling of plugin loading to make plugin a global property
2025-06-11 02:52:28 -04:00
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_ext
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99
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2001
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img
Revert "revert more general doc changes. those are moved to a separate branch for further edits."
2024-01-18 18:14:41 -05:00
JPG
add LAMMPS-GUI screenshot image
2025-05-02 00:21:41 -04:00
PDF
Update Colvars library to version 2025-04-18
2025-04-30 15:32:30 -04:00
.gitignore
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accel_styles.rst
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angle_amoeba.rst
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angle_charmm.rst
integrate into manual and add cross-references for CHARMM styles
2024-01-05 18:17:36 -05:00
angle_class2.rst
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angle_coeff.rst
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angle_cosine_buck6d.rst
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angle_cosine_delta.rst
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angle_cosine_periodic.rst
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angle_cosine_shift_exp.rst
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angle_cosine_shift.rst
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angle_cosine_squared_restricted.rst
update version tags for feature release
2024-04-16 19:47:12 -04:00
angle_cosine_squared.rst
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angle_cosine.rst
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angle_cross.rst
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angle_dipole.rst
bibliography cleanup
2024-08-14 10:32:46 -04:00
angle_fourier_simple.rst
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angle_fourier.rst
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angle_gaussian.rst
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angle_harmonic.rst
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angle_hybrid.rst
clarify that hybrid styles also do not write coeff data to data files
2024-07-30 08:59:51 -04:00
angle_lepton.rst
update version tags for feature release
2024-02-07 05:03:20 -05:00
angle_mesocnt.rst
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angle_mm3.rst
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angle_mwlc.rst
set version string to 4Feb2025
2025-01-30 17:22:28 -05:00
angle_none.rst
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angle_quartic.rst
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angle_spica.rst
updated pair style and angle style /kk in docs
2024-06-05 19:56:29 -04:00
angle_style.rst
mwlc angle documentation
2024-09-24 10:33:08 +08:00
angle_table.rst
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angle_write.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
angle_zero.rst
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atc_add_molecule.rst
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atc_add_species.rst
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atc_atom_element_map.rst
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atc_atom_weight.rst
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atc_atomic_charge.rst
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atc_boundary_dynamics.rst
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atc_boundary_faceset.rst
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atc_boundary_type.rst
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atc_consistent_fe_initialization.rst
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atc_control_localized_lambda.rst
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atc_control_momentum.rst
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atc_control_thermal.rst
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atc_decomposition.rst
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atc_electron_integration.rst
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atc_equilibrium_start.rst
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atc_extrinsic_exchange.rst
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atc_fe_md_boundary.rst
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atc_filter_scale.rst
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atc_filter_type.rst
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atc_fix_flux.rst
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atc_fix.rst
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atc_hardy_computes.rst
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atc_hardy_fields.rst
bibliography cleanup
2024-08-14 10:32:46 -04:00
atc_hardy_gradients.rst
bibliography cleanup
2024-08-14 10:32:46 -04:00
atc_hardy_kernel.rst
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atc_hardy_on_the_fly.rst
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atc_hardy_rates.rst
bibliography cleanup
2024-08-14 10:32:46 -04:00
atc_initial.rst
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atc_internal_element_set.rst
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atc_internal_quadrature.rst
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atc_kernel_bandwidth.rst
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atc_lumped_lambda_solve.rst
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atc_mask_direction.rst
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atc_mass_matrix.rst
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atc_material.rst
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atc_mesh_add_to_nodeset.rst
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atc_mesh_create_elementset.rst
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atc_mesh_create_faceset_box.rst
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atc_mesh_create_faceset_plane.rst
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atc_mesh_create_nodeset.rst
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atc_mesh_create.rst
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atc_mesh_delete_elements.rst
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atc_mesh_nodeset_to_elementset.rst
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atc_mesh_output.rst
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atc_mesh_quadrature.rst
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atc_mesh_read.rst
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atc_mesh_write.rst
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atc_output_boundary_integral.rst
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atc_output_contour_integral.rst
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atc_output_nodeset.rst
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atc_output_volume_integral.rst
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atc_output.rst
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atc_pair_interactions.rst
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atc_poisson_solver.rst
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atc_read_restart.rst
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atc_remove_molecule.rst
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atc_remove_source.rst
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atc_remove_species.rst
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atc_reset_atomic_reference.rst
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atc_reset_time.rst
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atc_sample_frequency.rst
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atc_set_reference_pe.rst
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atc_source_integration.rst
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atc_source.rst
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atc_temperature_definition.rst
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atc_time_filter.rst
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atc_time_integration.rst
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atc_track_displacement.rst
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atc_unfix_flux.rst
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atc_unfix.rst
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atc_write_atom_weights.rst
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atc_write_restart.rst
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atom_modify.rst
spelling fixes
2024-07-03 19:17:11 -04:00
atom_style.rst
tweak table widths for smoother display as PDF
2024-08-19 04:43:57 -04:00
balance.rst
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Bibliography.rst
whitespace
2024-08-15 22:55:07 -04:00
bond_bpm_rotational.rst
Adding missing settings to restart files
2025-02-26 13:04:06 -07:00
bond_bpm_spring_plastic.rst
Set pending version tags to 2Apr2025
2025-04-01 21:30:53 -04:00
bond_bpm_spring.rst
Merge conflict
2025-04-11 11:21:56 -06:00
bond_class2.rst
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bond_coeff.rst
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bond_fene_expand.rst
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bond_fene.rst
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bond_gaussian.rst
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bond_gromos.rst
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bond_harmonic_restrain.rst
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bond_harmonic_shift_cut.rst
correct and clarify statements about the potentials and their relations to each other
2025-03-10 06:26:37 -04:00
bond_harmonic_shift.rst
correct and clarify statements about the potentials and their relations to each other
2025-03-10 06:26:37 -04:00
bond_harmonic.rst
correct and clarify statements about the potentials and their relations to each other
2025-03-10 06:26:37 -04:00
bond_hybrid.rst
clarify that hybrid styles also do not write coeff data to data files
2024-07-30 08:59:51 -04:00
bond_lepton.rst
update version tags for feature release
2024-02-07 05:03:20 -05:00
bond_mesocnt.rst
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bond_mm3.rst
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bond_morse.rst
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bond_none.rst
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bond_nonlinear.rst
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bond_oxdna.rst
rename CG-DNA potential files
2024-06-20 14:33:26 -04:00
bond_quartic.rst
