From 74dade3ccb388d36cf10e416a0cc6e6d9070e9ea Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 5 Nov 2019 14:01:48 -0500 Subject: [PATCH 1/5] Change doc folder src -> txt, rst -> src --- doc/Makefile | 25 +++++++++--------- doc/{rst => src}/.gitignore | 0 doc/{rst => src}/Build.rst | 0 doc/{rst => src}/Build_basics.rst | 0 doc/{rst => src}/Build_cmake.rst | 0 doc/{rst => src}/Build_development.rst | 0 doc/{rst => src}/Build_extras.rst | 0 doc/{rst => src}/Build_link.rst | 0 doc/{rst => src}/Build_make.rst | 0 doc/{rst => src}/Build_package.rst | 0 doc/{rst => src}/Build_settings.rst | 0 doc/{rst => src}/Build_windows.rst | 0 doc/{rst => src}/Commands.rst | 0 doc/{rst => src}/Commands_all.rst | 0 doc/{rst => src}/Commands_bond.rst | 0 doc/{rst => src}/Commands_category.rst | 0 doc/{rst => src}/Commands_compute.rst | 0 doc/{rst => src}/Commands_fix.rst | 0 doc/{rst => src}/Commands_input.rst | 0 doc/{rst => src}/Commands_kspace.rst | 0 doc/{rst => src}/Commands_pair.rst | 0 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(100%) rename doc/{src => txt}/uncompute.txt (100%) rename doc/{src => txt}/undump.txt (100%) rename doc/{src => txt}/unfix.txt (100%) rename doc/{src => txt}/units.txt (100%) rename doc/{src => txt}/variable.txt (100%) rename doc/{src => txt}/velocity.txt (100%) rename doc/{src => txt}/write_coeff.txt (100%) rename doc/{src => txt}/write_data.txt (100%) rename doc/{src => txt}/write_dump.txt (100%) rename doc/{src => txt}/write_restart.txt (100%) diff --git a/doc/Makefile b/doc/Makefile index fc5e930121..5dcb070f4f 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -1,11 +1,12 @@ # Makefile for LAMMPS documentation SHELL = /bin/bash -BUILDDIR = ${PWD} -RSTDIR = $(BUILDDIR)/rst +BUILDDIR = ${CURDIR} +RSTDIR = $(BUILDDIR)/src +TXTDIR = $(BUILDDIR)/txt VENV = $(BUILDDIR)/docenv TXT2RST = $(VENV)/bin/txt2rst -ANCHORCHECK = $(VENV)/bin/doc_anchor_check +ANCHORCHECK = $(VENV)/bin/rst_anchor_check PYTHON = $(shell which python3) VIRTUALENV = virtualenv @@ -27,8 +28,8 @@ HAS_VIRTUALENV = YES endif SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') -SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt)) -OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) +SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt)) +OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst) .PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check @@ -53,7 +54,7 @@ clean-all: clean rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees clean: - rm -rf $(RSTDIR)/{Eqs,JPG,*.rst} html epub latex + rm -rf html epub latex rm -rf spelling clean-spelling: @@ -64,12 +65,10 @@ rst: clean $(OBJECTS) $(ANCHORCHECK) html: $(OBJECTS) $(ANCHORCHECK) @(\ . $(VENV)/bin/activate ;\ - cp -r src/JPG $(RSTDIR)/ ;\ - cp -r src/Eqs $(RSTDIR)/ ;\ sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\ echo "############################################" ;\ - doc_anchor_check src/*.txt ;\ - env LC_ALL=C grep -n '[^ -~]' src/*.txt ;\ + rst_anchor_check src/*.rst ;\ + env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\ echo "############################################" ;\ deactivate ;\ ) @@ -89,7 +88,7 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt @(\ . $(VENV)/bin/activate ;\ pip install sphinxcontrib-spelling ;\ - cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\ + cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\ sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\ deactivate ;\ ) @@ -126,7 +125,7 @@ pdf: $(OBJECTS) $(ANCHORCHECK) . $(VENV)/bin/activate ;\ sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\ echo "############################################" ;\ - doc_anchor_check src/*.txt ;\ + rst_anchor_check src/*.rst ;\ echo "############################################" ;\ deactivate ;\ ) @@ -163,7 +162,7 @@ fetch: anchor_check : $(ANCHORCHECK) @(\ . $(VENV)/bin/activate ;\ - doc_anchor_check src/*.txt ;\ + rst_anchor_check src/*.txt ;\ deactivate ;\ ) diff --git a/doc/rst/.gitignore b/doc/src/.gitignore similarity index 100% rename from doc/rst/.gitignore rename to doc/src/.gitignore diff --git a/doc/rst/Build.rst b/doc/src/Build.rst similarity index 100% rename from doc/rst/Build.rst rename to doc/src/Build.rst diff --git a/doc/rst/Build_basics.rst b/doc/src/Build_basics.rst similarity index 100% rename from doc/rst/Build_basics.rst rename to doc/src/Build_basics.rst diff --git a/doc/rst/Build_cmake.rst b/doc/src/Build_cmake.rst similarity index 100% rename from doc/rst/Build_cmake.rst rename to doc/src/Build_cmake.rst diff --git a/doc/rst/Build_development.rst b/doc/src/Build_development.rst similarity index 100% rename from doc/rst/Build_development.rst rename to doc/src/Build_development.rst 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a/doc/rst/comm_style.rst b/doc/src/comm_style.rst similarity index 100% rename from doc/rst/comm_style.rst rename to doc/src/comm_style.rst diff --git a/doc/rst/commands_list.rst b/doc/src/commands_list.rst similarity index 100% rename from doc/rst/commands_list.rst rename to doc/src/commands_list.rst diff --git a/doc/rst/compute.rst b/doc/src/compute.rst similarity index 100% rename from doc/rst/compute.rst rename to doc/src/compute.rst diff --git a/doc/rst/compute_ackland_atom.rst b/doc/src/compute_ackland_atom.rst similarity index 100% rename from doc/rst/compute_ackland_atom.rst rename to doc/src/compute_ackland_atom.rst diff --git a/doc/rst/compute_adf.rst b/doc/src/compute_adf.rst similarity index 100% rename from doc/rst/compute_adf.rst rename to doc/src/compute_adf.rst diff --git a/doc/rst/compute_angle.rst b/doc/src/compute_angle.rst similarity index 100% rename from doc/rst/compute_angle.rst rename to doc/src/compute_angle.rst diff --git a/doc/rst/compute_angle_local.rst b/doc/src/compute_angle_local.rst similarity index 100% rename from doc/rst/compute_angle_local.rst rename to doc/src/compute_angle_local.rst diff --git a/doc/rst/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst similarity index 100% rename from doc/rst/compute_angmom_chunk.rst rename to doc/src/compute_angmom_chunk.rst diff --git a/doc/rst/compute_basal_atom.rst b/doc/src/compute_basal_atom.rst similarity index 100% rename from doc/rst/compute_basal_atom.rst rename to doc/src/compute_basal_atom.rst diff --git a/doc/rst/compute_body_local.rst b/doc/src/compute_body_local.rst similarity index 100% rename from doc/rst/compute_body_local.rst rename to doc/src/compute_body_local.rst diff --git a/doc/rst/compute_bond.rst b/doc/src/compute_bond.rst similarity index 100% rename from doc/rst/compute_bond.rst rename to doc/src/compute_bond.rst diff --git a/doc/rst/compute_bond_local.rst b/doc/src/compute_bond_local.rst similarity index 100% rename from doc/rst/compute_bond_local.rst rename to doc/src/compute_bond_local.rst diff --git a/doc/rst/compute_centro_atom.rst b/doc/src/compute_centro_atom.rst similarity index 100% rename from doc/rst/compute_centro_atom.rst rename to doc/src/compute_centro_atom.rst diff --git a/doc/rst/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst similarity index 100% rename from doc/rst/compute_chunk_atom.rst