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lammps/doc/src
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Axel Kohlmeyer babec093ca Merge branch 'develop' into strip-style-suffix
2022-12-14 13:45:59 -05:00
..
_ext
…
99
…
2001
…
img
add examples import one image to manual
2022-05-08 21:15:32 -04:00
JPG
Convert PDLAMMPS user doc from latex to sphinx
2022-09-29 06:57:52 -04:00
PDF
Update PDF Colvars manual
2022-06-02 11:48:19 -04:00
.gitignore
…
accel_styles.rst
Math replacements and cosmetic edits to documentation
2022-09-01 01:01:46 -05:00
angle_amoeba.rst
fix documentation issues (spelling, references, non-ASCII chars)
2022-07-04 19:09:56 -04:00
angle_charmm.rst
avoid duplication of Accelerator package info in additional doc pages
2021-10-11 16:49:59 -06:00
angle_class2.rst
sync with current develop
2022-04-18 17:29:23 -06:00
angle_coeff.rst
more formatting/typesetting consistency
2022-09-03 04:17:22 -04:00
angle_cosine_buck6d.rst
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
angle_cosine_delta.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
angle_cosine_periodic.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
angle_cosine_shift_exp.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
angle_cosine_shift.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -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
…
angle_cross.rst
fix up mistyped package names
2021-07-03 16:19:15 -04:00
angle_dipole.rst
move some styles around
2021-07-09 16:54:00 -04:00
angle_fourier_simple.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
angle_fourier.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
angle_gaussian.rst
expand valid range of bond/angle style gaussian. update docs and tests.
2022-11-21 22:28:44 -05:00
angle_harmonic.rst
…
angle_hybrid.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
angle_mesocnt.rst
update versions strings for the next patch release
2022-09-14 16:29:10 -04:00
angle_mm3.rst
fix up mistyped package names
2021-07-03 16:19:15 -04:00
angle_none.rst
…
angle_quartic.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
angle_spica.rst
changed rstfile names, style names, and description about FF for SPICA
2022-07-08 16:54:01 +09:00
angle_style.rst
Merge branch 'lammps:develop' into mesocnt_stable
2022-08-29 12:45:20 +01:00
angle_table.rst
update to upstream
2021-05-21 16:15:31 -04:00
angle_zero.rst
Tweaks to documentation to make it more consistent and machine-readable
2022-08-19 19:25:15 -05:00
angles.rst
…
atc_add_molecule.rst
…
atc_add_species.rst
…
atc_atom_element_map.rst
…
atc_atom_weight.rst
…
atc_atomic_charge.rst
…
atc_boundary_dynamics.rst
…
atc_boundary_faceset.rst
…
atc_boundary_type.rst
…
atc_consistent_fe_initialization.rst
…
atc_control_localized_lambda.rst
…
atc_control_momentum.rst
…
atc_control_thermal.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
atc_decomposition.rst
…
atc_electron_integration.rst
…
atc_equilibrium_start.rst
…
atc_extrinsic_exchange.rst
…
atc_fe_md_boundary.rst
…
atc_filter_scale.rst
…
atc_filter_type.rst
…
atc_fix_flux.rst
…
atc_fix.rst
…
atc_hardy_computes.rst
…
atc_hardy_fields.rst
…
atc_hardy_gradients.rst
…
atc_hardy_kernel.rst
…
atc_hardy_on_the_fly.rst
…
atc_hardy_rates.rst
…
atc_initial.rst
…
atc_internal_element_set.rst
…
atc_internal_quadrature.rst
…
atc_kernel_bandwidth.rst
…
atc_lumped_lambda_solve.rst
…
atc_mask_direction.rst
…
atc_mass_matrix.rst
…
atc_material.rst
…
atc_mesh_add_to_nodeset.rst
…
atc_mesh_create_elementset.rst
…
atc_mesh_create_faceset_box.rst
…
atc_mesh_create_faceset_plane.rst
…
atc_mesh_create_nodeset.rst
…
atc_mesh_create.rst
…
atc_mesh_delete_elements.rst
…
atc_mesh_nodeset_to_elementset.rst
…
atc_mesh_output.rst
…
atc_mesh_quadrature.rst
…
atc_mesh_read.rst
…
atc_mesh_write.rst
…
atc_output_boundary_integral.rst
…
atc_output_contour_integral.rst
…
atc_output_nodeset.rst
…
atc_output_volume_integral.rst
…
atc_output.rst
Consistently use instead of
2020-11-10 14:04:49 +01:00
atc_pair_interactions.rst
…
atc_poisson_solver.rst
…
atc_read_restart.rst
…
atc_remove_molecule.rst
…
atc_remove_source.rst
…
atc_remove_species.rst
…
atc_reset_atomic_reference.rst
…
atc_reset_time.rst
…
atc_sample_frequency.rst
…
atc_set_reference_pe.rst
…
atc_source_integration.rst
…
atc_source.rst
…
atc_temperature_definition.rst
…
atc_time_filter.rst
…
atc_time_integration.rst
…
atc_track_displacement.rst
…
atc_unfix_flux.rst
…
atc_unfix.rst
…
atc_write_atom_weights.rst
…
atc_write_restart.rst
…
atom_modify.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
atom_style.rst
fix spelling and table format issues. re-wrap paragraphs in doc sources.
2022-10-10 17:26:13 -04:00
balance.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
Bibliography.rst
format DOI tags consistently
2022-09-26 11:41:22 -04:00
bond_bpm_rotational.rst
add .. versiondded:: tag to BPM package commands and restrictions text consistent
2022-11-07 22:57:32 -05:00
bond_bpm_spring.rst
add .. versiondded:: tag to BPM package commands and restrictions text consistent
2022-11-07 22:57:32 -05:00
bond_class2.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
bond_coeff.rst
Missing key word in fix/ave/chunk docs, edits to bond_coeff docs
2022-10-13 14:42:10 -05:00
bond_fene_expand.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
bond_fene.rst
clarify docs for bond style fene/nm/split and rename to fene/nm
2021-12-06 16:21:12 -05:00
bond_gaussian.rst
expand valid range of bond/angle style gaussian. update docs and tests.