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bond_rheo_shell.rst
fix typos
2025-03-12 11:56:40 -04:00
bond_special.rst
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bond_style.rst
Adding references to bpplastic bpm bond style
2025-02-04 15:42:01 -07:00
bond_table.rst
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bond_write.rst
doc pages 949-1220
2024-08-17 00:28:57 -04:00
bond_zero.rst
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boundary.rst
loads of spelling fixes
2023-12-01 15:54:54 -05:00
Build_basics.rst
remove CMAKE_TUNE_FLAGS
2025-04-06 07:06:20 -04:00
Build_cmake.rst
add note about need to run ldconfig on Linux system after make install
2025-03-17 23:33:39 -04:00
Build_development.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Build_diskspace.rst
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Build_extras.rst
Update docs for KOKKOS update
2025-03-31 12:36:40 -06:00
Build_link.rst
doc: more build section updates
2024-08-14 14:15:48 -06:00
Build_make.rst
adjust some wording for the removal of Python 2.x compatibility
2025-02-12 22:04:18 -05:00
Build_manual.rst
small clarification cherry-picked from PR #4502
2025-03-22 15:47:52 -04:00
Build_package.rst
make LAMMPS_ASYNC_IMD a CMake variable, too, and document it properly
2025-01-08 20:50:16 -05:00
Build_prerequisites.rst
address sphinx formatting issue due to added paragraph
2025-04-27 10:04:41 -04:00
Build_settings.rst
remove CMAKE_TUNE_FLAGS
2025-04-06 07:06:20 -04:00
Build_windows.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Build.rst
address sphinx formatting issue due to added paragraph
2025-04-27 10:04:41 -04:00
change_box.rst
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Classes_atom.rst
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Classes_input.rst
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Classes_lammps.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Classes.rst
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clear.rst
doc pages 949-1220
2024-08-17 00:28:57 -04:00
comm_modify.rst
remove multi/old from docs and print deprecation warning when used
2025-02-01 15:29:27 -05:00
comm_style.rst
doc pages 949-1220
2024-08-17 00:28:57 -04:00
Commands_all.rst
add docs for region2vmd command
2025-02-08 18:06:32 -05:00
Commands_bond.rst
Merge pull request #4482 from rbberger/dihedral_multi_harmonic_kokkos
2025-04-01 21:37:51 -04:00
Commands_category.rst
docs: update commands section
2024-08-16 12:54:53 -06:00
Commands_compute.rst
add compute vacf/chunk command
2025-02-16 22:43:28 -05:00
Commands_dump.rst
document extxyz dump style
2025-03-27 14:38:08 +01:00
Commands_fix.rst
Merge branch 'develop' into fix-set-command
2025-06-04 16:22:45 -04:00
Commands_input.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Commands_kspace.rst
remove redundant navigation
2024-08-19 13:28:01 -04:00
commands_list.rst
add docs for region2vmd command
2025-02-08 18:06:32 -05:00
Commands_pair.rst
Add OPENMP package version of pair style lj/pirani
2025-04-22 11:27:41 -04:00
Commands_parse.rst
docs: update commands section
2024-08-16 12:54:53 -06:00
Commands_removed.rst
Merge pull request #4574 from talinke/develop
2025-05-06 13:24:06 -04:00
Commands_structure.rst
use automatic numbering
2024-08-15 16:46:06 -04:00
Commands.rst
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compute_ackland_atom.rst
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compute_adf.rst
make computes rdf and adf error out multi cutoff neighbor lists if needed
2024-03-03 12:27:39 -05:00
compute_angle_local.rst
correct documentation to add "inputs local" to compute reduce commands on local data
2024-10-13 18:56:07 -04:00
compute_angle.rst
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compute_angmom_chunk.rst
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compute_ave_sphere_atom.rst
error out in compute ave/sphere/atom and efield/wolf/atom with multi-cutoff neighborlists
2024-03-03 12:46:20 -05:00
compute_basal_atom.rst
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compute_body_local.rst
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compute_bond_local.rst
reformulate description of force components
2025-05-17 21:15:48 -04:00
compute_bond.rst
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compute_born_matrix.rst
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compute_centro_atom.rst
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compute_chunk_atom.rst
Tweaked the description of numbering order
2025-03-15 14:09:38 -06:00
compute_chunk_spread_atom.rst
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compute_cluster_atom.rst
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compute_cna_atom.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
compute_cnp_atom.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
compute_com_chunk.rst
…
compute_com.rst
…
compute_composition_atom.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
compute_contact_atom.rst
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compute_coord_atom.rst
…
compute_count_type.rst
Update doc/src/compute_count_type.rst
2024-04-23 23:32:27 -04:00
compute_damage_atom.rst
…
compute_dihedral_local.rst
correct documentation to add "inputs local" to compute reduce commands on local data
2024-10-13 18:56:07 -04:00
compute_dihedral.rst
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compute_dilatation_atom.rst
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compute_dipole_chunk.rst
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compute_dipole.rst
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compute_displace_atom.rst
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compute_dpd_atom.rst
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compute_dpd.rst
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compute_edpd_temp_atom.rst
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compute_efield_atom.rst
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compute_efield_wolf_atom.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
compute_entropy_atom.rst
…
compute_erotate_asphere.rst
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compute_erotate_rigid.rst
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compute_erotate_sphere_atom.rst
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compute_erotate_sphere.rst
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compute_event_displace.rst
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compute_fabric.rst
incorporating feedback
2024-02-26 12:09:19 -07:00
compute_fep_ta.rst
…
compute_fep.rst
…
compute_gaussian_grid_local.rst
set version string to 4Feb2025
2025-01-30 17:22:28 -05:00
compute_global_atom.rst
…
compute_group_group.rst
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compute_gyration_chunk.rst
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compute_gyration_shape_chunk.rst
…
compute_gyration_shape.rst
…
compute_gyration.rst
…
compute_heat_flux.rst
…
compute_hexorder_atom.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
compute_hma.rst
…
compute_improper_local.rst
…
compute_improper.rst
…
compute_inertia_chunk.rst
…
compute_ke_atom_eff.rst
…
compute_ke_atom.rst
…
compute_ke_eff.rst
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compute_ke_rigid.rst
…
compute_ke.rst
…
compute_mliap.rst
fixed whitespace in docs
2024-03-22 16:51:27 -06:00
compute_modify.rst
…
compute_momentum.rst
…
compute_msd_chunk.rst
add compute vacf/chunk command
2025-02-16 22:43:28 -05:00
compute_msd_nongauss.rst
…
compute_msd.rst
add compute vacf/chunk command
2025-02-16 22:43:28 -05:00
compute_nbond_atom.rst
More updates for oxidation, more doc pages
2024-03-31 21:40:34 -06:00
compute_omega_chunk.rst
…
compute_orientorder_atom.rst
modernize boldface font selection in LaTeX sections
2025-03-13 22:14:07 -04:00
compute_pace.rst
update version tags for feature release
2024-02-07 05:03:20 -05:00
compute_pair_local.rst
reformulate description of force components
2025-05-17 21:15:48 -04:00
compute_pair.rst
…
compute_pe_atom.rst
…
compute_pe.rst
…
compute_plasticity_atom.rst
…
compute_pod_atom.rst
fix typo
2024-06-26 19:58:09 -04:00
compute_pressure_alchemy.rst
…
compute_pressure_uef.rst
…
compute_pressure.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
compute_property_atom.rst
Moving temp/heat keywords out of dump to compute prop/atom
2024-02-23 14:31:40 -07:00
compute_property_chunk.rst
…
compute_property_grid.rst
update release date to 21 November 2023
2023-11-19 05:40:05 -05:00
compute_property_local.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
compute_ptm_atom.rst
…
compute_rattlers_atom.rst
update version tags for feature release
2024-02-07 05:03:20 -05:00
compute_rdf.rst
compute_rdf: direct type label support
2024-05-12 16:11:36 -04:00
compute_reaxff_atom.rst
update version tags for feature release
2024-02-07 05:03:20 -05:00
compute_reduce_chunk.rst
Apply corrections from code review by @simongravelle
2024-10-14 08:19:53 -04:00
compute_reduce.rst
fix typo
2025-02-23 04:46:34 -05:00
compute_rheo_property_atom.rst
Typo in rheo doc
2025-04-19 10:55:19 -06:00
compute_rigid_local.rst
…
compute_saed.rst
correct dpi to get proper image scaling in PDF output
2023-12-02 16:34:32 -05:00
compute_slcsa_atom.rst
remove argument expansion since it would take only the first expanded argument only.
2025-03-26 04:11:51 -04:00
compute_slice.rst
…
compute_smd_contact_radius.rst
…
compute_smd_damage.rst
…
compute_smd_hourglass_error.rst
…
compute_smd_internal_energy.rst
…
compute_smd_plastic_strain_rate.rst
…
compute_smd_plastic_strain.rst
…
compute_smd_rho.rst
fix issues with compute smd/vol and related docs
2024-08-16 14:58:47 -04:00
compute_smd_tlsph_defgrad.rst
…
compute_smd_tlsph_dt.rst
…
compute_smd_tlsph_num_neighs.rst
…
compute_smd_tlsph_shape.rst
…
compute_smd_tlsph_strain_rate.rst
…
compute_smd_tlsph_strain.rst
…
compute_smd_tlsph_stress.rst
…
compute_smd_triangle_vertices.rst
…
compute_smd_ulsph_effm.rst
…
compute_smd_ulsph_num_neighs.rst
…
compute_smd_ulsph_strain_rate.rst
…
compute_smd_ulsph_strain.rst
…
compute_smd_ulsph_stress.rst
…
compute_smd_vol.rst
fix issues with compute smd/vol and related docs
2024-08-16 14:58:47 -04:00
compute_sna_atom.rst
modernize use of \it and \sf
2025-03-13 22:25:14 -04:00
compute_sph_e_atom.rst
add note about age of SPH package PDF add-on docs.
2024-12-10 23:00:30 -05:00
compute_sph_rho_atom.rst
add note about age of SPH package PDF add-on docs.
2024-12-10 23:00:30 -05:00
compute_sph_t_atom.rst
add note about age of SPH package PDF add-on docs.
