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jtclemm 3ea39f5a23 Update fix_nh.rst 
Removed mbox commands
2020-06-09 14:58:25 -06:00
..
_ext
update sphinx extension to automatically pad lists to fill tables and avoid errors processing the documentation
2020-01-21 11:39:29 -05:00
99
Fix typo
2020-03-14 13:57:48 +09:00
2001
Fix typo
2020-03-14 13:57:48 +09:00
Developer
move developer's guide tex sources back to src/Developer
2019-11-15 12:37:46 -05:00
JPG
Merge pull request #1981 from akohlmey/simplify_build_choices
2020-04-14 10:57:54 -04:00
PDF
Update Colvars to version 2020-02-27
2020-02-27 19:55:31 -05:00
.gitignore
start more detailed CMake howto document
2020-04-11 11:55:13 -04:00
angle_charmm.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
angle_class2.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_coeff.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_cosine_buck6d.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_cosine_delta.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_cosine_periodic.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_cosine_shift_exp.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_cosine_shift.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_cosine_squared.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_cosine.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_cross.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
angle_dipole.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_fourier_simple.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
angle_fourier.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
angle_harmonic.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_hybrid.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
angle_mm3.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
angle_none.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angle_quartic.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
angle_sdk.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
angle_style.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
angle_table.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
angle_zero.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
angles.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
atc_add_molecule.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_add_species.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_atom_element_map.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_atom_weight.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_atomic_charge.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_boundary_dynamics.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_boundary_faceset.rst
fix rst formatting issues
2020-03-19 15:48:46 -04:00
atc_boundary_type.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_consistent_fe_initialization.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_control_localized_lambda.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_control_momentum.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_control_thermal.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_decomposition.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_electron_integration.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_equilibrium_start.rst
next chunk of converted html files
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atc_extrinsic_exchange.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_fe_md_boundary.rst
next batch of converted files
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atc_filter_scale.rst
next chunk of converted html files
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atc_filter_type.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_fix_flux.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_fix.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_hardy_computes.rst
next chunk of converted atc doc files
2020-03-18 11:39:53 -04:00
atc_hardy_fields.rst
next chunk of converted atc doc files
2020-03-18 11:39:53 -04:00
atc_hardy_gradients.rst
next chunk of converted atc doc files
2020-03-18 11:39:53 -04:00
atc_hardy_kernel.rst
next chunk of converted atc doc files
2020-03-18 11:39:53 -04:00
atc_hardy_on_the_fly.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_hardy_rates.rst
next chunk of converted atc doc files
2020-03-18 11:39:53 -04:00
atc_initial.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_internal_element_set.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_internal_quadrature.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_kernel_bandwidth.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_lumped_lambda_solve.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_mask_direction.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_mass_matrix.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_material.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_mesh_add_to_nodeset.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_create_elementset.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_create_faceset_box.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_create_faceset_plane.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_create_nodeset.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_create.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_delete_elements.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_nodeset_to_elementset.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_output.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_mesh_quadrature.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_read.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_mesh_write.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_output_boundary_integral.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_output_contour_integral.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_output_nodeset.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_output_volume_integral.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_output.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_pair_interactions.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_poisson_solver.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_read_restart.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atc_remove_molecule.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_remove_source.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_remove_species.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_reset_atomic_reference.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_reset_time.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_sample_frequency.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_set_reference_pe.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_source_integration.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_source.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_temperature_definition.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_time_filter.rst
next chunk of converted html files
2020-03-16 07:34:56 -04:00
atc_time_integration.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_track_displacement.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
atc_unfix_flux.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_unfix.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
2020-03-13 11:06:11 -04:00
atc_write_atom_weights.rst
next batch of converted files
2020-03-19 14:39:00 -04:00
atc_write_restart.rst
some more converted atc fix_modify docs
2020-03-18 06:29:17 -04:00
atom_modify.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
atom_style.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
balance.rst
use list-table and figure to have side-by-side images
2020-04-13 10:30:01 -04:00
bond_class2.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_coeff.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
bond_fene_expand.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_fene.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_gromos.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_harmonic_shift_cut.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_harmonic_shift.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_harmonic.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_hybrid.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
bond_mm3.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
bond_morse.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_none.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_nonlinear.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_oxdna.rst
fix up some escaped '*' characters in "code-block" sections that do not need to be escaped
2020-03-24 11:35:21 -04:00
bond_quartic.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_style.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
bond_table.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
bond_write.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
bond_zero.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
bonds.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
boundary.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
box.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
Build_basics.rst
small tweaks and grammar corrections
2020-04-14 01:13:22 -04:00
Build_cmake.rst
small tweaks and grammar corrections
2020-04-14 01:13:22 -04:00
Build_development.rst
small tweaks and grammar corrections
2020-04-14 01:13:22 -04:00
Build_extras.rst
update Kokkos related documentation for Kokkos 3.1 and refactor build info a bit
2020-04-21 11:46:16 -04:00
Build_link.rst
update documentation for the changes to the build procedure
2020-04-09 15:43:05 -04:00
Build_make.rst
explain error message when using a non-c++11 compliant compiler.
