diff --git a/doc/Makefile b/doc/Makefile index fc5e93012156c071e8455b78e63a3671816d9138..5dcb070f4f5ddebbc17c893fbfcde5d77c468438 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/angles.rst b/doc/rst/angles.rst deleted file mode 100644 index 84a8fad6a8b6a0c056de5b238280473bfd01eb20..0000000000000000000000000000000000000000 --- a/doc/rst/angles.rst +++ /dev/null @@ -1,29 +0,0 @@ -Angle Styles -############ - - -.. toctree:: - :maxdepth: 1 - - 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 - diff --git a/doc/rst/bonds.rst b/doc/rst/bonds.rst deleted file mode 100644 index 55c97021719824a8338c22907464126428c031ca..0000000000000000000000000000000000000000 --- a/doc/rst/bonds.rst +++ /dev/null @@ -1,24 +0,0 @@ -Bond Styles -########### - - -.. toctree:: - :maxdepth: 1 - - 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 - diff --git a/doc/rst/computes.rst b/doc/rst/computes.rst deleted file mode 100644 index 1bb603f39cce9240cb3d0490ce06a8587697ad27..0000000000000000000000000000000000000000 --- a/doc/rst/computes.rst +++ /dev/null @@ -1,136 +0,0 @@ -Computes -######## - - -.. toctree:: - :maxdepth: 1 - - 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 - diff --git a/doc/rst/dihedrals.rst b/doc/rst/dihedrals.rst deleted file mode 100644 index e14399fcb6a4de60ebc378511b770b1aec25a0be..0000000000000000000000000000000000000000 --- a/doc/rst/dihedrals.rst +++ /dev/null @@ -1,39 +0,0 @@ -Dihedral Styles -############### - - -.. toctree:: - :maxdepth: 1 - - 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 - diff --git a/doc/rst/fixes.rst b/doc/rst/fixes.rst deleted file mode 100644 index 3678fcc8534c5d5840bf2d08ed801041808a37c7..0000000000000000000000000000000000000000 --- a/doc/rst/fixes.rst +++ /dev/null @@ -1,189 +0,0 @@ -Fixes -##### - - -.. toctree:: - :maxdepth: 1 - - 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 - diff --git a/doc/rst/impropers.rst b/doc/rst/impropers.rst deleted file mode 100644 index c524004fc4f0a9743cf883cd8d91d6fb910349aa..0000000000000000000000000000000000000000 --- a/doc/rst/impropers.rst +++ /dev/null @@ -1,22 +0,0 @@ -Improper Styles -############### - - -.. toctree:: - :maxdepth: 1 - - 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 - diff --git a/doc/rst/pairs.rst b/doc/rst/pairs.rst deleted file mode 100644 index 9124013161214b8cf2b69f819115e537c1a25011..0000000000000000000000000000000000000000 --- a/doc/rst/pairs.rst +++ /dev/null @@ -1,130 +0,0 @@ -Pair Styles -########### - - -.. toctree:: - :maxdepth: 1 - - 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 - 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 diff --git a/doc/rst/Build_extras.rst b/doc/src/Build_extras.rst similarity index 100% rename from doc/rst/Build_extras.rst rename to doc/src/Build_extras.rst diff --git a/doc/rst/Build_link.rst b/doc/src/Build_link.rst similarity index 100% rename from doc/rst/Build_link.rst rename to doc/src/Build_link.rst diff --git a/doc/rst/Build_make.rst b/doc/src/Build_make.rst similarity index 100% rename from doc/rst/Build_make.rst rename to doc/src/Build_make.rst diff --git a/doc/rst/Build_package.rst b/doc/src/Build_package.rst similarity index 100% rename from doc/rst/Build_package.rst rename to doc/src/Build_package.rst diff --git a/doc/rst/Build_settings.rst b/doc/src/Build_settings.rst similarity index 100% rename from doc/rst/Build_settings.rst rename to doc/src/Build_settings.rst diff --git a/doc/rst/Build_windows.rst b/doc/src/Build_windows.rst similarity index 100% rename from doc/rst/Build_windows.rst rename to doc/src/Build_windows.rst diff --git a/doc/rst/Commands.rst b/doc/src/Commands.rst similarity index 100% rename from doc/rst/Commands.rst rename to doc/src/Commands.rst diff --git a/doc/rst/Commands_all.rst b/doc/src/Commands_all.rst similarity index 100% rename from doc/rst/Commands_all.rst rename to doc/src/Commands_all.rst diff --git a/doc/rst/Commands_bond.rst b/doc/src/Commands_bond.rst similarity index 100% rename from doc/rst/Commands_bond.rst rename to doc/src/Commands_bond.rst diff --git a/doc/rst/Commands_category.rst b/doc/src/Commands_category.rst similarity index 100% rename from doc/rst/Commands_category.rst rename to doc/src/Commands_category.rst diff --git a/doc/rst/Commands_compute.rst b/doc/src/Commands_compute.rst similarity index 100% rename from doc/rst/Commands_compute.rst rename to doc/src/Commands_compute.rst diff --git a/doc/rst/Commands_fix.rst b/doc/src/Commands_fix.rst similarity index 100% rename from doc/rst/Commands_fix.rst rename to doc/src/Commands_fix.rst diff --git a/doc/rst/Commands_input.rst b/doc/src/Commands_input.rst similarity index 100% rename from doc/rst/Commands_input.rst rename to doc/src/Commands_input.rst diff --git a/doc/rst/Commands_kspace.rst b/doc/src/Commands_kspace.rst similarity index 100% rename from doc/rst/Commands_kspace.rst rename to doc/src/Commands_kspace.rst diff --git a/doc/rst/Commands_pair.rst b/doc/src/Commands_pair.rst similarity index 100% rename from doc/rst/Commands_pair.rst rename to doc/src/Commands_pair.rst diff --git a/doc/rst/Commands_parse.rst b/doc/src/Commands_parse.rst similarity index 100% rename from doc/rst/Commands_parse.rst rename to doc/src/Commands_parse.rst diff --git a/doc/rst/Commands_removed.rst b/doc/src/Commands_removed.rst similarity index 100% rename from doc/rst/Commands_removed.rst rename to doc/src/Commands_removed.rst diff --git a/doc/rst/Commands_structure.rst b/doc/src/Commands_structure.rst similarity index 100% rename from doc/rst/Commands_structure.rst rename to doc/src/Commands_structure.rst diff --git a/doc/rst/Errors.rst b/doc/src/Errors.rst similarity index 100% rename from doc/rst/Errors.rst rename to doc/src/Errors.rst diff --git a/doc/rst/Errors_bugs.rst b/doc/src/Errors_bugs.rst similarity index 100% rename from doc/rst/Errors_bugs.rst rename to doc/src/Errors_bugs.rst diff --git a/doc/rst/Errors_common.rst b/doc/src/Errors_common.rst similarity index 100% rename from doc/rst/Errors_common.rst rename to doc/src/Errors_common.rst diff --git a/doc/rst/Errors_messages.rst b/doc/src/Errors_messages.rst similarity index 100% rename from doc/rst/Errors_messages.rst rename to doc/src/Errors_messages.rst diff --git a/doc/rst/Errors_warnings.rst b/doc/src/Errors_warnings.rst similarity index 100% rename from doc/rst/Errors_warnings.rst rename to doc/src/Errors_warnings.rst diff --git a/doc/rst/Examples.rst b/doc/src/Examples.rst similarity index 100% rename from doc/rst/Examples.rst rename to doc/src/Examples.rst diff --git a/doc/rst/Howto.rst b/doc/src/Howto.rst similarity index 100% rename from doc/rst/Howto.rst rename to doc/src/Howto.rst diff --git a/doc/rst/Howto_2d.rst b/doc/src/Howto_2d.rst similarity index 100% rename from doc/rst/Howto_2d.rst rename to doc/src/Howto_2d.rst diff --git a/doc/rst/Howto_barostat.rst b/doc/src/Howto_barostat.rst similarity index 100% rename from doc/rst/Howto_barostat.rst rename to doc/src/Howto_barostat.rst diff --git a/doc/rst/Howto_bash.rst b/doc/src/Howto_bash.rst similarity index 100% rename from doc/rst/Howto_bash.rst rename to doc/src/Howto_bash.rst diff --git a/doc/rst/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst similarity index 100% rename from doc/rst/Howto_bioFF.rst rename to doc/src/Howto_bioFF.rst diff --git a/doc/rst/Howto_body.rst b/doc/src/Howto_body.rst similarity index 100% rename from doc/rst/Howto_body.rst rename to doc/src/Howto_body.rst diff --git a/doc/rst/Howto_chunk.rst b/doc/src/Howto_chunk.rst similarity index 100% rename from doc/rst/Howto_chunk.rst rename to doc/src/Howto_chunk.rst diff --git a/doc/rst/Howto_client_server.rst b/doc/src/Howto_client_server.rst similarity index 100% rename from doc/rst/Howto_client_server.rst rename to doc/src/Howto_client_server.rst diff --git a/doc/rst/Howto_coreshell.rst b/doc/src/Howto_coreshell.rst similarity index 100% rename from doc/rst/Howto_coreshell.rst rename to doc/src/Howto_coreshell.rst diff --git a/doc/rst/Howto_couple.rst b/doc/src/Howto_couple.rst similarity index 100% rename from doc/rst/Howto_couple.rst rename to doc/src/Howto_couple.rst diff --git a/doc/rst/Howto_diffusion.rst b/doc/src/Howto_diffusion.rst similarity index 100% rename from doc/rst/Howto_diffusion.rst rename to doc/src/Howto_diffusion.rst diff --git a/doc/rst/Howto_dispersion.rst b/doc/src/Howto_dispersion.rst similarity index 100% rename from doc/rst/Howto_dispersion.rst rename to doc/src/Howto_dispersion.rst diff --git a/doc/rst/Howto_drude.rst b/doc/src/Howto_drude.rst similarity index 100% rename from doc/rst/Howto_drude.rst rename to doc/src/Howto_drude.rst diff --git a/doc/rst/Howto_drude2.rst b/doc/src/Howto_drude2.rst similarity index 100% rename from doc/rst/Howto_drude2.rst rename to doc/src/Howto_drude2.rst diff --git a/doc/rst/Howto_elastic.rst b/doc/src/Howto_elastic.rst similarity index 100% rename from doc/rst/Howto_elastic.rst rename to doc/src/Howto_elastic.rst diff --git a/doc/rst/Howto_github.rst b/doc/src/Howto_github.rst similarity index 100% rename from doc/rst/Howto_github.rst rename to doc/src/Howto_github.rst diff --git a/doc/rst/Howto_granular.rst b/doc/src/Howto_granular.rst similarity index 100% rename from doc/rst/Howto_granular.rst rename to doc/src/Howto_granular.rst diff --git a/doc/rst/Howto_kappa.rst b/doc/src/Howto_kappa.rst similarity index 100% rename from doc/rst/Howto_kappa.rst rename to doc/src/Howto_kappa.rst diff --git a/doc/rst/Howto_library.rst b/doc/src/Howto_library.rst similarity index 100% rename from doc/rst/Howto_library.rst rename to doc/src/Howto_library.rst diff --git a/doc/rst/Howto_manifold.rst b/doc/src/Howto_manifold.rst similarity index 100% rename from doc/rst/Howto_manifold.rst rename to doc/src/Howto_manifold.rst diff --git a/doc/rst/Howto_multiple.rst b/doc/src/Howto_multiple.rst similarity index 100% rename from doc/rst/Howto_multiple.rst rename to doc/src/Howto_multiple.rst diff --git a/doc/rst/Howto_nemd.rst b/doc/src/Howto_nemd.rst similarity index 100% rename from doc/rst/Howto_nemd.rst rename to doc/src/Howto_nemd.rst diff --git a/doc/rst/Howto_output.rst b/doc/src/Howto_output.rst similarity index 100% rename from doc/rst/Howto_output.rst rename to doc/src/Howto_output.rst diff --git a/doc/rst/Howto_polarizable.rst b/doc/src/Howto_polarizable.rst similarity index 100% rename from doc/rst/Howto_polarizable.rst rename to doc/src/Howto_polarizable.rst diff --git a/doc/rst/Howto_pylammps.rst b/doc/src/Howto_pylammps.rst similarity index 100% rename from doc/rst/Howto_pylammps.rst rename to doc/src/Howto_pylammps.rst diff --git a/doc/rst/Howto_replica.rst b/doc/src/Howto_replica.rst similarity index 100% rename from doc/rst/Howto_replica.rst rename to doc/src/Howto_replica.rst diff --git a/doc/rst/Howto_restart.rst b/doc/src/Howto_restart.rst similarity index 100% rename from doc/rst/Howto_restart.rst rename to doc/src/Howto_restart.rst diff --git a/doc/rst/Howto_spc.rst b/doc/src/Howto_spc.rst similarity index 100% rename from doc/rst/Howto_spc.rst rename to doc/src/Howto_spc.rst diff --git a/doc/rst/Howto_spherical.rst b/doc/src/Howto_spherical.rst similarity index 100% rename from doc/rst/Howto_spherical.rst rename to doc/src/Howto_spherical.rst diff --git a/doc/rst/Howto_spins.rst b/doc/src/Howto_spins.rst similarity index 100% rename from doc/rst/Howto_spins.rst rename to doc/src/Howto_spins.rst diff --git a/doc/rst/Howto_temperature.rst b/doc/src/Howto_temperature.rst similarity index 100% rename from doc/rst/Howto_temperature.rst rename to doc/src/Howto_temperature.rst diff --git a/doc/rst/Howto_thermostat.rst b/doc/src/Howto_thermostat.rst similarity index 100% rename from doc/rst/Howto_thermostat.rst rename to doc/src/Howto_thermostat.rst diff --git a/doc/rst/Howto_tip3p.rst b/doc/src/Howto_tip3p.rst similarity index 100% rename from doc/rst/Howto_tip3p.rst rename to doc/src/Howto_tip3p.rst diff --git a/doc/rst/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst similarity index 100% rename from doc/rst/Howto_tip4p.rst rename to doc/src/Howto_tip4p.rst diff --git a/doc/rst/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst similarity index 100% rename from doc/rst/Howto_triclinic.rst rename to doc/src/Howto_triclinic.rst diff --git a/doc/rst/Howto_viscosity.rst b/doc/src/Howto_viscosity.rst similarity index 100% rename from doc/rst/Howto_viscosity.rst rename to doc/src/Howto_viscosity.rst