2024-12-10 23:00:30 -05:00
compute_spin.rst
…
compute_stress_atom.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
compute_stress_cartesian.rst
…
compute_stress_curvilinear.rst
fix typo
2024-11-27 01:45:42 -05:00
compute_stress_mop.rst
document restrictions for bonded interactions
2024-10-23 12:35:50 -04:00
compute_tally.rst
…
compute_tdpd_cc_atom.rst
…
compute_temp_asphere.rst
fix spelling and formatting issues
2024-08-21 20:18:28 -04:00
compute_temp_body.rst
better explanations of vector outputs for compute temp commands
2024-08-21 12:46:45 -06:00
compute_temp_chunk.rst
whitespace fix in doc
2025-01-08 22:45:38 -08:00
compute_temp_com.rst
better explanations of vector outputs for compute temp commands
2024-08-21 12:46:45 -06:00
compute_temp_cs.rst
fix spelling and formatting issues
2024-08-21 20:18:28 -04:00
compute_temp_deform_eff.rst
better explanations of vector outputs for compute temp commands
2024-08-21 12:46:45 -06:00
compute_temp_deform.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
compute_temp_drude.rst
…
compute_temp_eff.rst
…
compute_temp_partial.rst
fix typo in compute_temp_partial.rst
2024-11-06 11:27:45 +01:00
compute_temp_profile.rst
fix spelling and formatting issues
2024-08-21 20:18:28 -04:00
compute_temp_ramp.rst
fix spelling and formatting issues
2024-08-21 20:18:28 -04:00
compute_temp_region_eff.rst
fix spelling and formatting issues
2024-08-21 20:18:28 -04:00
compute_temp_region.rst
better explanations of vector outputs for compute temp commands
2024-08-21 12:46:45 -06:00
compute_temp_rotate.rst
better explanations of vector outputs for compute temp commands
2024-08-21 12:46:45 -06:00
compute_temp_sphere.rst
better explanations of vector outputs for compute temp commands
2024-08-21 12:46:45 -06:00
compute_temp_uef.rst
…
compute_temp.rst
whitespace
2024-08-26 11:38:26 -04:00
compute_ti.rst
…
compute_torque_chunk.rst
…
compute_vacf_chunk.rst
Set pending version tags to 2Apr2025
2025-04-01 21:30:53 -04:00
compute_vacf.rst
add compute vacf/chunk command
2025-02-16 22:43:28 -05:00
compute_vcm_chunk.rst
…
compute_viscosity_cos.rst
better explanations of vector outputs for compute temp commands
2024-08-21 12:46:45 -06:00
compute_voronoi_atom.rst
update release date to 21 November 2023
2023-11-19 05:40:05 -05:00
compute_xrd.rst
recreate compute xrd mesh image with reasonable dpi setting and used PNG format
2023-12-01 00:37:42 -05:00
compute.rst
add compute vacf/chunk command
2025-02-16 22:43:28 -05:00
Cplusplus.rst
…
create_atoms.rst
clarify
2025-04-11 12:34:31 -04:00
create_bonds.rst
…
create_box.rst
Last batch of edits
2024-08-16 14:03:40 -06:00
delete_atoms.rst
restore original delete_atoms implementation. new version spun off as PR #4492
2025-03-08 17:52:26 -05:00
delete_bonds.rst
discuss that only turning off bonds can lead to "bond atom missing" errors
2025-01-18 09:08:08 -05:00
Developer_atom.rst
Edits to developer doc files
2024-08-14 10:41:52 -06:00
Developer_code_design.rst
Merge pull request #4446 from jtclemm/small-patches
2025-01-30 12:51:50 -05:00
Developer_comm_ops.rst
Updating developer comm doc page to include bond and optional args
2024-11-05 15:53:48 -07:00
Developer_flow.rst
small correction
2025-01-23 11:20:36 -05:00
Developer_grid.rst
doc pages 949-1220
2024-08-17 00:28:57 -04:00
Developer_internal.rst
small update to internal command documentation
2025-03-25 04:37:15 -04:00
Developer_notes.rst
some tweaks for local table of contents
2025-03-26 20:09:54 -04:00
Developer_org.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Developer_par_comm.rst
Edits to developer doc files
2024-08-14 10:41:52 -06:00
Developer_par_long.rst
Edits to developer doc files
2024-08-14 10:41:52 -06:00
Developer_par_neigh.rst
Edits to developer doc files
2024-08-14 10:41:52 -06:00
Developer_par_openmp.rst
Edits to developer doc files
2024-08-14 10:41:52 -06:00
Developer_par_part.rst
…
Developer_parallel.rst
…
Developer_platform.rst
include new platform call in docs
2023-12-14 11:21:09 -05:00
Developer_plugins.rst
Merge branch 'develop' into plumed-plugin
2024-08-20 11:09:18 -04:00
Developer_unittest.rst
update for more clarity
2025-01-08 10:04:06 -05:00
Developer_updating.rst
show use of Domain::minimum_image_big() in second example block
2025-05-31 23:36:36 -04:00
Developer_utils.rst
implement an utils::print() function similar to fmt::print()
2025-01-23 00:03:30 -05:00
Developer_write_command.rst
add commented example for implementing a command style
2024-09-04 08:23:29 -04:00
Developer_write_fix.rst
implement an utils::print() function similar to fmt::print()
2025-01-23 00:03:30 -05:00
Developer_write_pair.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Developer_write.rst
Add document describing how to implement a new command style
2024-09-04 05:47:59 -04:00
Developer.rst
document some internal styles
2025-03-04 23:15:41 -05:00
dielectric.rst
…
dihedral_charmm.rst
integrate into manual and add cross-references for CHARMM styles
2024-01-05 18:17:36 -05:00
dihedral_class2.rst
…
dihedral_coeff.rst
…
dihedral_cosine_shift_exp.rst
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dihedral_cosine_squared_restricted.rst
update version tags for feature release
2024-04-16 19:47:12 -04:00
dihedral_fourier.rst
…
dihedral_harmonic.rst
…
dihedral_helix.rst
…
dihedral_hybrid.rst
clarify that hybrid styles also do not write coeff data to data files
2024-07-30 08:59:51 -04:00
dihedral_lepton.rst
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dihedral_multi_harmonic.rst
add missing index
2025-04-04 03:41:22 -04:00
dihedral_nharmonic.rst
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dihedral_none.rst
…
dihedral_opls.rst
…
dihedral_quadratic.rst
…
dihedral_spherical.rst
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dihedral_style.rst
Update dihedral_style.rst
2024-03-29 11:18:11 +01:00
dihedral_table.rst
…
dihedral_write.rst
…
dihedral_zero.rst
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dimension.rst
…
displace_atoms.rst
…
dump_adios.rst
…
dump_cfg_uef.rst
…
dump_h5md.rst
…
dump_image.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
dump_modify.rst
More doc
2025-03-28 10:58:54 +01:00
dump_molfile.rst
…
dump_netcdf.rst
…
dump_vtk.rst
…
dump.rst
update a couple more pending version tags
2025-04-02 14:20:57 -04:00
dumps.rst
populate dump style index by moving commands off of commands_list.rst
2024-08-14 11:06:35 -04:00
dynamical_matrix.rst
…
echo.rst
…
Errors_bugs.rst
…
Errors_common.rst
Added mention of the MatSci forum in the Errors_common introduction
2024-08-14 20:49:49 +02:00
Errors_debug.rst
add info on how to debug if LAMMPS seems stuck
2025-01-08 12:24:13 -05:00
Errors_details.rst
improve warning and explanation about too short communication cutoff
2025-04-30 16:46:22 -04:00
Errors_messages.rst
Merge remote-tracking branch 'github/develop' into errors-more-cleanup
2025-03-19 01:39:22 -04:00
Errors_warnings.rst
remove leftover pieces of obsolete warning
2025-03-22 15:42:51 -04:00
Errors.rst
…
Examples.rst
Adding auxetic/incompressible bpm demo
2025-01-30 14:54:59 -07:00
fitpod_command.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
fix_accelerate_cos.rst
small doc fixes
2024-08-13 20:47:46 -04:00
fix_acks2_reaxff.rst