rename to doc/src/compute_chunk_atom.rst diff --git a/doc/rst/compute_chunk_spread_atom.rst b/doc/src/compute_chunk_spread_atom.rst similarity index 100% rename from doc/rst/compute_chunk_spread_atom.rst rename to doc/src/compute_chunk_spread_atom.rst diff --git a/doc/rst/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst similarity index 100% rename from doc/rst/compute_cluster_atom.rst rename to doc/src/compute_cluster_atom.rst diff --git a/doc/rst/compute_cna_atom.rst b/doc/src/compute_cna_atom.rst similarity index 100% rename from doc/rst/compute_cna_atom.rst rename to doc/src/compute_cna_atom.rst diff --git a/doc/rst/compute_cnp_atom.rst b/doc/src/compute_cnp_atom.rst similarity index 100% rename from doc/rst/compute_cnp_atom.rst rename to doc/src/compute_cnp_atom.rst diff --git a/doc/rst/compute_com.rst b/doc/src/compute_com.rst similarity index 100% rename from doc/rst/compute_com.rst rename to doc/src/compute_com.rst diff --git a/doc/rst/compute_com_chunk.rst b/doc/src/compute_com_chunk.rst similarity index 100% rename from doc/rst/compute_com_chunk.rst rename to doc/src/compute_com_chunk.rst diff --git a/doc/rst/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst similarity index 100% rename from doc/rst/compute_contact_atom.rst rename to doc/src/compute_contact_atom.rst diff --git a/doc/rst/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst similarity index 100% rename from doc/rst/compute_coord_atom.rst rename to doc/src/compute_coord_atom.rst diff --git a/doc/rst/compute_damage_atom.rst b/doc/src/compute_damage_atom.rst similarity index 100% rename from doc/rst/compute_damage_atom.rst rename to doc/src/compute_damage_atom.rst diff --git a/doc/rst/compute_dihedral.rst b/doc/src/compute_dihedral.rst similarity index 100% rename from doc/rst/compute_dihedral.rst rename to doc/src/compute_dihedral.rst diff --git a/doc/rst/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst similarity index 100% rename from doc/rst/compute_dihedral_local.rst rename to doc/src/compute_dihedral_local.rst diff --git a/doc/rst/compute_dilatation_atom.rst b/doc/src/compute_dilatation_atom.rst similarity index 100% rename from doc/rst/compute_dilatation_atom.rst rename to doc/src/compute_dilatation_atom.rst diff --git a/doc/rst/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst similarity index 100% rename from doc/rst/compute_dipole_chunk.rst rename to doc/src/compute_dipole_chunk.rst diff --git a/doc/rst/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst similarity index 100% rename from doc/rst/compute_displace_atom.rst rename to doc/src/compute_displace_atom.rst diff --git a/doc/rst/compute_dpd.rst b/doc/src/compute_dpd.rst similarity index 100% rename from doc/rst/compute_dpd.rst rename to doc/src/compute_dpd.rst diff --git a/doc/rst/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst similarity index 100% rename from doc/rst/compute_dpd_atom.rst rename to doc/src/compute_dpd_atom.rst diff --git a/doc/rst/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst similarity index 100% rename from doc/rst/compute_edpd_temp_atom.rst rename to doc/src/compute_edpd_temp_atom.rst diff --git a/doc/rst/compute_entropy_atom.rst b/doc/src/compute_entropy_atom.rst similarity index 100% rename from doc/rst/compute_entropy_atom.rst rename to doc/src/compute_entropy_atom.rst diff --git a/doc/rst/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst similarity index 100% rename from doc/rst/compute_erotate_asphere.rst rename to doc/src/compute_erotate_asphere.rst diff --git a/doc/rst/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst similarity index 100% rename from doc/rst/compute_erotate_rigid.rst rename to doc/src/compute_erotate_rigid.rst diff --git a/doc/rst/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst similarity index 100% rename from doc/rst/compute_erotate_sphere.rst rename to doc/src/compute_erotate_sphere.rst diff --git a/doc/rst/compute_erotate_sphere_atom.rst b/doc/src/compute_erotate_sphere_atom.rst similarity index 100% rename from doc/rst/compute_erotate_sphere_atom.rst rename to doc/src/compute_erotate_sphere_atom.rst diff --git a/doc/rst/compute_event_displace.rst b/doc/src/compute_event_displace.rst similarity index 100% rename from doc/rst/compute_event_displace.rst rename to doc/src/compute_event_displace.rst diff --git a/doc/rst/compute_fep.rst b/doc/src/compute_fep.rst similarity index 100% rename from doc/rst/compute_fep.rst rename to doc/src/compute_fep.rst diff --git a/doc/rst/compute_global_atom.rst b/doc/src/compute_global_atom.rst similarity index 100% rename from doc/rst/compute_global_atom.rst rename to doc/src/compute_global_atom.rst diff --git a/doc/rst/compute_group_group.rst b/doc/src/compute_group_group.rst similarity index 100% rename from doc/rst/compute_group_group.rst rename to doc/src/compute_group_group.rst diff --git a/doc/rst/compute_gyration.rst b/doc/src/compute_gyration.rst similarity index 100% rename from doc/rst/compute_gyration.rst rename to doc/src/compute_gyration.rst diff --git a/doc/rst/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst similarity index 100% rename from doc/rst/compute_gyration_chunk.rst rename to doc/src/compute_gyration_chunk.rst diff --git a/doc/rst/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst similarity index 100% rename from doc/rst/compute_gyration_shape.rst rename to doc/src/compute_gyration_shape.rst diff --git a/doc/rst/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst similarity index 100% rename from doc/rst/compute_heat_flux.rst rename to doc/src/compute_heat_flux.rst diff --git a/doc/rst/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst similarity index 100% rename from doc/rst/compute_hexorder_atom.rst rename to doc/src/compute_hexorder_atom.rst diff --git a/doc/rst/compute_hma.rst b/doc/src/compute_hma.rst similarity index 100% rename from doc/rst/compute_hma.rst rename to doc/src/compute_hma.rst diff --git a/doc/rst/compute_improper.rst b/doc/src/compute_improper.rst similarity index 100% rename from doc/rst/compute_improper.rst rename to doc/src/compute_improper.rst diff --git a/doc/rst/compute_improper_local.rst b/doc/src/compute_improper_local.rst similarity index 100% rename from doc/rst/compute_improper_local.rst rename to doc/src/compute_improper_local.rst diff --git a/doc/rst/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst similarity index 100% rename from doc/rst/compute_inertia_chunk.rst rename to doc/src/compute_inertia_chunk.rst diff --git a/doc/rst/compute_ke.rst b/doc/src/compute_ke.rst similarity index 100% rename from doc/rst/compute_ke.rst rename to doc/src/compute_ke.rst diff --git a/doc/rst/compute_ke_atom.rst b/doc/src/compute_ke_atom.rst similarity index 100% rename from doc/rst/compute_ke_atom.rst rename to doc/src/compute_ke_atom.rst diff --git a/doc/rst/compute_ke_atom_eff.rst b/doc/src/compute_ke_atom_eff.rst similarity index 100% rename from doc/rst/compute_ke_atom_eff.rst rename to doc/src/compute_ke_atom_eff.rst diff --git a/doc/rst/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst similarity index 100% rename from