2020-04-12 16:32:40 -04:00
Build_package.rst
add link target
2020-04-11 12:43:00 -04:00
Build_settings.rst
some more typesetting improvements
2020-03-13 19:41:33 -04:00
Build_windows.rst
update docs for updated CMake support with MinGW
2020-03-19 11:09:27 -04:00
Build.rst
update build overview
2020-04-11 22:20:35 -04:00
change_box.rst
document the image flag reset for switching boundaries
2020-04-27 10:51:53 -04:00
clear.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
comm_modify.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
comm_style.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
Commands_all.rst
updating the Commands_all, adding kim_property command
2020-03-16 08:18:19 -05:00
Commands_bond.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
Commands_category.rst
convert lists to tables for more compact presentation
2020-02-28 18:52:13 +01:00
Commands_compute.rst
Merge pull request #2019 from z-gong/viscosity
2020-05-04 17:42:31 -04:00
Commands_fix.rst
Add documents and minor fix for USER-VISCOSITY package
2020-04-24 14:41:03 +02:00
Commands_input.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Commands_kspace.rst
remove backslash escapes for underscore in doc references
2020-01-23 16:52:38 -05:00
commands_list.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
Commands_pair.rst
add missing pair style. Coulombic/Coulombics -> Coulomb for consistency
2020-04-13 10:38:09 -04:00
Commands_parse.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
Commands_removed.rst
use consistent capitalization with NVIDIA
2020-04-10 23:20:10 -04:00
Commands_structure.rst
remove trailing whitespace from documentation sources
2020-03-10 15:51:06 -04:00
Commands.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
compute_ackland_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_adf.rst
replace "xxxn't" with "xxx not"
2020-03-18 07:02:34 -04:00
compute_angle_local.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_angle.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_angmom_chunk.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_basal_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_body_local.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_bond_local.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_bond.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_centro_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_chunk_atom.rst
some more fixups
2020-03-13 17:02:59 -04:00
compute_chunk_spread_atom.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_cluster_atom.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_cna_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_cnp_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_com_chunk.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_com.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_contact_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_coord_atom.rst
Update docs
2020-05-01 07:53:41 -06:00
compute_damage_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_dihedral_local.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_dihedral.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_dilatation_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_dipole_chunk.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_displace_atom.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_dpd_atom.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
compute_dpd.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_edpd_temp_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_entropy_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
2020-03-12 01:11:38 -04:00
compute_erotate_asphere.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_erotate_rigid.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_erotate_sphere_atom.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_erotate_sphere.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_event_displace.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_fep.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_global_atom.rst
some more fixups
2020-03-13 17:02:59 -04:00
compute_group_group.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_gyration_chunk.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_gyration_shape_chunk.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_gyration_shape.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_gyration.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_heat_flux.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_hexorder_atom.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_hma.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_improper_local.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_improper.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_inertia_chunk.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_ke_atom_eff.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
compute_ke_atom.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_ke_eff.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_ke_rigid.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_ke.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_meso_e_atom.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_meso_rho_atom.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_meso_t_atom.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_modify.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
compute_momentum.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_msd_chunk.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_msd_nongauss.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_msd.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_omega_chunk.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_orientorder_atom.rst
Add missing paramemter to compute_orientorder_atom docs
2020-05-01 08:01:29 -06:00
compute_pair_local.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_pair.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_pe_atom.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_pe.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_plasticity_atom.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_pressure_cylinder.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_pressure_uef.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_pressure.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_property_atom.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_property_chunk.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_property_local.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_ptm_atom.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_rdf.rst
replace "xxxn't" with "xxx not"
2020-03-18 07:02:34 -04:00
compute_reduce_chunk.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_reduce.rst
some more fixups
2020-03-13 17:02:59 -04:00
compute_rigid_local.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_saed.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_slice.rst
some more fixups
2020-03-13 17:02:59 -04:00