diff --git a/doc/rst/Howto_viz.rst b/doc/src/Howto_viz.rst similarity index 100% rename from doc/rst/Howto_viz.rst rename to doc/src/Howto_viz.rst diff --git a/doc/rst/Howto_walls.rst b/doc/src/Howto_walls.rst similarity index 100% rename from doc/rst/Howto_walls.rst rename to doc/src/Howto_walls.rst diff --git a/doc/rst/Install.rst b/doc/src/Install.rst similarity index 100% rename from doc/rst/Install.rst rename to doc/src/Install.rst diff --git a/doc/rst/Install_git.rst b/doc/src/Install_git.rst similarity index 100% rename from doc/rst/Install_git.rst rename to doc/src/Install_git.rst diff --git a/doc/rst/Install_linux.rst b/doc/src/Install_linux.rst similarity index 100% rename from doc/rst/Install_linux.rst rename to doc/src/Install_linux.rst diff --git a/doc/rst/Install_mac.rst b/doc/src/Install_mac.rst similarity index 100% rename from doc/rst/Install_mac.rst rename to doc/src/Install_mac.rst diff --git a/doc/rst/Install_patch.rst b/doc/src/Install_patch.rst similarity index 100% rename from doc/rst/Install_patch.rst rename to doc/src/Install_patch.rst diff --git a/doc/rst/Install_svn.rst b/doc/src/Install_svn.rst similarity index 100% rename from doc/rst/Install_svn.rst rename to doc/src/Install_svn.rst diff --git a/doc/rst/Install_tarball.rst b/doc/src/Install_tarball.rst similarity index 100% rename from doc/rst/Install_tarball.rst rename to doc/src/Install_tarball.rst diff --git a/doc/rst/Install_windows.rst b/doc/src/Install_windows.rst similarity index 100% rename from doc/rst/Install_windows.rst rename to doc/src/Install_windows.rst diff --git a/doc/rst/Intro.rst b/doc/src/Intro.rst similarity index 100% rename from doc/rst/Intro.rst rename to doc/src/Intro.rst diff --git a/doc/rst/Intro_authors.rst b/doc/src/Intro_authors.rst similarity index 100% rename from doc/rst/Intro_authors.rst rename to doc/src/Intro_authors.rst diff --git a/doc/rst/Intro_features.rst b/doc/src/Intro_features.rst similarity index 100% rename from doc/rst/Intro_features.rst rename to doc/src/Intro_features.rst diff --git a/doc/rst/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst similarity index 100% rename from doc/rst/Intro_nonfeatures.rst rename to doc/src/Intro_nonfeatures.rst diff --git a/doc/rst/Intro_opensource.rst b/doc/src/Intro_opensource.rst similarity index 100% rename from doc/rst/Intro_opensource.rst rename to doc/src/Intro_opensource.rst diff --git a/doc/rst/Intro_overview.rst b/doc/src/Intro_overview.rst similarity index 100% rename from doc/rst/Intro_overview.rst rename to doc/src/Intro_overview.rst diff --git a/doc/rst/Intro_website.rst b/doc/src/Intro_website.rst similarity index 100% rename from doc/rst/Intro_website.rst rename to doc/src/Intro_website.rst diff --git a/doc/rst/Manual.rst b/doc/src/Manual.rst similarity index 98% rename from doc/rst/Manual.rst rename to doc/src/Manual.rst index c5485271e1585a0b67e097fdd9cac02be7a260c4..dd67a13427bc2aaac9705104678f637b88d84aaa 100644 --- a/doc/rst/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/src/Manual.txt b/doc/src/Manual.txt deleted file mode 100644 index 041a481547cd5a3e6e8ce948508487037568bc17..0000000000000000000000000000000000000000 --- a/doc/src/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 - - - - diff --git a/doc/rst/Manual_build.rst b/doc/src/Manual_build.rst similarity index 100% rename from doc/rst/Manual_build.rst rename to doc/src/Manual_build.rst diff --git a/doc/rst/Manual_version.rst b/doc/src/Manual_version.rst similarity index 100% rename from doc/rst/Manual_version.rst rename to doc/src/Manual_version.rst diff --git a/doc/rst/Modify.rst b/doc/src/Modify.rst similarity index 100% rename from doc/rst/Modify.rst rename to doc/src/Modify.rst diff --git a/doc/rst/Modify_atom.rst b/doc/src/Modify_atom.rst similarity index 100% rename from doc/rst/Modify_atom.rst rename to doc/src/Modify_atom.rst diff --git a/doc/rst/Modify_body.rst b/doc/src/Modify_body.rst similarity index 100% rename from doc/rst/Modify_body.rst rename to doc/src/Modify_body.rst diff --git a/doc/rst/Modify_bond.rst b/doc/src/Modify_bond.rst similarity index 100% rename from doc/rst/Modify_bond.rst rename to doc/src/Modify_bond.rst diff --git a/doc/rst/Modify_command.rst b/doc/src/Modify_command.rst similarity index 100% rename from doc/rst/Modify_command.rst rename to doc/src/Modify_command.rst diff --git a/doc/rst/Modify_compute.rst b/doc/src/Modify_compute.rst similarity index 100% rename from doc/rst/Modify_compute.rst rename to doc/src/Modify_compute.rst diff --git a/doc/rst/Modify_contribute.rst b/doc/src/Modify_contribute.rst similarity index 100% rename from doc/rst/Modify_contribute.rst rename to doc/src/Modify_contribute.rst diff --git a/doc/rst/Modify_dump.rst b/doc/src/Modify_dump.rst similarity index 100% rename from doc/rst/Modify_dump.rst rename to doc/src/Modify_dump.rst diff --git a/doc/rst/Modify_fix.rst b/doc/src/Modify_fix.rst similarity index 100% rename from doc/rst/Modify_fix.rst rename to doc/src/Modify_fix.rst diff --git a/doc/rst/Modify_kspace.rst b/doc/src/Modify_kspace.rst similarity index 100% rename from doc/rst/Modify_kspace.rst rename to doc/src/Modify_kspace.rst diff --git a/doc/rst/Modify_min.rst b/doc/src/Modify_min.rst similarity index 100% rename from doc/rst/Modify_min.rst rename to doc/src/Modify_min.rst diff --git a/doc/rst/Modify_overview.rst b/doc/src/Modify_overview.rst similarity index 100% rename from doc/rst/Modify_overview.rst rename to doc/src/Modify_overview.rst diff --git a/doc/rst/Modify_pair.rst b/doc/src/Modify_pair.rst similarity index 100% rename from doc/rst/Modify_pair.rst rename to doc/src/Modify_pair.rst diff --git a/doc/rst/Modify_region.rst b/doc/src/Modify_region.rst similarity index 100% rename from doc/rst/Modify_region.rst rename to doc/src/Modify_region.rst diff --git a/doc/rst/Modify_thermo.rst b/doc/src/Modify_thermo.rst similarity index 100% rename from doc/rst/Modify_thermo.rst rename to doc/src/Modify_thermo.rst diff --git a/doc/rst/Modify_variable.rst b/doc/src/Modify_variable.rst similarity index 100% rename from doc/rst/Modify_variable.rst rename to doc/src/Modify_variable.rst diff --git a/doc/rst/Packages.rst b/doc/src/Packages.rst similarity index 100% rename from doc/rst/Packages.rst rename to doc/src/Packages.rst diff --git a/doc/rst/Packages_details.rst b/doc/src/Packages_details.rst similarity index 100% rename from doc/rst/Packages_details.rst rename to doc/src/Packages_details.rst diff --git a/doc/rst/Packages_standard.rst b/doc/src/Packages_standard.rst similarity index 100% rename from doc/rst/Packages_standard.rst rename to doc/src/Packages_standard.rst diff --git a/doc/rst/Packages_user.rst b/doc/src/Packages_user.rst similarity index 100% rename from doc/rst/Packages_user.rst rename to doc/src/Packages_user.rst diff --git a/doc/rst/Python_call.rst b/doc/src/Python_call.rst similarity index 100% rename from doc/rst/Python_call.rst rename to doc/src/Python_call.rst diff --git a/doc/rst/Python_examples.rst b/doc/src/Python_examples.rst similarity index 100% rename from doc/rst/Python_examples.rst rename to doc/src/Python_examples.rst diff --git a/doc/rst/Python_head.rst b/doc/src/Python_head.rst similarity index 100% rename from doc/rst/Python_head.rst rename to doc/src/Python_head.rst diff --git a/doc/rst/Python_install.rst b/doc/src/Python_install.rst similarity index 100% rename from doc/rst/Python_install.rst rename to doc/src/Python_install.rst diff --git a/doc/rst/Python_library.rst b/doc/src/Python_library.rst similarity index 100% rename from doc/rst/Python_library.rst rename to doc/src/Python_library.rst diff --git a/doc/rst/Python_mpi.rst b/doc/src/Python_mpi.rst similarity index 100% rename from doc/rst/Python_mpi.rst rename to doc/src/Python_mpi.rst diff --git a/doc/rst/Python_overview.rst b/doc/src/Python_overview.rst similarity index 100% rename from doc/rst/Python_overview.rst rename to doc/src/Python_overview.rst diff --git a/doc/rst/Python_pylammps.rst b/doc/src/Python_pylammps.rst similarity index 100% rename from doc/rst/Python_pylammps.rst rename to doc/src/Python_pylammps.rst diff --git a/doc/rst/Python_run.rst b/doc/src/Python_run.rst similarity index 100% rename from doc/rst/Python_run.rst rename to doc/src/Python_run.rst diff --git a/doc/rst/Python_shlib.rst b/doc/src/Python_shlib.rst similarity index 100% rename from doc/rst/Python_shlib.rst rename to doc/src/Python_shlib.rst diff --git a/doc/rst/Python_test.rst b/doc/src/Python_test.rst similarity index 100% rename from doc/rst/Python_test.rst rename to doc/src/Python_test.rst diff --git a/doc/rst/Run_basics.rst b/doc/src/Run_basics.rst similarity index 100% rename from doc/rst/Run_basics.rst rename to doc/src/Run_basics.rst diff --git a/doc/rst/Run_head.rst b/doc/src/Run_head.rst similarity index 100% rename from doc/rst/Run_head.rst rename to doc/src/Run_head.rst diff --git a/doc/rst/Run_options.rst b/doc/src/Run_options.rst similarity index 100% rename from doc/rst/Run_options.rst rename to doc/src/Run_options.rst diff --git a/doc/rst/Run_output.rst b/doc/src/Run_output.rst similarity index 100% rename from doc/rst/Run_output.rst rename to doc/src/Run_output.rst diff --git a/doc/rst/Run_windows.rst b/doc/src/Run_windows.rst similarity index 100% rename from doc/rst/Run_windows.rst rename to doc/src/Run_windows.rst diff --git a/doc/rst/Speed.rst b/doc/src/Speed.rst similarity index 100% rename from doc/rst/Speed.rst rename to doc/src/Speed.rst diff --git a/doc/rst/Speed_bench.rst b/doc/src/Speed_bench.rst similarity index 100% rename from doc/rst/Speed_bench.rst rename to doc/src/Speed_bench.rst diff --git a/doc/rst/Speed_compare.rst b/doc/src/Speed_compare.rst similarity index 100% rename from doc/rst/Speed_compare.rst rename to doc/src/Speed_compare.rst diff --git a/doc/rst/Speed_gpu.rst b/doc/src/Speed_gpu.rst similarity index 100% rename from doc/rst/Speed_gpu.rst rename to doc/src/Speed_gpu.rst diff --git a/doc/rst/Speed_intel.rst b/doc/src/Speed_intel.rst similarity index 100% rename from doc/rst/Speed_intel.rst rename to doc/src/Speed_intel.rst diff --git a/doc/rst/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst similarity index 100% rename from doc/rst/Speed_kokkos.rst rename to doc/src/Speed_kokkos.rst diff --git a/doc/rst/Speed_measure.rst b/doc/src/Speed_measure.rst similarity index 100% rename from doc/rst/Speed_measure.rst rename to doc/src/Speed_measure.rst diff --git a/doc/rst/Speed_omp.rst b/doc/src/Speed_omp.rst similarity index 100% rename from doc/rst/Speed_omp.rst rename to doc/src/Speed_omp.rst diff --git a/doc/rst/Speed_opt.rst b/doc/src/Speed_opt.rst similarity index 100% rename from doc/rst/Speed_opt.rst rename to doc/src/Speed_opt.rst diff --git a/doc/rst/Speed_packages.rst b/doc/src/Speed_packages.rst similarity index 100% rename from doc/rst/Speed_packages.rst rename to doc/src/Speed_packages.rst diff --git a/doc/rst/Speed_tips.rst b/doc/src/Speed_tips.rst similarity index 100% rename from doc/rst/Speed_tips.rst rename to doc/src/Speed_tips.rst diff --git a/doc/rst/Tools.rst b/doc/src/Tools.rst similarity index 100% rename from doc/rst/Tools.rst rename to doc/src/Tools.rst diff --git a/doc/rst/angle_charmm.rst b/doc/src/angle_charmm.rst similarity index 100% rename from doc/rst/angle_charmm.rst rename to doc/src/angle_charmm.rst diff --git a/doc/rst/angle_class2.rst b/doc/src/angle_class2.rst similarity index 100% rename from doc/rst/angle_class2.rst rename to doc/src/angle_class2.rst diff --git a/doc/rst/angle_coeff.rst b/doc/src/angle_coeff.rst similarity index 100% rename from doc/rst/angle_coeff.rst rename to doc/src/angle_coeff.rst diff --git a/doc/rst/angle_cosine.rst b/doc/src/angle_cosine.rst similarity index 100% rename from doc/rst/angle_cosine.rst rename to doc/src/angle_cosine.rst diff --git a/doc/rst/angle_cosine_buck6d.rst b/doc/src/angle_cosine_buck6d.rst similarity index 100% rename from doc/rst/angle_cosine_buck6d.rst rename to doc/src/angle_cosine_buck6d.rst diff --git a/doc/rst/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst similarity index 100% rename from doc/rst/angle_cosine_delta.rst rename to doc/src/angle_cosine_delta.rst diff --git a/doc/rst/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst similarity index 100% rename from doc/rst/angle_cosine_periodic.rst rename to doc/src/angle_cosine_periodic.rst diff --git a/doc/rst/angle_cosine_shift.rst