rename fix qeqr/reaxff to fix qeq/rel/reaxff
2025-03-29 18:40:47 -04:00
fix_adapt_fep.rst
add note that pair_coeff settings used for fix adapt must be set explicitly
2024-11-14 15:26:46 -05:00
fix_adapt.rst
Update extract(), document, and test
2025-04-22 11:28:17 -04:00
fix_add_heat.rst
Fixing errors in add heat
2024-08-09 15:36:27 -06:00
fix_addforce.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
fix_addtorque.rst
…
fix_alchemy.rst
…
fix_amoeba_bitorsion.rst
fix errors in fix amoeba/pitorsion doc page
2024-06-21 07:51:49 -06:00
fix_amoeba_pitorsion.rst
one more change
2024-06-21 08:00:50 -06:00
fix_append_atoms.rst
…
fix_atc.rst
…
fix_atom_swap.rst
spelling
2024-10-23 21:10:34 -04:00
fix_ave_atom.rst
more consistent fix average notation
2024-08-18 15:04:58 -06:00
fix_ave_chunk.rst
include space in custom formats to show how spaces can be used to separate columns
2025-03-10 13:30:08 -04:00
fix_ave_correlate_long.rst
small correction for wildcard expansion
2025-05-20 21:18:07 -04:00
fix_ave_correlate.rst
Fix constant i for type first
2025-03-12 08:14:48 +10:00
fix_ave_grid.rst
spelling
2024-08-18 17:36:11 -04:00
fix_ave_histo.rst
convert lists with global values from fixes to use automatic numbering
2024-08-13 20:59:57 -04:00
fix_ave_moments.rst
Fix typo in doc/src/fix_ave_moments.rst
2025-05-29 14:39:39 -04:00
fix_ave_spatial_sphere.rst
small doc fixes
2024-08-13 20:47:46 -04:00
fix_ave_spatial.rst
small doc fixes
2024-08-13 20:47:46 -04:00
fix_ave_time.rst
include space in custom formats to show how spaces can be used to separate columns
2025-03-10 13:30:08 -04:00
fix_aveforce.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
fix_balance.rst
Update fix_balance.rst
2024-08-16 23:44:17 -04:00
fix_bocs.rst
more doc reformatting
2024-08-14 01:34:42 -04:00
fix_bond_break.rst
bond/break: direct type label support
2024-05-11 16:40:40 -04:00
fix_bond_create.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
fix_bond_react.rst
Set pending version tags to 2Apr2025
2025-04-01 21:30:53 -04:00
fix_bond_swap.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
fix_box_relax.rst
more doc reformatting
2024-08-14 01:34:42 -04:00
fix_brownian.rst
…
fix_charge_regulation.rst
convert lists with global values from fixes to use automatic numbering
2024-08-13 20:59:57 -04:00
fix_cmap.rst
Update fix_cmap.rst
2024-10-04 13:04:52 -04:00
fix_colvars.rst
apply special treatment for fix colvars/kk as suggested by @stanmoore1
2024-11-16 11:14:18 -05:00
fix_controller.rst
…
fix_damping_cundall.rst
more doc reformatting
2024-08-14 01:34:42 -04:00
fix_deform_pressure.rst
more bibliography updates
2024-08-14 23:45:59 -04:00
fix_deform.rst
add warning about overflowing image flags and how to prevent that
2024-07-12 23:43:14 -04:00
fix_deposit.rst
restore numerical examples
2024-04-23 10:13:50 -04:00
fix_dpd_energy.rst
final set of bibliography updates
2024-08-15 22:52:42 -04:00
fix_dpd_source.rst
…
fix_drag.rst
…
fix_drude_transform.rst
…
fix_drude.rst
…
fix_dt_reset.rst
…
fix_efield_lepton.rst
set version string to 4Feb2025
2025-01-30 17:22:28 -05:00
fix_efield.rst
Name change, add example
2024-11-12 11:40:07 -05:00
fix_ehex.rst
…
fix_electrode.rst
Merge branch 'develop' into electrode
2024-07-03 15:17:43 -04:00
fix_electron_stopping.rst
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fix_enforce2d.rst
…
fix_eos_cv.rst
…
fix_eos_table_rx.rst
fix a few more .rst formatting issues flagged by pandoc
2025-03-15 12:35:12 -04:00
fix_eos_table.rst
…
fix_evaporate.rst
…
fix_external.rst
improve expanded fix external docs
2024-11-27 01:55:11 -05:00
fix_ffl.rst
…
fix_filter_corotate.rst
…
fix_flow_gauss.rst
…
fix_freeze.rst
…
fix_gcmc.rst
clarification of min/max keywords in fix gcmc
2024-09-26 11:08:59 -04:00
fix_gjf.rst
add missing versionadded tag
2025-05-07 02:00:40 -04:00
fix_gld.rst
modernize boldface font selection in LaTeX sections
2025-03-13 22:14:07 -04:00
fix_gle.rst
…
fix_gravity.rst
…
fix_grem.rst
…
fix_halt.rst
Set pending version tags to 2Apr2025
2025-04-01 21:30:53 -04:00
fix_heat_flow.rst
Documentation for fix add/heat
2024-04-24 13:04:51 -06:00
fix_heat.rst
…
fix_hyper_global.rst
resolve some issues in .rst files detected by pandoc
2025-03-15 12:00:53 -04:00
fix_hyper_local.rst
resolve some issues in .rst files detected by pandoc
2025-03-15 12:00:53 -04:00
fix_imd.rst
set version string to 4Feb2025
2025-01-30 17:22:28 -05:00
fix_indent.rst
improve fix indent documentation
2024-07-06 09:55:22 -04:00
fix_ipi.rst
correct capitalization
2024-06-25 13:33:29 -04:00
fix_langevin_drude.rst
more bibliography updates
2024-08-14 23:45:59 -04:00
fix_langevin_eff.rst
…
fix_langevin_spin.rst
…
fix_langevin.rst
Updated fix langevin algorithm citation
2025-04-29 15:03:49 -07:00
fix_lb_fluid.rst
modernize boldface font selection in LaTeX sections
2025-03-13 22:14:07 -04:00
fix_lb_momentum.rst
…
fix_lb_viscous.rst
…
fix_lineforce.rst
…
fix_manifoldforce.rst
…
fix_mdi_qm.rst
…
fix_mdi_qmmm.rst
…
fix_meso_move.rst
update pending version tags with planned release date
2024-08-25 16:39:13 -04:00
fix_modify_atc_commands.rst
…
fix_modify.rst
Set pending version tags to 2Apr2025
2025-04-01 21:30:53 -04:00
fix_mol_swap.rst
convert lists with global values from fixes to use automatic numbering
2024-08-13 20:59:57 -04:00
fix_momentum.rst
…
fix_move.rst
Set pending version tags to 2Apr2025
2025-04-01 21:30:53 -04:00
fix_msst.rst
…
fix_mvv_dpd.rst
update pending version tags with planned release date
2024-08-25 16:39:13 -04:00
fix_neb_spin.rst
bibliography cleanup
2024-08-14 10:32:46 -04:00
fix_neb.rst
key word -> keyword
2025-03-14 06:59:33 -04:00
fix_neighbor_swap.rst
Additional edits
2025-05-09 14:53:27 -06:00
fix_nh_eff.rst
…
fix_nh_uef.rst
Update fix_nh_uef.rst
2023-12-06 08:14:12 -05:00
fix_nh.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
fix_nonaffine_displacement.rst
documenting fix nonaffine/disp's incompatability with rerun
2024-09-26 13:06:32 -06:00
fix_nph_asphere.rst
…
fix_nph_body.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
fix_nph_sphere.rst
…
fix_nphug.rst
…
fix_npt_asphere.rst
…
fix_npt_body.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
fix_npt_cauchy.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
fix_npt_sphere.rst
…
fix_numdiff_virial.rst
…
fix_numdiff.rst
…
fix_nve_asphere_noforce.rst
…
fix_nve_asphere.rst
…
fix_nve_awpmd.rst
…
fix_nve_body.rst
…
fix_nve_bpm_sphere.rst
…
fix_nve_dot.rst
…
fix_nve_dotc_langevin.rst
…
fix_nve_eff.rst
…
fix_nve_limit.rst
Update fix_nve_limit.rst
2024-10-04 13:05:26 -04:00
fix_nve_line.rst
…
fix_nve_manifold_rattle.rst
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fix_nve_noforce.rst
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fix_nve_sphere.rst
…
fix_nve_spin.rst
…
fix_nve_tri.rst
…
fix_nve.rst
…
fix_nvk.rst
…
fix_nvt_asphere.rst
…
fix_nvt_body.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
fix_nvt_manifold_rattle.rst
…
fix_nvt_sllod_eff.rst
…
fix_nvt_sllod.rst
…
fix_nvt_sphere.rst
…
fix_oneway.rst
…
fix_orient_eco.rst
…
fix_orient.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
fix_pafi.rst
…
fix_pair.rst
…
fix_phonon.rst
clarify docs about fix phonon dependency on KSPACE
2023-12-10 15:27:50 -05:00
fix_pimd.rst
Set pending version tags to 2Apr2025