compute_smd_contact_radius.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_smd_damage.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_smd_hourglass_error.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_smd_internal_energy.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_smd_plastic_strain_rate.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_smd_plastic_strain.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_smd_rho.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_smd_tlsph_defgrad.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_smd_tlsph_dt.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_smd_tlsph_num_neighs.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_smd_tlsph_shape.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_smd_tlsph_strain_rate.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_smd_tlsph_strain.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_smd_tlsph_stress.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_smd_triangle_vertices.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_smd_ulsph_num_neighs.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
compute_smd_ulsph_strain_rate.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
compute_smd_ulsph_strain.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
compute_smd_ulsph_stress.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
compute_smd_vol.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_sna_atom.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_spin.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_stress_atom.rst
add more explicit note about lack of support for pair styles in compute centroid/stress/atom
2020-04-21 12:44:13 -04:00
compute_stress_mop.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_tally.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_tdpd_cc_atom.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_asphere.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_body.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_chunk.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_com.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_cs.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_deform_eff.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_deform.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_drude.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_temp_eff.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_partial.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_profile.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_ramp.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_region_eff.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_region.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_rotate.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_sphere.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp_uef.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_temp.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_ti.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_torque_chunk.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_vacf.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_vcm_chunk.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
compute_viscosity_cos.rst
Minor fix in doc
2020-04-30 19:00:37 +02:00
compute_voronoi_atom.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute_xrd.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
compute.rst
Add documents and minor fix for USER-VISCOSITY package
2020-04-24 14:41:03 +02:00
computes.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
create_atoms.rst
replace "xxxn't" with "xxx not"
2020-03-18 07:02:34 -04:00
create_bonds.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
create_box.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
delete_atoms.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
delete_bonds.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dielectric.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
dihedral_charmm.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedral_class2.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
dihedral_coeff.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedral_cosine_shift_exp.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
dihedral_fourier.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedral_harmonic.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
dihedral_helix.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
dihedral_hybrid.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedral_multi_harmonic.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
dihedral_nharmonic.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedral_none.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
dihedral_opls.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
dihedral_quadratic.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedral_spherical.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedral_style.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedral_table_cut.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedral_table.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedral_zero.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedrals.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
dimension.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
displace_atoms.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dump_adios.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dump_cfg_uef.rst
convert all remaining compute styles to use code-block instead of parsed literal
2020-03-12 01:56:13 -04:00
dump_h5md.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dump_image.rst
some more fixups
2020-03-13 17:02:59 -04:00
dump_modify.rst
replace "xxxn't" with "xxx not"
2020-03-18 07:02:34 -04:00
dump_molfile.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
dump_netcdf.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
dump_vtk.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dump.rst
replace "xxxn't" with "xxx not"
2020-03-18 07:02:34 -04:00
dynamical_matrix.rst
Merge pull request #1891 from charlessievers/fix_numerical_differentiation
2020-03-18 23:31:18 -04:00
echo.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
Errors_bugs.rst
provide info about including debug support in executable and a stack trace debug tutorial
2020-04-12 15:34:00 -04:00
Errors_common.rst
replace "xxxn't" with "xxx not"
2020-03-18 07:02:34 -04:00
Errors_debug.rst
remove tabs
2020-04-12 16:32:16 -04:00
Errors_messages.rst
Merge pull request #1874 from akohlmey/generalize-box-change-detect
2020-04-15 11:14:45 -04:00
Errors_warnings.rst
Merge branch 'master' into restart-consistency
2020-03-18 20:30:00 -04:00
Errors.rst
provide info about including debug support in executable and a stack trace debug tutorial
2020-04-12 15:34:00 -04:00
Examples.rst
Some more code-blocks instead of parsed-literal
2020-03-13 18:38:47 -04:00
fix_accelerate_cos.rst
add add check to refuse running with 2d systems and document it.