2022-11-21 22:28:44 -05:00
bond_gromos.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
bond_harmonic_shift_cut.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
bond_harmonic_shift.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
bond_harmonic.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
bond_hybrid.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
bond_mesocnt.rst
update versions strings for the next patch release
2022-09-14 16:29:10 -04:00
bond_mm3.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
bond_morse.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
bond_none.rst
…
bond_nonlinear.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
bond_oxdna.rst
Merge pull request #2924 from ohenrich/cg-dna
2021-09-07 14:12:07 -04:00
bond_quartic.rst
clarify LJ energy function component of the quartic bond style
2022-09-30 19:48:56 -04:00
bond_special.rst
move some styles around
2021-07-09 16:54:00 -04:00
bond_style.rst
spelling
2022-08-30 14:44:01 -04:00
bond_table.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
bond_write.rst
…
bond_zero.rst
Tweaks to documentation to make it more consistent and machine-readable
2022-08-19 19:25:15 -05:00
bonds.rst
…
boundary.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
Build_basics.rst
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
Build_cmake.rst
Document multi-configuration build support in CMake
2021-11-04 16:32:21 -04:00
Build_development.rst
add CMake check that will refuse compilation of unit tests or skip tests
2022-10-17 18:11:30 -04:00
Build_diskspace.rst
update documentation to refer to the new branch names (develop, release)
2021-10-10 04:39:16 -04:00
Build_extras.rst
add missing entry to table
2022-12-13 09:22:02 -05:00
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
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
Build_manual.rst
spelling
2022-10-03 09:55:20 -04:00
Build_package.rst
more information about compiling LAMMPS on windows
2022-05-19 00:06:00 -04:00
Build_settings.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Build_windows.rst
more information about compiling LAMMPS on windows
2022-05-19 00:06:00 -04:00
Build.rst
notes on reducing disk space requirements when building LAMMPS from source
2021-08-25 22:51:21 -04:00
change_box.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Classes_atom.rst
…
Classes_input.rst
…
Classes_lammps.rst
…
Classes.rst
update header texts
2020-10-14 23:28:28 -04:00
clear.rst
delete atomfile style variables with clear command
2022-10-18 07:34:06 -04:00
comm_modify.rst
Tweaks to documentation to make it more consistent and machine-readable
2022-08-19 19:25:15 -05:00
comm_style.rst
…
Commands_all.rst
Update documentation
2022-12-01 00:11:21 -05:00
Commands_bond.rst
added bond_style mesocnt documentation, corrected pair_style mesocnt documentation and added mesocnt styles in style indices
2022-08-15 18:44:31 +02:00
Commands_category.rst
update documentation for removal of box command
2022-11-21 14:04:58 -05:00
Commands_compute.rst
update pod doc
2022-11-20 12:30:11 -05:00
Commands_dump.rst
properly integrate the new file into the document toctree
2022-07-15 17:51:36 -04:00
Commands_fix.rst
rename doc file for all electrode fixes to fix_electrode.rst
2022-12-04 16:10:02 -05:00
Commands_input.rst
add -skiprun command line flag that sets a timeout so that run and minimizations loops are skipped
2021-09-03 11:21:42 -04:00
Commands_kspace.rst
add a table with list of dump styles
2022-07-15 14:47:45 -06:00
commands_list.rst
Update documentation
2022-12-01 00:11:21 -05:00
Commands_pair.rst
Update doc to reflect a change in the pair style name
2022-11-29 20:20:42 -05:00
Commands_parse.rst
clarification on what constituets single, double, and triple quotes.
2022-08-03 01:50:11 -04:00
Commands_removed.rst
provide backward compatible URLs to reduce 404 errors on www.lammps.org
2022-12-13 05:28:28 -05:00
Commands_structure.rst
…
Commands.rst
properly integrate the new file into the document toctree
2022-07-15 17:51:36 -04:00
compute_ackland_atom.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
compute_adf.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
compute_angle_local.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
compute_angle.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
compute_angmom_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_ave_sphere_atom.rst
add some more versionadded tags, now mostly complete for 2022
2022-09-25 09:41:55 -04:00
compute_basal_atom.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
compute_body_local.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
compute_bond_local.rst
Fixing merge conflicts
2022-09-03 12:35:32 -06:00
compute_bond.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
compute_born_matrix.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_centro_atom.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
compute_chunk_atom.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
compute_chunk_spread_atom.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
compute_cluster_atom.rst
More math and code-block edits
2022-08-15 23:48:30 -05:00
compute_cna_atom.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
compute_cnp_atom.rst
Updates to fix code-block at top, math, and anything else I found
2022-08-15 20:17:36 -05:00
compute_com_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_com.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_contact_atom.rst
More math and code-block edits
2022-08-15 23:48:30 -05:00
compute_coord_atom.rst
Tweaks to documentation to make it more consistent and machine-readable
2022-08-19 19:25:15 -05:00
compute_damage_atom.rst
reference the Howto from the rest of the manual. Spelling fixes.
2022-09-29 07:43:01 -04:00
compute_dihedral_local.rst
More math and code-block edits
2022-08-15 23:48:30 -05:00
compute_dihedral.rst
More math and code-block edits
2022-08-15 23:48:30 -05:00
compute_dilatation_atom.rst
reference the Howto from the rest of the manual. Spelling fixes.
2022-09-29 07:43:01 -04:00
compute_dipole_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_dipole.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_displace_atom.rst
Fixed remaining discrepancies between lists of keywords and doc of them
2022-10-13 23:00:13 -05:00
compute_dpd_atom.rst
More math and code-block edits
2022-08-15 23:48:30 -05:00
compute_dpd.rst
More math and code-block edits
2022-08-15 23:48:30 -05:00
compute_edpd_temp_atom.rst
More math and code-block edits
2022-08-15 23:48:30 -05:00
compute_efield_atom.rst
More math and code-block edits
2022-08-15 23:48:30 -05:00
compute_entropy_atom.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
compute_erotate_asphere.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_erotate_rigid.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_erotate_sphere_atom.rst
More math and code-block edits
2022-08-15 23:48:30 -05:00
compute_erotate_sphere.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_event_displace.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_fabric.rst
Tweaks to documentation to make it more consistent and machine-readable
2022-08-19 19:25:15 -05:00
compute_fep_ta.rst
add some more versionadded tags, now mostly complete for 2022
2022-09-25 09:41:55 -04:00
compute_fep.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_global_atom.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_group_group.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_gyration_chunk.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_gyration_shape_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_gyration_shape.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_gyration.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_heat_flux.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_hexorder_atom.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_hma.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_improper_local.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_improper.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_inertia_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_ke_atom_eff.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_ke_atom.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_ke_eff.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_ke_rigid.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_ke.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_mesont.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_mliap.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_modify.rst
Changed a couple of "dof" to "DOF" as per Axel's preference
2022-08-22 23:29:24 -05:00
compute_momentum.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_msd_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_msd_nongauss.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_msd.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_nbond_atom.rst
add .. versiondded:: tag to BPM package commands and restrictions text consistent
2022-11-07 22:57:32 -05:00
compute_omega_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_orientorder_atom.rst
After running "make fix-whitespace"
2022-08-22 21:41:12 -05:00
compute_pair_local.rst
correct docs for compute pair/local dx/dy/dz to reflect the code behavior
2022-11-28 14:12:30 -05:00
compute_pair.rst
merged in develop
2022-09-07 14:12:26 -06:00
compute_pe_atom.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_pe.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_plasticity_atom.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_pressure_uef.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_pressure.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_property_atom.rst
update versions strings for the next patch release
2022-09-14 16:29:10 -04:00
compute_property_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_property_local.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_ptm_atom.rst
Math replacements; code-block LAMMPS; clarity and parsing-friendly edits
2022-08-16 20:29:12 -05:00
compute_rdf.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_reduce_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_reduce.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_rigid_local.rst
make compute rigid/local consistent with other "possible attributes" docs
2022-10-17 14:51:10 -05:00
compute_saed.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