2025-04-01 21:30:53 -04:00
fix_planeforce.rst
…
fix_plumed.rst
fix cut-n-paste issue
2023-09-14 00:27:35 -04:00
fix_poems.rst
…
fix_polarize.rst
…
fix_pour.rst
Changing pour insertion note box
2024-09-26 20:02:47 -06:00
fix_precession_spin.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
fix_press_berendsen.rst
…
fix_press_langevin.rst
Update fix_press_langevin.rst to include full equation 13
2025-02-18 17:15:01 +01:00
fix_print.rst
…
fix_propel_self.rst
…
fix_property_atom.rst
Moving temp/heat keywords out of dump to compute prop/atom
2024-02-23 14:31:40 -07:00
fix_python_invoke.rst
add missing doc section for fix python/invoke
2025-01-29 23:57:44 -07:00
fix_python_move.rst
…
fix_qbmsst.rst
…
fix_qeq_comb.rst
…
fix_qeq_reaxff.rst
rename fix qeqr/reaxff to fix qeq/rel/reaxff
2025-03-29 18:40:47 -04:00
fix_qeq_rel_reaxff.rst
clarify and rewrap
2025-05-07 15:47:35 -04:00
fix_qeq.rst
Update fix_qeq.rst
2025-03-12 15:15:35 -07:00
fix_qmmm.rst
…
fix_qtb.rst
…
fix_qtpie_reaxff.rst
Add self-citation
2025-05-02 13:52:17 +01:00
fix_reaxff_bonds.rst
Set pending version tags to 2Apr2025
2025-04-01 21:30:53 -04:00
fix_reaxff_species.rst
add note that dynamic groups are only supported without averaging
2025-02-26 11:12:58 -05:00
fix_recenter.rst
Update fix_recenter.rst
2024-10-04 13:05:48 -04:00
fix_restrain.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
fix_rheo_oxidation.rst
update pending version tags with planned release date
2024-08-25 16:39:13 -04:00
fix_rheo_pressure.rst
doc fixes
2024-11-26 15:55:08 -07:00
fix_rheo_thermal.rst
doc fixes
2024-11-26 15:55:08 -07:00
fix_rheo_viscosity.rst
doc fixes
2024-11-26 15:55:08 -07:00
fix_rheo.rst
address spelling issues
2024-12-14 17:10:22 -05:00
fix_rhok.rst
…
fix_rigid_meso.rst
update pending version tags with planned release date
2024-08-25 16:39:13 -04:00
fix_rigid.rst
Merge branch 'develop' into general-triclinic
2023-12-06 07:01:55 -05:00
fix_rx.rst
…
fix_saed_vtk.rst
…
fix_set.rst
correct incorrect reference to command
2025-05-29 05:24:00 -04:00
fix_setforce.rst
…
fix_sgcmc.rst
Fixed doc page
2025-04-19 18:21:39 -06:00
fix_shake.rst
update pending version tags with planned release date
2024-08-25 16:39:13 -04:00
fix_shardlow.rst
final set of bibliography updates
2024-08-15 22:52:42 -04:00
fix_smd_adjust_dt.rst
…
fix_smd_integrate_tlsph.rst
update pending version tags with planned release date
2024-08-25 16:39:13 -04:00
fix_smd_integrate_ulsph.rst
update pending version tags with planned release date
2024-08-25 16:39:13 -04:00
fix_smd_move_triangulated_surface.rst
…
fix_smd_setvel.rst
…
fix_smd_wall_surface.rst
…
fix_smd.rst
…
fix_sph_stationary.rst
add note about age of SPH package PDF add-on docs.
2024-12-10 23:00:30 -05:00
fix_sph.rst
add note about age of SPH package PDF add-on docs.
2024-12-10 23:00:30 -05:00
fix_spring_chunk.rst
…
fix_spring_rg.rst
…
fix_spring_self.rst
document KOKKOS restriction of fix spring/self
2024-11-15 15:22:19 -05:00
fix_spring.rst
…
fix_srd.rst
some more documentation updates for bibliography
2024-08-14 14:57:53 -04:00
fix_store_force.rst
rewrap docs
2024-07-11 13:39:44 -04:00
fix_store_state.rst
…
fix_temp_berendsen.rst
Update docs
2023-12-11 12:55:06 -07:00
fix_temp_csvr.rst
…
fix_temp_rescale_eff.rst
…
fix_temp_rescale.rst
Update docs
2023-12-11 12:55:06 -07:00
fix_tfmc.rst
…
fix_tgnh_drude.rst
…
fix_thermal_conductivity.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
fix_ti_spring.rst
…
fix_tmd.rst
…
fix_ttm.rst
fix ttm doc formatting fixes
2024-03-29 02:50:30 -04:00
fix_tune_kspace.rst
…
fix_vector.rst
…
fix_viscosity.rst
…
fix_viscous_sphere.rst
…
fix_viscous.rst
…
fix_wall_body_polygon.rst
…
fix_wall_body_polyhedron.rst
…
fix_wall_ees.rst
bibliography cleanup
2024-08-14 10:32:46 -04:00
fix_wall_flow.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
fix_wall_gran_region.rst
spelling fixes and updates for the manual
2025-01-29 16:39:53 -05:00
fix_wall_gran.rst
spelling fixes and updates for the manual
2025-01-29 16:39:53 -05:00
fix_wall_piston.rst
key word -> keyword
2025-03-14 06:59:33 -04:00
fix_wall_reflect_stochastic.rst
…
fix_wall_reflect.rst
…
fix_wall_region.rst
Update fix_wall_region.rst
2024-10-04 13:06:32 -04:00
fix_wall_srd.rst
…
fix_wall.rst
…
fix_widom.rst
convert lists with global values from fixes to use automatic numbering
2024-08-13 20:59:57 -04:00
fix.rst
Merge branch 'develop' into fix-set-command
2025-06-04 16:22:45 -04:00
Fortran.rst
refactor handling of plugin loading to make plugin a global property
2025-06-11 02:52:28 -04:00
geturl.rst
discuss using a proxy with geturl, e.g. on a cluster compute node
2025-04-03 18:45:14 -04:00
group2ndx.rst
fix typo
2024-09-11 06:34:15 -04:00
group.rst
cleanup, clarification and re-wrap of doc file sections
2024-10-13 18:56:41 -04:00
Howto_2d.rst
one more doc page
2024-04-08 10:53:14 -06:00
Howto_amoeba.rst
…
Howto_barostat.rst
Adding reference to deform/pressure in barostat howto
2024-12-19 15:15:39 -07:00
Howto_bioFF.rst
continue refactoring for bio force field and water moldel discussions
2025-05-17 23:30:18 -04:00
Howto_body.rst
correct typos and remove duplicate text
2024-04-10 12:56:43 -06:00
Howto_bpm.rst
Adding references to bpplastic bpm bond style
2025-02-04 15:42:01 -07:00
Howto_broken_bonds.rst
…
Howto_bulk2slab.rst
add disclaimer and improve some formulations
2025-03-25 15:42:11 -04:00
Howto_chunk.rst
cleanup, clarification and re-wrap of doc file sections
2024-10-13 18:56:41 -04:00
Howto_cmake.rst
remove CMAKE_TUNE_FLAGS
2025-04-06 07:06:20 -04:00
Howto_coreshell.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
Howto_couple.rst
docs: start with howto section
2024-08-18 07:59:29 -06:00
Howto_diffusion.rst
docs: complete howto review
2024-08-18 13:20:00 -06:00
Howto_dispersion.rst
…
Howto_drude2.rst
…
Howto_drude.rst
…
Howto_elastic.rst
add some more advertisement for LAMMPS-GUI
2024-08-18 18:55:59 -04:00
Howto_FFgeneral.rst
continue refactoring for bio force field and water moldel discussions
2025-05-17 23:30:18 -04:00
Howto_github.rst
Add mini ToC for HowTo only and reorganize the introduction
2025-04-12 00:47:35 -04:00
Howto_granular.rst
Moving temp/heat keywords out of dump to compute prop/atom
2024-02-23 14:31:40 -07:00
Howto_grid.rst
…
Howto_kappa.rst
docs: complete howto review
2024-08-18 13:20:00 -06:00
Howto_lammps_gui.rst
open available error URLs with double click or from context menu
2025-04-28 18:25:40 -04:00
Howto_library.rst
…
Howto_manifold.rst
…
Howto_mdi.rst
…
Howto_moltemplate.rst
make spellchecker happy
2025-03-25 14:55:30 -04:00
Howto_multiple.rst
docs: start with howto section
2024-08-18 07:59:29 -06:00
Howto_nemd.rst
…
Howto_output.rst
…
Howto_peri.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
Howto_polarizable.rst
…
Howto_pylammps.rst
python: doc and example updates
2024-12-12 23:27:07 -07:00
Howto_python.rst
document how to address "externally managed environment" errors with install-python
2025-03-18 20:20:56 -04:00
Howto_replica.rst
…
Howto_restart.rst
docs: start with howto section
2024-08-18 07:59:29 -06:00
Howto_rheo.rst
Updating rheo citation information
2024-11-11 11:42:50 -07:00
Howto_spc.rst
continue refactoring for bio force field and water moldel discussions
2025-05-17 23:30:18 -04:00