2020-04-30 12:46:16 -04:00
fix_adapt_fep.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_adapt.rst
Merge branch 'master' into fixadapt
2020-04-11 16:24:13 -04:00
fix_addforce.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_addtorque.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_append_atoms.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_atc.rst
final batch of converted AtC doc files
2020-03-19 15:36:45 -04:00
fix_atom_swap.rst
replace "xxxn't" with "xxx not"
2020-03-18 07:02:34 -04:00
fix_ave_atom.rst
some more fixups
2020-03-13 17:02:59 -04:00
fix_ave_chunk.rst
some more fixups
2020-03-13 17:02:59 -04:00
fix_ave_correlate_long.rst
manually incorporate fixes for ave/correlate/long from PR #2066
2020-05-04 08:18:56 -04:00
fix_ave_correlate.rst
some more fixups
2020-03-13 17:02:59 -04:00
fix_ave_histo.rst
some more fixups
2020-03-13 17:02:59 -04:00
fix_ave_time.rst
some more fixups
2020-03-13 17:02:59 -04:00
fix_aveforce.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_balance.rst
use list-table and figure to have side-by-side images
2020-04-13 10:30:01 -04:00
fix_bocs.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_bond_break.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_bond_create.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_bond_react.rst
Update fix_bond_react.rst
2020-04-26 13:08:40 -06:00
fix_bond_swap.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_box_relax.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_client_md.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_cmap.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_colvars.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_controller.rst
some more fixups
2020-03-13 17:02:59 -04:00
fix_deform.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_deposit.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_dpd_energy.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_dpd_source.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_drag.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_drude_transform.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_drude.rst
finish updating docs for fixes using code-block plus a few other improvements
2020-03-11 12:58:57 -04:00
fix_dt_reset.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_efield.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_ehex.rst
replace "xxxn't" with "xxx not"
2020-03-18 07:02:34 -04:00
fix_electron_stopping.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_enforce2d.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_eos_cv.rst
finish updating docs for fixes using code-block plus a few other improvements
2020-03-11 12:58:57 -04:00
fix_eos_table_rx.rst
finish updating docs for fixes using code-block plus a few other improvements
2020-03-11 12:58:57 -04:00
fix_eos_table.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_evaporate.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_external.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_ffl.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_filter_corotate.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_flow_gauss.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_freeze.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_gcmc.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_gld.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_gle.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_gravity.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_grem.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_halt.rst
support diskfree option to "fix halt" also on BSD variants
2020-05-03 02:34:40 -04:00
fix_heat.rst
make description of eflux as a variable less convoluted
2020-04-22 08:13:27 -04:00
fix_hyper_global.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_hyper_local.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_imd.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_indent.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_ipi.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_langevin_drude.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_langevin_eff.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_langevin_spin.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_langevin.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_latte.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_lb_fluid.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_lb_momentum.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_lb_pc.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_lb_rigid_pc_sphere.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_lb_viscous.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_lineforce.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_manifoldforce.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_meso_move.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_meso_stationary.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_meso.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_modify_atc_commands.rst
Convert a first set of AtC documentation html files to rst and add infrastructure files and links
2020-03-12 14:26:04 -04:00
fix_modify.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_momentum.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_move.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_mscg.rst
finish updating docs for fixes using code-block plus a few other improvements
2020-03-11 12:58:57 -04:00
fix_msst.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_mvv_dpd.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_neb_spin.rst
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fix_neb.rst
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fix_nh_uef.rst
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fix_nh.rst
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fix_nph_asphere.rst
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fix_numdiff.rst
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fix_oneway.rst
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fix_phonon.rst
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fix_pour.rst
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fix_precession_spin.rst
Merge branch 'clean-master2' of github.com:julient31/lammps into neel-rework
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fix_press_berendsen.rst
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fix_print.rst
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fix_qeq.rst
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fix_qmmm.rst
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fix_qtb.rst