doc/rst/compute_ke_eff.rst rename to doc/src/compute_ke_eff.rst diff --git a/doc/rst/compute_ke_rigid.rst b/doc/src/compute_ke_rigid.rst similarity index 100% rename from doc/rst/compute_ke_rigid.rst rename to doc/src/compute_ke_rigid.rst diff --git a/doc/rst/compute_meso_e_atom.rst b/doc/src/compute_meso_e_atom.rst similarity index 100% rename from doc/rst/compute_meso_e_atom.rst rename to doc/src/compute_meso_e_atom.rst diff --git a/doc/rst/compute_meso_rho_atom.rst b/doc/src/compute_meso_rho_atom.rst similarity index 100% rename from doc/rst/compute_meso_rho_atom.rst rename to doc/src/compute_meso_rho_atom.rst diff --git a/doc/rst/compute_meso_t_atom.rst b/doc/src/compute_meso_t_atom.rst similarity index 100% rename from doc/rst/compute_meso_t_atom.rst rename to doc/src/compute_meso_t_atom.rst diff --git a/doc/rst/compute_modify.rst b/doc/src/compute_modify.rst similarity index 100% rename from doc/rst/compute_modify.rst rename to doc/src/compute_modify.rst diff --git a/doc/rst/compute_momentum.rst b/doc/src/compute_momentum.rst similarity index 100% rename from doc/rst/compute_momentum.rst rename to doc/src/compute_momentum.rst diff --git a/doc/rst/compute_msd.rst b/doc/src/compute_msd.rst similarity index 100% rename from doc/rst/compute_msd.rst rename to doc/src/compute_msd.rst diff --git a/doc/rst/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst similarity index 100% rename from doc/rst/compute_msd_chunk.rst rename to doc/src/compute_msd_chunk.rst diff --git a/doc/rst/compute_msd_nongauss.rst b/doc/src/compute_msd_nongauss.rst similarity index 100% rename from doc/rst/compute_msd_nongauss.rst rename to doc/src/compute_msd_nongauss.rst diff --git a/doc/rst/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst similarity index 100% rename from doc/rst/compute_omega_chunk.rst rename to doc/src/compute_omega_chunk.rst diff --git a/doc/rst/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst similarity index 100% rename from doc/rst/compute_orientorder_atom.rst rename to doc/src/compute_orientorder_atom.rst diff --git a/doc/rst/compute_pair.rst b/doc/src/compute_pair.rst similarity index 100% rename from doc/rst/compute_pair.rst rename to doc/src/compute_pair.rst diff --git a/doc/rst/compute_pair_local.rst b/doc/src/compute_pair_local.rst similarity index 100% rename from doc/rst/compute_pair_local.rst rename to 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b/doc/src/compute_pressure_uef.rst similarity index 100% rename from doc/rst/compute_pressure_uef.rst rename to doc/src/compute_pressure_uef.rst diff --git a/doc/rst/compute_property_atom.rst b/doc/src/compute_property_atom.rst similarity index 100% rename from doc/rst/compute_property_atom.rst rename to doc/src/compute_property_atom.rst diff --git a/doc/rst/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst similarity index 100% rename from doc/rst/compute_property_chunk.rst rename to doc/src/compute_property_chunk.rst diff --git a/doc/rst/compute_property_local.rst b/doc/src/compute_property_local.rst similarity index 100% rename from doc/rst/compute_property_local.rst rename to doc/src/compute_property_local.rst diff --git a/doc/rst/compute_ptm_atom.rst b/doc/src/compute_ptm_atom.rst similarity index 100% rename from doc/rst/compute_ptm_atom.rst rename to doc/src/compute_ptm_atom.rst diff --git a/doc/rst/compute_rdf.rst b/doc/src/compute_rdf.rst similarity index 100% rename from doc/rst/compute_rdf.rst rename to doc/src/compute_rdf.rst diff --git a/doc/rst/compute_reduce.rst b/doc/src/compute_reduce.rst similarity index 100% rename from doc/rst/compute_reduce.rst rename to doc/src/compute_reduce.rst diff --git a/doc/rst/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst similarity index 100% rename from doc/rst/compute_reduce_chunk.rst rename to doc/src/compute_reduce_chunk.rst diff --git a/doc/rst/compute_rigid_local.rst b/doc/src/compute_rigid_local.rst similarity index 100% rename from doc/rst/compute_rigid_local.rst rename to doc/src/compute_rigid_local.rst diff --git a/doc/rst/compute_saed.rst b/doc/src/compute_saed.rst similarity index 100% rename from doc/rst/compute_saed.rst rename to doc/src/compute_saed.rst diff --git a/doc/rst/compute_slice.rst b/doc/src/compute_slice.rst similarity index 100% rename from doc/rst/compute_slice.rst rename to doc/src/compute_slice.rst diff --git a/doc/rst/compute_smd_contact_radius.rst 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a/doc/src/pair_meso.txt b/doc/txt/pair_meso.txt similarity index 100% rename from doc/src/pair_meso.txt rename to doc/txt/pair_meso.txt diff --git a/doc/src/pair_mgpt.txt b/doc/txt/pair_mgpt.txt similarity index 100% rename from doc/src/pair_mgpt.txt rename to doc/txt/pair_mgpt.txt diff --git a/doc/src/pair_mie.txt b/doc/txt/pair_mie.txt similarity index 100% rename from doc/src/pair_mie.txt rename to doc/txt/pair_mie.txt diff --git a/doc/src/pair_mm3_switch3_coulgauss.txt b/doc/txt/pair_mm3_switch3_coulgauss.txt similarity index 100% rename from doc/src/pair_mm3_switch3_coulgauss.txt rename to doc/txt/pair_mm3_switch3_coulgauss.txt diff --git a/doc/src/pair_modify.txt b/doc/txt/pair_modify.txt similarity index 100% rename from doc/src/pair_modify.txt rename to doc/txt/pair_modify.txt diff --git a/doc/src/pair_momb.txt b/doc/txt/pair_momb.txt similarity index 100% rename from doc/src/pair_momb.txt rename to doc/txt/pair_momb.txt diff --git a/doc/src/pair_morse.txt b/doc/txt/pair_morse.txt similarity index 100% rename from doc/src/pair_morse.txt rename to doc/txt/pair_morse.txt diff --git a/doc/src/pair_multi_lucy.txt b/doc/txt/pair_multi_lucy.txt similarity index 100% rename from doc/src/pair_multi_lucy.txt rename to doc/txt/pair_multi_lucy.txt diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/txt/pair_multi_lucy_rx.txt similarity index 100% rename from doc/src/pair_multi_lucy_rx.txt rename to doc/txt/pair_multi_lucy_rx.txt diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/txt/pair_nb3b_harmonic.txt similarity index 100% rename from doc/src/pair_nb3b_harmonic.txt rename to doc/txt/pair_nb3b_harmonic.txt diff --git a/doc/src/pair_nm.txt b/doc/txt/pair_nm.txt similarity index 100% rename from doc/src/pair_nm.txt rename to doc/txt/pair_nm.txt diff --git a/doc/src/pair_none.txt b/doc/txt/pair_none.txt similarity index 100% rename from doc/src/pair_none.txt rename to doc/txt/pair_none.txt diff --git a/doc/src/pair_oxdna.txt b/doc/txt/pair_oxdna.txt similarity index 100% rename from doc/src/pair_oxdna.txt rename to doc/txt/pair_oxdna.txt diff --git a/doc/src/pair_oxdna2.txt b/doc/txt/pair_oxdna2.txt similarity index 100% rename from doc/src/pair_oxdna2.txt rename to doc/txt/pair_oxdna2.txt diff --git a/doc/src/pair_peri.txt b/doc/txt/pair_peri.txt similarity index 100% rename from doc/src/pair_peri.txt rename to doc/txt/pair_peri.txt diff --git a/doc/src/pair_polymorphic.txt b/doc/txt/pair_polymorphic.txt similarity index 100% rename from doc/src/pair_polymorphic.txt rename to doc/txt/pair_polymorphic.txt diff --git a/doc/src/pair_python.txt b/doc/txt/pair_python.txt similarity index 100% rename from doc/src/pair_python.txt rename to