compute_slice.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_contact_radius.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_damage.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_hourglass_error.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_internal_energy.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_plastic_strain_rate.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_plastic_strain.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_rho.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_tlsph_defgrad.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_tlsph_dt.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_tlsph_num_neighs.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_tlsph_shape.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_tlsph_strain_rate.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_tlsph_strain.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_tlsph_stress.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_triangle_vertices.rst
Updates documentation files to make them more consistent and some typo fixes (round 1)
2022-08-05 23:03:09 -05:00
compute_smd_ulsph_effm.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_ulsph_num_neighs.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_ulsph_strain_rate.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_ulsph_strain.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_ulsph_stress.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_smd_vol.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_sna_atom.rst
add versionadded/versionchanged markers for features from 15Sep2022 and 3Aug2022
2022-09-25 03:20:29 -04:00
compute_sph_e_atom.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_sph_rho_atom.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_sph_t_atom.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_spin.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
compute_stress_atom.rst
add example for a 1-d pressure profile
2022-08-29 17:04:48 -04:00
compute_stress_mop.rst
More cosmetic edits to documentation
2022-08-18 19:25:06 -05:00
compute_stress_profile.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_tally.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_tdpd_cc_atom.rst
More cosmetic edits to documentation
2022-08-18 19:25:06 -05:00
compute_temp_asphere.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_body.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_com.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_cs.rst
correct inconsistent spelling of name
2022-09-23 10:33:44 -04:00
compute_temp_deform_eff.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_deform.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_drude.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_eff.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_partial.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_profile.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_ramp.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
compute_temp_region_eff.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_region.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_rotate.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_sphere.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_temp_uef.rst
Finished edits on computes (whew!); builds with no errors or warnings
2022-08-19 00:25:06 -05:00
compute_temp.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_ti.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_torque_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_vacf.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_vcm_chunk.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_viscosity_cos.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
compute_voronoi_atom.rst
Fixed remaining discrepancies between lists of keywords and doc of them
2022-10-13 23:00:13 -05:00
compute_xrd.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
compute.rst
update pod doc
2022-11-20 12:30:11 -05:00
computes.rst
…
Cplusplus.rst
…
create_atoms.rst
Fixed remaining discrepancies between lists of keywords and doc of them
2022-10-13 23:00:13 -05:00
create_bonds.rst
Edits to documentation files for consistency and math
2022-08-19 23:49:44 -05:00
create_box.rst
update documentation for removal of box command
2022-11-21 14:04:58 -05:00
delete_atoms.rst
fix sphinx formatting issue
2022-11-28 14:00:26 -05:00
delete_bonds.rst
Fixed remaining discrepancies between lists of keywords and doc of them
2022-10-13 23:00:13 -05:00
Developer_code_design.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Developer_comm_ops.rst
update docs
2022-02-25 14:13:03 -05:00
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
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Developer_org.rst
remove obsolete TODO item
2022-03-03 06:43:52 -05:00
Developer_par_comm.rst
break large file into multiple smaller files by section and add toctree
2021-09-05 21:57:03 -04:00
Developer_par_long.rst
use larger version of FFT grid comm image
2021-09-06 15:50:02 -04:00
Developer_par_neigh.rst
fix typo
2021-09-05 22:10:00 -04:00
Developer_par_openmp.rst
add discussion of OpenMP parallelization
2021-09-06 09:52:19 -04:00
Developer_par_part.rst
break large file into multiple smaller files by section and add toctree
2021-09-05 21:57:03 -04:00
Developer_parallel.rst
update some formulations as suggested by @sjplimp
2021-09-23 13:51:06 -04:00
Developer_platform.rst
implement and use a platform neutral abstraction of unsetenv(3)
2021-11-03 10:53:45 -04:00
Developer_plugins.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Developer_unittest.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Developer_updating.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Developer_utils.rst
Merge branch 'develop' into strip-style-suffix
2022-12-14 13:45:59 -05:00
Developer_write.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Developer.rst
Initial version of an LAMMPS older version code update guide
2022-07-22 00:03:34 -04:00
dielectric.rst
Edits to documentation files for consistency and math
2022-08-19 23:49:44 -05:00
dihedral_charmm.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
dihedral_class2.rst
…
dihedral_coeff.rst
more formatting/typesetting consistency
2022-09-03 04:17:22 -04:00
dihedral_cosine_shift_exp.rst
move some styles around
2021-07-09 16:54:00 -04:00
dihedral_fourier.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
dihedral_harmonic.rst
…
dihedral_helix.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
dihedral_hybrid.rst
update docs for hybrid style updates
2021-08-02 21:53:31 -04:00
dihedral_multi_harmonic.rst
…
dihedral_nharmonic.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
dihedral_none.rst
…
dihedral_opls.rst
…
dihedral_quadratic.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
dihedral_spherical.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
dihedral_style.rst
Edits to documentation files for consistency and math
2022-08-19 23:49:44 -05:00
dihedral_table.rst
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
dihedral_zero.rst
Updates documentation files to make them more consistent and some typo fixes (round 1)
2022-08-05 23:03:09 -05:00
dihedrals.rst
…
dimension.rst
Edits to documentation files for consistency and math
2022-08-19 23:49:44 -05:00
displace_atoms.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
dump_adios.rst
Math replacements and cosmetic edits to documentation
2022-09-01 01:01:46 -05:00
dump_cfg_uef.rst
Math replacements and cosmetic edits to documentation
2022-09-01 01:01:46 -05:00
dump_h5md.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
dump_image.rst
fix typo
2022-11-23 12:55:51 -05:00
dump_modify.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
dump_molfile.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
dump_netcdf.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
dump_vtk.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
dump.rst
fix typo
2022-10-14 04:44:49 -04:00
dumps.rst
also index dump styles
2022-07-15 22:58:49 -04:00
dynamical_matrix.rst
update docs
2021-12-14 09:13:05 -05:00
echo.rst
Minor edits to doc pages for echo group if
2022-08-21 22:19:30 -05:00
Errors_bugs.rst
remove references to the mailing list in the manual and replace with forum link, if needed
2022-03-29 07:01:00 -04:00
Errors_common.rst
update URLs in source code and manual
2021-05-24 14:18:20 -04:00
Errors_debug.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Errors_details.rst
add documentation for new error and warning policy
2022-04-23 16:40:28 -04:00
Errors_messages.rst
Update Errors_messages.rst
2022-09-07 00:02:31 -04:00
Errors_warnings.rst
Update Errors_warnings.rst
2022-07-13 11:51:50 -04:00
Errors.rst
add utility to print url with pointer to error message
2022-04-22 05:25:50 -04:00
Examples.rst
Merge branch 'develop' into BPM
2022-04-11 12:18:34 -04:00
fitpod_command.rst
update fitpod doc
2022-12-02 17:42:49 -05:00
fix_accelerate_cos.rst
Math replacements and cosmetic edits to documentation
2022-09-01 01:01:46 -05:00
fix_acks2_reaxff.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
fix_adapt_fep.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
fix_adapt.rst
add some more versionadded tags, now mostly complete for 2022
2022-09-25 09:41:55 -04:00
fix_addforce.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
fix_addtorque.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
fix_amoeba_bitorsion.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
fix_amoeba_pitorsion.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
fix_append_atoms.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
fix_atc.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
fix_atom_swap.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
fix_ave_atom.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
fix_ave_chunk.rst
Missing key word in fix/ave/chunk docs, edits to bond_coeff docs
2022-10-13 14:42:10 -05:00
fix_ave_correlate_long.rst
Math-related edits and code-block swaps; checkd builds for pdf and html docs
2022-09-02 17:44:45 -05:00
fix_ave_correlate.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
fix_ave_histo.rst
Missing keyword in fix_ave_histo doc
2022-10-13 14:48:26 -05:00
fix_ave_spatial_sphere.rst
provide backward compatible URLs to reduce 404 errors on www.lammps.org
2022-12-13 05:28:28 -05:00
fix_ave_spatial.rst
provide backward compatible URLs to reduce 404 errors on www.lammps.org
2022-12-13 05:28:28 -05:00
fix_ave_time.rst
missing format keyword in fix ave/time doc
2022-10-13 14:51:30 -05:00
fix_aveforce.rst
Math-related edits and code-block swaps; checkd builds for pdf and html docs
2022-09-02 17:44:45 -05:00
fix_balance.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
fix_bocs.rst
removed an extra space
2022-10-14 18:27:21 -05:00
fix_bond_break.rst
Missed one I->i edit
2022-10-14 18:04:49 -05:00
fix_bond_create.rst
Updated docs for fixes bond/break, bond/create, and bond/react for math/etc.