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fix_reaxc_bonds.rst
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fix_recenter.rst
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fix_restrain.rst
same doc change for "lbond" option
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fix_rhok.rst
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fix_rx.rst
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fix_saed_vtk.rst
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fix_setforce.rst
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fix_smd_wall_surface.rst
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fix_spring_chunk.rst
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fix_spring_self.rst
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fix_spring.rst
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fix_srd.rst
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fix_temp_berendsen.rst
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fix_temp_csvr.rst
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fix_tfmc.rst
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fix_tune_kspace.rst
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fix_vector.rst
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fix_viscosity.rst
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fix_wall_body_polyhedron.rst
Fixed the doc page for fix wall/body/polyhedron
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fix_wall.rst
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fix.rst
Add documents and minor fix for USER-VISCOSITY package
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fixes.rst
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group2ndx.rst
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group.rst
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Howto_2d.rst
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Howto_barostat.rst
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Howto_bash.rst
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Howto_bioFF.rst
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Howto_chunk.rst
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Howto_client_server.rst
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Howto_cmake.rst
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Howto_coreshell.rst
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Howto_dispersion.rst
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Howto_drude2.rst
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Howto_elastic.rst
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Howto_github.rst
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Howto_granular.rst
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Howto_kappa.rst
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Howto_library.rst
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Howto_manifold.rst
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Howto_multiple.rst
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Howto_nemd.rst
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Howto_output.rst
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Howto_polarizable.rst
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Howto_pylammps.rst
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Howto_replica.rst
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Howto_restart.rst
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Howto_spc.rst
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Howto_spherical.rst
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Howto_spins.rst
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Howto_temperature.rst
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Howto_thermostat.rst
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Howto_tip3p.rst
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Howto_tip4p.rst
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Howto_triclinic.rst
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Howto_viscosity.rst
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Howto_viz.rst
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Howto_walls.rst
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Howto.rst
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hyper.rst
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if.rst
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improper_class2.rst
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improper_coeff.rst
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improper_cossq.rst
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improper_cvff.rst
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improper_distance.rst
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improper_distharm.rst
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improper_fourier.rst
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improper_harmonic.rst
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improper_hybrid.rst
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improper_inversion_harmonic.rst
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improper_none.rst
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improper_ring.rst
some minor fixups
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improper_sqdistharm.rst
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improper_style.rst
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improper_umbrella.rst
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improper_zero.rst
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impropers.rst
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include.rst
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info.rst
more conversion of parsed-literal to code-block and a bunch of other issues
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Install_conda.rst
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Install_git.rst
some more typesetting improvements
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Install_linux.rst
Add explaination of potenentials directory behavior for lmp_daily
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Install_mac.rst
tweaks
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Install_patch.rst
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Install_tarball.rst
some more typesetting improvements
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Install_windows.rst
some more typesetting improvements
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Install.rst
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Intro_authors.rst