doc/txt/pair_python.txt diff --git a/doc/src/pair_quip.txt b/doc/txt/pair_quip.txt similarity index 100% rename from doc/src/pair_quip.txt rename to doc/txt/pair_quip.txt diff --git a/doc/src/pair_reaxc.txt b/doc/txt/pair_reaxc.txt similarity index 100% rename from doc/src/pair_reaxc.txt rename to 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similarity index 100% rename from doc/src/pair_smd_triangulated_surface.txt rename to doc/txt/pair_smd_triangulated_surface.txt diff --git a/doc/src/pair_smd_ulsph.txt b/doc/txt/pair_smd_ulsph.txt similarity index 100% rename from doc/src/pair_smd_ulsph.txt rename to doc/txt/pair_smd_ulsph.txt diff --git a/doc/src/pair_smtbq.txt b/doc/txt/pair_smtbq.txt similarity index 100% rename from doc/src/pair_smtbq.txt rename to doc/txt/pair_smtbq.txt diff --git a/doc/src/pair_snap.txt b/doc/txt/pair_snap.txt similarity index 100% rename from doc/src/pair_snap.txt rename to doc/txt/pair_snap.txt diff --git a/doc/src/pair_soft.txt b/doc/txt/pair_soft.txt similarity index 100% rename from doc/src/pair_soft.txt rename to doc/txt/pair_soft.txt diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/txt/pair_sph_heatconduction.txt similarity index 100% rename from doc/src/pair_sph_heatconduction.txt rename to doc/txt/pair_sph_heatconduction.txt diff --git a/doc/src/pair_sph_idealgas.txt b/doc/txt/pair_sph_idealgas.txt similarity index 100% rename from doc/src/pair_sph_idealgas.txt rename to doc/txt/pair_sph_idealgas.txt diff --git a/doc/src/pair_sph_lj.txt b/doc/txt/pair_sph_lj.txt similarity index 100% rename from doc/src/pair_sph_lj.txt rename to doc/txt/pair_sph_lj.txt diff --git a/doc/src/pair_sph_rhosum.txt b/doc/txt/pair_sph_rhosum.txt similarity index 100% rename from doc/src/pair_sph_rhosum.txt rename to doc/txt/pair_sph_rhosum.txt diff --git a/doc/src/pair_sph_taitwater.txt b/doc/txt/pair_sph_taitwater.txt similarity index 100% rename from doc/src/pair_sph_taitwater.txt rename to doc/txt/pair_sph_taitwater.txt diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/txt/pair_sph_taitwater_morris.txt similarity index 100% rename from doc/src/pair_sph_taitwater_morris.txt rename to doc/txt/pair_sph_taitwater_morris.txt diff --git a/doc/src/pair_spin_dipole.txt b/doc/txt/pair_spin_dipole.txt similarity index 100% rename from doc/src/pair_spin_dipole.txt rename to doc/txt/pair_spin_dipole.txt diff --git a/doc/src/pair_spin_dmi.txt b/doc/txt/pair_spin_dmi.txt similarity index 100% rename from doc/src/pair_spin_dmi.txt rename to doc/txt/pair_spin_dmi.txt diff --git a/doc/src/pair_spin_exchange.txt b/doc/txt/pair_spin_exchange.txt similarity index 100% rename from doc/src/pair_spin_exchange.txt rename to doc/txt/pair_spin_exchange.txt diff --git a/doc/src/pair_spin_magelec.txt b/doc/txt/pair_spin_magelec.txt similarity index 100% rename from doc/src/pair_spin_magelec.txt rename to doc/txt/pair_spin_magelec.txt diff --git a/doc/src/pair_spin_neel.txt b/doc/txt/pair_spin_neel.txt similarity index 100% rename from doc/src/pair_spin_neel.txt rename to doc/txt/pair_spin_neel.txt diff --git a/doc/src/pair_srp.txt b/doc/txt/pair_srp.txt similarity index 100% rename from doc/src/pair_srp.txt rename to doc/txt/pair_srp.txt diff --git a/doc/src/pair_style.txt b/doc/txt/pair_style.txt similarity index 100% rename from doc/src/pair_style.txt rename to 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rename from doc/src/server.txt rename to doc/txt/server.txt diff --git a/doc/src/server_mc.txt b/doc/txt/server_mc.txt similarity index 100% rename from doc/src/server_mc.txt rename to doc/txt/server_mc.txt diff --git a/doc/src/server_md.txt b/doc/txt/server_md.txt similarity index 100% rename from doc/src/server_md.txt rename to doc/txt/server_md.txt diff --git a/doc/src/set.txt b/doc/txt/set.txt similarity index 100% rename from doc/src/set.txt rename to doc/txt/set.txt diff --git a/doc/src/shell.txt b/doc/txt/shell.txt similarity index 100% rename from doc/src/shell.txt rename to doc/txt/shell.txt diff --git a/doc/src/special_bonds.txt b/doc/txt/special_bonds.txt similarity index 100% rename from doc/src/special_bonds.txt rename to doc/txt/special_bonds.txt diff --git a/doc/src/suffix.txt b/doc/txt/suffix.txt similarity index 100% rename from doc/src/suffix.txt rename to doc/txt/suffix.txt diff --git a/doc/src/tad.txt b/doc/txt/tad.txt similarity index 100% rename from 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b/doc/txt/third_order.txt similarity index 100% rename from doc/src/third_order.txt rename to doc/txt/third_order.txt diff --git a/doc/src/timer.txt b/doc/txt/timer.txt similarity index 100% rename from doc/src/timer.txt rename to doc/txt/timer.txt diff --git a/doc/src/timestep.txt b/doc/txt/timestep.txt similarity index 100% rename from doc/src/timestep.txt rename to doc/txt/timestep.txt diff --git a/doc/src/uncompute.txt b/doc/txt/uncompute.txt similarity index 100% rename from doc/src/uncompute.txt rename to doc/txt/uncompute.txt diff --git a/doc/src/undump.txt b/doc/txt/undump.txt similarity index 100% rename from doc/src/undump.txt rename to doc/txt/undump.txt diff --git a/doc/src/unfix.txt b/doc/txt/unfix.txt similarity index 100% rename from doc/src/unfix.txt rename to doc/txt/unfix.txt diff --git a/doc/src/units.txt b/doc/txt/units.txt similarity index 100% rename from doc/src/units.txt rename to doc/txt/units.txt diff --git a/doc/src/variable.txt b/doc/txt/variable.txt similarity index 100% rename from doc/src/variable.txt rename to doc/txt/variable.txt diff --git a/doc/src/velocity.txt b/doc/txt/velocity.txt similarity index 100% rename from doc/src/velocity.txt rename to doc/txt/velocity.txt diff --git a/doc/src/write_coeff.txt b/doc/txt/write_coeff.txt similarity index 100% rename from doc/src/write_coeff.txt rename to doc/txt/write_coeff.txt diff --git a/doc/src/write_data.txt b/doc/txt/write_data.txt similarity index 100% rename from doc/src/write_data.txt rename to doc/txt/write_data.txt diff --git a/doc/src/write_dump.txt b/doc/txt/write_dump.txt similarity index 100% rename from doc/src/write_dump.txt rename to doc/txt/write_dump.txt diff --git a/doc/src/write_restart.txt b/doc/txt/write_restart.txt similarity index 100% rename from doc/src/write_restart.txt rename to doc/txt/write_restart.txt -- GitLab From 423a3bb99f9f8f294670c2f5a0f2516b3cd0c190 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 5 Nov 2019 14:22:17 -0500 Subject: [PATCH 2/5] Add initial version of updated tools from #1533 --- .../lammpsdoc/eqImg2mathjaxInline.py | 238 ++++++++++++++++++ .../converters/lammpsdoc/rst_anchor_check.py | 64 +++++ doc/utils/converters/setup.py | 2 +- 3 files changed, 303 insertions(+), 1 deletion(-) create mode 100644 doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py create mode 100644 doc/utils/converters/lammpsdoc/rst_anchor_check.py diff --git a/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py new file mode 100644 index 0000000000..6db83da7fd --- /dev/null +++ b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py @@ -0,0 +1,238 @@ +#! /usr/bin/env python3 +# LAMMPS Documentation Utilities +# +# Scan for duplicate anchor labels in documentation files +# +# Copyright (C) 2019 E. Anne Gunn +# Based largely on doc_anchor_check.py by Richard Berger +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +import argparse +import os +import re +import sys + + +# We only want to replace image lines where image is +# pulled from Eqs subfolder +image_pattern = re.compile(r'.