2022-10-14 17:40:22 -05:00
fix_bond_react.rst
merged 3 doc pages for reset_atoms command
2022-11-28 10:32:53 -07:00
fix_bond_swap.rst
add note to doc page about sticker site model
2022-09-12 09:41:29 -06:00
fix_box_relax.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_brownian.rst
Fixed a couple more mathbf->boldsymbol errors in fix brownian doc
2022-10-15 10:47:33 -05:00
fix_charge_regulation.rst
whitespace
2022-01-28 14:48:34 -05:00
fix_cmap.rst
doc pages for AMOEBA/HIPPO
2022-04-18 16:38:41 -06:00
fix_colvars.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_controller.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_damping_cundall.rst
add Note to damping/cundall documentation about fix order. Remove fix order warning from fix viscous/sphere
2022-03-23 14:59:43 -05:00
fix_deform.rst
doc page edit
2022-04-04 08:59:40 -06:00
fix_deposit.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_dpd_energy.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_dpd_source.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_drag.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_drude_transform.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_drude.rst
update docs for renames examples folders
2021-06-29 11:31:57 -04:00
fix_dt_reset.rst
bug fixes to make a series of test inputs run correctly
2021-12-08 16:44:51 -07:00
fix_efield.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_ehex.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_electrode.rst
rename doc file for all electrode fixes to fix_electrode.rst
2022-12-04 16:10:02 -05:00
fix_electron_stopping.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_enforce2d.rst
…
fix_eos_cv.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_eos_table_rx.rst
refer to temperature more consistently with :math:T instead of *T*
2022-08-23 05:26:07 -04:00
fix_eos_table.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_evaporate.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_external.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
fix_ffl.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_filter_corotate.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_flow_gauss.rst
Updates documentation files to make them more consistent and some typo fixes (round 1)
2022-08-05 23:03:09 -05:00
fix_freeze.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_gcmc.rst
refer to temperature more consistently with :math:T instead of *T*
2022-08-23 05:26:07 -04:00
fix_gld.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_gle.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
fix_gravity.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_grem.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_halt.rst
use MBytes consistently
2021-08-26 01:00:08 -04:00
fix_heat.rst
…
fix_hyper_global.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_hyper_local.rst
consistently use prefactor instead of pre-factor (the former was more common)
2022-05-17 16:20:10 -04:00
fix_imd.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_indent.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_ipi.rst
error out when reduced units are used with fix ipi or fix pimd
2022-11-24 13:17:11 -05:00
fix_langevin_drude.rst
Consolidate "Jiang" citations
2021-12-06 14:07:36 -05:00
fix_langevin_eff.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_langevin_spin.rst
Correcting some aspects of the SPIN package documentation.
2022-09-26 07:43:19 +02:00
fix_langevin.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_latte.rst
add versionadded/versionchanged markers for features from 15Sep2022 and 3Aug2022
2022-09-25 03:20:29 -04:00
fix_lb_fluid.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_lb_momentum.rst
upgrade of lb/fluid fix
2021-12-01 14:31:57 -05:00
fix_lb_viscous.rst
update citation references
2022-03-04 18:16:02 -05:00
fix_lineforce.rst
…
fix_manifoldforce.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_mdi_qm.rst
add some more versionadded tags, now mostly complete for 2022
2022-09-25 09:41:55 -04:00
fix_meso_move.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_modify_atc_commands.rst
…
fix_modify.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_mol_swap.rst
fix spelling and make consistent
2021-10-13 19:25:09 -04:00
fix_momentum.rst
fix minor documentation issues
2022-05-11 13:23:59 -04:00
fix_move.rst
add "transrot" style to fix move that allows to do translation and rotation at the same time
2022-04-02 18:34:17 -04:00
fix_mscg.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_msst.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_mvv_dpd.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_neb_spin.rst
…
fix_neb.rst
Merge branch 'master' into collected-small-changes
2021-07-27 11:15:00 -04:00
fix_nh_eff.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nh_uef.rst
update documentation for removal of box command
2022-11-21 14:04:58 -05:00
fix_nh.rst
use k_B for Boltzmann constant
2022-08-23 00:04:25 -04:00
fix_nph_asphere.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nph_body.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nph_sphere.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nphug.rst
refer to temperature more consistently with :math:T instead of *T*
2022-08-23 05:26:07 -04:00
fix_npt_asphere.rst
clarify doc pages for thermostatting fixes to mention regions
2021-09-30 16:55:22 -06:00
fix_npt_body.rst
clarify doc pages for thermostatting fixes to mention regions
2021-09-30 16:55:22 -06:00
fix_npt_cauchy.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_npt_sphere.rst
additional tweaks to clarify fix sphere doc pages
2022-07-28 16:30:00 -06:00
fix_numdiff_virial.rst
add some more versionadded tags, now mostly complete for 2022
2022-09-25 09:41:55 -04:00
fix_numdiff.rst
Finished debugging, testing, documenting
2022-01-28 18:34:30 -07:00
fix_nve_asphere_noforce.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nve_asphere.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nve_awpmd.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nve_body.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nve_bpm_sphere.rst
add .. versiondded:: tag to BPM package commands and restrictions text consistent
2022-11-07 22:57:32 -05:00
fix_nve_dot.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nve_dotc_langevin.rst
refer to temperature more consistently with :math:T instead of *T*
2022-08-23 05:26:07 -04:00
fix_nve_eff.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nve_limit.rst
…
fix_nve_line.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nve_manifold_rattle.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
fix_nve_noforce.rst
move back to src for dependencies
2021-07-27 15:53:35 -04:00
fix_nve_sphere.rst
additional tweaks to clarify fix sphere doc pages
2022-07-28 16:30:00 -06:00
fix_nve_spin.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nve_tri.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nve.rst
doc fixes: spelling and links
2022-04-23 07:34:44 -04:00
fix_nvk.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nvt_asphere.rst
clarify doc pages for thermostatting fixes to mention regions
2021-09-30 16:55:22 -06:00
fix_nvt_body.rst
clarify doc pages for thermostatting fixes to mention regions
2021-09-30 16:55:22 -06:00
fix_nvt_manifold_rattle.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
fix_nvt_sllod_eff.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_nvt_sllod.rst
Finished debugging, testing, documenting
2022-01-28 18:34:30 -07:00
fix_nvt_sphere.rst
additional tweaks to clarify fix sphere doc pages
2022-07-28 16:30:00 -06:00
fix_oneway.rst
Updates documentation files to make them more consistent and some typo fixes (round 1)
2022-08-05 23:03:09 -05:00
fix_orient_eco.rst
fix a few typos with :doc: references
2022-09-04 17:27:32 -04:00
fix_orient.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_pafi.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_pair.rst
Revert "update documentation: explain fix_modify pair every N"
2022-10-03 19:43:37 +02:00
fix_phonon.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
fix_pimd.rst
error out when reduced units are used with fix ipi or fix pimd
2022-11-24 13:17:11 -05:00
fix_planeforce.rst
…
fix_plumed.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_poems.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_polarize.rst
fix spelling and table format issues. re-wrap paragraphs in doc sources.