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Intro_features.rst
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Intro_nonfeatures.rst
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Intro_opensource.rst
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Intro_overview.rst
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Intro_website.rst
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Intro.rst
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jump.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
kim_commands.rst
correct spelling
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kspace_modify.rst
replace '\_' with '_' in plain text where possible
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kspace_style.rst
Merge pull request #1938 from akohlmey/doc-remove-backslash-underscore
2020-03-13 21:01:04 -04:00
label.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
lattice.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
log.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
Manual_build.rst
Some more code-blocks instead of parsed-literal
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Manual_version.rst
update lammps.sandia.gov URLs to use https://
2020-03-12 00:28:28 -04:00
Manual.rst
Convert a first set of AtC documentation html files to rst and add infrastructure files and links
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mass.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
message.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
min_modify.rst
Merge branch 'clean-master2' of github.com:julient31/lammps into neel-rework
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min_spin.rst
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min_style.rst
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minimize.rst
handle not previously flagged false positives
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Modify_atom.rst
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Modify_body.rst
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Modify_bond.rst
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Modify_command.rst
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Modify_compute.rst
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Modify_contribute.rst
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Modify_dump.rst
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Modify_fix.rst
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Modify_kspace.rst
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Modify_min.rst
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Modify_overview.rst
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Modify_pair.rst
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Modify_region.rst
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2020-03-13 16:34:57 -04:00
Modify_thermo.rst
delete empty lines at the end of files
2020-01-31 14:03:52 -05:00
Modify_variable.rst
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2020-03-10 15:56:11 -04:00
Modify.rst
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2020-03-10 15:56:11 -04:00
molecule.rst
Merge branch 'master' into atc-doc-to-rst
2020-03-19 11:28:02 -04:00
neb_spin.rst
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neb.rst
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neigh_modify.rst
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neighbor.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
newton.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
next.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
package.rst
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Packages_details.rst
move fix_accelerate_cos and compute_viscosity_cos to USER-MISC
2020-04-24 15:30:20 +02:00
Packages_standard.rst
update lammps.sandia.gov URLs to use https://
2020-03-12 00:28:28 -04:00
Packages_user.rst
update plumed URLs to use https://
2020-03-12 00:32:44 -04:00
Packages.rst
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2020-03-10 15:56:11 -04:00
pair_adp.rst
updating the pair potential docs, adding reference to OpenKIM
2020-03-17 16:07:22 -05:00
pair_agni.rst
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pair_airebo.rst
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pair_atm.rst
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pair_awpmd.rst
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pair_beck.rst
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2020-03-13 16:34:57 -04:00
pair_body_nparticle.rst
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pair_body_rounded_polygon.rst
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pair_body_rounded_polyhedron.rst
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pair_bop.rst
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pair_born.rst
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pair_brownian.rst
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pair_buck6d_coul_gauss.rst
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pair_buck_long.rst
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pair_buck.rst
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2020-03-13 16:34:57 -04:00
pair_charmm.rst
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2020-03-13 16:34:57 -04:00
pair_class2.rst
fix up some escaped '*' characters in "code-block" sections that do not need to be escaped
2020-03-24 11:35:21 -04:00
pair_coeff.rst
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pair_colloid.rst
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pair_comb.rst
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2020-03-18 07:02:34 -04:00
pair_cosine_squared.rst
Fix typo in latex formula (cosine was not squared)
2020-04-11 17:17:48 +01:00
pair_coul_diel.rst
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pair_coul_shield.rst
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2020-03-13 16:34:57 -04:00
pair_coul_slater.rst
update coul/slater docs to align with recent changes in upstream
2020-03-18 21:07:57 -04:00
pair_coul.rst
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pair_cs.rst
Update pair_cs.rst
2020-04-07 18:50:53 +02:00
pair_dipole.rst
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pair_dpd_fdt.rst
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pair_dpd.rst
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pair_drip.rst
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pair_dsmc.rst
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pair_e3b.rst
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2020-03-13 16:34:57 -04:00
pair_eam.rst
updating the pair potential docs, adding reference to OpenKIM
