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lammps/doc/src
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Richard Berger e6f7a99ae2 Update Python_examples.rst
2020-07-22 16:27:04 -04:00
..
_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
one more permission fix
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2001
Fix typo
2020-03-14 13:57:48 +09:00
Developer
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
img
Update Python_examples.rst
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JPG
Update Python_examples.rst
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PDF
Update Colvars to version 2020-02-27
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.gitignore
start more detailed CMake howto document
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accel_styles.rst
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angle_charmm.rst
clarify units for energy terms with angles
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angle_class2.rst
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angle_coeff.rst
import updates to the manual from the progguide branch
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angle_cosine_buck6d.rst
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angle_cosine_delta.rst
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angle_cosine_periodic.rst
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angle_cosine_shift_exp.rst
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angle_cosine_shift.rst
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angle_cosine_squared.rst
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angle_cosine.rst
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angle_cross.rst
clarify units for energy terms with angles
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angle_dipole.rst
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angle_fourier_simple.rst
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angle_fourier.rst
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angle_harmonic.rst
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angle_hybrid.rst
replace '\_' with '_' in plain text where possible
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angle_mm3.rst
clarify units for energy terms with angles
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angle_none.rst
collapse multiple empty lines into a single empty line
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angle_quartic.rst
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angle_sdk.rst
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angle_style.rst
replace '\_' with '_' in plain text where possible
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angle_table.rst
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angle_zero.rst
collapse multiple empty lines into a single empty line
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angles.rst
collapse multiple empty lines into a single empty line
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atc_add_molecule.rst
final batch of converted AtC doc files
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atc_add_species.rst
final batch of converted AtC doc files
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atc_atom_element_map.rst
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atc_atom_weight.rst
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atc_atomic_charge.rst
final batch of converted AtC doc files
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atc_boundary_dynamics.rst
final batch of converted AtC doc files
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atc_boundary_faceset.rst
fix rst formatting issues
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atc_boundary_type.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_consistent_fe_initialization.rst
final batch of converted AtC doc files
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atc_control_localized_lambda.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_control_momentum.rst
import updates to the manual from the progguide branch
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atc_control_thermal.rst
import updates to the manual from the progguide branch
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atc_decomposition.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_electron_integration.rst
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atc_equilibrium_start.rst
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atc_extrinsic_exchange.rst
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atc_fe_md_boundary.rst
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atc_filter_scale.rst
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atc_filter_type.rst
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atc_fix_flux.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_fix.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_hardy_computes.rst
next chunk of converted atc doc files
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atc_hardy_fields.rst
import updates to the manual from the progguide branch
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atc_hardy_gradients.rst
import updates to the manual from the progguide branch
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atc_hardy_kernel.rst
import updates to the manual from the progguide branch
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atc_hardy_on_the_fly.rst
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atc_hardy_rates.rst
import updates to the manual from the progguide branch
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atc_initial.rst
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atc_internal_element_set.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_internal_quadrature.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_kernel_bandwidth.rst
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atc_lumped_lambda_solve.rst
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atc_mask_direction.rst
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atc_mass_matrix.rst
final batch of converted AtC doc files
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atc_material.rst
final batch of converted AtC doc files
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atc_mesh_add_to_nodeset.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_mesh_create_elementset.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_mesh_create_faceset_box.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_mesh_create_faceset_plane.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_mesh_create_nodeset.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_mesh_create.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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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
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atc_mesh_output.rst
some more converted atc fix_modify docs
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atc_mesh_quadrature.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_mesh_read.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_mesh_write.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_output_boundary_integral.rst
some more converted atc fix_modify docs
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atc_output_contour_integral.rst
some more converted atc fix_modify docs
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atc_output_nodeset.rst
some more converted atc fix_modify docs
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atc_output_volume_integral.rst
some more converted atc fix_modify docs
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atc_output.rst
some more converted atc fix_modify docs
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atc_pair_interactions.rst
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atc_poisson_solver.rst
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atc_read_restart.rst
some more converted atc fix_modify docs
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atc_remove_molecule.rst
final batch of converted AtC doc files
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atc_remove_source.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_remove_species.rst
import updates to the manual from the progguide branch
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atc_reset_atomic_reference.rst
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atc_reset_time.rst