*image:: Eqs/(.*)\.jpg') +tex_eq_pattern = re.compile(r'\$\$') +latex_begin_eq_pattern = re.compile(r'\\begin{equation}') +latex_end_eq_pattern = re.compile(r'\\end{equation}') +latex_begin_eqArray_pattern = re.compile(r'\\begin{eqnarray\*}') +latex_end_eqArray_pattern = re.compile(r'\\end{eqnarray\*}') + +imageMarker = ">>>image was here" +image_marker_pattern = re.compile(r'>>>image was here') +align_pattern = re.compile(r'.*:align: center') + +modifiedFileFolder = "src/modifiedRst/" +# Since this is a proof of concept implementation, +# skip any rst files that are known to cause problems +skipFileList = ["pair_tersoff_zbl.rst"] + +runReport = { +} + + +def checkForEquationStart(texLine): + eqType = None + texMatch = tex_eq_pattern.match(texLine) + if texMatch: + eqType = "texMatch" + else: + eqMatch = latex_begin_eq_pattern.match(texLine) + if eqMatch: + eqType = "eqMatch" + else: + eqArrayMatch = latex_begin_eqArray_pattern.match(texLine) + if eqArrayMatch: + eqType = "eqArrayMatch" + return eqType + + +def checkForEquationEnd(texLine, eqType): + endPattern = tex_eq_pattern + if eqType == "texMatch": + endPattern = tex_eq_pattern + elif eqType == "eqMatch": + endPattern = latex_end_eq_pattern + elif eqType == "eqArrayMatch": + endPattern = latex_end_eqArray_pattern + else: + print("***error: unexpected eqType %s, will look for tex delimiter" % eqType) + + endMatch = endPattern.match(texLine) + endFound = endMatch is not None + if endFound: + print("found pattern end, line: %s" % texLine) + return endFound + + +def startMathjax(): + mathjaxLines = [] + mathjaxLines.append(".. math::\n\n") + return mathjaxLines + + +def endMathjax(mathjaxLines): + mathjaxLines.append("\n") + mathjaxLines.append("%s\n" % imageMarker) + return mathjaxLines + + +def processFile(filename): + print("in processFile for filename: %s" % filename) + imageCount = 0 + + modifiedFileLines = [] + doWriteModifiedFile = False + with open(filename, 'rt') as f: + for line_number, line in enumerate(f): + m = image_pattern.match(line) + if m: + fileroot = m.group(1) + print("fileroot: {0}".format(fileroot)) + imageCount += 1 + texFilename = "src/Eqs/{0}.tex".format(fileroot) + print("will try to open %s" % texFilename) + eqType = None + eqLines = [] + try: + with open(texFilename, 'rt', encoding='utf-8') as t: + print("%s file opened ok" % texFilename) + eqLines = startMathjax() + try: + for dummy, texLine in enumerate(t): + #print(texLine) + if eqType == None: + eqType = checkForEquationStart(texLine) + if eqType != None: + print("equation type: {0}".format(eqType)) + else: + endFound = checkForEquationEnd(texLine, eqType) + if endFound != True: + eqLines.append(texLine) + else: + eqType = None + eqLines = endMathjax(eqLines) + print("Equation lines will be:") + print("-----------------------------") + print(*eqLines, sep="\n") + print("-----------------------------") + except UnicodeDecodeError: + print("UnicodeDecodeError reading file file %s, image markup will be left in place" % texFilename) + break + except EnvironmentError: + error = "could not open source tex file {0}, line: {1}".format(texFilename, line) + print(error) + print("image markup will be left in place") + if filename not in runReport: + runReport[filename] = [] + runReport[filename].append(error) + # put the image line we could not replace back into the output + eqLines.append(line) + if len(eqLines) > 0: + modifiedFileLines.extend(eqLines) + doWriteModifiedFile = True + eqLines = [] + else: + # not an equation line, so simply queue it up for output as is + modifiedFileLines.append(line) + if doWriteModifiedFile: + #print(*modifiedFileLines, sep="\n") + print("modifiedFileLines has %d lines before align center cleanup" % len(modifiedFileLines)) + # First, go through the file and pull out the lines where there is + # now an image file marker followed by an align center directive + deleteLines = [] + for lineNumber, line in enumerate(modifiedFileLines): + m = image_marker_pattern.match(line) + if m: + print("found image marker in line %d" % lineNumber) + n = align_pattern.match(modifiedFileLines[lineNumber+1]) + if n: + print("found align center") + deleteLines.append(lineNumber) + deleteLines.append(lineNumber+1) + #When deleting, always work from the back of the list to the front + for lineNumber in reversed(deleteLines): + print(lineNumber) + del modifiedFileLines[lineNumber] + print("modifiedFileLines has %d lines after align center cleanup" % len(modifiedFileLines)) + # Now we can actually write out the new contents + try: + if not os.path.exists(modifiedFileFolder): + os.makedirs(modifiedFileFolder) + nameParts = filename.split("/") + filenamePos = len(nameParts) - 1 + modFilePath = "{0}{1}".format(modifiedFileFolder, nameParts[filenamePos]) + modRst = open(modFilePath, "w") + for rstLine in modifiedFileLines: + modRst.write(rstLine) + modRst.close() + except OSError: + print('Error: Creating directory. ' + modifiedFileFolder) + return imageCount + + +def main(): + fileCount = 0 + totalImageCount = 0 + + parser = argparse.ArgumentParser(description='replace image markup in rst files with inline mathjax markup from .txt source of images') + parser.add_argument('files', metavar='file', nargs='+', help='one or more files to scan') + parsed_args = parser.parse_args() + + # TODO: make originalRst folder and copy src/*.rst files into it + + # Because we may decide to add files to the skip list between runs, + # if we have more than one file to process, + # remove the modified file folder so we don't end up with + # zombie modifications + if len(parsed_args.files) > 1: + for outputFile in os.listdir(modifiedFileFolder): + filePath = os.path.join(modifiedFileFolder, outputFile) + try: + if os.path.isfile(filePath): + os.unlink(filePath) + except Exception as e: + print(e) + sys.exit(1) + + for filename in parsed_args.files: + doSkip = False + for skipName in skipFileList: + if filename.find(skipName) != -1: + print("skipping file: %s" % filename) + doSkip = True + runReport[filename] = ["skipped based on skipFileList"] + break + if not doSkip: + fileCount += 1 + ic = processFile(filename) + totalImageCount += ic + + print("============================================") + print("Processed %d rst files." % fileCount) + print("Found %d image lines." % totalImageCount) + + for fileKey in runReport: + print("--------------------------------------------") + print("run report for %s:" % fileKey) + print(*runReport[fileKey], sep="\n") + + print("============================================") + +if __name__ == "__main__": + main() diff --git a/doc/utils/converters/lammpsdoc/rst_anchor_check.py b/doc/utils/converters/lammpsdoc/rst_anchor_check.py new file mode 100644 index 0000000000..9c097e7d0e --- /dev/null +++ b/doc/utils/converters/lammpsdoc/rst_anchor_check.py @@ -0,0 +1,64 @@ +#! /usr/bin/env python3 +# LAMMPS Documentation Utilities +# +# Scan for duplicate anchor labels in documentation files +# +# Copyright (C) 2017 Richard Berger +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +import re +import sys +import argparse + +def main(): + parser = argparse.ArgumentParser(description='scan for duplicate anchor labels in documentation files') + parser.add_argument('files', metavar='file', nargs='+', help='one or more files to scan') + parsed_args = parser.parse_args() + + anchor_pattern = re.compile(r'^\.