b/doc/src/angle_cosine_shift.rst similarity index 100% rename from doc/rst/angle_cosine_shift.rst rename to doc/src/angle_cosine_shift.rst diff --git a/doc/rst/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst similarity index 100% rename from doc/rst/angle_cosine_shift_exp.rst rename to doc/src/angle_cosine_shift_exp.rst diff --git a/doc/rst/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst similarity index 100% rename from doc/rst/angle_cosine_squared.rst rename to doc/src/angle_cosine_squared.rst diff --git a/doc/rst/angle_cross.rst b/doc/src/angle_cross.rst similarity index 100% rename from doc/rst/angle_cross.rst rename to doc/src/angle_cross.rst diff --git a/doc/rst/angle_dipole.rst b/doc/src/angle_dipole.rst similarity index 100% rename from doc/rst/angle_dipole.rst rename to doc/src/angle_dipole.rst diff --git a/doc/rst/angle_fourier.rst b/doc/src/angle_fourier.rst similarity index 100% rename from doc/rst/angle_fourier.rst rename to doc/src/angle_fourier.rst diff --git a/doc/rst/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst similarity index 100% rename from doc/rst/angle_fourier_simple.rst rename to doc/src/angle_fourier_simple.rst diff --git a/doc/rst/angle_harmonic.rst b/doc/src/angle_harmonic.rst similarity index 100% rename from doc/rst/angle_harmonic.rst rename to doc/src/angle_harmonic.rst diff --git a/doc/rst/angle_hybrid.rst b/doc/src/angle_hybrid.rst similarity index 100% rename from doc/rst/angle_hybrid.rst rename to doc/src/angle_hybrid.rst diff --git a/doc/rst/angle_mm3.rst b/doc/src/angle_mm3.rst similarity index 100% rename from doc/rst/angle_mm3.rst rename to doc/src/angle_mm3.rst diff --git a/doc/rst/angle_none.rst b/doc/src/angle_none.rst similarity index 100% rename from doc/rst/angle_none.rst rename to doc/src/angle_none.rst diff --git a/doc/rst/angle_quartic.rst b/doc/src/angle_quartic.rst similarity index 100% rename from doc/rst/angle_quartic.rst rename to doc/src/angle_quartic.rst diff --git a/doc/rst/angle_sdk.rst b/doc/src/angle_sdk.rst similarity index 100% rename from doc/rst/angle_sdk.rst rename to doc/src/angle_sdk.rst diff --git a/doc/rst/angle_style.rst b/doc/src/angle_style.rst similarity index 100% rename from doc/rst/angle_style.rst rename to doc/src/angle_style.rst diff --git a/doc/rst/angle_table.rst b/doc/src/angle_table.rst similarity index 100% rename from doc/rst/angle_table.rst rename to doc/src/angle_table.rst diff --git a/doc/rst/angle_zero.rst b/doc/src/angle_zero.rst similarity index 100% rename from doc/rst/angle_zero.rst rename to doc/src/angle_zero.rst diff --git a/doc/src/angles.rst b/doc/src/angles.rst new file mode 100644 index 0000000000000000000000000000000000000000..79c52a552570f5f738cddc7b0da2bee4650fef05 --- /dev/null +++ b/doc/src/angles.rst @@ -0,0 +1,9 @@ +Angle Styles +############ + + +.. toctree:: + :maxdepth: 1 + :glob: + + angle_* diff --git a/doc/src/angles.txt b/doc/src/angles.txt deleted file mode 100644 index 3d8a47b2ebceb834ca91aec44d81dd42f5b4c9e2..0000000000000000000000000000000000000000 --- a/doc/src/angles.txt +++ /dev/null @@ -1,30 +0,0 @@ -Angle Styles :h1 - - diff --git a/doc/rst/atom_modify.rst b/doc/src/atom_modify.rst similarity index 100% rename from doc/rst/atom_modify.rst rename to doc/src/atom_modify.rst diff --git a/doc/rst/atom_style.rst b/doc/src/atom_style.rst similarity index 100% rename from doc/rst/atom_style.rst rename to doc/src/atom_style.rst diff --git a/doc/rst/balance.rst b/doc/src/balance.rst similarity index 100% rename from doc/rst/balance.rst rename to doc/src/balance.rst diff --git a/doc/rst/bond_class2.rst b/doc/src/bond_class2.rst similarity index 100% rename from doc/rst/bond_class2.rst rename to doc/src/bond_class2.rst diff --git a/doc/rst/bond_coeff.rst b/doc/src/bond_coeff.rst similarity index 100% rename from doc/rst/bond_coeff.rst rename to doc/src/bond_coeff.rst diff --git a/doc/rst/bond_fene.rst b/doc/src/bond_fene.rst similarity index 100% rename from doc/rst/bond_fene.rst rename to doc/src/bond_fene.rst diff --git a/doc/rst/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst similarity index 100% rename from doc/rst/bond_fene_expand.rst rename to doc/src/bond_fene_expand.rst diff --git a/doc/rst/bond_gromos.rst b/doc/src/bond_gromos.rst similarity index 100% rename from doc/rst/bond_gromos.rst rename to doc/src/bond_gromos.rst diff --git a/doc/rst/bond_harmonic.rst b/doc/src/bond_harmonic.rst similarity index 100% rename from doc/rst/bond_harmonic.rst rename to doc/src/bond_harmonic.rst diff --git a/doc/rst/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst similarity index 100% rename from doc/rst/bond_harmonic_shift.rst rename to doc/src/bond_harmonic_shift.rst diff --git a/doc/rst/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst similarity index 100% rename from doc/rst/bond_harmonic_shift_cut.rst rename to doc/src/bond_harmonic_shift_cut.rst diff --git a/doc/rst/bond_hybrid.rst b/doc/src/bond_hybrid.rst similarity index 100% rename from doc/rst/bond_hybrid.rst rename to doc/src/bond_hybrid.rst diff --git a/doc/rst/bond_mm3.rst b/doc/src/bond_mm3.rst similarity index 100% rename from doc/rst/bond_mm3.rst rename to doc/src/bond_mm3.rst diff --git a/doc/rst/bond_morse.rst b/doc/src/bond_morse.rst similarity index 100% rename from doc/rst/bond_morse.rst rename to doc/src/bond_morse.rst diff --git a/doc/rst/bond_none.rst b/doc/src/bond_none.rst similarity index 100% rename from doc/rst/bond_none.rst rename to doc/src/bond_none.rst diff --git a/doc/rst/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst similarity index 100% rename from doc/rst/bond_nonlinear.rst rename to doc/src/bond_nonlinear.rst diff --git a/doc/rst/bond_oxdna.rst b/doc/src/bond_oxdna.rst similarity index 100% rename from doc/rst/bond_oxdna.rst rename to doc/src/bond_oxdna.rst diff --git a/doc/rst/bond_quartic.rst b/doc/src/bond_quartic.rst similarity index 100% rename from doc/rst/bond_quartic.rst rename to doc/src/bond_quartic.rst diff --git a/doc/rst/bond_style.rst b/doc/src/bond_style.rst similarity index 100% rename from doc/rst/bond_style.rst rename to doc/src/bond_style.rst diff --git a/doc/rst/bond_table.rst b/doc/src/bond_table.rst similarity index 100% rename from doc/rst/bond_table.rst rename to doc/src/bond_table.rst diff --git a/doc/rst/bond_write.rst b/doc/src/bond_write.rst similarity index 100% rename from doc/rst/bond_write.rst rename to doc/src/bond_write.rst diff --git a/doc/rst/bond_zero.rst b/doc/src/bond_zero.rst similarity index 100% rename from doc/rst/bond_zero.rst rename to doc/src/bond_zero.rst diff --git a/doc/src/bonds.rst b/doc/src/bonds.rst new file mode 100644 index 0000000000000000000000000000000000000000..3019e0c177b8ce344097502816f83b32dcae3250 --- /dev/null +++ b/doc/src/bonds.rst @@ -0,0 +1,9 @@ +Bond Styles +########### + + +.. toctree:: + :maxdepth: 1 + :glob: + + bond_* diff --git a/doc/src/bonds.txt b/doc/src/bonds.txt deleted file mode 100644 index 48896e711c3bcdc57dd637c00ec0d285a6914f61..0000000000000000000000000000000000000000 --- a/doc/src/bonds.txt +++ /dev/null @@ -1,25 +0,0 @@ -Bond Styles :h1 - - diff --git a/doc/rst/boundary.rst b/doc/src/boundary.rst similarity index 100% rename from doc/rst/boundary.rst rename to doc/src/boundary.rst diff --git a/doc/rst/box.rst b/doc/src/box.rst similarity index 100% rename from doc/rst/box.rst rename to doc/src/box.rst diff --git a/doc/rst/change_box.rst b/doc/src/change_box.rst similarity index 100% rename from doc/rst/change_box.rst rename to doc/src/change_box.rst diff --git a/doc/rst/clear.rst b/doc/src/clear.rst similarity index 100% rename from doc/rst/clear.rst rename to doc/src/clear.rst diff --git a/doc/rst/comm_modify.rst b/doc/src/comm_modify.rst similarity index 100% rename from doc/rst/comm_modify.rst rename to doc/src/comm_modify.rst diff --git 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 doc/src/compute_pair_local.rst diff --git a/doc/rst/compute_pe.rst b/doc/src/compute_pe.rst similarity index 100% rename from doc/rst/compute_pe.rst rename to doc/src/compute_pe.rst diff --git a/doc/rst/compute_pe_atom.rst b/doc/src/compute_pe_atom.rst similarity index 100% rename from doc/rst/compute_pe_atom.rst rename to doc/src/compute_pe_atom.rst diff --git a/doc/rst/compute_plasticity_atom.rst b/doc/src/compute_plasticity_atom.rst similarity index 100% rename from doc/rst/compute_plasticity_atom.rst rename to doc/src/compute_plasticity_atom.rst diff --git a/doc/rst/compute_pressure.rst b/doc/src/compute_pressure.rst similarity index 100% rename from doc/rst/compute_pressure.rst rename to doc/src/compute_pressure.rst diff --git a/doc/rst/compute_pressure_cylinder.rst b/doc/src/compute_pressure_cylinder.rst similarity index 100% rename from doc/rst/compute_pressure_cylinder.rst rename to doc/src/compute_pressure_cylinder.rst diff --git a/doc/rst/compute_pressure_uef.rst 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 b/doc/src/compute_smd_contact_radius.rst similarity index 100% rename from doc/rst/compute_smd_contact_radius.rst rename to doc/src/compute_smd_contact_radius.rst diff --git a/doc/rst/compute_smd_damage.rst b/doc/src/compute_smd_damage.rst similarity index 100% rename from doc/rst/compute_smd_damage.rst rename to doc/src/compute_smd_damage.rst diff --git a/doc/rst/compute_smd_hourglass_error.rst b/doc/src/compute_smd_hourglass_error.rst similarity index 100% rename from doc/rst/compute_smd_hourglass_error.rst rename to doc/src/compute_smd_hourglass_error.rst diff --git a/doc/rst/compute_smd_internal_energy.rst b/doc/src/compute_smd_internal_energy.rst similarity index 100% rename from doc/rst/compute_smd_internal_energy.rst rename to doc/src/compute_smd_internal_energy.rst diff --git a/doc/rst/compute_smd_plastic_strain.rst b/doc/src/compute_smd_plastic_strain.rst similarity index 100% rename from doc/rst/compute_smd_plastic_strain.rst rename to doc/src/compute_smd_plastic_strain.rst diff --git a/doc/rst/compute_smd_plastic_strain_rate.rst b/doc/src/compute_smd_plastic_strain_rate.rst similarity index 100% rename from doc/rst/compute_smd_plastic_strain_rate.rst rename to doc/src/compute_smd_plastic_strain_rate.rst diff --git a/doc/rst/compute_smd_rho.rst b/doc/src/compute_smd_rho.rst similarity index 100% rename from doc/rst/compute_smd_rho.rst rename to doc/src/compute_smd_rho.rst diff --git a/doc/rst/compute_smd_tlsph_defgrad.rst b/doc/src/compute_smd_tlsph_defgrad.rst similarity index 100% rename from doc/rst/compute_smd_tlsph_defgrad.rst rename to doc/src/compute_smd_tlsph_defgrad.rst diff --git a/doc/rst/compute_smd_tlsph_dt.rst b/doc/src/compute_smd_tlsph_dt.rst similarity index 100% rename from doc/rst/compute_smd_tlsph_dt.rst rename to doc/src/compute_smd_tlsph_dt.rst diff --git a/doc/rst/compute_smd_tlsph_num_neighs.rst b/doc/src/compute_smd_tlsph_num_neighs.rst similarity index 100% rename from doc/rst/compute_smd_tlsph_num_neighs.rst rename to doc/src/compute_smd_tlsph_num_neighs.rst diff --git a/doc/rst/compute_smd_tlsph_shape.rst b/doc/src/compute_smd_tlsph_shape.rst similarity index 100% rename from doc/rst/compute_smd_tlsph_shape.rst rename to doc/src/compute_smd_tlsph_shape.rst diff --git a/doc/rst/compute_smd_tlsph_strain.rst b/doc/src/compute_smd_tlsph_strain.rst similarity index 100% rename from doc/rst/compute_smd_tlsph_strain.rst rename to doc/src/compute_smd_tlsph_strain.rst diff --git a/doc/rst/compute_smd_tlsph_strain_rate.rst b/doc/src/compute_smd_tlsph_strain_rate.rst similarity index 100% rename from doc/rst/compute_smd_tlsph_strain_rate.rst rename to doc/src/compute_smd_tlsph_strain_rate.rst diff --git a/doc/rst/compute_smd_tlsph_stress.rst b/doc/src/compute_smd_tlsph_stress.rst similarity index 100% rename from doc/rst/compute_smd_tlsph_stress.rst rename to doc/src/compute_smd_tlsph_stress.rst diff --git a/doc/rst/compute_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst similarity index 100% rename from doc/rst/compute_smd_triangle_vertices.rst rename to doc/src/compute_smd_triangle_vertices.rst diff --git a/doc/rst/compute_smd_ulsph_num_neighs.rst b/doc/src/compute_smd_ulsph_num_neighs.rst similarity index 100% rename from doc/rst/compute_smd_ulsph_num_neighs.rst rename to doc/src/compute_smd_ulsph_num_neighs.rst diff --git a/doc/rst/compute_smd_ulsph_strain.rst b/doc/src/compute_smd_ulsph_strain.rst similarity index 100% rename from