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atc_sample_frequency.rst
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atc_set_reference_pe.rst
import updates to the manual from the progguide branch
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atc_source_integration.rst
final batch of converted AtC doc files
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atc_source.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_temperature_definition.rst
final batch of converted AtC doc files
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atc_time_filter.rst
next chunk of converted html files
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atc_time_integration.rst
import updates to the manual from the progguide branch
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atc_track_displacement.rst
final batch of converted AtC doc files
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atc_unfix_flux.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_unfix.rst
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs
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atc_write_atom_weights.rst
next batch of converted files
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atc_write_restart.rst
some more converted atc fix_modify docs
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atom_modify.rst
replace '\_' with '_' in plain text where possible
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atom_style.rst
Merge branch 'master' into feature-cnt
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balance.rst
use list-table and figure to have side-by-side images
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bond_class2.rst
Replace common text block with include
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bond_coeff.rst
import updates to the manual from the progguide branch
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bond_fene_expand.rst
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bond_fene.rst
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bond_gromos.rst
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bond_harmonic_shift_cut.rst
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bond_harmonic_shift.rst
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bond_harmonic.rst
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bond_hybrid.rst
replace '\_' with '_' in plain text where possible
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bond_mm3.rst
replace '\_' with '_' in plain text where possible
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bond_morse.rst
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bond_none.rst
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bond_nonlinear.rst
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bond_oxdna.rst
fix up some escaped '*' characters in "code-block" sections that do not need to be escaped
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bond_quartic.rst
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bond_style.rst
replace '\_' with '_' in plain text where possible
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bond_table.rst
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bond_write.rst
document the use and generation of "DATE:" and "UNITS:" tags
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bond_zero.rst
replace '\_' with '_' in plain text where possible
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bonds.rst
collapse multiple empty lines into a single empty line
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boundary.rst
import updates to the manual from the progguide branch
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box.rst
import updates to the manual from the progguide branch
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Build_basics.rst
don't set CMAKE_TUNE_FLAGS to anything by default
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Build_cmake.rst
one more correction for cmake --build
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Build_development.rst
Merge branch 'master' into test-updates
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Build_extras.rst
update CMake script for GPU package to include handling of Arch 8.0 and CUDA 11
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Build_link.rst
import updates to the manual from the progguide branch
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Build_make.rst
explain error message when using a non-c++11 compliant compiler.
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Build_package.rst
add and document new "download" preset
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Build_settings.rst
make subheaders and typesetting more consistent
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Build_windows.rst
Update Windows Subsystem for Linux Tutorial
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Build.rst
update build overview
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change_box.rst
document the image flag reset for switching boundaries
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clear.rst
collapse multiple empty lines into a single empty line
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comm_modify.rst
replace '\_' with '_' in plain text where possible
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comm_style.rst
collapse multiple empty lines into a single empty line
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Commands_all.rst
rename reset_ids command to reset_atom_ids
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Commands_bond.rst
collapse multiple empty lines into a single empty line
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Commands_category.rst
convert lists to tables for more compact presentation
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Commands_compute.rst
Merge pull request #2211 from athomps/compute-mliap
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Commands_fix.rst
Merge pull request #2230 from evoyiatzis/widom
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Commands_input.rst
import updates to the manual from the progguide branch
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Commands_kspace.rst
remove backslash escapes for underscore in doc references
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commands_list.rst
rename reset_ids command to reset_atom_ids
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Commands_pair.rst
Split pair_lj.rst into three files
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Commands_parse.rst
replace '\_' with '_' in plain text where possible
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Commands_removed.rst
use consistent capitalization with NVIDIA
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Commands_structure.rst
remove trailing whitespace from documentation sources
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Commands.rst
collapse multiple empty lines into a single empty line
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compute_ackland_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
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compute_adf.rst
import updates to the manual from the progguide branch
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compute_angle_local.rst
replace '\_' with '_' in plain text where possible
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compute_angle.rst
replace '\_' with '_' in plain text where possible
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compute_angmom_chunk.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
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compute_basal_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
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compute_body_local.rst
replace '\_' with '_' in plain text where possible
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compute_bond_local.rst
replace '\_' with '_' in plain text where possible
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compute_bond.rst
replace '\_' with '_' in plain text where possible
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compute_centro_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
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compute_chunk_atom.rst
add option to compute chunk/atom to access the number of chunks as a global scalar
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compute_chunk_spread_atom.rst
replace '\_' with '_' in plain text where possible