2020-03-17 16:07:22 -05:00
pair_edip.rst
replace "xxxn't" with "xxx not"
2020-03-18 07:02:34 -04:00
pair_eff.rst
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pair_eim.rst
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2020-03-13 16:34:57 -04:00
pair_exp6_rx.rst
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pair_extep.rst
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pair_fep_soft.rst
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pair_gauss.rst
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pair_gayberne.rst
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pair_gran.rst
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pair_granular.rst
use american english spelling
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pair_gromacs.rst
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pair_gw.rst
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pair_hbond_dreiding.rst
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pair_hybrid.rst
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2020-03-13 16:34:57 -04:00
pair_ilp_graphene_hbn.rst
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pair_kim.rst
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pair_kolmogorov_crespi_full.rst
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pair_kolmogorov_crespi_z.rst
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pair_lcbop.rst
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pair_lebedeva_z.rst
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pair_line_lj.rst
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pair_list.rst
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pair_lj96.rst
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pair_lj_cubic.rst
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pair_lj_expand.rst
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pair_lj_long.rst
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pair_lj_smooth_linear.rst
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pair_lj_smooth.rst
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pair_lj_switch3_coulgauss_long.rst
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pair_lj.rst
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pair_local_density.rst
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pair_lubricate.rst
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pair_lubricateU.rst
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pair_mdf.rst
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pair_meam_spline.rst
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2020-03-13 16:34:57 -04:00
pair_meam_sw_spline.rst
fix up some escaped '*' characters in "code-block" sections that do not need to be escaped
2020-03-24 11:35:21 -04:00
pair_meamc.rst
MEAM/C: improve error messages and documentation
2020-03-26 17:20:23 +01:00
pair_mesocnt.rst
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2020-03-13 16:34:57 -04:00
pair_mesodpd.rst
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pair_mgpt.rst
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pair_mie.rst
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2020-03-13 16:34:57 -04:00
pair_mm3_switch3_coulgauss_long.rst
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2020-03-13 16:34:57 -04:00
pair_modify.rst
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2020-03-13 16:34:57 -04:00
pair_momb.rst
update docs to cleanly translate
2020-04-16 18:17:38 -04:00
pair_morse.rst
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2020-03-13 16:34:57 -04:00
pair_multi_lucy_rx.rst
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pair_multi_lucy.rst
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2020-03-13 16:34:57 -04:00
pair_nb3b_harmonic.rst
fix up some escaped '*' characters in "code-block" sections that do not need to be escaped
2020-03-24 11:35:21 -04:00
pair_nm.rst
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pair_none.rst
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pair_oxdna2.rst
collapse multiple empty lines into a single empty line
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pair_oxdna.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
pair_oxrna2.rst
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2020-03-10 15:56:11 -04:00
pair_peri.rst
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2020-03-13 16:34:57 -04:00
pair_polymorphic.rst
fix two more typos
2020-04-19 16:37:52 -04:00
pair_python.rst
fix up some escaped '*' characters in "code-block" sections that do not need to be escaped
2020-03-24 11:35:21 -04:00
pair_quip.rst
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2020-03-13 16:34:57 -04:00
pair_reaxc.rst
make MIN_HBONDS define for reax/c configurable via an input option
2020-05-01 23:22:48 -04:00
pair_resquared.rst
some more fixups
2020-03-13 17:02:59 -04:00
pair_sdk.rst
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2020-03-13 16:34:57 -04:00
pair_sdpd_taitwater_isothermal.rst
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pair_smd_hertz.rst
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pair_smd_tlsph.rst
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pair_smd_triangulated_surface.rst
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pair_smd_ulsph.rst
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pair_smtbq.rst
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pair_snap.rst
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pair_soft.rst
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pair_sph_heatconduction.rst
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pair_sph_idealgas.rst
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pair_sph_lj.rst
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pair_sph_rhosum.rst
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pair_sph_taitwater_morris.rst
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pair_sph_taitwater.rst
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pair_spin_dipole.rst
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pair_spin_dmi.rst
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pair_spin_exchange.rst
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2020-03-13 16:34:57 -04:00
pair_spin_magelec.rst
fix up some escaped '*' characters in "code-block" sections that do not need to be escaped
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pair_spin_neel.rst
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pair_srp.rst
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2020-03-13 16:34:57 -04:00
pair_style.rst
add missing pair style. Coulombic/Coulombics -> Coulomb for consistency