doc/rst/compute_smd_ulsph_strain.rst rename to doc/src/compute_smd_ulsph_strain.rst diff --git a/doc/rst/compute_smd_ulsph_strain_rate.rst b/doc/src/compute_smd_ulsph_strain_rate.rst similarity index 100% rename from doc/rst/compute_smd_ulsph_strain_rate.rst rename to doc/src/compute_smd_ulsph_strain_rate.rst diff --git a/doc/rst/compute_smd_ulsph_stress.rst b/doc/src/compute_smd_ulsph_stress.rst similarity index 100% rename from doc/rst/compute_smd_ulsph_stress.rst rename to doc/src/compute_smd_ulsph_stress.rst diff --git a/doc/rst/compute_smd_vol.rst b/doc/src/compute_smd_vol.rst similarity index 100% rename from doc/rst/compute_smd_vol.rst rename to doc/src/compute_smd_vol.rst diff --git a/doc/rst/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst similarity index 100% rename from doc/rst/compute_sna_atom.rst rename to doc/src/compute_sna_atom.rst diff --git a/doc/rst/compute_spin.rst b/doc/src/compute_spin.rst similarity index 100% rename from doc/rst/compute_spin.rst rename to doc/src/compute_spin.rst diff --git a/doc/rst/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst similarity index 100% rename from doc/rst/compute_stress_atom.rst rename to doc/src/compute_stress_atom.rst diff --git a/doc/rst/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst similarity index 100% rename from doc/rst/compute_stress_mop.rst rename to doc/src/compute_stress_mop.rst diff --git a/doc/rst/compute_tally.rst b/doc/src/compute_tally.rst similarity index 100% rename from doc/rst/compute_tally.rst rename to doc/src/compute_tally.rst diff --git a/doc/rst/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst similarity index 100% rename from doc/rst/compute_tdpd_cc_atom.rst rename to doc/src/compute_tdpd_cc_atom.rst diff --git a/doc/rst/compute_temp.rst b/doc/src/compute_temp.rst similarity index 100% rename from doc/rst/compute_temp.rst rename to doc/src/compute_temp.rst diff --git a/doc/rst/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst similarity index 100% rename from doc/rst/compute_temp_asphere.rst rename to doc/src/compute_temp_asphere.rst diff --git a/doc/rst/compute_temp_body.rst b/doc/src/compute_temp_body.rst similarity index 100% rename from doc/rst/compute_temp_body.rst rename to doc/src/compute_temp_body.rst diff --git a/doc/rst/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst similarity index 100% rename from doc/rst/compute_temp_chunk.rst rename to doc/src/compute_temp_chunk.rst diff --git a/doc/rst/compute_temp_com.rst b/doc/src/compute_temp_com.rst similarity index 100% rename from doc/rst/compute_temp_com.rst rename to doc/src/compute_temp_com.rst diff --git a/doc/rst/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst similarity index 100% rename from doc/rst/compute_temp_cs.rst rename to doc/src/compute_temp_cs.rst diff --git a/doc/rst/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst similarity index 100% rename from doc/rst/compute_temp_deform.rst rename to doc/src/compute_temp_deform.rst diff --git a/doc/rst/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst similarity index 100% rename from doc/rst/compute_temp_deform_eff.rst rename to doc/src/compute_temp_deform_eff.rst diff --git a/doc/rst/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst similarity index 100% rename from doc/rst/compute_temp_drude.rst rename to doc/src/compute_temp_drude.rst diff --git a/doc/rst/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst similarity index 100% rename from doc/rst/compute_temp_eff.rst rename to doc/src/compute_temp_eff.rst diff --git a/doc/rst/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst similarity index 100% rename from doc/rst/compute_temp_partial.rst rename to doc/src/compute_temp_partial.rst diff --git a/doc/rst/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst similarity index 100% rename from doc/rst/compute_temp_profile.rst rename to doc/src/compute_temp_profile.rst diff --git a/doc/rst/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst similarity index 100% rename from doc/rst/compute_temp_ramp.rst rename to doc/src/compute_temp_ramp.rst diff --git a/doc/rst/compute_temp_region.rst b/doc/src/compute_temp_region.rst similarity index 100% rename from doc/rst/compute_temp_region.rst rename to doc/src/compute_temp_region.rst diff --git a/doc/rst/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst similarity index 100% rename from doc/rst/compute_temp_region_eff.rst rename to doc/src/compute_temp_region_eff.rst diff --git a/doc/rst/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst similarity index 100% rename from doc/rst/compute_temp_rotate.rst rename to doc/src/compute_temp_rotate.rst diff --git a/doc/rst/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst similarity index 100% rename from doc/rst/compute_temp_sphere.rst rename to doc/src/compute_temp_sphere.rst diff --git a/doc/rst/compute_temp_uef.rst b/doc/src/compute_temp_uef.rst similarity index 100% rename from doc/rst/compute_temp_uef.rst rename to doc/src/compute_temp_uef.rst diff --git a/doc/rst/compute_ti.rst b/doc/src/compute_ti.rst similarity index 100% rename from doc/rst/compute_ti.rst rename to doc/src/compute_ti.rst diff --git a/doc/rst/compute_torque_chunk.rst b/doc/src/compute_torque_chunk.rst similarity index 100% rename from doc/rst/compute_torque_chunk.rst rename to doc/src/compute_torque_chunk.rst diff --git a/doc/rst/compute_vacf.rst b/doc/src/compute_vacf.rst similarity index 100% rename from doc/rst/compute_vacf.rst rename to doc/src/compute_vacf.rst diff --git a/doc/rst/compute_vcm_chunk.rst b/doc/src/compute_vcm_chunk.rst similarity index 100% rename from doc/rst/compute_vcm_chunk.rst rename to doc/src/compute_vcm_chunk.rst diff --git a/doc/rst/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst similarity index 100% rename from doc/rst/compute_voronoi_atom.rst rename to doc/src/compute_voronoi_atom.rst diff --git a/doc/rst/compute_xrd.rst b/doc/src/compute_xrd.rst similarity index 100% rename from doc/rst/compute_xrd.rst rename to doc/src/compute_xrd.rst diff --git a/doc/src/computes.rst b/doc/src/computes.rst new file mode 100644 index 0000000000000000000000000000000000000000..1c1819a444db76dad68f176ec412b53028313d14 --- /dev/null +++ b/doc/src/computes.rst @@ -0,0 +1,9 @@ +Computes +######## + + +.. toctree:: + :maxdepth: 1 + :glob: + + compute_* diff --git a/doc/rst/create_atoms.rst b/doc/src/create_atoms.rst similarity index 100% rename from doc/rst/create_atoms.rst rename to doc/src/create_atoms.rst diff --git a/doc/rst/create_bonds.rst b/doc/src/create_bonds.rst similarity index 100% rename from doc/rst/create_bonds.rst rename to doc/src/create_bonds.rst diff --git a/doc/rst/create_box.rst b/doc/src/create_box.rst similarity index 100% rename from doc/rst/create_box.rst rename to doc/src/create_box.rst diff --git a/doc/rst/delete_atoms.rst b/doc/src/delete_atoms.rst similarity index 100% rename from doc/rst/delete_atoms.rst rename to doc/src/delete_atoms.rst diff --git a/doc/rst/delete_bonds.rst b/doc/src/delete_bonds.rst similarity index 100% rename from doc/rst/delete_bonds.rst rename to doc/src/delete_bonds.rst diff --git a/doc/rst/dielectric.rst b/doc/src/dielectric.rst similarity index 100% rename from doc/rst/dielectric.rst rename to doc/src/dielectric.rst diff --git a/doc/rst/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst similarity index 100% rename from doc/rst/dihedral_charmm.rst rename to doc/src/dihedral_charmm.rst diff --git a/doc/rst/dihedral_class2.rst b/doc/src/dihedral_class2.rst similarity index 100% rename from doc/rst/dihedral_class2.rst rename to doc/src/dihedral_class2.rst diff --git a/doc/rst/dihedral_coeff.rst b/doc/src/dihedral_coeff.rst similarity index 100% rename from doc/rst/dihedral_coeff.rst rename to doc/src/dihedral_coeff.rst diff --git a/doc/rst/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst similarity index 100% rename from doc/rst/dihedral_cosine_shift_exp.rst rename to doc/src/dihedral_cosine_shift_exp.rst diff --git a/doc/rst/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst similarity index 100% rename from doc/rst/dihedral_fourier.rst rename to doc/src/dihedral_fourier.rst diff --git a/doc/rst/dihedral_harmonic.rst b/doc/src/dihedral_harmonic.rst similarity index 100% rename from doc/rst/dihedral_harmonic.rst rename to doc/src/dihedral_harmonic.rst diff --git a/doc/rst/dihedral_helix.rst b/doc/src/dihedral_helix.rst similarity index 100% rename from doc/rst/dihedral_helix.rst rename to doc/src/dihedral_helix.rst diff --git a/doc/rst/dihedral_hybrid.rst b/doc/src/dihedral_hybrid.rst similarity index 100% rename from doc/rst/dihedral_hybrid.rst rename to doc/src/dihedral_hybrid.rst diff --git a/doc/rst/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst similarity index 100% rename from doc/rst/dihedral_multi_harmonic.rst rename to doc/src/dihedral_multi_harmonic.rst diff --git a/doc/rst/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst similarity index 100% rename from doc/rst/dihedral_nharmonic.rst rename to doc/src/dihedral_nharmonic.rst diff --git a/doc/rst/dihedral_none.rst b/doc/src/dihedral_none.rst similarity index 100% rename from doc/rst/dihedral_none.rst rename to doc/src/dihedral_none.rst diff --git a/doc/rst/dihedral_opls.rst b/doc/src/dihedral_opls.rst similarity index 100% rename from doc/rst/dihedral_opls.rst rename to doc/src/dihedral_opls.rst diff --git a/doc/rst/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst similarity index 100% rename from doc/rst/dihedral_quadratic.rst rename to doc/src/dihedral_quadratic.rst diff --git a/doc/rst/dihedral_spherical.rst b/doc/src/dihedral_spherical.rst similarity index 100% rename from doc/rst/dihedral_spherical.rst rename to doc/src/dihedral_spherical.rst diff --git a/doc/rst/dihedral_style.rst b/doc/src/dihedral_style.rst similarity index 100% rename from doc/rst/dihedral_style.rst rename to doc/src/dihedral_style.rst diff --git a/doc/rst/dihedral_table.rst b/doc/src/dihedral_table.rst similarity index 100% rename from doc/rst/dihedral_table.rst rename to doc/src/dihedral_table.rst diff --git a/doc/rst/dihedral_table_cut.rst b/doc/src/dihedral_table_cut.rst similarity index 100% rename from doc/rst/dihedral_table_cut.rst rename to doc/src/dihedral_table_cut.rst diff --git a/doc/rst/dihedral_zero.rst b/doc/src/dihedral_zero.rst similarity index 100% rename from doc/rst/dihedral_zero.rst rename to doc/src/dihedral_zero.rst diff --git a/doc/src/dihedrals.rst b/doc/src/dihedrals.rst new file mode 100644 index 0000000000000000000000000000000000000000..bab913f1c2d0b38f64acea2fa0137a0ac993ee56 --- /dev/null +++ b/doc/src/dihedrals.rst @@ -0,0 +1,9 @@ +Dihedral Styles +############### + + +.. toctree:: + :maxdepth: 1 + :glob: + + dihedral_* diff --git a/doc/src/dihedrals.txt b/doc/src/dihedrals.txt deleted file mode 100644 index a862bf50a0a9c357ffeed1129e3b67423259447c..0000000000000000000000000000000000000000 --- a/doc/src/dihedrals.txt +++ /dev/null @@ -1,40 +0,0 @@ -Dihedral Styles :h1 - - diff --git a/doc/rst/dimension.rst b/doc/src/dimension.rst similarity index 100% rename from doc/rst/dimension.rst rename to doc/src/dimension.rst diff --git a/doc/rst/displace_atoms.rst b/doc/src/displace_atoms.rst similarity index 100% rename from doc/rst/displace_atoms.rst rename to doc/src/displace_atoms.rst diff --git a/doc/rst/dump.rst b/doc/src/dump.rst similarity index 100% rename from doc/rst/dump.rst rename to doc/src/dump.rst diff --git a/doc/rst/dump_adios.rst b/doc/src/dump_adios.rst similarity index 100% rename from doc/rst/dump_adios.rst rename to doc/src/dump_adios.rst diff --git a/doc/rst/dump_cfg_uef.rst b/doc/src/dump_cfg_uef.rst similarity index 100% rename from doc/rst/dump_cfg_uef.rst rename to doc/src/dump_cfg_uef.rst diff --git a/doc/rst/dump_h5md.rst b/doc/src/dump_h5md.rst similarity index 100% rename from doc/rst/dump_h5md.rst rename to doc/src/dump_h5md.rst diff --git a/doc/rst/dump_image.rst b/doc/src/dump_image.rst similarity index 100% rename from doc/rst/dump_image.rst rename to doc/src/dump_image.rst diff --git a/doc/rst/dump_modify.rst b/doc/src/dump_modify.rst similarity index 100% rename from doc/rst/dump_modify.rst rename to doc/src/dump_modify.rst diff --git a/doc/rst/dump_molfile.rst b/doc/src/dump_molfile.rst similarity index 100% rename from doc/rst/dump_molfile.rst rename to doc/src/dump_molfile.rst diff --git