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compute_cluster_atom.rst
minor adjustments to new reset_mol_ids command
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compute_cna_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
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compute_cnp_atom.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
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compute_com_chunk.rst
convert more LAMMPS script examples to use code-block instead of parsed-literal
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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
Replace common text block with include
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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
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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
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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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
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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
Split pair_lj.rst into three files
2020-07-01 14:27:06 -04:00
compute_global_atom.rst
some more fixups
2020-03-13 17:02:59 -04:00
compute_group_group.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
fix typo
2020-05-21 01:13:03 -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_mesont.rst
Fix whitespace
2020-06-16 07:20:09 -04:00
compute_mliap.rst
whitespace fixes
2020-07-16 19:03:30 -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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
compute_msd_nongauss.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
compute_msd.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
Replace common text block with include
2020-07-21 17:38:56 -04:00
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 common text block with include
2020-07-21 17:38:56 -04:00
compute_property_atom.rst
Fix whitespace
2020-06-16 07:20:09 -04:00
compute_property_chunk.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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_effm.rst
add minimal doc page for compute smd/ulsph/effm
2020-07-01 18:44:24 -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
whitespace fixes
2020-07-07 20:25:59 -04:00
compute_sph_e_atom.rst
renaming of variables and command names in USER-SPH
2020-04-30 16:40:09 -06:00
compute_sph_rho_atom.rst
renaming of variables and command names in USER-SPH
2020-04-30 16:40:09 -06:00
compute_sph_t_atom.rst
renaming of variables and command names in USER-SPH
2020-04-30 16:40:09 -06:00
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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
Replace common text block with include
2020-07-21 17:38:56 -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 common text block with include
2020-07-21 17:38:56 -04:00
compute_ti.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
Merge pull request #2211 from athomps/compute-mliap
2020-07-06 12:47:41 -04:00
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
rename reset_ids command to reset_atom_ids
2020-07-07 13:32:00 -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 common text block with include
2020-07-21 17:38:56 -04:00
dihedral_class2.rst
Replace common text block with include
2020-07-21 17:38:56 -04:00
dihedral_coeff.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
dihedral_cosine_shift_exp.rst
Replace common text block with include
2020-07-21 17:38:56 -04:00
dihedral_fourier.rst
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2020-07-21 17:38:56 -04:00
dihedral_harmonic.rst
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2020-07-21 17:38:56 -04:00
dihedral_helix.rst
Replace common text block with include
2020-07-21 17:38:56 -04:00
dihedral_hybrid.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
dihedral_multi_harmonic.rst
Replace common text block with include
2020-07-21 17:38:56 -04:00
dihedral_nharmonic.rst
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2020-07-21 17:38:56 -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
Replace common text block with include
2020-07-21 17:38:56 -04:00
dihedral_quadratic.rst
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2020-07-21 17:38:56 -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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
dihedral_table.rst
Replace common text block with include
2020-07-21 17:38:56 -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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
dump_modify.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
Errors_messages.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
Errors_warnings.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
Split pair_lj.rst into three files
2020-07-01 14:27:06 -04:00
fix_adapt.rst
Split pair_lj.rst into three files
2020-07-01 14:27:06 -04:00
fix_addforce.rst
Replace common text block with include
2020-07-21 17:38:56 -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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
fix_ave_histo.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
fix_ave_time.rst
some more fixups
2020-03-13 17:02:59 -04:00
fix_aveforce.rst
Replace common text block with include
2020-07-21 17:38:56 -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
reformat and rephrase text about availability of fix bond/create/angle only keyword
2020-07-15 21:32:22 -04:00
fix_bond_react.rst
fix permissions
2020-06-06 10:44:09 -04:00
fix_bond_swap.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_box_relax.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
fix_client_md.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_cmap.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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 common text block with include
2020-07-21 17:38:56 -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 common text block with include
2020-07-21 17:38:56 -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 common text block with include
2020-07-21 17:38:56 -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
Replace common text block with include
2020-07-21 17:38:56 -04:00
fix_eos_table.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -04:00
fix_evaporate.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_external.rst
import updates to the manual from the progguide branch
2020-06-14 11:25:02 -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 common text block with include
2020-07-21 17:38:56 -04:00
fix_gcmc.rst
make frenkel book anchors globally unique
2020-07-15 20:56:50 -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 common text block with include
2020-07-21 17:38:56 -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
use proper units (fmsec -> fs, psec -> ps and so on)
2020-05-21 01:13:15 -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
use proper units (fmsec -> fs, psec -> ps and so on)
2020-05-21 01:13:15 -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 common text block with include
2020-07-21 17:38:56 -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
use proper units (fmsec -> fs, psec -> ps and so on)
2020-05-21 01:13:15 -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 common text block with include
2020-07-21 17:38:56 -04:00
fix_move.rst
use proper units (fmsec -> fs, psec -> ps and so on)
2020-05-21 01:13:15 -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
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_neb.rst
replace '\_' with '_' in plain text where possible
2020-03-13 16:34:57 -04:00
fix_nh_eff.rst
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fix.rst
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fixes.rst
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group2ndx.rst
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group.rst
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hyper.rst
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if.rst
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include.rst
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info.rst
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Install_patch.rst
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Install_windows.rst
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Install.rst
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Intro_authors.rst
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jump.rst