Howto_spherical.rst
…
Howto_spins.rst
…
Howto_structured_data.rst
docs: complete howto review
2024-08-18 13:20:00 -06:00
Howto_temperature.rst
…
Howto_thermostat.rst
Name change: langevin/gjf to gjf
2025-04-29 12:00:06 -07:00
Howto_tip3p.rst
tweak table widths for smoother display as PDF
2024-08-19 04:43:57 -04:00
Howto_tip4p.rst
continue refactoring for bio force field and water moldel discussions
2025-05-17 23:30:18 -04:00
Howto_tip5p.rst
tweak table widths for smoother display as PDF
2024-08-19 04:43:57 -04:00
Howto_triclinic.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
Howto_type_labels.rst
Update Howto_type_labels.rst
2024-04-16 00:20:18 -04:00
Howto_viscosity.rst
docs: complete howto review
2024-08-18 13:20:00 -06:00
Howto_viz.rst
docs: start with howto section
2024-08-18 07:59:29 -06:00
Howto_walls.rst
…
Howto_wsl.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Howto.rst
continue refactoring for bio force field and water moldel discussions
2025-05-17 23:30:18 -04:00
hyper.rst
…
if.rst
doc pages 949-1220
2024-08-17 00:28:57 -04:00
improper_amoeba.rst
find more misformatted references in ReST sources
2023-10-26 04:46:33 -04:00
improper_class2.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
improper_coeff.rst
…
improper_cossq.rst
improper styles moved to EXTRA-MOLECULE
2024-05-16 15:08:02 -04:00
improper_cvff.rst
…
improper_distance.rst
improper styles moved to EXTRA-MOLECULE
2024-05-16 15:08:02 -04:00
improper_distharm.rst
…
improper_fourier.rst
improper styles moved to EXTRA-MOLECULE
2024-05-16 15:08:02 -04:00
improper_harmonic.rst
…
improper_hybrid.rst
clarify that hybrid styles also do not write coeff data to data files
2024-07-30 08:59:51 -04:00
improper_inversion_harmonic.rst
…
improper_none.rst
…
improper_ring.rst
improper styles moved to EXTRA-MOLECULE
2024-05-16 15:08:02 -04:00
improper_sqdistharm.rst
…
improper_style.rst
doc pages 949-1220
2024-08-17 00:28:57 -04:00
improper_umbrella.rst
…
improper_zero.rst
…
include.rst
doc pages 949-1220
2024-08-17 00:28:57 -04:00
info.rst
doc pages 949-1220
2024-08-17 00:28:57 -04:00
Install_conda.rst
…
Install_git.rst
GitHub has stopped support for subversion in 2024. Remove note from 2016.
2025-04-24 18:42:19 -04:00
Install_linux.rst
Remove lammps-shell tool as it has been superseded by LAMMPS-GUI
2024-07-22 06:43:10 -04:00
Install_mac.rst
Update macOS info
2025-03-19 13:57:49 +01:00
Install_tarball.rst
docs: update install section
2024-08-14 00:03:10 -06:00
Install_windows.rst
docs: update install section
2024-08-14 00:03:10 -06:00
Install.rst
docs: update commands section
2024-08-16 12:54:53 -06:00
Intro_authors.rst
small clarifications and corrections. Sync with current state of affairs
2025-05-19 11:31:42 -04:00
Intro_citing.rst
add DOIs for recent stable releases
2024-03-11 22:40:21 -04:00
Intro_features.rst
small tweak
2024-04-16 20:07:30 -04:00
Intro_nonfeatures.rst
spelling
2024-08-19 08:45:56 -04:00
Intro_opensource.rst
small tweak to license text
2024-08-20 21:12:14 -04:00
Intro_overview.rst
small updates and clarifications
2025-03-27 12:52:48 -04:00
Intro_portability.rst
small clarifications and corrections. Sync with current state of affairs
2025-05-19 11:31:42 -04:00
Intro_website.rst
…
Intro.rst
…
jump.rst
…
kim_commands.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
kspace_modify.rst
doc fix for kspace_modify from @ndtrung81
2025-01-23 10:06:37 -05:00
kspace_style.rst
whitespace
2024-02-05 17:22:53 -05:00
label.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
labelmap.rst
Mention bonded force field primer from typelabel paper in bioFF howto
2024-06-26 07:27:11 -04:00
lattice.rst
better documention and error checking for 2d general triclinic
2024-04-08 10:43:20 -06:00
lepton_expression.rst
…
Library_add.rst
remove references to -DLAMMPS_SMALLSMALL and trigger error when used
2025-03-14 10:20:31 -04:00
Library_atoms.rst
first try at implementing lammps_extract_atom_size()
2024-08-30 22:50:42 -04:00
Library_config.rst
…
Library_create.rst
refactor handling of plugin loading to make plugin a global property
2025-06-11 02:52:28 -04:00
Library_execute.rst
add missing lammps_expand() function
2025-01-13 19:13:34 -05:00
Library_neighbor.rst
…
Library_objects.rst
library: update new function signatures to use void* instead of bigint
2025-01-19 16:06:33 -07:00
Library_properties.rst
update docs for new library function
2024-07-16 19:08:01 -04:00
Library_scatter.rst
…
Library_utility.rst
have Error::set_show_error() return the previous setting
2025-03-24 04:13:24 -04:00
Library.rst
python: update examples and docs
2024-12-12 23:27:07 -07:00
log.rst
doc pages 949-1220
2024-08-17 00:28:57 -04:00
Manual_version.rst
small updates and clarifications
2025-03-27 12:52:48 -04:00
Manual.rst
white on black title. Make page 1 show up in PDF sidebar
2024-08-19 16:26:38 -04:00
mass.rst
…
mdi.rst
tweak table widths for smoother display as PDF
2024-08-19 04:43:57 -04:00
min_modify.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
min_spin.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
min_style.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
minimize.rst
modernize use of \it and \sf
2025-03-13 22:25:14 -04:00
Modify_atom.rst
Edits to modify doc files
2024-08-13 20:17:26 -06:00
Modify_body.rst
…
Modify_bond.rst
…
Modify_command.rst
…
Modify_compute.rst
list post_constructor methods and modernize description
2025-04-03 13:47:53 -04:00
Modify_contribute.rst
Edits to modify doc files
2024-08-13 20:17:26 -06:00
Modify_dump.rst
…
Modify_fix.rst
list post_constructor methods and modernize description
2025-04-03 13:47:53 -04:00
Modify_gran_sub_mod.rst
tweak table widths for smoother display as PDF
2024-08-19 04:43:57 -04:00
Modify_kspace.rst
…
Modify_min.rst
…
Modify_overview.rst
Edits to modify doc files
2024-08-13 20:17:26 -06:00
Modify_pair.rst
Address akohlmey comments
2025-04-21 10:06:50 -06:00
Modify_region.rst
…
Modify_requirements.rst
adjust some wording for the removal of Python 2.x compatibility
2025-02-12 22:04:18 -05:00
Modify_style.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Modify_thermo.rst
Edits to modify doc files
2024-08-13 20:17:26 -06:00
Modify_variable.rst
…
Modify.rst
…
molecule.rst
tweak table widths for smoother display as PDF
2024-08-19 04:43:57 -04:00
neb_spin.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
neb.rst
Fixed typo in NEB documentation (energy units --> dimensionless)
2024-01-24 14:52:42 -05:00
neigh_modify.rst
update pending version tags with planned release date
2024-08-25 16:39:13 -04:00
neighbor.rst
remove multi/old from docs and print deprecation warning when used
2025-02-01 15:29:27 -05:00
newton.rst
…
next.rst
…
package.rst
fix a few more .rst formatting issues flagged by pandoc
2025-03-15 12:35:12 -04:00
Packages_details.rst
adjust some wording for the removal of Python 2.x compatibility
2025-02-12 22:04:18 -05:00
Packages_list.rst
docs: fixup Packages_list.rst table
2024-08-18 07:41:06 -06:00
Packages.rst
…
pair_adp.rst
…
pair_agni.rst
…
pair_aip_water_2dm.rst
modernize boldface font selection in LaTeX sections
2025-03-13 22:14:07 -04:00
pair_airebo.rst
small corrections
2024-02-22 09:15:18 -05:00
pair_amoeba.rst
…
pair_atm.rst