a/doc/rst/dump_netcdf.rst b/doc/src/dump_netcdf.rst similarity index 100% rename from doc/rst/dump_netcdf.rst rename to doc/src/dump_netcdf.rst diff --git a/doc/rst/dump_vtk.rst b/doc/src/dump_vtk.rst similarity index 100% rename from doc/rst/dump_vtk.rst rename to doc/src/dump_vtk.rst diff --git a/doc/rst/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst similarity index 100% rename from doc/rst/dynamical_matrix.rst rename to doc/src/dynamical_matrix.rst diff --git a/doc/rst/echo.rst b/doc/src/echo.rst similarity index 100% rename from doc/rst/echo.rst rename to doc/src/echo.rst diff --git a/doc/rst/fix.rst b/doc/src/fix.rst similarity index 100% rename from doc/rst/fix.rst rename to doc/src/fix.rst diff --git a/doc/rst/fix_adapt.rst b/doc/src/fix_adapt.rst similarity index 100% rename from doc/rst/fix_adapt.rst rename to doc/src/fix_adapt.rst diff --git a/doc/rst/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst similarity index 100% rename from doc/rst/fix_adapt_fep.rst rename to doc/src/fix_adapt_fep.rst diff --git a/doc/rst/fix_addforce.rst b/doc/src/fix_addforce.rst similarity index 100% rename from doc/rst/fix_addforce.rst rename to doc/src/fix_addforce.rst diff --git a/doc/rst/fix_addtorque.rst b/doc/src/fix_addtorque.rst similarity index 100% rename from doc/rst/fix_addtorque.rst rename to doc/src/fix_addtorque.rst diff --git a/doc/rst/fix_append_atoms.rst b/doc/src/fix_append_atoms.rst similarity index 100% rename from doc/rst/fix_append_atoms.rst rename to doc/src/fix_append_atoms.rst diff --git a/doc/rst/fix_atc.rst b/doc/src/fix_atc.rst similarity index 100% rename from doc/rst/fix_atc.rst rename to doc/src/fix_atc.rst diff --git a/doc/rst/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst similarity index 100% rename from doc/rst/fix_atom_swap.rst rename to doc/src/fix_atom_swap.rst diff --git a/doc/rst/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst similarity index 100% rename from doc/rst/fix_ave_atom.rst rename to doc/src/fix_ave_atom.rst diff --git a/doc/rst/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst similarity index 100% rename from doc/rst/fix_ave_chunk.rst rename to doc/src/fix_ave_chunk.rst diff --git a/doc/rst/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst similarity index 100% rename from doc/rst/fix_ave_correlate.rst rename to doc/src/fix_ave_correlate.rst diff --git a/doc/rst/fix_ave_correlate_long.rst b/doc/src/fix_ave_correlate_long.rst similarity index 100% rename from doc/rst/fix_ave_correlate_long.rst rename to doc/src/fix_ave_correlate_long.rst diff --git a/doc/rst/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst similarity index 100% rename from doc/rst/fix_ave_histo.rst rename to doc/src/fix_ave_histo.rst diff --git a/doc/rst/fix_ave_time.rst b/doc/src/fix_ave_time.rst similarity index 100% rename from doc/rst/fix_ave_time.rst rename to doc/src/fix_ave_time.rst diff --git a/doc/rst/fix_aveforce.rst b/doc/src/fix_aveforce.rst similarity index 100% rename from doc/rst/fix_aveforce.rst rename to doc/src/fix_aveforce.rst diff --git a/doc/rst/fix_balance.rst b/doc/src/fix_balance.rst similarity index 100% rename from doc/rst/fix_balance.rst rename to doc/src/fix_balance.rst diff --git a/doc/rst/fix_bocs.rst b/doc/src/fix_bocs.rst similarity index 100% rename from doc/rst/fix_bocs.rst rename to doc/src/fix_bocs.rst diff --git a/doc/rst/fix_bond_break.rst b/doc/src/fix_bond_break.rst similarity index 100% rename from doc/rst/fix_bond_break.rst rename to doc/src/fix_bond_break.rst diff --git a/doc/rst/fix_bond_create.rst b/doc/src/fix_bond_create.rst similarity index 100% rename from doc/rst/fix_bond_create.rst rename to doc/src/fix_bond_create.rst diff --git a/doc/rst/fix_bond_react.rst b/doc/src/fix_bond_react.rst similarity index 100% rename from doc/rst/fix_bond_react.rst rename to doc/src/fix_bond_react.rst diff --git a/doc/rst/fix_bond_swap.rst b/doc/src/fix_bond_swap.rst similarity index 100% rename from doc/rst/fix_bond_swap.rst rename to doc/src/fix_bond_swap.rst diff --git a/doc/rst/fix_box_relax.rst b/doc/src/fix_box_relax.rst similarity index 100% rename from doc/rst/fix_box_relax.rst rename to doc/src/fix_box_relax.rst diff --git a/doc/rst/fix_client_md.rst b/doc/src/fix_client_md.rst similarity index 100% rename from doc/rst/fix_client_md.rst rename to doc/src/fix_client_md.rst diff --git a/doc/rst/fix_cmap.rst b/doc/src/fix_cmap.rst similarity index 100% rename from doc/rst/fix_cmap.rst rename to doc/src/fix_cmap.rst diff --git a/doc/rst/fix_colvars.rst b/doc/src/fix_colvars.rst similarity index 100% rename from doc/rst/fix_colvars.rst rename to doc/src/fix_colvars.rst diff --git a/doc/rst/fix_controller.rst b/doc/src/fix_controller.rst similarity index 100% rename from doc/rst/fix_controller.rst rename to doc/src/fix_controller.rst diff --git a/doc/rst/fix_deform.rst b/doc/src/fix_deform.rst similarity index 100% rename from doc/rst/fix_deform.rst rename to doc/src/fix_deform.rst diff --git a/doc/rst/fix_deposit.rst b/doc/src/fix_deposit.rst similarity index 100% rename from doc/rst/fix_deposit.rst rename to doc/src/fix_deposit.rst diff --git a/doc/rst/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst similarity index 100% rename from doc/rst/fix_dpd_energy.rst rename to doc/src/fix_dpd_energy.rst diff --git a/doc/rst/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst similarity index 100% rename from doc/rst/fix_dpd_source.rst rename to doc/src/fix_dpd_source.rst diff --git a/doc/rst/fix_drag.rst b/doc/src/fix_drag.rst similarity index 100% rename from doc/rst/fix_drag.rst rename to doc/src/fix_drag.rst diff --git a/doc/rst/fix_drude.rst b/doc/src/fix_drude.rst similarity index 100% rename from doc/rst/fix_drude.rst rename to doc/src/fix_drude.rst diff --git a/doc/rst/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst similarity index 100% rename from doc/rst/fix_drude_transform.rst rename to doc/src/fix_drude_transform.rst diff --git a/doc/rst/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst similarity index 100% rename from doc/rst/fix_dt_reset.rst rename to doc/src/fix_dt_reset.rst diff --git a/doc/rst/fix_efield.rst b/doc/src/fix_efield.rst similarity index 100% rename from doc/rst/fix_efield.rst rename to doc/src/fix_efield.rst diff --git a/doc/rst/fix_ehex.rst b/doc/src/fix_ehex.rst similarity index 100% rename from doc/rst/fix_ehex.rst rename to doc/src/fix_ehex.rst diff --git a/doc/rst/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst similarity index 100% rename from doc/rst/fix_electron_stopping.rst rename to doc/src/fix_electron_stopping.rst diff --git a/doc/rst/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst similarity index 100% rename from doc/rst/fix_enforce2d.rst rename to doc/src/fix_enforce2d.rst diff --git a/doc/rst/fix_eos_cv.rst b/doc/src/fix_eos_cv.rst similarity index 100% rename from doc/rst/fix_eos_cv.rst rename to doc/src/fix_eos_cv.rst diff --git a/doc/rst/fix_eos_table.rst b/doc/src/fix_eos_table.rst similarity index 100% rename from doc/rst/fix_eos_table.rst rename to doc/src/fix_eos_table.rst diff --git a/doc/rst/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst similarity index 100% rename from doc/rst/fix_eos_table_rx.rst rename to doc/src/fix_eos_table_rx.rst diff --git a/doc/rst/fix_evaporate.rst b/doc/src/fix_evaporate.rst similarity index 100% rename from doc/rst/fix_evaporate.rst rename to doc/src/fix_evaporate.rst diff --git a/doc/rst/fix_external.rst b/doc/src/fix_external.rst similarity index 100% rename from doc/rst/fix_external.rst rename to doc/src/fix_external.rst diff --git a/doc/rst/fix_ffl.rst b/doc/src/fix_ffl.rst similarity index 100% rename from doc/rst/fix_ffl.rst rename to doc/src/fix_ffl.rst diff --git a/doc/rst/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst similarity index 100% rename from doc/rst/fix_filter_corotate.rst rename to doc/src/fix_filter_corotate.rst diff --git a/doc/rst/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst similarity index 100% rename from doc/rst/fix_flow_gauss.rst rename to doc/src/fix_flow_gauss.rst diff --git a/doc/rst/fix_freeze.rst b/doc/src/fix_freeze.rst similarity index 100% rename from doc/rst/fix_freeze.rst rename to doc/src/fix_freeze.rst diff --git a/doc/rst/fix_gcmc.rst b/doc/src/fix_gcmc.rst similarity index 100% rename from doc/rst/fix_gcmc.rst rename to doc/src/fix_gcmc.rst diff --git a/doc/rst/fix_gld.rst b/doc/src/fix_gld.rst similarity index 100% rename from doc/rst/fix_gld.rst rename to doc/src/fix_gld.rst diff --git a/doc/rst/fix_gle.rst b/doc/src/fix_gle.rst similarity index 100% rename from doc/rst/fix_gle.rst rename to doc/src/fix_gle.rst diff --git a/doc/rst/fix_gravity.rst b/doc/src/fix_gravity.rst similarity index 100% rename from doc/rst/fix_gravity.rst rename to doc/src/fix_gravity.rst diff --git a/doc/rst/fix_grem.rst b/doc/src/fix_grem.rst similarity index 100% rename from doc/rst/fix_grem.rst rename to doc/src/fix_grem.rst diff --git a/doc/rst/fix_halt.rst b/doc/src/fix_halt.rst similarity index 100% rename from doc/rst/fix_halt.rst rename to doc/src/fix_halt.rst diff --git a/doc/rst/fix_heat.rst b/doc/src/fix_heat.rst similarity index 100% rename from doc/rst/fix_heat.rst rename to doc/src/fix_heat.rst diff --git a/doc/rst/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst similarity index 100% rename from doc/rst/fix_hyper_global.rst rename to doc/src/fix_hyper_global.rst diff --git a/doc/rst/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst similarity index 100% rename from doc/rst/fix_hyper_local.rst rename to doc/src/fix_hyper_local.rst diff --git a/doc/rst/fix_imd.rst b/doc/src/fix_imd.rst similarity index 100% rename from doc/rst/fix_imd.rst rename to doc/src/fix_imd.rst diff --git a/doc/rst/fix_indent.rst b/doc/src/fix_indent.rst similarity index 100% rename from doc/rst/fix_indent.rst rename to doc/src/fix_indent.rst diff --git a/doc/rst/fix_ipi.rst b/doc/src/fix_ipi.rst similarity index 100% rename from doc/rst/fix_ipi.rst rename to doc/src/fix_ipi.rst diff --git a/doc/rst/fix_langevin.rst b/doc/src/fix_langevin.rst similarity index 100% rename from doc/rst/fix_langevin.rst rename to doc/src/fix_langevin.rst diff --git a/doc/rst/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst similarity index 100% rename from doc/rst/fix_langevin_drude.rst rename to doc/src/fix_langevin_drude.rst diff --git a/doc/rst/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst similarity index 100% rename from doc/rst/fix_langevin_eff.rst rename to doc/src/fix_langevin_eff.rst diff --git a/doc/rst/fix_langevin_spin.rst b/doc/src/fix_langevin_spin.rst similarity index 100% rename from doc/rst/fix_langevin_spin.rst rename to doc/src/fix_langevin_spin.rst diff --git a/doc/rst/fix_latte.rst b/doc/src/fix_latte.rst similarity index 100% rename from doc/rst/fix_latte.rst rename to doc/src/fix_latte.rst diff --git a/doc/rst/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst similarity index 100% rename from doc/rst/fix_lb_fluid.rst rename to doc/src/fix_lb_fluid.rst diff --git a/doc/rst/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst similarity index 100% rename from doc/rst/fix_lb_momentum.rst rename to doc/src/fix_lb_momentum.rst diff --git a/doc/rst/fix_lb_pc.rst b/doc/src/fix_lb_pc.rst similarity index 100% rename from doc/rst/fix_lb_pc.rst rename to doc/src/fix_lb_pc.rst diff --git a/doc/rst/fix_lb_rigid_pc_sphere.rst b/doc/src/fix_lb_rigid_pc_sphere.rst similarity index 100% rename from doc/rst/fix_lb_rigid_pc_sphere.rst rename to doc/src/fix_lb_rigid_pc_sphere.rst diff --git a/doc/rst/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst similarity index 100% rename from doc/rst/fix_lb_viscous.rst rename to doc/src/fix_lb_viscous.rst diff --git a/doc/rst/fix_lineforce.rst b/doc/src/fix_lineforce.rst similarity index 100% rename from doc/rst/fix_lineforce.rst rename to doc/src/fix_lineforce.rst diff --git a/doc/rst/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst similarity index 100% rename from doc/rst/fix_manifoldforce.rst rename to doc/src/fix_manifoldforce.rst diff --git a/doc/rst/fix_meso.rst b/doc/src/fix_meso.rst similarity index 100% rename from doc/rst/fix_meso.rst rename to doc/src/fix_meso.rst diff --git a/doc/rst/fix_meso_move.rst b/doc/src/fix_meso_move.rst similarity index 100% rename from doc/rst/fix_meso_move.rst rename to