2020-04-13 10:38:09 -04:00
pair_sw.rst
replace "xxxn't" with "xxx not"
2020-03-18 07:02:34 -04:00
pair_table_rx.rst
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pair_table.rst
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pair_tersoff_mod.rst
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pair_tersoff_zbl.rst
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pair_tersoff.rst
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pair_thole.rst
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pair_tri_lj.rst
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pair_ufm.rst
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pair_vashishta.rst
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pair_write.rst
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pair_yukawa_colloid.rst
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pair_yukawa.rst
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pair_zbl.rst
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pair_zero.rst
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pairs.rst
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partition.rst
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prd.rst
clarified AMD quote from review paper
2020-04-29 16:14:52 -06:00
print.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
processors.rst
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Python_call.rst
Some more code-blocks instead of parsed-literal
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Python_examples.rst
some more fixups
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Python_head.rst
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Python_install.rst
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Python_library.rst
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Python_mpi.rst
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Python_overview.rst
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Python_pylammps.rst
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Python_run.rst
delete empty lines at the end of files
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Python_shlib.rst
update instructions in Python doc section
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Python_test.rst
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python.rst
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quit.rst
more conversion of parsed-literal to code-block and a bunch of other issues
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read_data.rst
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read_dump.rst
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read_restart.rst
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region.rst
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replicate.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
rerun.rst
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reset_ids.rst
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reset_timestep.rst
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restart.rst
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Run_basics.rst
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Run_head.rst
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Run_options.rst
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Run_output.rst
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run_style.rst
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Run_windows.rst
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run.rst
more conversion of parsed-literal to code-block and a bunch of other issues
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server_mc.rst
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server_md.rst
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server.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
set.rst
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2020-03-13 16:34:57 -04:00
shell.rst
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2020-03-18 07:02:49 -04:00
special_bonds.rst
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Speed_bench.rst
update lammps.sandia.gov URLs to use https://
2020-03-12 00:28:28 -04:00
Speed_compare.rst
use consistent capitalization with NVIDIA
2020-04-10 23:20:10 -04:00
Speed_gpu.rst
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Speed_intel.rst
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2020-03-13 18:38:47 -04:00
Speed_kokkos.rst
update Kokkos related documentation for Kokkos 3.1 and refactor build info a bit
2020-04-21 11:46:16 -04:00
Speed_measure.rst
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Speed_omp.rst
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Speed_opt.rst
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2020-03-13 18:38:47 -04:00
Speed_packages.rst
use consistent capitalization with NVIDIA
2020-04-10 23:20:10 -04:00
Speed_tips.rst
delete empty lines at the end of files
2020-01-31 14:03:52 -05:00
Speed.rst
update lammps.sandia.gov URLs to use https://
2020-03-12 00:28:28 -04:00
suffix.rst
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2020-03-13 16:34:57 -04:00
tad.rst
clarified AMD quote from review paper
2020-04-29 16:14:52 -06:00
temper_grem.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
temper_npt.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
temper.rst
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thermo_modify.rst
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thermo_style.rst
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thermo.rst
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2020-03-13 16:34:57 -04:00
third_order.rst
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timer.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
timestep.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
Tools.rst
do not advertise multiple targets in cmbuild wrapper
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uncompute.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
undump.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
unfix.rst
more conversion of parsed-literal to code-block and a bunch of other issues
2020-03-12 08:11:10 -04:00
units.rst
collapse multiple empty lines into a single empty line
2020-03-10 15:56:11 -04:00
variable.rst
some more fixups
2020-03-13 17:02:59 -04:00
velocity.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
write_coeff.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
write_data.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
write_dump.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
write_restart.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00