\. _(.*):$') + anchors = {} + + for filename in parsed_args.files: + #print("filename: %s" % filename) + with open(filename, 'rt') as f: + for line_number, line in enumerate(f): + m = anchor_pattern.match(line) + if m: + label = m.group(1) + #print("found label: %s" % label) + if label in anchors: + anchors[label].append((filename, line_number+1)) + else: + anchors[label] = [(filename, line_number+1)] + + print("found %d anchor labels" % len(anchors)) + + count = 0 + + for label in sorted(anchors.keys()): + if len(anchors[label]) > 1: + print(label) + count += 1 + for filename, line_number in anchors[label]: + print(" - %s:%d" % (filename, line_number)) + + + if count > 0: + print("Found %d anchor label errors." % count) + sys.exit(1) + else: + print("No anchor label errors.") + +if __name__ == "__main__": + main() diff --git a/doc/utils/converters/setup.py b/doc/utils/converters/setup.py index f4656a7f69..d85669bcc1 100644 --- a/doc/utils/converters/setup.py +++ b/doc/utils/converters/setup.py @@ -13,6 +13,6 @@ setup(name='LAMMPS Documentation Utilities', entry_points = { "console_scripts": ['txt2html = lammpsdoc.txt2html:main', 'txt2rst = lammpsdoc.txt2rst:main', - 'doc_anchor_check = lammpsdoc.doc_anchor_check:main '] + 'rst_anchor_check = lammpsdoc.rst_anchor_check:main '] }, ) -- GitLab From 5e6694f3bcda89237fe8cb96903abfdd81413df2 Mon Sep 17 00:00:00 2001 From: Anne Gunn Date: Fri, 21 Jun 2019 08:34:32 -0600 Subject: [PATCH 3/5] Re-enabled conversion of equations arrays. Disabled works even worse --- .../lammpsdoc/eqImg2mathjaxInline.py | 41 +++++++++++++------ 1 file changed, 29 insertions(+), 12 deletions(-) diff --git a/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py index 6db83da7fd..353eed8b6e 100644 --- a/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py +++ b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py @@ -21,6 +21,7 @@ import argparse import os import re +import shutil import sys @@ -37,7 +38,8 @@ imageMarker = ">>>image was here" image_marker_pattern = re.compile(r'>>>image was here') align_pattern = re.compile(r'.*:align: center') -modifiedFileFolder = "src/modifiedRst/" +modifiedRstFolder = "src/modifiedRst/" +safeRstFolder = "src/safeRst/" # Since this is a proof of concept implementation, # skip any rst files that are known to cause problems skipFileList = ["pair_tersoff_zbl.rst"] @@ -151,7 +153,13 @@ def processFile(filename): # not an equation line, so simply queue it up for output as is modifiedFileLines.append(line) if doWriteModifiedFile: - #print(*modifiedFileLines, sep="\n") + # We're going to write out a modified file, so first copy the original rst + # file into the original file folder. + nameParts = filename.split("/") + filenamePos = len(nameParts) - 1 + safeFilePath = "{0}{1}".format(safeRstFolder, nameParts[filenamePos]) + shutil.copyfile(filename, safeFilePath) + print("modifiedFileLines has %d lines before align center cleanup" % len(modifiedFileLines)) # First, go through the file and pull out the lines where there is # now an image file marker followed by an align center directive @@ -172,17 +180,13 @@ def processFile(filename): print("modifiedFileLines has %d lines after align center cleanup" % len(modifiedFileLines)) # Now we can actually write out the new contents try: - if not os.path.exists(modifiedFileFolder): - os.makedirs(modifiedFileFolder) - nameParts = filename.split("/") - filenamePos = len(nameParts) - 1 - modFilePath = "{0}{1}".format(modifiedFileFolder, nameParts[filenamePos]) + modFilePath = "{0}{1}".format(modifiedRstFolder, nameParts[filenamePos]) modRst = open(modFilePath, "w") for rstLine in modifiedFileLines: modRst.write(rstLine) modRst.close() except OSError: - print('Error: Creating directory. ' + modifiedFileFolder) + print('Error: Creating directory. ' + modifiedRstFolder) return imageCount @@ -193,16 +197,28 @@ def main(): parser = argparse.ArgumentParser(description='replace image markup in rst files with inline mathjax markup from .txt source of images') parser.add_argument('files', metavar='file', nargs='+', help='one or more files to scan') parsed_args = parser.parse_args() + print(parsed_args) - # TODO: make originalRst folder and copy src/*.rst files into it + if not os.path.exists(safeRstFolder): + os.makedirs(safeRstFolder) + if not os.path.exists(modifiedRstFolder): + os.makedirs(modifiedRstFolder) # Because we may decide to add files to the skip list between runs, # if we have more than one file to process, - # remove the modified file folder so we don't end up with + # files from both original and modified folders # zombie modifications if len(parsed_args.files) > 1: - for outputFile in os.listdir(modifiedFileFolder): - filePath = os.path.join(modifiedFileFolder, outputFile) + for outputFile in os.listdir(modifiedRstFolder): + filePath = os.path.join(modifiedRstFolder, outputFile) + try: + if os.path.isfile(filePath): + os.unlink(filePath) + except Exception as e: + print(e) + sys.exit(1) + for safeFile in os.listdir(safeRstFolder): + filePath = os.path.join(safeRstFolder, safeFile) try: if os.path.isfile(filePath): os.unlink(filePath) @@ -211,6 +227,7 @@ def main(): sys.exit(1) for filename in parsed_args.files: + print("filename: %s" % filename) doSkip = False for skipName in skipFileList: if filename.find(skipName) != -1: -- GitLab From c756e472aeab235f7ea7e939b45dba5abccddb73 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 5 Nov 2019 15:34:57 -0500 Subject: [PATCH 4/5] Remove Manual.txt and use variable for version --- doc/src/Manual.rst | 4 +- doc/txt/Manual.txt | 124 --------------------------------------------- 2 files changed, 2 insertions(+), 126 deletions(-) delete mode 100644 doc/txt/Manual.txt diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index c5485271e1..dd67a13427 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -1,8 +1,8 @@ LAMMPS Documentation #################### -30 Oct 2019 version -******************* +|version| version +***************** :doc:`What is a LAMMPS version? ` diff --git a/doc/txt/Manual.txt b/doc/txt/Manual.txt deleted file mode 100644 index 041a481547..0000000000 --- a/doc/txt/Manual.txt +++ /dev/null @@ -1,124 +0,0 @@ - - -LAMMPS Users Manual - - - - - - - -