doc/src/fix_meso_move.rst diff --git a/doc/rst/fix_meso_stationary.rst b/doc/src/fix_meso_stationary.rst similarity index 100% rename from doc/rst/fix_meso_stationary.rst rename to doc/src/fix_meso_stationary.rst diff --git a/doc/rst/fix_modify.rst b/doc/src/fix_modify.rst similarity index 100% rename from doc/rst/fix_modify.rst rename to doc/src/fix_modify.rst diff --git a/doc/rst/fix_momentum.rst b/doc/src/fix_momentum.rst similarity index 100% rename from doc/rst/fix_momentum.rst rename to doc/src/fix_momentum.rst diff --git a/doc/rst/fix_move.rst b/doc/src/fix_move.rst similarity index 100% rename from doc/rst/fix_move.rst rename to doc/src/fix_move.rst diff --git a/doc/rst/fix_mscg.rst b/doc/src/fix_mscg.rst similarity index 100% rename from doc/rst/fix_mscg.rst rename to doc/src/fix_mscg.rst diff --git a/doc/rst/fix_msst.rst b/doc/src/fix_msst.rst similarity index 100% rename from doc/rst/fix_msst.rst rename to doc/src/fix_msst.rst diff --git a/doc/rst/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst similarity index 100% rename from doc/rst/fix_mvv_dpd.rst rename to doc/src/fix_mvv_dpd.rst diff --git a/doc/rst/fix_neb.rst b/doc/src/fix_neb.rst similarity index 100% rename from doc/rst/fix_neb.rst rename to doc/src/fix_neb.rst diff --git a/doc/rst/fix_neb_spin.rst b/doc/src/fix_neb_spin.rst similarity index 100% rename from doc/rst/fix_neb_spin.rst rename to doc/src/fix_neb_spin.rst diff --git a/doc/rst/fix_nh.rst b/doc/src/fix_nh.rst similarity index 100% rename from doc/rst/fix_nh.rst rename to doc/src/fix_nh.rst diff --git a/doc/rst/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst similarity index 100% rename from doc/rst/fix_nh_eff.rst rename to doc/src/fix_nh_eff.rst diff --git a/doc/rst/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst similarity index 100% rename from doc/rst/fix_nh_uef.rst rename to doc/src/fix_nh_uef.rst diff --git a/doc/rst/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst similarity index 100% rename from doc/rst/fix_nph_asphere.rst rename to doc/src/fix_nph_asphere.rst diff --git a/doc/rst/fix_nph_body.rst b/doc/src/fix_nph_body.rst similarity index 100% rename from doc/rst/fix_nph_body.rst rename to doc/src/fix_nph_body.rst diff --git a/doc/rst/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst similarity index 100% rename from doc/rst/fix_nph_sphere.rst rename to doc/src/fix_nph_sphere.rst diff --git a/doc/rst/fix_nphug.rst b/doc/src/fix_nphug.rst similarity index 100% rename from doc/rst/fix_nphug.rst rename to doc/src/fix_nphug.rst diff --git a/doc/rst/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst similarity index 100% rename from doc/rst/fix_npt_asphere.rst rename to doc/src/fix_npt_asphere.rst diff --git a/doc/rst/fix_npt_body.rst b/doc/src/fix_npt_body.rst similarity index 100% rename from doc/rst/fix_npt_body.rst rename to doc/src/fix_npt_body.rst diff --git a/doc/rst/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst similarity index 100% rename from doc/rst/fix_npt_sphere.rst rename to doc/src/fix_npt_sphere.rst diff --git a/doc/rst/fix_nve.rst b/doc/src/fix_nve.rst similarity index 100% rename from doc/rst/fix_nve.rst rename to doc/src/fix_nve.rst diff --git a/doc/rst/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst similarity index 100% rename from doc/rst/fix_nve_asphere.rst rename to doc/src/fix_nve_asphere.rst diff --git a/doc/rst/fix_nve_asphere_noforce.rst b/doc/src/fix_nve_asphere_noforce.rst similarity index 100% rename from doc/rst/fix_nve_asphere_noforce.rst rename to doc/src/fix_nve_asphere_noforce.rst diff --git a/doc/rst/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst similarity index 100% rename from doc/rst/fix_nve_awpmd.rst rename to doc/src/fix_nve_awpmd.rst diff --git a/doc/rst/fix_nve_body.rst b/doc/src/fix_nve_body.rst similarity index 100% rename from doc/rst/fix_nve_body.rst rename to doc/src/fix_nve_body.rst diff --git a/doc/rst/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst similarity index 100% rename from doc/rst/fix_nve_dot.rst rename to doc/src/fix_nve_dot.rst diff --git a/doc/rst/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst similarity index 100% rename from doc/rst/fix_nve_dotc_langevin.rst rename to doc/src/fix_nve_dotc_langevin.rst diff --git a/doc/rst/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst similarity index 100% rename from doc/rst/fix_nve_eff.rst rename to doc/src/fix_nve_eff.rst diff --git a/doc/rst/fix_nve_limit.rst b/doc/src/fix_nve_limit.rst similarity index 100% rename from doc/rst/fix_nve_limit.rst rename to doc/src/fix_nve_limit.rst diff --git a/doc/rst/fix_nve_line.rst b/doc/src/fix_nve_line.rst similarity index 100% rename from doc/rst/fix_nve_line.rst rename to doc/src/fix_nve_line.rst diff --git a/doc/rst/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst similarity index 100% rename from doc/rst/fix_nve_manifold_rattle.rst rename to doc/src/fix_nve_manifold_rattle.rst diff --git a/doc/rst/fix_nve_noforce.rst b/doc/src/fix_nve_noforce.rst similarity index 100% rename from doc/rst/fix_nve_noforce.rst rename to doc/src/fix_nve_noforce.rst diff --git a/doc/rst/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst similarity index 100% rename from doc/rst/fix_nve_sphere.rst rename to doc/src/fix_nve_sphere.rst diff --git a/doc/rst/fix_nve_spin.rst b/doc/src/fix_nve_spin.rst similarity index 100% rename from doc/rst/fix_nve_spin.rst rename to doc/src/fix_nve_spin.rst diff --git a/doc/rst/fix_nve_tri.rst b/doc/src/fix_nve_tri.rst similarity index 100% rename from doc/rst/fix_nve_tri.rst rename to doc/src/fix_nve_tri.rst diff --git a/doc/rst/fix_nvk.rst b/doc/src/fix_nvk.rst similarity index 100% rename from doc/rst/fix_nvk.rst rename to doc/src/fix_nvk.rst diff --git a/doc/rst/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst similarity index 100% rename from doc/rst/fix_nvt_asphere.rst rename to doc/src/fix_nvt_asphere.rst diff --git a/doc/rst/fix_nvt_body.rst b/doc/src/fix_nvt_body.rst similarity index 100% rename from doc/rst/fix_nvt_body.rst rename to doc/src/fix_nvt_body.rst diff --git a/doc/rst/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst similarity index 100% rename from doc/rst/fix_nvt_manifold_rattle.rst rename to doc/src/fix_nvt_manifold_rattle.rst diff --git a/doc/rst/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst similarity index 100% rename from doc/rst/fix_nvt_sllod.rst rename to doc/src/fix_nvt_sllod.rst diff --git a/doc/rst/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst similarity index 100% rename from doc/rst/fix_nvt_sllod_eff.rst rename to doc/src/fix_nvt_sllod_eff.rst diff --git a/doc/rst/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst similarity index 100% rename from doc/rst/fix_nvt_sphere.rst rename to doc/src/fix_nvt_sphere.rst diff --git a/doc/rst/fix_oneway.rst b/doc/src/fix_oneway.rst similarity index 100% rename from doc/rst/fix_oneway.rst rename to doc/src/fix_oneway.rst diff --git a/doc/rst/fix_orient.rst b/doc/src/fix_orient.rst similarity index 100% rename from doc/rst/fix_orient.rst rename to doc/src/fix_orient.rst diff --git a/doc/rst/fix_phonon.rst b/doc/src/fix_phonon.rst similarity index 100% rename from doc/rst/fix_phonon.rst rename to doc/src/fix_phonon.rst diff --git a/doc/rst/fix_pimd.rst b/doc/src/fix_pimd.rst similarity index 100% rename from doc/rst/fix_pimd.rst rename to doc/src/fix_pimd.rst diff --git a/doc/rst/fix_planeforce.rst b/doc/src/fix_planeforce.rst similarity index 100% rename from doc/rst/fix_planeforce.rst rename to doc/src/fix_planeforce.rst diff --git a/doc/rst/fix_plumed.rst b/doc/src/fix_plumed.rst similarity index 100% rename from doc/rst/fix_plumed.rst rename to doc/src/fix_plumed.rst diff --git a/doc/rst/fix_poems.rst b/doc/src/fix_poems.rst similarity index 100% rename from doc/rst/fix_poems.rst rename to doc/src/fix_poems.rst diff --git a/doc/rst/fix_pour.rst b/doc/src/fix_pour.rst similarity index 100% rename from doc/rst/fix_pour.rst rename to doc/src/fix_pour.rst diff --git a/doc/rst/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst similarity index 100% rename from doc/rst/fix_precession_spin.rst rename to doc/src/fix_precession_spin.rst diff --git a/doc/rst/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst similarity index 100% rename from doc/rst/fix_press_berendsen.rst rename to doc/src/fix_press_berendsen.rst diff --git a/doc/rst/fix_print.rst b/doc/src/fix_print.rst similarity index 100% rename from doc/rst/fix_print.rst rename to doc/src/fix_print.rst diff --git a/doc/rst/fix_property_atom.rst b/doc/src/fix_property_atom.rst similarity index 100% rename from doc/rst/fix_property_atom.rst rename to doc/src/fix_property_atom.rst diff --git a/doc/rst/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst similarity index 100% rename from doc/rst/fix_python_invoke.rst rename to doc/src/fix_python_invoke.rst diff --git a/doc/rst/fix_python_move.rst b/doc/src/fix_python_move.rst similarity index 100% rename from doc/rst/fix_python_move.rst rename to doc/src/fix_python_move.rst diff --git a/doc/rst/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst similarity index 100% rename from doc/rst/fix_qbmsst.rst rename to doc/src/fix_qbmsst.rst diff --git a/doc/rst/fix_qeq.rst b/doc/src/fix_qeq.rst similarity index 100% rename from doc/rst/fix_qeq.rst rename to doc/src/fix_qeq.rst diff --git a/doc/rst/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst similarity index 100% rename from doc/rst/fix_qeq_comb.rst rename to doc/src/fix_qeq_comb.rst diff --git a/doc/rst/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst similarity index 100% rename from doc/rst/fix_qeq_reax.rst rename to doc/src/fix_qeq_reax.rst diff --git a/doc/rst/fix_qmmm.rst b/doc/src/fix_qmmm.rst similarity index 100% rename from doc/rst/fix_qmmm.rst rename to doc/src/fix_qmmm.rst diff --git a/doc/rst/fix_qtb.rst b/doc/src/fix_qtb.rst similarity index 100% rename from doc/rst/fix_qtb.rst rename to doc/src/fix_qtb.rst diff --git a/doc/rst/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst similarity index 100% rename from doc/rst/fix_reaxc_bonds.rst rename to doc/src/fix_reaxc_bonds.rst diff --git a/doc/rst/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst similarity index 100% rename from doc/rst/fix_reaxc_species.rst rename to doc/src/fix_reaxc_species.rst diff --git a/doc/rst/fix_recenter.rst b/doc/src/fix_recenter.rst similarity index 100% rename from doc/rst/fix_recenter.rst rename to doc/src/fix_recenter.rst diff --git a/doc/rst/fix_restrain.rst b/doc/src/fix_restrain.rst similarity index 100% rename from doc/rst/fix_restrain.rst rename to doc/src/fix_restrain.rst diff --git a/doc/rst/fix_rhok.rst b/doc/src/fix_rhok.rst similarity index 100% rename from doc/rst/fix_rhok.rst rename to doc/src/fix_rhok.rst diff --git a/doc/rst/fix_rigid.rst b/doc/src/fix_rigid.rst similarity index 100% rename from doc/rst/fix_rigid.rst rename to doc/src/fix_rigid.rst diff --git a/doc/rst/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst similarity index 100% rename from doc/rst/fix_rigid_meso.rst rename to doc/src/fix_rigid_meso.rst diff --git a/doc/rst/fix_rx.rst b/doc/src/fix_rx.rst similarity index 100% rename from doc/rst/fix_rx.rst rename to doc/src/fix_rx.rst diff --git a/doc/rst/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst similarity index 100% rename from doc/rst/fix_saed_vtk.rst rename to doc/src/fix_saed_vtk.rst diff --git a/doc/rst/fix_setforce.rst b/doc/src/fix_setforce.rst similarity index 100% rename from doc/rst/fix_setforce.rst rename to doc/src/fix_setforce.rst diff --git a/doc/rst/fix_shake.rst b/doc/src/fix_shake.rst similarity index 100% rename from doc/rst/fix_shake.rst rename to doc/src/fix_shake.rst diff --git a/doc/rst/fix_shardlow.rst b/doc/src/fix_shardlow.rst similarity index 100% rename from doc/rst/fix_shardlow.rst rename to doc/src/fix_shardlow.rst diff --git a/doc/rst/fix_smd.rst b/doc/src/fix_smd.rst similarity index 100% rename from doc/rst/fix_smd.rst rename to doc/src/fix_smd.rst diff --git a/doc/rst/fix_smd_adjust_dt.rst b/doc/src/fix_smd_adjust_dt.rst similarity index 100% rename from doc/rst/fix_smd_adjust_dt.rst rename to doc/src/fix_smd_adjust_dt.rst diff --git a/doc/rst/fix_smd_integrate_tlsph.rst b/doc/src/fix_smd_integrate_tlsph.rst similarity index 100% rename from doc/rst/fix_smd_integrate_tlsph.rst rename to