2022-10-10 17:26:13 -04:00
fix_pour.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_precession_spin.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_press_berendsen.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_print.rst
adding of timer-style variables and associated doc pages
2022-05-06 11:21:36 -06:00
fix_propel_self.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_property_atom.rst
Updates documentation files to make them more consistent and some typo fixes (round 1)
2022-08-05 23:03:09 -05:00
fix_python_invoke.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_python_move.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_qbmsst.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_qeq_comb.rst
update the note based on the suggestion by @athomps
2022-02-18 11:38:05 -05:00
fix_qeq_reaxff.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
fix_qeq.rst
update the note based on the suggestion by @athomps
2022-02-18 11:38:05 -05:00
fix_qmmm.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
fix_qtb.rst
use MBytes consistently
2021-08-26 01:00:08 -04:00
fix_reaxff_bonds.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_reaxff_species.rst
clarify how reaxff/species decides when to reneighbor
2022-07-06 00:45:36 -04:00
fix_recenter.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_restrain.rst
consistently use prefactor instead of pre-factor (the former was more common)
2022-05-17 16:20:10 -04:00
fix_rhok.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_rigid_meso.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_rigid.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_rx.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_saed_vtk.rst
fix saed/vtk does not use the overwrite option anywhere
2021-10-04 17:22:58 -04:00
fix_setforce.rst
avoid duplication of Accelerator package info in additional doc pages
2021-10-11 16:49:59 -06:00
fix_shake.rst
add versionadded/versionchanged markers for features from 15Sep2022 and 3Aug2022
2022-09-25 03:20:29 -04:00
fix_shardlow.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_smd_adjust_dt.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_smd_integrate_tlsph.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_smd_integrate_ulsph.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_smd_move_triangulated_surface.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_smd_setvel.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_smd_wall_surface.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_smd.rst
Updating MISC to EXTRA-X in doc files
2021-12-13 12:27:00 -07:00
fix_sph_stationary.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_sph.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -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
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
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
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_store_force.rst
…
fix_store_state.rst
resolved merge conflicts with master
2021-08-17 11:55:33 -06:00
fix_temp_berendsen.rst
clarify doc pages for thermostatting fixes to mention regions
2021-09-30 16:55:22 -06:00
fix_temp_csvr.rst
clarify doc pages for thermostatting fixes to mention regions
2021-09-30 16:55:22 -06:00
fix_temp_rescale_eff.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_temp_rescale.rst
clarify doc pages for thermostatting fixes to mention regions
2021-09-30 16:55:22 -06:00
fix_tfmc.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_tgnh_drude.rst
clarify doc pages for thermostatting fixes to mention regions
2021-09-30 16:55:22 -06:00
fix_thermal_conductivity.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_ti_spring.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_tmd.rst
modernize parsing in fix tmd, add support for comments and empty lines
2022-03-31 07:36:50 -04:00
fix_ttm.rst
fix typo
2022-04-22 11:27:08 -04:00
fix_tune_kspace.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_vector.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_viscosity.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_viscous_sphere.rst
add support for determining damping scale factor from atom-style variable
2022-03-23 10:43:26 -04:00
fix_viscous.rst
refer to temperature more consistently with :math:T instead of *T*
2022-08-23 05:26:07 -04:00
fix_wall_body_polygon.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_wall_body_polyhedron.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_wall_ees.rst
consistently use prefactor instead of pre-factor (the former was more common)
2022-05-17 16:20:10 -04:00
fix_wall_gran_region.rst
cosmetic changes for consistency
2021-09-07 19:12:59 -04:00
fix_wall_gran.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_wall_piston.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_wall_reflect_stochastic.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_wall_reflect.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_wall_region.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_wall_srd.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
fix_wall.rst
made keyword lists and descriptions consistent for all fix styles
2022-10-13 19:20:08 -05:00
fix_widom.rst
refer to temperature more consistently with :math:T instead of *T*
2022-08-23 05:26:07 -04:00
fix.rst
rename doc file for all electrode fixes to fix_electrode.rst
2022-12-04 16:10:02 -05:00
fixes.rst
…
Fortran.rst
set pending version info in docs to 3Nov2022
2022-11-01 06:00:05 -04:00
group2ndx.rst
Updates documentation files to make them more consistent and some typo fixes (round 1)
2022-08-05 23:03:09 -05:00
group.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
Howto_2d.rst
…
Howto_amoeba.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Howto_barostat.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Howto_bioFF.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Howto_body.rst
fix miscalculated example
2022-05-20 01:06:21 -04:00
Howto_bpm.rst
fix some minor documentation issues
2022-09-21 09:41:55 -04:00
Howto_broken_bonds.rst
permissions
2022-04-12 18:43:47 -04:00
Howto_chunk.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Howto_cmake.rst
get rid of references to USER-MISC in the general discussion
2021-07-25 10:03:16 -04:00
Howto_coreshell.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Howto_couple.rst
remove broken links in the manual from removing packages
2022-04-08 17:27:01 -04:00
Howto_diffusion.rst
…
Howto_dispersion.rst
…
Howto_drude2.rst
Consolidate "Jiang" citations
2021-12-06 14:07:36 -05:00
Howto_drude.rst
Update docs for TGNH
2020-11-14 17:08:26 +01:00
Howto_elastic.rst
Added some self-citations for key contributors
2022-02-25 17:03:45 -07:00
Howto_github.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Howto_granular.rst
whitespace
2021-06-10 23:16:44 -04:00
Howto_kappa.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Howto_library.rst
rename sections to User Guide and Programmer Guide
2020-10-15 12:00:36 -04:00
Howto_manifold.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Howto_mdi.rst
fix spelling in MDI docs
2022-06-28 13:58:42 -04:00
Howto_multiple.rst
…
Howto_nemd.rst
…
Howto_output.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Howto_peri.rst
make equation references explicit since .. math:: + 🏷️ does not work with latex
2022-09-29 13:54:09 -04:00
Howto_polarizable.rst
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
Howto_pylammps.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Howto_replica.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Howto_restart.rst
…
Howto_spc.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Howto_spherical.rst
…
Howto_spins.rst
whitespace
2022-09-26 13:12:04 -04:00
Howto_structured_data.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Howto_temperature.rst
…
Howto_thermostat.rst
integrate platform sub-namespace into source code and documentation
2021-10-02 16:55:11 -04:00
Howto_tip3p.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Howto_tip4p.rst
update TIP4P howto
2022-10-27 07:02:16 -04:00
Howto_triclinic.rst
update documentation for removal of box command
2022-11-21 14:04:58 -05:00
Howto_type_labels.rst
update versions strings for the next patch release
2022-09-14 16:29:10 -04:00
Howto_viscosity.rst
formatting corrections and minor tweaks to the Argon viscosity howto
2022-07-01 09:26:23 -04:00
Howto_viz.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Howto_walls.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Howto_wsl.rst
rename "minimal" preset to "basic"
2021-06-30 20:39:17 -04:00
Howto.rst
Convert PDLAMMPS user doc from latex to sphinx
2022-09-29 06:57:52 -04:00
hyper.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
if.rst
Minor edits to doc pages for echo group if
2022-08-21 22:19:30 -05:00