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kim_commands.rst
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kspace_modify.rst
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kspace_style.rst
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label.rst
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lattice.rst
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log.rst
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Manual_build.rst
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Manual.rst
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mass.rst
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message.rst
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min_modify.rst
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minimize.rst
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molecule.rst
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neb_spin.rst
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neb.rst
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neigh_modify.rst
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neighbor.rst
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newton.rst
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next.rst
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package.rst
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Packages_details.rst
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Packages_standard.rst
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Packages_user.rst
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Packages.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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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_buck6d_coul_gauss.rst
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pair_buck_long.rst
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pair_buck.rst
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pair_class2.rst
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pair_coeff.rst
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pair_colloid.rst
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pair_comb.rst
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pair_cosine_squared.rst
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pair_coul_diel.rst
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pair_coul_shield.rst
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pair_dsmc.rst
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pair_e3b.rst
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pair_eff.rst
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pair_eim.rst
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pair_exp6_rx.rst
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pair_gw.rst
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pair_hybrid.rst
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pair_kim.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.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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pair_meam_sw_spline.rst
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pair_meamc.rst
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pair_mesocnt.rst
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pair_mesodpd.rst
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pair_mesont_tpm.rst
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pair_mgpt.rst
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pair_mie.rst
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pair_mliap.rst
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pair_modify.rst
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pair_momb.rst
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pair_morse.rst
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pair_multi_lucy_rx.rst
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pair_multi_lucy.rst
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pair_nb3b_harmonic.rst
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pair_nm.rst
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pair_none.rst
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pair_oxdna2.rst
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pair_peri.rst
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pair_polymorphic.rst
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pair_python.rst
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pair_quip.rst
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pair_resquared.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_spin_dipole.rst
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pair_spin_exchange.rst
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pair_spin_magelec.rst
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pair_spin_neel.rst
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pair_srp.rst
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pair_style.rst
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pair_sw.rst
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pair_table_rx.rst
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pair_table.rst
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pair_tri_lj.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_zero.rst
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pairs.rst
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partition.rst
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prd.rst
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print.rst
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processors.rst
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python.rst
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quit.rst
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read_data.rst
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read_dump.rst
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region.rst
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replicate.rst
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rerun.rst
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restart.rst
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run_style.rst
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run.rst
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server_mc.rst
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server_md.rst
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server.rst
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set.rst
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shell.rst
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special_bonds.rst
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Speed_bench.rst
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Speed_compare.rst
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Speed_gpu.rst
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Speed_intel.rst
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Speed_opt.rst
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Speed_packages.rst
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Speed.rst
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suffix.rst
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tad.rst
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temper_grem.rst
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temper_npt.rst
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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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third_order.rst
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timer.rst
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timestep.rst
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Tools.rst
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uncompute.rst
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undump.rst
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unfix.rst
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units.rst
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variable.rst
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velocity.rst
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write_coeff.rst
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write_data.rst
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write_dump.rst
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write_restart.rst
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