Merge pull request #4262 from jrgissing/type-labels-for-pair_style_commands
2024-08-19 15:02:23 -04:00
pair_awpmd.rst
…
pair_beck.rst
make more cases specifying cutoff Rc/r_c consistent
2023-12-01 05:49:20 -05:00
pair_body_nparticle.rst
…
pair_body_rounded_polygon.rst
…
pair_body_rounded_polyhedron.rst
correct typo and link in body particles doc
2023-11-16 10:35:02 -07:00
pair_bop.rst
fix a few more .rst formatting issues flagged by pandoc
2025-03-15 12:35:12 -04:00
pair_born_gauss.rst
fix cut-n-paste doc issue
2024-07-26 10:35:07 -04:00
pair_born.rst
…
pair_bpm_spring.rst
Merge branch 'develop' into BPM
2025-02-04 16:02:57 -07:00
pair_brownian.rst
doc
2024-10-04 11:35:46 -05:00
pair_buck6d_coul_gauss.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
pair_buck_long.rst
…
pair_buck.rst
…
pair_charmm.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
pair_class2.rst
…
pair_coeff.rst
…
pair_colloid.rst
…
pair_comb.rst
…
pair_cosine_squared.rst
Edits/corrections to doc pages 2315-2589
2024-08-15 09:38:58 -05:00
pair_coul_diel.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
pair_coul_shield.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
pair_coul_slater.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
pair_coul_tt.rst
…
pair_coul.rst
Merge branch 'develop' into collected-small-fixes
2025-03-13 03:06:14 -04:00
pair_cs.rst
…
pair_dielectric.rst
…
pair_dipole.rst
Merge branch 'doc-pdf' of https://github.com/ndtrung81/lammps into collected-small-fixes
2024-08-15 13:37:11 -04:00
pair_dispersion_d3.rst
Set pending version tags to 2Apr2025
2025-04-01 21:30:53 -04:00
pair_dpd_coul_slater_long.rst
Merge branch 'develop' into next-release
2024-06-26 19:50:27 -04:00
pair_dpd_ext.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
pair_dpd_fdt.rst
final set of bibliography updates
2024-08-15 22:52:42 -04:00
pair_dpd.rst
Edits/corrections to doc pages 2315-2589
2024-08-15 09:38:58 -05:00
pair_drip.rst
…
pair_dsmc.rst
document requirement of per-type masses
2024-02-22 04:34:22 -05:00
pair_e3b.rst
convert e3b and srp
2024-08-08 18:57:53 -04:00
pair_eam.rst
rephrase warning about EAM deansity exceeding tabulated embedding term
2024-04-16 23:02:29 -04:00
pair_edip.rst
…
pair_eff.rst
Edits/corrections to doc pages 2315-2589
2024-08-15 09:38:58 -05:00
pair_eim.rst
fix a few more .rst formatting issues flagged by pandoc
2025-03-15 12:35:12 -04:00
pair_exp6_rx.rst
…
pair_extep.rst
Edits/corrections to doc pages 2315-2589
2024-08-15 09:38:58 -05:00
pair_fep_soft.rst
Merge pull request #4262 from jrgissing/type-labels-for-pair_style_commands
2024-08-19 15:02:23 -04:00
pair_gauss.rst
…
pair_gayberne.rst
…
pair_gran.rst
Edits/corrections to doc pages 2315-2589
2024-08-15 09:38:58 -05:00
pair_granular.rst
address spelling issues
2025-05-05 20:22:00 -04:00
pair_gromacs.rst
…
pair_gw.rst
…
pair_harmonic_cut.rst
…
pair_hbond_dreiding.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
pair_hdnnp.rst
bibliography cleanup
2024-08-14 10:32:46 -04:00
pair_hybrid.rst
clarify use of pair-wise additive pair style requirement as go-between for many-body potentials.
2025-05-28 11:22:39 -04:00
pair_ilp_graphene_hbn.rst
modernize boldface font selection in LaTeX sections
2025-03-13 22:14:07 -04:00
pair_ilp_tmd.rst
modernize boldface font selection in LaTeX sections
2025-03-13 22:14:07 -04:00
pair_kim.rst
…
pair_kolmogorov_crespi_full.rst
modernize boldface font selection in LaTeX sections
2025-03-13 22:14:07 -04:00
pair_kolmogorov_crespi_z.rst
final set of bibliography updates
2024-08-15 22:52:42 -04:00
pair_lcbop.rst
…
pair_lebedeva_z.rst
…
pair_lepton.rst
fix typo, cut-n-paste error, and add clarification
2024-01-18 14:32:40 -05:00
pair_line_lj.rst
…
pair_list.rst
…
pair_lj96.rst
…
pair_lj_cubic.rst
…
pair_lj_cut_coul.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
pair_lj_cut_sphere.rst
…
pair_lj_cut_tip4p.rst
Merge pull request #4262 from jrgissing/type-labels-for-pair_style_commands
2024-08-19 15:02:23 -04:00
pair_lj_expand_sphere.rst
…
pair_lj_expand.rst
…
pair_lj_long.rst
Merge pull request #4262 from jrgissing/type-labels-for-pair_style_commands
2024-08-19 15:02:23 -04:00
pair_lj_pirani.rst
correct reference
2025-04-28 22:20:57 -04:00
pair_lj_relres.rst
…
pair_lj_smooth_linear.rst
use r_c consistently
2023-12-01 05:43:42 -05:00
pair_lj_smooth.rst
spelling
2025-05-06 12:05:12 -04:00
pair_lj_switch3_coulgauss_long.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
pair_lj.rst
update documentation for new "make fasthtml"
2025-03-12 17:50:27 -04:00
pair_local_density.rst
…
pair_lubricate.rst
update docs to make wall fix restrictions more explicit
2024-08-16 16:29:45 -04:00
pair_lubricateU.rst
update docs to make wall fix restrictions more explicit
2024-08-16 16:29:45 -04:00
pair_mdf.rst
…
pair_meam_spline.rst
…
pair_meam_sw_spline.rst
…
pair_meam.rst
small grammar tweak
2024-08-08 21:27:06 -04:00
pair_mesocnt.rst
…
pair_mesodpd.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
pair_mgpt.rst
modernize boldface font selection in LaTeX sections
2025-03-13 22:14:07 -04:00
pair_mie.rst
update documentation according to accelerated style include check
2024-10-04 13:54:04 -04:00
pair_mliap.rst
consistently use a :class: qualifier for admonitions
2025-01-30 03:54:26 -05:00
pair_modify.rst
…
pair_momb.rst
…
pair_morse.rst
use r_c consistently
2023-12-01 05:36:25 -05:00
pair_multi_lucy_rx.rst
…
pair_multi_lucy.rst
…
pair_nb3b.rst
consolidate nb3b pair style docs
2023-11-03 22:39:42 -04:00
pair_nm.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
pair_none.rst
…
pair_oxdna2.rst
rename CG-DNA potential files
2024-06-20 14:33:26 -04:00
pair_oxdna.rst
rename CG-DNA potential files
2024-06-20 14:33:26 -04:00
pair_oxrna2.rst
rename CG-DNA potential files
2024-06-20 14:33:26 -04:00
pair_pace.rst
update pair_pace.rst documentation page
2023-11-25 23:37:01 +01:00
pair_pedone.rst
Edits/corrections to doc pages 2315-2589
2024-08-15 09:38:58 -05:00
pair_peri.rst
…
pair_pod.rst
various documentation fixups, dedup references, wrap paragraphs, adjust underlines, add missing index
2024-06-26 07:26:03 -04:00
pair_polymorphic.rst
bibliography cleanup
2024-08-14 10:32:46 -04:00
pair_python.rst
…
pair_quip.rst
strip off common namespace components from index entries
2024-08-14 12:18:17 -04:00
pair_rann.rst
some more documentation updates for bibliography
2024-08-14 14:57:53 -04:00
pair_reaxff.rst
add tip for addressing memory management issues with ReaxFF
2025-01-30 03:57:30 -05:00
pair_rebomos.rst
update version tags for feature release
2024-04-16 19:47:12 -04:00
pair_resquared.rst
…
pair_rheo_solid.rst
update pending version tags with planned release date
2024-08-25 16:39:13 -04:00
pair_rheo.rst
update pending version tags with planned release date
2024-08-25 16:39:13 -04:00
pair_saip_metal.rst
modernize boldface font selection in LaTeX sections
2025-03-13 22:14:07 -04:00
pair_sdpd_taitwater_isothermal.rst
…
pair_smatb.rst
…
pair_smd_hertz.rst
…
pair_smd_tlsph.rst
…
pair_smd_triangulated_surface.rst
…
pair_smd_ulsph.rst
…
pair_smtbq.rst
…
pair_snap.rst
some more documentation updates for bibliography
2024-08-14 14:57:53 -04:00
pair_soft.rst
Update docs
2024-06-05 09:00:01 -06:00
pair_sph_heatconduction.rst
add note about age of SPH package PDF add-on docs.