improper_amoeba.rst
fix documentation issues (spelling, references, non-ASCII chars)
2022-07-04 19:09:56 -04:00
improper_class2.rst
…
improper_coeff.rst
more formatting/typesetting consistency
2022-09-03 04:17:22 -04:00
improper_cossq.rst
move some styles around
2021-07-09 16:54:00 -04:00
improper_cvff.rst
…
improper_distance.rst
move some styles around
2021-07-09 16:54:00 -04:00
improper_distharm.rst
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
improper_fourier.rst
move some styles around
2021-07-09 16:54:00 -04:00
improper_harmonic.rst
avoid duplication of Accelerator package info in additional doc pages
2021-10-11 16:49:59 -06:00
improper_hybrid.rst
Updates documentation files to make them more consistent and some typo fixes (round 1)
2022-08-05 23:03:09 -05:00
improper_inversion_harmonic.rst
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
improper_none.rst
…
improper_ring.rst
move some styles around
2021-07-09 16:54:00 -04:00
improper_sqdistharm.rst
move some styles around
2021-07-09 16:54:00 -04:00
improper_style.rst
doc pages for AMOEBA/HIPPO
2022-04-18 16:38:41 -06:00
improper_umbrella.rst
…
improper_zero.rst
…
impropers.rst
…
include.rst
…
info.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Install_conda.rst
use upper case LAMMPS as the name of the package consistently
2022-09-24 03:45:23 -04:00
Install_git.rst
update github managers.
2022-03-18 11:37:49 -04:00
Install_linux.rst
clarify whom to contact with questions about pre-built binaries. update ubuntu info
2022-07-24 18:12:04 -04:00
Install_mac.rst
remove src/MESSAGE package and supporting dirs and doc pages
2022-04-07 15:44:48 -06:00
Install_tarball.rst
update URL for downloading old LAMMPS versions
2022-03-24 17:02:07 -04:00
Install_windows.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Install.rst
clarify whom to contact with questions about pre-built binaries. update ubuntu info
2022-07-24 18:12:04 -04:00
Intro_authors.rst
update sjplimp's email and homepage
2022-09-24 05:02:53 -04:00
Intro_citing.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Intro_features.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Intro_nonfeatures.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Intro_opensource.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Intro_overview.rst
update overview text
2021-08-24 23:02:49 -04:00
Intro_website.rst
remove references to the mailing list in the manual and replace with forum link, if needed
2022-03-29 07:01:00 -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
…
kim_commands.rst
reorder punctuation and quotation characters for clarity
2022-09-12 19:02:46 -04:00
kspace_modify.rst
Fixed remaining discrepancies between lists of keywords and doc of them
2022-10-13 23:00:13 -05:00
kspace_style.rst
rename doc file for all electrode fixes to fix_electrode.rst
2022-12-04 16:10:02 -05:00
label.rst
add reference
2022-07-26 09:19:45 -04:00
labelmap.rst
update versions strings for the next patch release
2022-09-14 16:29:10 -04:00
lattice.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
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
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Library_create.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Library_execute.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
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
Finished docs for everything currently implemented
2022-09-29 09:14:49 -05:00
Library_properties.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Library_scatter.rst
add python interface with optional numpy support for lammps_gather_bonds()
2021-07-26 22:40:21 -04:00
Library_utility.rst
c-library functions should be always present, documented, and lowercase
2022-09-24 03:07:24 -04:00
Library.rst
add note about the plugin version of the C library interface
2022-10-31 14:42:12 -04:00
log.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Manual_version.rst
clarifications and corrections for the discussion of the main git branches
2021-11-17 06:58:44 -05:00
Manual.rst
Fixed typo in Manual.rst
2022-10-21 10:59:48 -05:00
mass.rst
direct type label support for mass command
2021-12-08 16:04:22 -05:00
mdi.rst
Doc edits for mdi.rst
2022-10-04 18:49:35 -05:00
min_modify.rst
whitespace
2022-09-26 13:12:04 -04:00
min_spin.rst
Correcting some aspects of the SPIN package documentation.
2022-09-26 07:43:19 +02:00
min_style.rst
fix underline
2022-05-19 23:06:54 -04:00
minimize.rst
discuss why one would want to use check = no during minimization
2022-08-17 16:00:00 -04:00
Modify_atom.rst
update docs for adding atom styles to refactored process
2022-04-14 11:48:18 -04:00
Modify_body.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Modify_bond.rst
expand docs for bond/angle/dihedral/improper styles
2022-11-07 23:52:23 -05:00
Modify_command.rst
update docs for change in class topology
2021-04-13 17:47:21 -04:00
Modify_compute.rst
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
Modify_contribute.rst
remove references to the mailing list in the manual and replace with forum link, if needed
2022-03-29 07:01:00 -04:00
Modify_dump.rst
…
Modify_fix.rst
document missing call
2022-07-27 22:13:14 -04:00
Modify_kspace.rst
…
Modify_min.rst
…
Modify_overview.rst
link Modify overview paragraph to Code design page
2022-02-27 11:29:19 -05:00
Modify_pair.rst
update list of functions and add list of flags for pair styles
2022-11-07 16:10:12 -05:00
Modify_region.rst
…
Modify_style.rst
document preference to not use "alternative tokens"
2022-10-30 22:07:43 -04:00
Modify_thermo.rst
update documentation for modifying LAMMPS to reflect changes to Thermo class
2022-03-19 18:06:56 -04:00
Modify_variable.rst
update documentation for modifying LAMMPS to reflect changes to Thermo class
2022-03-19 18:06:56 -04:00
Modify.rst
small rewording
2022-02-28 12:17:20 -05:00
molecule.rst
document type label support for Shake Bond Types
2022-09-06 23:27:03 -04:00
neb_spin.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
neb.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
neigh_modify.rst
update wording and fix typo
2022-10-14 10:21:48 -04:00
neighbor.rst
cross-reference neighbor multi and point out differences and benefits
2022-07-13 03:11:40 -04:00
newton.rst
…
next.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
package.rst
Resolve conflicts with devel branch
2022-08-05 23:30:41 -05:00
Packages_details.rst
Merge pull request #3449 from cesmix-mit/pod
2022-12-05 12:29:13 -05:00
Packages_list.rst
Merge pull request #3449 from cesmix-mit/pod
2022-12-05 12:29:13 -05:00
Packages.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_adp.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
pair_agni.rst
avoid duplication of Accelerator package info in additional doc pages
2021-10-11 16:49:59 -06:00
pair_airebo.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
pair_amoeba.rst
set pending version info in docs to 3Nov2022
2022-11-01 06:00:05 -04:00
pair_atm.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_awpmd.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_beck.rst
forgot to move pair style beck to EXTRA-PAIR
2021-07-28 18:33:33 -04:00
pair_body_nparticle.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_body_rounded_polygon.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_body_rounded_polyhedron.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_bop.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_born.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_bpm_spring.rst
add .. versiondded:: tag to BPM package commands and restrictions text consistent
2022-11-07 22:57:32 -05:00
pair_brownian.rst
Updates documentation files to make them more consistent and some typo fixes (round 1)
2022-08-05 23:03:09 -05:00
pair_buck6d_coul_gauss.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_buck_long.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_buck.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_charmm.rst
use kcal consistently
2022-10-01 21:05:16 -04:00
pair_class2.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_coeff.rst
more formatting/typesetting consistency
2022-09-03 04:17:22 -04:00
pair_colloid.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_comb.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_cosine_squared.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_coul_diel.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_coul_shield.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_coul_slater.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_coul_tt.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_coul.rst
fix typo and reformat
2022-12-07 20:41:33 -05:00
pair_cs.rst
update broken URLs
2022-09-26 12:09:45 -04:00
pair_dielectric.rst
fix spelling and table format issues. re-wrap paragraphs in doc sources.