doc/src/fix_smd_integrate_tlsph.rst diff --git a/doc/rst/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst similarity index 100% rename from doc/rst/fix_smd_integrate_ulsph.rst rename to doc/src/fix_smd_integrate_ulsph.rst diff --git a/doc/rst/fix_smd_move_triangulated_surface.rst b/doc/src/fix_smd_move_triangulated_surface.rst similarity index 100% rename from doc/rst/fix_smd_move_triangulated_surface.rst rename to doc/src/fix_smd_move_triangulated_surface.rst diff --git a/doc/rst/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst similarity index 100% rename from doc/rst/fix_smd_setvel.rst rename to doc/src/fix_smd_setvel.rst diff --git a/doc/rst/fix_smd_wall_surface.rst b/doc/src/fix_smd_wall_surface.rst similarity index 100% rename from doc/rst/fix_smd_wall_surface.rst rename to doc/src/fix_smd_wall_surface.rst diff --git a/doc/rst/fix_spring.rst b/doc/src/fix_spring.rst similarity index 100% rename from doc/rst/fix_spring.rst rename to doc/src/fix_spring.rst diff --git a/doc/rst/fix_spring_chunk.rst b/doc/src/fix_spring_chunk.rst similarity index 100% rename from doc/rst/fix_spring_chunk.rst rename to doc/src/fix_spring_chunk.rst diff --git a/doc/rst/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst similarity index 100% rename from doc/rst/fix_spring_rg.rst rename to doc/src/fix_spring_rg.rst diff --git a/doc/rst/fix_spring_self.rst b/doc/src/fix_spring_self.rst similarity index 100% rename from doc/rst/fix_spring_self.rst rename to doc/src/fix_spring_self.rst diff --git a/doc/rst/fix_srd.rst b/doc/src/fix_srd.rst similarity index 100% rename from doc/rst/fix_srd.rst rename to doc/src/fix_srd.rst diff --git a/doc/rst/fix_store_force.rst b/doc/src/fix_store_force.rst similarity index 100% rename from doc/rst/fix_store_force.rst rename to doc/src/fix_store_force.rst diff --git a/doc/rst/fix_store_state.rst b/doc/src/fix_store_state.rst similarity index 100% rename from doc/rst/fix_store_state.rst rename to doc/src/fix_store_state.rst diff --git a/doc/rst/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst similarity index 100% rename from doc/rst/fix_temp_berendsen.rst rename to doc/src/fix_temp_berendsen.rst diff --git a/doc/rst/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst similarity index 100% rename from doc/rst/fix_temp_csvr.rst rename to doc/src/fix_temp_csvr.rst diff --git a/doc/rst/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst similarity index 100% rename from doc/rst/fix_temp_rescale.rst rename to doc/src/fix_temp_rescale.rst diff --git a/doc/rst/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst similarity index 100% rename from doc/rst/fix_temp_rescale_eff.rst rename to doc/src/fix_temp_rescale_eff.rst diff --git a/doc/rst/fix_tfmc.rst b/doc/src/fix_tfmc.rst similarity index 100% rename from doc/rst/fix_tfmc.rst rename to doc/src/fix_tfmc.rst diff --git a/doc/rst/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst similarity index 100% rename from doc/rst/fix_thermal_conductivity.rst rename to doc/src/fix_thermal_conductivity.rst diff --git a/doc/rst/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst similarity index 100% rename from doc/rst/fix_ti_spring.rst rename to doc/src/fix_ti_spring.rst diff --git a/doc/rst/fix_tmd.rst b/doc/src/fix_tmd.rst similarity index 100% rename from doc/rst/fix_tmd.rst rename to doc/src/fix_tmd.rst diff --git a/doc/rst/fix_ttm.rst b/doc/src/fix_ttm.rst similarity index 100% rename from doc/rst/fix_ttm.rst rename to doc/src/fix_ttm.rst diff --git a/doc/rst/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst similarity index 100% rename from doc/rst/fix_tune_kspace.rst rename to doc/src/fix_tune_kspace.rst diff --git a/doc/rst/fix_vector.rst b/doc/src/fix_vector.rst similarity index 100% rename from doc/rst/fix_vector.rst rename to doc/src/fix_vector.rst diff --git a/doc/rst/fix_viscosity.rst b/doc/src/fix_viscosity.rst similarity index 100% rename from doc/rst/fix_viscosity.rst rename to doc/src/fix_viscosity.rst diff --git a/doc/rst/fix_viscous.rst b/doc/src/fix_viscous.rst similarity index 100% rename from doc/rst/fix_viscous.rst rename to doc/src/fix_viscous.rst diff --git a/doc/rst/fix_wall.rst b/doc/src/fix_wall.rst similarity index 100% rename from doc/rst/fix_wall.rst rename to doc/src/fix_wall.rst diff --git a/doc/rst/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst similarity index 100% rename from doc/rst/fix_wall_body_polygon.rst rename to doc/src/fix_wall_body_polygon.rst diff --git a/doc/rst/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst similarity index 100% rename from doc/rst/fix_wall_body_polyhedron.rst rename to doc/src/fix_wall_body_polyhedron.rst diff --git a/doc/rst/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst similarity index 100% rename from doc/rst/fix_wall_ees.rst rename to doc/src/fix_wall_ees.rst diff --git a/doc/rst/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst similarity index 100% rename from doc/rst/fix_wall_gran.rst rename to doc/src/fix_wall_gran.rst diff --git a/doc/rst/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst similarity index 100% rename from doc/rst/fix_wall_gran_region.rst rename to doc/src/fix_wall_gran_region.rst diff --git a/doc/rst/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst similarity index 100% rename from doc/rst/fix_wall_piston.rst rename to doc/src/fix_wall_piston.rst diff --git a/doc/rst/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst similarity index 100% rename from doc/rst/fix_wall_reflect.rst rename to doc/src/fix_wall_reflect.rst diff --git a/doc/rst/fix_wall_region.rst b/doc/src/fix_wall_region.rst similarity index 100% rename from doc/rst/fix_wall_region.rst rename to doc/src/fix_wall_region.rst diff --git a/doc/rst/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst similarity index 100% rename from doc/rst/fix_wall_srd.rst rename to doc/src/fix_wall_srd.rst diff --git a/doc/src/fixes.rst b/doc/src/fixes.rst new file mode 100644 index 0000000000000000000000000000000000000000..5a85738c45128d4f7fac91e4bebc92916704b7ea --- /dev/null +++ b/doc/src/fixes.rst @@ -0,0 +1,9 @@ +Fixes +##### + + +.. toctree:: + :maxdepth: 1 + :glob: + + fix_* diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt deleted file mode 100644 index d966b9a225cca510a0ce61daff21099a75a01e26..0000000000000000000000000000000000000000 --- a/doc/src/fixes.txt +++ /dev/null @@ -1,190 +0,0 @@ -Fixes :h1 - - diff --git a/doc/rst/group.rst b/doc/src/group.rst similarity index 100% rename from doc/rst/group.rst rename to doc/src/group.rst diff --git a/doc/rst/group2ndx.rst b/doc/src/group2ndx.rst similarity index 100% rename from doc/rst/group2ndx.rst rename to doc/src/group2ndx.rst diff --git a/doc/rst/hyper.rst b/doc/src/hyper.rst similarity index 100% rename from doc/rst/hyper.rst rename to doc/src/hyper.rst diff --git a/doc/rst/if.rst b/doc/src/if.rst similarity index 100% rename from doc/rst/if.rst rename to doc/src/if.rst diff --git a/doc/rst/improper_class2.rst b/doc/src/improper_class2.rst similarity index 100% rename from doc/rst/improper_class2.rst rename to doc/src/improper_class2.rst diff --git a/doc/rst/improper_coeff.rst b/doc/src/improper_coeff.rst similarity index 100% rename from doc/rst/improper_coeff.rst rename to doc/src/improper_coeff.rst diff --git a/doc/rst/improper_cossq.rst b/doc/src/improper_cossq.rst similarity index 100% rename from doc/rst/improper_cossq.rst rename to doc/src/improper_cossq.rst diff --git a/doc/rst/improper_cvff.rst b/doc/src/improper_cvff.rst similarity index 100% rename from doc/rst/improper_cvff.rst rename to doc/src/improper_cvff.rst diff --git a/doc/rst/improper_distance.rst b/doc/src/improper_distance.rst similarity index 100% rename from doc/rst/improper_distance.rst rename to doc/src/improper_distance.rst diff --git a/doc/rst/improper_distharm.rst b/doc/src/improper_distharm.rst similarity index 100% rename from doc/rst/improper_distharm.rst rename to doc/src/improper_distharm.rst diff --git a/doc/rst/improper_fourier.rst b/doc/src/improper_fourier.rst similarity index 100% rename from doc/rst/improper_fourier.rst rename to doc/src/improper_fourier.rst diff --git a/doc/rst/improper_harmonic.rst b/doc/src/improper_harmonic.rst similarity index 100% rename from doc/rst/improper_harmonic.rst rename to doc/src/improper_harmonic.rst diff --git a/doc/rst/improper_hybrid.rst b/doc/src/improper_hybrid.rst similarity index 100% rename from doc/rst/improper_hybrid.rst rename to doc/src/improper_hybrid.rst diff --git a/doc/rst/improper_inversion_harmonic.rst b/doc/src/improper_inversion_harmonic.rst similarity index 100% rename from doc/rst/improper_inversion_harmonic.rst rename to doc/src/improper_inversion_harmonic.rst diff --git a/doc/rst/improper_none.rst b/doc/src/improper_none.rst similarity index 100% rename from doc/rst/improper_none.rst rename to doc/src/improper_none.rst diff --git a/doc/rst/improper_ring.rst b/doc/src/improper_ring.rst similarity index 100% rename from doc/rst/improper_ring.rst rename to doc/src/improper_ring.rst diff --git a/doc/rst/improper_sqdistharm.rst b/doc/src/improper_sqdistharm.rst similarity index 100% rename from doc/rst/improper_sqdistharm.rst rename to doc/src/improper_sqdistharm.rst diff --git a/doc/rst/improper_style.rst b/doc/src/improper_style.rst similarity index 100% rename from doc/rst/improper_style.rst rename to doc/src/improper_style.rst diff --git a/doc/rst/improper_umbrella.rst b/doc/src/improper_umbrella.rst similarity index 100% rename from doc/rst/improper_umbrella.rst rename to doc/src/improper_umbrella.rst diff --git a/doc/rst/improper_zero.rst b/doc/src/improper_zero.rst similarity index 100% rename from doc/rst/improper_zero.rst rename to doc/src/improper_zero.rst diff --git a/doc/src/impropers.rst b/doc/src/impropers.rst new file mode 100644 index 0000000000000000000000000000000000000000..93b4776d2cd9a0e1d141749a5cdd643f23c588c8 --- /dev/null +++ b/doc/src/impropers.rst @@ -0,0 +1,9 @@ +Improper Styles +############### + + +.. toctree:: + :maxdepth: 1 + :glob: + + improper_* diff --git a/doc/rst/include.rst b/doc/src/include.rst similarity index 100% rename from doc/rst/include.rst rename to doc/src/include.rst diff --git a/doc/rst/info.rst b/doc/src/info.rst similarity index 100% rename from doc/rst/info.rst rename to doc/src/info.rst diff --git a/doc/rst/jump.rst b/doc/src/jump.rst similarity index 100% rename from doc/rst/jump.rst rename to doc/src/jump.rst diff --git a/doc/rst/kim_commands.rst b/doc/src/kim_commands.rst similarity index 100% rename from doc/rst/kim_commands.rst rename to doc/src/kim_commands.rst diff --git a/doc/rst/kspace_modify.rst b/doc/src/kspace_modify.rst similarity index 100% rename from doc/rst/kspace_modify.rst rename to doc/src/kspace_modify.rst diff --git a/doc/rst/kspace_style.rst b/doc/src/kspace_style.rst similarity index 100% rename from doc/rst/kspace_style.rst rename to doc/src/kspace_style.rst diff --git a/doc/rst/label.rst b/doc/src/label.rst similarity index 100% rename from doc/rst/label.rst rename to doc/src/label.rst diff --git a/doc/rst/lattice.rst b/doc/src/lattice.rst similarity index 100% rename from doc/rst/lattice.rst rename to doc/src/lattice.rst diff --git a/doc/rst/log.rst b/doc/src/log.rst similarity index 100% rename from doc/rst/log.rst rename to doc/src/log.rst diff --git a/doc/rst/mass.rst b/doc/src/mass.rst similarity index 100% rename from doc/rst/mass.rst rename to doc/src/mass.rst diff --git a/doc/rst/message.rst b/doc/src/message.rst similarity index 100% rename from doc/rst/message.rst rename to doc/src/message.rst diff --git a/doc/rst/min_modify.rst b/doc/src/min_modify.rst similarity index 100% rename from doc/rst/min_modify.rst rename to doc/src/min_modify.rst diff --git a/doc/rst/min_spin.rst b/doc/src/min_spin.rst similarity index 100% rename from doc/rst/min_spin.rst rename to doc/src/min_spin.rst diff --git a/doc/rst/min_style.rst b/doc/src/min_style.rst similarity index 100% rename from doc/rst/min_style.rst rename to doc/src/min_style.rst diff --git a/doc/rst/minimize.rst b/doc/src/minimize.rst similarity index 100% rename from doc/rst/minimize.rst rename to doc/src/minimize.rst diff --git a/doc/rst/molecule.rst b/doc/src/molecule.rst similarity index 100% rename from doc/rst/molecule.rst rename to doc/src/molecule.rst diff --git a/doc/rst/neb.rst b/doc/src/neb.rst similarity