- - - -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html#comm) - -:line - -LAMMPS Documentation :c,h1 -30 Oct 2019 version :c,h2 - -"What is a LAMMPS version?"_Manual_version.html - -LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel -Simulator. - -LAMMPS is a classical molecular dynamics simulation code with a focus -on materials modeling. It was designed to run efficiently on parallel -computers. It was developed originally at Sandia National -Laboratories, a US Department of Energy facility. The majority of -funding for LAMMPS has come from the US Department of Energy (DOE). -LAMMPS is an open-source code, distributed freely under the terms of -the GNU Public License (GPL). - -The "LAMMPS website"_lws has a variety of information about the code. -It includes links to an on-line version of this manual, a "mailing -list"_http://lammps.sandia.gov/mail.html where users can post -questions, and a "GitHub site"_https://github.com/lammps/lammps where -all LAMMPS development is coordinated. - -:line - -The content for this manual is part of the LAMMPS distribution. You -can build a local copy of the Manual as HTML pages or a PDF file, by -following the steps on the "Manual build"_Manual_build.html doc page. -There is also a "Developer.pdf"_Developer.pdf document which gives -a brief description of the basic code structure of LAMMPS. - -:line - -Once you are familiar with LAMMPS, you may want to bookmark "this -page"_Commands.html since it gives quick access to a doc page for -every LAMMPS command. - - - - -"Introduction"_Intro.html :olb,l -"Install LAMMPS"_Install.html :l -"Build LAMMPS"_Build.html :l -"Run LAMMPS"_Run_head.html :l -"Commands"_Commands.html :l -"Optional packages"_Packages.html :l -"Accelerate performance"_Speed.html :l -"How-to discussions"_Howto.html :l -"Example scripts"_Examples.html :l -"Auxiliary tools"_Tools.html :l -"Modify & extend LAMMPS"_Modify.html :l -"Use Python with LAMMPS"_Python_head.html :l -"Errors"_Errors.html :l -"Building the LAMMPS manual"_Manual_build.html :l -:ole - - - - -- GitLab From c3e52c3c8cced95f63fcf87b14c1e96aec362175 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 5 Nov 2019 15:48:00 -0500 Subject: [PATCH 5/5] Use globs for style lists --- doc/src/angles.rst | 24 +----- doc/src/bonds.rst | 19 +---- doc/src/computes.rst | 131 +---------------------------- doc/src/dihedrals.rst | 34 +------- doc/src/fixes.rst | 184 +--------------------------------------- doc/src/impropers.rst | 17 +--- doc/src/pairs.rst | 125 +-------------------------- doc/txt/angles.txt | 30 ------- doc/txt/bonds.txt | 25 ------ doc/txt/dihedrals.txt | 40 --------- doc/txt/fixes.txt | 190 ------------------------------------------ doc/txt/pairs.txt | 131 ----------------------------- 12 files changed, 14 insertions(+), 936 deletions(-) delete mode 100644 doc/txt/angles.txt delete mode 100644 doc/txt/bonds.txt delete mode 100644 doc/txt/dihedrals.txt delete mode 100644 doc/txt/fixes.txt delete mode 100644 doc/txt/pairs.txt diff --git a/doc/src/angles.rst b/doc/src/angles.rst index 84a8fad6a8..79c52a5525 100644 --- a/doc/src/angles.rst +++ b/doc/src/angles.rst @@ -4,26 +4,6 @@ Angle Styles .. toctree:: :maxdepth: 1 + :glob: - angle_charmm - angle_class2 - angle_cosine - angle_cosine_buck6d - angle_cosine_delta - angle_cosine_periodic - angle_cosine_shift - angle_cosine_shift_exp - angle_cosine_squared - angle_cross - angle_dipole - angle_fourier - angle_fourier_simple - angle_harmonic - angle_hybrid - angle_mm3 - angle_none - angle_quartic - angle_sdk - angle_table - angle_zero - + angle_* diff --git a/doc/src/bonds.rst b/doc/src/bonds.rst index 55c9702171..3019e0c177 100644 --- a/doc/src/bonds.rst +++ b/doc/src/bonds.rst @@ -4,21 +4,6 @@ Bond Styles .. toctree:: :maxdepth: 1 + :glob: - bond_class2 - bond_fene - bond_fene_expand - bond_gromos - bond_harmonic - bond_harmonic_shift - bond_harmonic_shift_cut - bond_hybrid - bond_mm3 - bond_morse - bond_none - bond_nonlinear - bond_oxdna - bond_quartic - bond_table - bond_zero - + bond_* diff --git a/doc/src/computes.rst b/doc/src/computes.rst index 1bb603f39c..1c1819a444 100644 --- a/doc/src/computes.rst +++ b/doc/src/computes.rst @@ -4,133 +4,6 @@ Computes .. toctree:: :maxdepth: 1 + :glob: - compute_ackland_atom - compute_adf - compute_angle - compute_angle_local - compute_angmom_chunk - compute_basal_atom - compute_body_local - compute_bond - compute_bond_local - compute_centro_atom - compute_chunk_atom - compute_chunk_spread_atom - compute_cluster_atom - compute_cna_atom - compute_cnp_atom - compute_com - compute_com_chunk - compute_contact_atom - compute_coord_atom - compute_damage_atom - compute_dihedral - compute_dihedral_local - compute_dilatation_atom - compute_dipole_chunk - compute_displace_atom - compute_dpd - compute_dpd_atom - compute_edpd_temp_atom - compute_entropy_atom - compute_erotate_asphere - compute_erotate_rigid - compute_erotate_sphere - compute_erotate_sphere_atom - compute_event_displace - compute_fep - compute_global_atom - compute_group_group - compute_gyration - compute_gyration_chunk - compute_gyration_shape - compute_heat_flux - compute_hexorder_atom - compute_hma - compute_improper - compute_improper_local - compute_inertia_chunk - compute_ke - compute_ke_atom - compute_ke_atom_eff - compute_ke_eff - compute_ke_rigid - compute_meso_e_atom - compute_meso_rho_atom - compute_meso_t_atom - compute_momentum - compute_msd - compute_msd_chunk - compute_msd_nongauss - compute_omega_chunk - compute_orientorder_atom - compute_pair - compute_pair_local - compute_pe - compute_pe_atom - compute_plasticity_atom - compute_pressure - compute_pressure_cylinder - compute_pressure_uef - compute_property_atom - compute_property_chunk - compute_property_local - compute_ptm_atom - compute_rdf - compute_reduce - compute_reduce_chunk - compute_rigid_local - compute_saed - compute_slice - compute_smd_contact_radius - compute_smd_damage - compute_smd_hourglass_error - compute_smd_internal_energy - compute_smd_plastic_strain - compute_smd_plastic_strain_rate - compute_smd_rho - compute_smd_tlsph_defgrad - compute_smd_tlsph_dt - compute_smd_tlsph_num_neighs - compute_smd_tlsph_shape - compute_smd_tlsph_strain - compute_smd_tlsph_strain_rate - compute_smd_tlsph_stress - compute_smd_triangle_vertices - compute_smd_ulsph_num_neighs - compute_smd_ulsph_strain - compute_smd_ulsph_strain_rate - compute_smd_ulsph_stress - compute_smd_vol - compute_sna_atom - compute_spin - compute_stress_atom - compute_stress_mop - compute_tally - compute_tdpd_cc_atom - compute_temp - compute_temp_asphere - compute_temp_body - compute_temp_chunk - compute_temp_com - compute_temp_cs - compute_temp_deform - compute_temp_deform_eff - compute_temp_drude - compute_temp_eff - compute_temp_partial - compute_temp_profile - compute_temp_ramp - compute_temp_region - compute_temp_region_eff - compute_temp_rotate - compute_temp_sphere - compute_temp_uef - compute_ti - compute_torque_chunk - compute_vacf - compute_vcm_chunk - compute_voronoi_atom - compute_xrd - + compute_* diff --git a/doc/src/dihedrals.rst b/doc/src/dihedrals.rst index e14399fcb6..bab913f1c2 100644 --- a/doc/src/dihedrals.rst +++ b/doc/src/dihedrals.rst @@ -4,36 +4,6 @@ Dihedral Styles .. toctree:: :maxdepth: 1 + :glob: - dihedral_charmm - dihedral_class2 - dihedral_cosine_shift_exp - dihedral_fourier - dihedral_harmonic - dihedral_helix - dihedral_hybrid - dihedral_multi_harmonic - dihedral_nharmonic - dihedral_none - dihedral_opls - dihedral_quadratic - dihedral_spherical - dihedral_table - dihedral_table_cut - dihedral_zero - dihedral_charmm - dihedral_class2 - dihedral_cosine_shift_exp - dihedral_fourier - dihedral_harmonic - dihedral_helix - dihedral_hybrid - dihedral_multi_harmonic - dihedral_nharmonic - dihedral_none - dihedral_opls - dihedral_quadratic - dihedral_spherical - dihedral_table - dihedral_zero - + dihedral_* diff --git a/doc/src/fixes.rst b/doc/src/fixes.rst index 3678fcc853..5a85738c45 100644 --- a/doc/src/fixes.rst +++ b/doc/src/fixes.rst @@ -4,186 +4,6 @@ Fixes .. toctree:: :maxdepth: 1 + :glob: - fix_adapt - fix_adapt_fep - fix_addforce - fix_addtorque - fix_append_atoms - fix_atc - fix_atom_swap - fix_ave_atom - fix_ave_chunk - fix_ave_correlate - fix_ave_correlate_long - fix_ave_histo - fix_ave_time - fix_aveforce - fix_balance - fix_bocs - fix_bond_break - fix_bond_create - fix_bond_swap - fix_bond_react - fix_box_relax - fix_client_md - fix_cmap - fix_colvars - fix_controller - fix_deform - fix_deposit - fix_drag - fix_drude - fix_drude_transform - fix_dpd_energy - fix_dpd_source - fix_dt_reset - fix_efield - fix_ehex - fix_electron_stopping - fix_enforce2d - fix_eos_cv - fix_eos_table - fix_eos_table_rx - fix_evaporate - fix_external - fix_ffl - fix_filter_corotate - fix_flow_gauss - fix_freeze - fix_gcmc - fix_gld - fix_gle - fix_gravity - fix_grem - fix_halt - fix_heat - fix_hyper_global - fix_hyper_local - fix_imd - fix_indent - fix_ipi - fix_langevin - fix_langevin_drude - fix_langevin_eff - fix_langevin_spin - fix_latte - fix_lb_fluid - fix_lb_momentum - fix_lb_pc - fix_lb_rigid_pc_sphere - fix_lb_viscous - fix_lineforce - fix_manifoldforce - fix_meso - fix_meso_move - fix_meso_stationary - fix_momentum - fix_move - fix_mscg - fix_msst - fix_mvv_dpd - fix_neb - fix_neb_spin - fix_nh - fix_nh_eff - fix_nh_uef - fix_nph_asphere - fix_nph_body - fix_nph_sphere - fix_nphug - fix_npt_asphere - fix_npt_body - fix_npt_sphere - fix_nve - fix_nve_asphere - fix_nve_asphere_noforce - fix_nve_awpmd - fix_nve_body - fix_nve_dot - fix_nve_dotc_langevin - fix_nve_eff - fix_nve_limit - fix_nve_line - fix_nve_manifold_rattle - fix_nve_noforce - fix_nve_sphere - fix_nve_spin - fix_nve_tri - fix_nvk - fix_nvt_asphere - fix_nvt_body - fix_nvt_manifold_rattle - fix_nvt_sllod - fix_nvt_sllod_eff - fix_nvt_sphere - fix_oneway - fix_orient - fix_phonon - fix_pimd - fix_planeforce - fix_plumed - fix_poems - fix_pour - fix_precession_spin - fix_press_berendsen - fix_print - fix_property_atom - fix_python_invoke - fix_python_move - fix_qbmsst - fix_qeq - fix_qeq_comb - fix_qeq_reax - fix_qmmm - fix_qtb - fix_reaxc_bonds - fix_reaxc_species - fix_recenter - fix_restrain - fix_rhok - fix_rigid - fix_rigid_meso - fix_rx - fix_saed_vtk - fix_setforce - fix_shake - fix_shardlow - fix_smd - fix_smd_adjust_dt - fix_smd_integrate_tlsph - fix_smd_integrate_ulsph - fix_smd_move_triangulated_surface - fix_smd_setvel - fix_smd_wall_surface - fix_spring - fix_spring_chunk - fix_spring_rg - fix_spring_self - fix_srd - fix_store_force - fix_store_state - fix_temp_berendsen - fix_temp_csvr - fix_temp_rescale - fix_temp_rescale_eff - fix_tfmc - fix_thermal_conductivity - fix_ti_spring - fix_tmd - fix_ttm - fix_tune_kspace - fix_vector - fix_viscosity - fix_viscous - fix_wall - fix_wall_body_polygon - fix_wall_body_polyhedron - fix_wall_ees - fix_wall_gran - fix_wall_gran_region - fix_wall_piston - fix_wall_reflect - fix_wall_region - fix_wall_srd - + fix_* diff --git a/doc/src/impropers.rst b/doc/src/impropers.rst index c524004fc4..93b4776d2c 100644 --- a/doc/src/impropers.rst +++ b/doc/src/impropers.rst @@ -4,19 +4,6 @@ Improper Styles .. toctree:: :maxdepth: 1 + :glob: - improper_class2 - improper_cossq - improper_cvff - improper_distance - improper_distharm - improper_fourier - improper_harmonic - improper_hybrid - improper_inversion_harmonic - improper_none - improper_ring - improper_umbrella - improper_sqdistharm - improper_zero - + improper_* diff --git a/doc/src/pairs.rst b/doc/src/pairs.rst index 9124013161..4fdf2b2c69 100644 --- a/doc/src/pairs.rst +++ b/doc/src/pairs.rst @@ -4,127 +4,6 @@ Pair Styles .. toctree:: :maxdepth: 1 + :glob: - pair_adp - pair_agni - pair_airebo - pair_atm - pair_awpmd - pair_beck - pair_body_nparticle - pair_body_rounded_polygon - pair_body_rounded_polyhedron - pair_bop - pair_born - pair_brownian - pair_buck - pair_buck_long - pair_buck6d_coul_gauss - pair_charmm - pair_class2 - pair_colloid - pair_comb - pair_cosine_squared - pair_coul - pair_coul_diel - pair_coul_shield - pair_cs - pair_dipole - pair_dpd - pair_dpd_fdt - pair_drip - pair_dsmc - pair_e3b - pair_eam - pair_edip - pair_eff - pair_eim - pair_exp6_rx - pair_extep - pair_fep_soft - pair_gauss - pair_gayberne - pair_gran - pair_granular - pair_gromacs - pair_gw - pair_hbond_dreiding - pair_hybrid - pair_ilp_graphene_hbn - pair_kim - pair_kolmogorov_crespi_full - pair_kolmogorov_crespi_z - pair_lcbop - pair_lebedeva_z - pair_line_lj - pair_list - pair_lj - pair_lj96 - pair_lj_cubic - pair_lj_expand - pair_lj_long - pair_lj_smooth - pair_lj_smooth_linear - pair_lj_switch3_coulgauss - pair_local_density - pair_lubricate - pair_lubricateU - pair_mdf - pair_meamc - pair_meam_spline - pair_meam_sw_spline - pair_meso - pair_mgpt - pair_mie - pair_mm3_switch3_coulgauss - pair_momb - pair_morse - pair_multi_lucy - pair_multi_lucy_rx - pair_nb3b_harmonic - pair_nm - pair_none - pair_oxdna - pair_oxdna2 - pair_peri - pair_polymorphic - pair_python - pair_quip - pair_reaxc - pair_resquared - pair_sdk - pair_sdpd_taitwater_isothermal - pair_smd_hertz - pair_smd_tlsph - pair_smd_triangulated_surface - pair_smd_ulsph - pair_smtbq - pair_snap - pair_soft - pair_sph_heatconduction - pair_sph_idealgas - pair_sph_lj - pair_sph_rhosum - pair_sph_taitwater - pair_sph_taitwater_morris - pair_spin_dipole - pair_spin_dmi - pair_spin_exchange - pair_spin_magelec - pair_spin_neel - pair_srp - pair_sw - pair_table - pair_table_rx - pair_tersoff - pair_tersoff_mod - pair_tersoff_zbl - pair_thole - pair_tri_lj - pair_ufm - pair_vashishta - pair_yukawa - pair_yukawa_colloid - pair_zbl - pair_zero - + pair_* diff --git a/doc/txt/angles.txt b/doc/txt/angles.txt deleted file mode 100644 index 3d8a47b2eb..0000000000 --- a/doc/txt/angles.txt +++ /dev/null @@ -1,30 +0,0 @@ -Angle Styles :h1 - - diff --git a/doc/txt/bonds.txt b/doc/txt/bonds.txt deleted file mode 100644 index 48896e711c..0000000000 --- a/doc/txt/bonds.txt +++ /dev/null @@ -1,25 +0,0 @@ -Bond Styles :h1 - - diff --git a/doc/txt/dihedrals.txt b/doc/txt/dihedrals.txt deleted file mode 100644 index a862bf50a0..0000000000 --- a/doc/txt/dihedrals.txt +++ /dev/null @@ -1,40 +0,0 @@ -Dihedral Styles :h1 - - diff --git a/doc/txt/fixes.txt b/doc/txt/fixes.txt deleted file mode 100644 index d966b9a225..0000000000 --- a/doc/txt/fixes.txt +++ /dev/null @@ -1,190 +0,0 @@ -Fixes :h1 - - diff --git a/doc/txt/pairs.txt b/doc/txt/pairs.txt deleted file mode 100644 index 1f8f130e48..0000000000 --- a/doc/txt/pairs.txt +++ /dev/null @@ -1,131 +0,0 @@ -Pair Styles :h1 - - -- GitLab