2022-10-10 17:26:13 -04:00
pair_dipole.rst
update dipole pair style examples and docs
2022-10-17 19:05:17 -04:00
pair_dpd_ext.rst
use k_B for Boltzmann constant
2022-08-23 00:04:25 -04:00
pair_dpd_fdt.rst
fix multiple typesetting issues and make consistent
2022-09-14 23:26:01 -04:00
pair_dpd.rst
fix multiple typesetting issues and make consistent
2022-09-14 23:26:01 -04:00
pair_drip.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_dsmc.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_e3b.rst
fix some docs formatting issues
2022-06-08 12:47:30 -04:00
pair_eam.rst
set pending version info in docs to 3Nov2022
2022-11-01 06:00:05 -04:00
pair_edip.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_eff.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_eim.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_exp6_rx.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_extep.rst
…
pair_fep_soft.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_gauss.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_gayberne.rst
additional formatting updates
2022-09-21 15:58:12 -04:00
pair_gran.rst
consistently use prefactor instead of pre-factor (the former was more common)
2022-05-17 16:20:10 -04:00
pair_granular.rst
more consistency
2022-10-15 15:35:29 -04:00
pair_gromacs.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
pair_gw.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_harmonic_cut.rst
add some more versionadded tags, now mostly complete for 2022
2022-09-25 09:41:55 -04:00
pair_hbond_dreiding.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_hdnnp.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_hybrid.rst
improve pair hybrid documentation with respect to mixing
2021-11-19 14:18:55 -05:00
pair_ilp_graphene_hbn.rst
integrate better into manual and traditional build system
2022-04-22 11:38:55 -04:00
pair_ilp_tmd.rst
add some more versionadded tags, now mostly complete for 2022
2022-09-25 09:41:55 -04:00
pair_kim.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_kolmogorov_crespi_full.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_kolmogorov_crespi_z.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lcbop.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lebedeva_z.rst
whitespace
2021-11-04 16:48:29 -04:00
pair_line_lj.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_list.rst
correct implementation of quartic potential in pair style list
2022-10-21 02:25:40 -04:00
pair_lj96.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lj_cubic.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lj_cut_coul.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lj_cut_tip4p.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lj_expand.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lj_long.rst
update a citation
2022-04-12 12:59:25 -06:00
pair_lj_relres.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lj_smooth_linear.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lj_smooth.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lj_switch3_coulgauss_long.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lj.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_local_density.rst
correct docs for pair style local/density
2021-12-08 00:22:37 -05:00
pair_lubricate.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_lubricateU.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_mdf.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_meam_spline.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_meam_sw_spline.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_meam.rst
update broken URLs
2022-09-26 12:09:45 -04:00
pair_mesocnt.rst
update versions strings for the next patch release
2022-09-14 16:29:10 -04:00
pair_mesodpd.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_mesont_tpm.rst
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
pair_mgpt.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_mie.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_mliap.rst
Merge pull request #3511 from akohlmey/next_patch_release
2022-11-03 11:53:08 -04:00
pair_modify.rst
add versionadded/versionchanged markers for features from 15Sep2022 and 3Aug2022
2022-09-25 03:20:29 -04:00
pair_momb.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_morse.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_multi_lucy_rx.rst
consistently use prefactor instead of pre-factor (the former was more common)
2022-05-17 16:20:10 -04:00
pair_multi_lucy.rst
consistently use prefactor instead of pre-factor (the former was more common)
2022-05-17 16:20:10 -04:00
pair_nb3b_harmonic.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_nm.rst
make consistent with other reference
2022-01-03 18:26:56 -05:00
pair_none.rst
clarify the description of pair style none
2022-05-20 07:14:05 -04:00
pair_oxdna2.rst
Merge pull request #2924 from ohenrich/cg-dna
2021-09-07 14:12:07 -04:00
pair_oxdna.rst
Merge pull request #2924 from ohenrich/cg-dna
2021-09-07 14:12:07 -04:00
pair_oxrna2.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_pace.rst
small upd to pair/extrapolation docs example
2022-10-27 11:56:12 +02:00
pair_peri.rst
reference the Howto from the rest of the manual. Spelling fixes.