2024-12-10 23:00:30 -05:00
pair_sph_idealgas.rst
add note about age of SPH package PDF add-on docs.
2024-12-10 23:00:30 -05:00
pair_sph_lj.rst
add note about age of SPH package PDF add-on docs.
2024-12-10 23:00:30 -05:00
pair_sph_rhosum.rst
add note about age of SPH package PDF add-on docs.
2024-12-10 23:00:30 -05:00
pair_sph_taitwater_morris.rst
add note about age of SPH package PDF add-on docs.
2024-12-10 23:00:30 -05:00
pair_sph_taitwater.rst
add note about age of SPH package PDF add-on docs.
2024-12-10 23:00:30 -05:00
pair_spica.rst
updated pair style and angle style /kk in docs
2024-06-05 19:56:29 -04:00
pair_spin_dipole.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
pair_spin_dmi.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
pair_spin_exchange.rst
modernize LaTeX for formatting text in math mode
2025-03-12 17:14:11 -04:00
pair_spin_magelec.rst
…
pair_spin_neel.rst
…
pair_srp.rst
convert e3b and srp
2024-08-08 18:57:53 -04:00
pair_style.rst
Update pair_style.rst
2025-04-22 14:47:24 +02:00
pair_sw_angle_table.rst
…
pair_sw.rst
…
pair_table_rx.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
pair_table.rst
…
pair_tersoff_mod.rst
…
pair_tersoff_zbl.rst
…
pair_tersoff.rst
…
pair_thole.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
pair_threebody_table.rst
…
pair_tracker.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
pair_tri_lj.rst
…
pair_uf3.rst
update version tags for next feature release
2024-06-25 13:30:38 -04:00
pair_ufm.rst
…
pair_vashishta.rst
…
pair_wf_cut.rst
…
pair_write.rst
type label support for pair_write
2024-08-06 23:51:49 -04:00
pair_ylz.rst
…
pair_yukawa_colloid.rst
Add accelerator package text
2023-10-12 12:52:57 -06:00
pair_yukawa.rst
…
pair_zbl.rst
…
pair_zero.rst
…
partition.rst
…
plugin.rst
refactor handling of plugin loading to make plugin a global property
2025-06-11 02:52:28 -04:00
prd.rst
…
print.rst
…
processors.rst
spelling
2024-03-17 15:13:13 -04:00
Python_atoms.rst
python: doc and example updates
2024-12-12 23:27:07 -07:00
Python_call.rst
…
Python_config.rst
…
Python_create.rst
python: doc and example updates
2024-12-12 23:27:07 -07:00
Python_error.rst
misc doc fixes to python section
2024-08-13 16:30:33 -06:00
Python_examples.rst
…
Python_execute.rst
python: doc and example updates
2024-12-12 23:27:07 -07:00
Python_ext.rst
…
Python_formats.rst
…
Python_head.rst
python: doc and example updates
2024-12-12 23:27:07 -07:00
Python_install.rst
Set pending version tags to 2Apr2025
2025-04-01 21:30:53 -04:00
Python_jupyter.rst
small fixes for the manual
2024-12-14 17:12:51 -05:00
Python_launch.rst
improve phrasing
2025-04-10 10:49:27 -04:00
Python_module.rst
python: doc and example updates
2024-12-12 23:27:07 -07:00
Python_neighbor.rst
misc doc fixes to python section
2024-08-13 16:30:33 -06:00
Python_objects.rst
python: doc and example updates
2024-12-12 23:27:07 -07:00
Python_overview.rst
adjust some wording for the removal of Python 2.x compatibility
2025-02-12 22:04:18 -05:00
Python_properties.rst
whitespace
2024-12-14 16:58:58 -05:00
Python_run.rst
…
Python_scatter.rst
improve docs and use dtype as parameter name to avoid confusion with type
2025-04-04 10:41:35 -04:00
Python_trouble.rst
…
python.rst
…
quit.rst
…
read_data.rst
mass replace 2 -> two, and 3 -> three where it can be safely detecte
2024-08-17 08:15:58 -04:00
read_dump.rst
some more fixes and rewording
2024-09-30 15:42:34 -04:00
read_restart.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
region2vmd.rst
Set pending version tags to 2Apr2025
2025-04-01 21:30:53 -04:00
region.rst
add block to list of regions with all-variable shape options
2025-02-26 10:42:52 -05:00
replicate.rst
spelling fixes
2024-05-13 13:43:50 -04:00
rerun.rst
…
reset_atoms.rst
reset_atoms: one more grammar tweak
2024-07-06 18:03:43 -04:00
reset_timestep.rst
…
restart.rst
…
Run_basics.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Run_formats.rst
small tweaks
2025-03-29 15:56:34 -04:00
Run_head.rst
Start general document about file formats
2024-09-25 23:15:20 -04:00
Run_options.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Run_output.rst
clarify and explain that there may not be neighbor list statistics data
2025-02-01 09:19:33 -05:00
run_style.rst
improve error message
2024-08-21 17:48:01 -04:00
Run_windows.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
run.rst
add renieigbor option to fix set
2025-05-26 16:22:52 -06:00
set.rst
new doc page for fix set command with example
2025-05-02 16:13:01 -06:00
shell.rst
…
special_bonds.rst
…
Speed_bench.rst
docs: update speed section
2024-08-16 14:09:32 -06:00
Speed_compare.rst
provide some more talking points for comparison of KOKKOS and GPU package
2025-05-25 05:04:37 -04:00
Speed_gpu.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Speed_intel.rst
add updates/corrections, improve formatting
2024-12-27 03:50:51 -05:00
Speed_kokkos.rst
integrate and adapt contents from PR #4028 by @alphataubio
2025-01-15 06:05:25 -05:00
Speed_measure.rst
correct discuss FFT benchmark timing for PPPM
2025-05-27 23:40:52 -04:00
Speed_omp.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Speed_opt.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
Speed_packages.rst
docs: update speed section
2024-08-16 14:09:32 -06:00
Speed_tips.rst
…
Speed.rst
…
suffix.rst
use command-line consistently where applicable and drop "line" where not
2024-12-27 04:03:41 -05:00
tad.rst
…
temper_grem.rst
…
temper_npt.rst
…
temper.rst
…
thermo_modify.rst
more tweaks
2024-04-08 16:25:17 -06:00
thermo_style.rst
small doc formatting and spelling fixes
2024-04-16 19:33:14 -04:00
thermo.rst
…
third_order.rst
…
timer.rst
key word -> keyword
2025-03-14 06:59:33 -04:00
timestep.rst
…
Tools.rst
small update
2025-05-02 00:30:22 -04:00
uncompute.rst
…
undump.rst
…
unfix.rst
…
units.rst
…
variable.rst
move documentation of sign() function to logical location and add version tag
2025-03-02 12:40:32 -05:00
velocity.rst
…
write_coeff.rst
…
write_data.rst
clarify that all hybrid styles do not write Coeff sections
2024-07-30 05:45:24 -04:00
write_dump.rst
…
write_restart.rst
more doc page updates for general tri
2023-11-16 16:35:16 -07:00