2022-09-29 07:43:01 -04:00
pair_pod.rst
whitespace
2022-12-01 00:32:13 -05:00
pair_polymorphic.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_python.rst
add harmonic/cut to python example folder. small tweaks to docs and examples
2022-03-18 17:58:30 -04:00
pair_quip.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
pair_rann.rst
Updates documentation files to make them more consistent and some typo fixes (round 1)
2022-08-05 23:03:09 -05:00
pair_reaxff.rst
Update docs
2022-03-04 13:10:25 -07:00
pair_resquared.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_saip_metal.rst
add some more versionadded tags, now mostly complete for 2022
2022-09-25 09:41:55 -04:00
pair_sdpd_taitwater_isothermal.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_smatb.rst
add some .. versionadded:: statements to indicate the version a feature was added
2022-08-01 03:54:39 -04:00
pair_smd_hertz.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_smd_tlsph.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_smd_triangulated_surface.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_smd_ulsph.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_smtbq.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
pair_snap.rst
Completed inner cutoff, KOKKOS still in progress
2022-04-21 17:30:12 -06:00
pair_soft.rst
consistently use prefactor instead of pre-factor (the former was more common)
2022-05-17 16:20:10 -04:00
pair_sph_heatconduction.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_sph_idealgas.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_sph_lj.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_sph_rhosum.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_sph_taitwater_morris.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_sph_taitwater.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_spica.rst
whitespace
2022-07-15 12:16:15 -04:00
pair_spin_dipole.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_spin_dmi.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_spin_exchange.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_spin_magelec.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_spin_neel.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_srp.rst
add versionadded/versionchanged markers for features from 15Sep2022 and 3Aug2022
2022-09-25 03:20:29 -04:00
pair_style.rst
Update doc to reflect a change in the pair style name
2022-11-29 20:20:42 -05:00
pair_sw_angle_table.rst
add some .. versionadded:: statements to indicate the version a feature was added
2022-08-01 03:54:39 -04:00
pair_sw.rst
fix broken link and clarify
2022-11-28 15:53:31 -05:00
pair_table_rx.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_table.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_tersoff_mod.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_tersoff_zbl.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_tersoff.rst
make documentation of a few pair styles more consistent with the rest
2021-11-29 15:57:11 -05:00
pair_thole.rst
make documentation of a few pair styles more consistent with the rest
2021-11-29 15:57:11 -05:00
pair_threebody_table.rst
add some .. versionadded:: statements to indicate the version a feature was added
2022-08-01 03:54:39 -04:00
pair_tracker.rst
fix typo
2022-12-10 09:59:49 -05:00
pair_tri_lj.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_ufm.rst
refer to temperature more consistently with :math:T instead of *T*
2022-08-23 05:26:07 -04:00
pair_vashishta.rst
make documentation of a few pair styles more consistent with the rest
2021-11-29 15:57:11 -05:00
pair_wf_cut.rst
offset is not used (by construction of the potential)
2022-08-05 07:20:44 -04:00
pair_write.rst
update comment about pair_write restrictions
2022-01-21 10:47:49 -05:00
pair_ylz.rst
correct a grammatical error
2022-11-17 23:25:04 +08:00
pair_yukawa_colloid.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_yukawa.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
pair_zbl.rst
make \AA macro available in :math: for HTML and PDF
2022-10-01 20:58:48 -04:00
pair_zero.rst
Add docs
2022-10-03 11:57:47 -06:00
pairs.rst
…
partition.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
plugin.rst
add some more versionadded tags, now mostly complete for 2022
2022-09-25 09:41:55 -04:00
prd.rst
Fixed remaining discrepancies between lists of keywords and doc of them
2022-10-13 23:00:13 -05:00
print.rst
adding of timer-style variables and associated doc pages
2022-05-06 11:21:36 -06:00
processors.rst
Fixed remaining discrepancies between lists of keywords and doc of them
2022-10-13 23:00:13 -05:00
Python_atoms.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Python_call.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Python_config.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Python_create.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Python_error.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Python_examples.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Python_execute.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
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
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Python_install.rst
update some more version change timestamps
2022-03-19 20:20:30 -04:00
Python_launch.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Python_module.rst
fix errors/typos in manual
2021-04-02 21:00:42 -04:00
Python_neighbor.rst
Fix whitespace
2022-10-03 12:45:18 -06:00
Python_objects.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Python_overview.rst
Update docs
2020-12-17 11:57:40 -05:00
Python_properties.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Python_run.rst
Add extra space in Python_run.rst
2020-10-16 17:20:38 -04:00
Python_scatter.rst
use consistent pygments language tags
2022-12-04 16:59:17 -05:00
Python_trouble.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
python.rst
add versionchanged tag to "python source" docs
2022-11-15 17:15:07 -05:00
quit.rst
…
read_data.rst
update documentation for removal of box command
2022-11-21 14:04:58 -05:00
read_dump.rst
add versionadded/versionchanged markers for features from 15Sep2022 and 3Aug2022
2022-09-25 03:20:29 -04:00
read_restart.rst
remove any remap related documentation. add paragraph about file compatibility
2022-06-22 14:22:23 -04:00
region.rst
add some more versionadded tags, now mostly complete for 2022
2022-09-25 09:41:55 -04:00
replicate.rst
…
rerun.rst
allow for command-line setting of initial temp
2021-08-26 11:52:07 -06:00
reset_atoms.rst
whitespace
2022-11-28 14:05:03 -05:00
reset_timestep.rst
remove NULL option for reset_timestep
2022-05-04 16:21:06 -04:00
restart.rst
spelling
2022-09-13 11:43:09 -04:00
Run_basics.rst
format mpirun/mpiexec consistently
2022-10-04 08:55:53 -04:00
Run_head.rst
…
Run_options.rst
add versionadded marker
2022-11-15 03:46:50 -05:00
Run_output.rst
also print atom-step/s performance metric
2022-10-13 16:32:41 -04:00
run_style.rst
fix typo and remove correspondign false positive
2022-10-13 05:47:08 -04:00
Run_windows.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
run.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
set.rst
update versions strings for the next patch release
2022-09-14 16:29:10 -04:00
shell.rst
add support for '-f' option to shell rm built-in command
2022-03-17 15:17:44 -04:00
special_bonds.rst
Merge branch 'develop' into amoeba-ak
2022-05-28 05:24:02 -04:00
Speed_bench.rst
update URLs in source code and manual
2021-05-24 14:18:20 -04:00
Speed_compare.rst
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
Speed_gpu.rst
format mpirun/mpiexec consistently
2022-10-04 08:55:53 -04:00
Speed_intel.rst
convert URLs to https where possible, check URLs for bit rot and update or remove
2022-09-24 08:02:18 -04:00
Speed_kokkos.rst
format mpirun/mpiexec consistently
2022-10-04 08:55:53 -04:00
Speed_measure.rst
correct docs about how to get synchronized timings
2022-06-22 10:24:56 -04:00
Speed_omp.rst
format mpirun/mpiexec consistently
2022-10-04 08:55:53 -04:00
Speed_opt.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Speed_packages.rst
make capitalization consistent
2022-09-30 19:53:11 -04:00
Speed_tips.rst
…
Speed.rst
update title in reference to accelerator section
2021-10-11 17:26:24 -04:00
suffix.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
tad.rst
Fixed remaining discrepancies between lists of keywords and doc of them
2022-10-13 23:00:13 -05:00
temper_grem.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
temper_npt.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
temper.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
thermo_modify.rst
Minor documentation edits
2022-10-06 22:12:33 -05:00
thermo_style.rst
remove discussion of mode
2022-04-25 17:01:15 -06:00
thermo.rst
refactor thermo output processing and add new yaml thermo style
2022-03-19 16:39:09 -04:00
third_order.rst
replace image with embedded latex text
2022-05-04 17:50:25 -04:00
timer.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
timestep.rst
fix up some more package designations and clean up some legacy formatting
2021-07-25 20:23:37 -04:00
Tools.rst
add utility to detect pending version tags in .. versionadded/changed::
2022-09-25 03:51:54 -04:00
uncompute.rst
…
undump.rst
…
unfix.rst
…
units.rst
use kcal consistently
2022-10-01 21:05:16 -04:00
variable.rst
delete atomfile style variables with clear command
2022-10-18 07:34:06 -04:00
velocity.rst
Fixed remaining discrepancies between lists of keywords and doc of them
2022-10-13 23:00:13 -05:00
write_coeff.rst
…
write_data.rst
de-doc multiple label maps
2022-08-09 12:01:47 -04:00
write_dump.rst
…
write_restart.rst
document both, CMake and traditional procedure to enable MPIIO
2020-10-11 12:18:26 -04:00