index 100% rename from doc/rst/neb.rst rename to doc/src/neb.rst diff --git a/doc/rst/neb_spin.rst b/doc/src/neb_spin.rst similarity index 100% rename from doc/rst/neb_spin.rst rename to doc/src/neb_spin.rst diff --git a/doc/rst/neigh_modify.rst b/doc/src/neigh_modify.rst similarity index 100% rename from doc/rst/neigh_modify.rst rename to doc/src/neigh_modify.rst diff --git a/doc/rst/neighbor.rst b/doc/src/neighbor.rst similarity index 100% rename from doc/rst/neighbor.rst rename to doc/src/neighbor.rst diff --git a/doc/rst/newton.rst b/doc/src/newton.rst similarity index 100% rename from doc/rst/newton.rst rename to doc/src/newton.rst diff --git a/doc/rst/next.rst b/doc/src/next.rst similarity index 100% rename from doc/rst/next.rst rename to doc/src/next.rst diff --git a/doc/rst/package.rst b/doc/src/package.rst similarity index 100% rename from doc/rst/package.rst rename to doc/src/package.rst diff --git a/doc/rst/pair_adp.rst b/doc/src/pair_adp.rst similarity index 100% rename from doc/rst/pair_adp.rst rename to doc/src/pair_adp.rst diff --git a/doc/rst/pair_agni.rst b/doc/src/pair_agni.rst similarity index 100% rename from doc/rst/pair_agni.rst rename to doc/src/pair_agni.rst diff --git a/doc/rst/pair_airebo.rst b/doc/src/pair_airebo.rst similarity index 100% rename from doc/rst/pair_airebo.rst rename to doc/src/pair_airebo.rst diff --git a/doc/rst/pair_atm.rst b/doc/src/pair_atm.rst similarity index 100% rename from doc/rst/pair_atm.rst rename to doc/src/pair_atm.rst diff --git a/doc/rst/pair_awpmd.rst b/doc/src/pair_awpmd.rst similarity index 100% rename from doc/rst/pair_awpmd.rst rename to doc/src/pair_awpmd.rst diff --git a/doc/rst/pair_beck.rst b/doc/src/pair_beck.rst similarity index 100% rename from doc/rst/pair_beck.rst rename to doc/src/pair_beck.rst diff --git a/doc/rst/pair_body_nparticle.rst b/doc/src/pair_body_nparticle.rst similarity index 100% rename from doc/rst/pair_body_nparticle.rst rename to doc/src/pair_body_nparticle.rst diff --git a/doc/rst/pair_body_rounded_polygon.rst b/doc/src/pair_body_rounded_polygon.rst similarity index 100% rename from doc/rst/pair_body_rounded_polygon.rst rename to doc/src/pair_body_rounded_polygon.rst diff --git a/doc/rst/pair_body_rounded_polyhedron.rst b/doc/src/pair_body_rounded_polyhedron.rst similarity index 100% rename from doc/rst/pair_body_rounded_polyhedron.rst rename to doc/src/pair_body_rounded_polyhedron.rst diff --git a/doc/rst/pair_bop.rst b/doc/src/pair_bop.rst similarity index 100% rename from doc/rst/pair_bop.rst rename to doc/src/pair_bop.rst diff --git a/doc/rst/pair_born.rst b/doc/src/pair_born.rst similarity index 100% rename from doc/rst/pair_born.rst rename to doc/src/pair_born.rst diff --git a/doc/rst/pair_brownian.rst b/doc/src/pair_brownian.rst similarity index 100% rename from doc/rst/pair_brownian.rst rename to doc/src/pair_brownian.rst diff --git a/doc/rst/pair_buck.rst b/doc/src/pair_buck.rst similarity index 100% rename from doc/rst/pair_buck.rst rename to doc/src/pair_buck.rst diff --git a/doc/rst/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst similarity index 100% rename from doc/rst/pair_buck6d_coul_gauss.rst rename to doc/src/pair_buck6d_coul_gauss.rst diff --git a/doc/rst/pair_buck_long.rst b/doc/src/pair_buck_long.rst similarity index 100% rename from doc/rst/pair_buck_long.rst rename to doc/src/pair_buck_long.rst diff --git a/doc/rst/pair_charmm.rst b/doc/src/pair_charmm.rst similarity index 100% rename from doc/rst/pair_charmm.rst rename to doc/src/pair_charmm.rst diff --git a/doc/rst/pair_class2.rst b/doc/src/pair_class2.rst similarity index 100% rename from doc/rst/pair_class2.rst rename to doc/src/pair_class2.rst diff --git a/doc/rst/pair_coeff.rst b/doc/src/pair_coeff.rst similarity index 100% rename from doc/rst/pair_coeff.rst rename to doc/src/pair_coeff.rst diff --git a/doc/rst/pair_colloid.rst b/doc/src/pair_colloid.rst similarity index 100% rename from doc/rst/pair_colloid.rst rename to doc/src/pair_colloid.rst diff --git a/doc/rst/pair_comb.rst b/doc/src/pair_comb.rst similarity index 100% rename from doc/rst/pair_comb.rst rename to doc/src/pair_comb.rst diff --git a/doc/rst/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst similarity index 100% rename from doc/rst/pair_cosine_squared.rst rename to doc/src/pair_cosine_squared.rst diff --git a/doc/rst/pair_coul.rst b/doc/src/pair_coul.rst similarity index 100% rename from doc/rst/pair_coul.rst rename to doc/src/pair_coul.rst diff --git a/doc/rst/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst similarity index 100% rename from doc/rst/pair_coul_diel.rst rename to doc/src/pair_coul_diel.rst diff --git a/doc/rst/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst similarity index 100% rename from doc/rst/pair_coul_shield.rst rename to doc/src/pair_coul_shield.rst diff --git a/doc/rst/pair_cs.rst b/doc/src/pair_cs.rst similarity index 100% rename from doc/rst/pair_cs.rst rename to doc/src/pair_cs.rst diff --git a/doc/rst/pair_dipole.rst b/doc/src/pair_dipole.rst similarity index 100% rename from doc/rst/pair_dipole.rst rename to doc/src/pair_dipole.rst diff --git a/doc/rst/pair_dpd.rst b/doc/src/pair_dpd.rst similarity index 100% rename from doc/rst/pair_dpd.rst rename to doc/src/pair_dpd.rst diff --git a/doc/rst/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst similarity index 100% rename from doc/rst/pair_dpd_fdt.rst rename to doc/src/pair_dpd_fdt.rst diff --git a/doc/rst/pair_drip.rst b/doc/src/pair_drip.rst similarity index 100% rename from doc/rst/pair_drip.rst rename to doc/src/pair_drip.rst diff --git a/doc/rst/pair_dsmc.rst b/doc/src/pair_dsmc.rst similarity index 100% rename from doc/rst/pair_dsmc.rst rename to doc/src/pair_dsmc.rst diff --git a/doc/rst/pair_e3b.rst b/doc/src/pair_e3b.rst similarity index 100% rename from doc/rst/pair_e3b.rst rename to doc/src/pair_e3b.rst diff --git a/doc/rst/pair_eam.rst b/doc/src/pair_eam.rst similarity index 100% rename from doc/rst/pair_eam.rst rename to doc/src/pair_eam.rst diff --git a/doc/rst/pair_edip.rst b/doc/src/pair_edip.rst similarity index 100% rename from doc/rst/pair_edip.rst rename to doc/src/pair_edip.rst diff --git a/doc/rst/pair_eff.rst b/doc/src/pair_eff.rst similarity index 100% rename from doc/rst/pair_eff.rst rename to doc/src/pair_eff.rst diff --git a/doc/rst/pair_eim.rst b/doc/src/pair_eim.rst similarity index 100% rename from doc/rst/pair_eim.rst rename to doc/src/pair_eim.rst diff --git a/doc/rst/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst similarity index 100% rename from doc/rst/pair_exp6_rx.rst rename to doc/src/pair_exp6_rx.rst diff --git a/doc/rst/pair_extep.rst b/doc/src/pair_extep.rst similarity index 100% rename from doc/rst/pair_extep.rst rename to doc/src/pair_extep.rst diff --git a/doc/rst/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst similarity index 100% rename from doc/rst/pair_fep_soft.rst rename to doc/src/pair_fep_soft.rst diff --git a/doc/rst/pair_gauss.rst b/doc/src/pair_gauss.rst similarity index 100% rename from doc/rst/pair_gauss.rst rename to doc/src/pair_gauss.rst diff --git a/doc/rst/pair_gayberne.rst b/doc/src/pair_gayberne.rst similarity index 100% rename from doc/rst/pair_gayberne.rst rename to doc/src/pair_gayberne.rst diff --git a/doc/rst/pair_gran.rst b/doc/src/pair_gran.rst similarity index 100% rename from doc/rst/pair_gran.rst rename to doc/src/pair_gran.rst diff --git a/doc/rst/pair_granular.rst b/doc/src/pair_granular.rst similarity index 100% rename from doc/rst/pair_granular.rst rename to doc/src/pair_granular.rst diff --git a/doc/rst/pair_gromacs.rst b/doc/src/pair_gromacs.rst similarity index 100% rename from doc/rst/pair_gromacs.rst rename to doc/src/pair_gromacs.rst diff --git a/doc/rst/pair_gw.rst b/doc/src/pair_gw.rst similarity index 100% rename from doc/rst/pair_gw.rst rename to doc/src/pair_gw.rst diff --git a/doc/rst/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst similarity index 100% rename from doc/rst/pair_hbond_dreiding.rst rename to doc/src/pair_hbond_dreiding.rst diff --git a/doc/rst/pair_hybrid.rst b/doc/src/pair_hybrid.rst similarity index 100% rename from doc/rst/pair_hybrid.rst rename to doc/src/pair_hybrid.rst diff --git a/doc/rst/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst similarity index 100% rename from doc/rst/pair_ilp_graphene_hbn.rst rename to doc/src/pair_ilp_graphene_hbn.rst diff --git a/doc/rst/pair_kim.rst b/doc/src/pair_kim.rst similarity index 100% rename from doc/rst/pair_kim.rst rename to doc/src/pair_kim.rst diff --git a/doc/rst/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst similarity index 100% rename from doc/rst/pair_kolmogorov_crespi_full.rst rename to doc/src/pair_kolmogorov_crespi_full.rst diff --git a/doc/rst/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst similarity index 100% rename from doc/rst/pair_kolmogorov_crespi_z.rst rename to doc/src/pair_kolmogorov_crespi_z.rst diff --git a/doc/rst/pair_lcbop.rst b/doc/src/pair_lcbop.rst similarity index 100% rename from doc/rst/pair_lcbop.rst rename to doc/src/pair_lcbop.rst diff --git a/doc/rst/pair_lebedeva_z.rst b/doc/src/pair_lebedeva_z.rst similarity index 100% rename from doc/rst/pair_lebedeva_z.rst rename to doc/src/pair_lebedeva_z.rst diff --git a/doc/rst/pair_line_lj.rst b/doc/src/pair_line_lj.rst similarity index 100% rename from doc/rst/pair_line_lj.rst rename to doc/src/pair_line_lj.rst diff --git a/doc/rst/pair_list.rst b/doc/src/pair_list.rst similarity index 100% rename from doc/rst/pair_list.rst rename to doc/src/pair_list.rst diff --git a/doc/rst/pair_lj.rst b/doc/src/pair_lj.rst similarity index 100% rename from doc/rst/pair_lj.rst rename to doc/src/pair_lj.rst diff --git a/doc/rst/pair_lj96.rst b/doc/src/pair_lj96.rst similarity index 100% rename from doc/rst/pair_lj96.rst rename to doc/src/pair_lj96.rst diff --git a/doc/rst/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst similarity index 100% rename from doc/rst/pair_lj_cubic.rst rename to doc/src/pair_lj_cubic.rst diff --git a/doc/rst/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst similarity index 100% rename from doc/rst/pair_lj_expand.rst rename to doc/src/pair_lj_expand.rst diff --git a/doc/rst/pair_lj_long.rst b/doc/src/pair_lj_long.rst similarity index 100% rename from doc/rst/pair_lj_long.rst rename to doc/src/pair_lj_long.rst diff --git a/doc/rst/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst similarity index 100% rename from doc/rst/pair_lj_smooth.rst rename to doc/src/pair_lj_smooth.rst diff --git a/doc/rst/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst similarity index 100% rename from doc/rst/pair_lj_smooth_linear.rst rename to doc/src/pair_lj_smooth_linear.rst diff --git a/doc/rst/pair_lj_switch3_coulgauss.rst b/doc/src/pair_lj_switch3_coulgauss.rst similarity index 100% rename from doc/rst/pair_lj_switch3_coulgauss.rst rename to doc/src/pair_lj_switch3_coulgauss.rst diff --git a/doc/rst/pair_local_density.rst b/doc/src/pair_local_density.rst similarity index 100% rename from doc/rst/pair_local_density.rst rename to doc/src/pair_local_density.rst diff --git a/doc/rst/pair_lubricate.rst b/doc/src/pair_lubricate.rst similarity index 100% rename from doc/rst/pair_lubricate.rst rename to doc/src/pair_lubricate.rst diff --git a/doc/rst/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst similarity index 100% rename from doc/rst/pair_lubricateU.rst rename to doc/src/pair_lubricateU.rst diff --git a/doc/rst/pair_mdf.rst b/doc/src/pair_mdf.rst similarity index 100% rename from doc/rst/pair_mdf.rst rename to doc/src/pair_mdf.rst diff --git a/doc/rst/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst similarity index 100% rename from doc/rst/pair_meam_spline.rst rename to doc/src/pair_meam_spline.rst diff --git a/doc/rst/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst similarity index 100% rename from doc/rst/pair_meam_sw_spline.rst rename to doc/src/pair_meam_sw_spline.rst diff --git a/doc/rst/pair_meamc.rst b/doc/src/pair_meamc.rst similarity index 100% rename from doc/rst/pair_meamc.rst rename to doc/src/pair_meamc.rst diff --git a/doc/rst/pair_meso.rst b/doc/src/pair_meso.rst similarity index 100% rename from doc/rst/pair_meso.rst rename to doc/src/pair_meso.rst diff --git a/doc/rst/pair_mgpt.rst b/doc/src/pair_mgpt.rst similarity index 100% rename from doc/rst/pair_mgpt.rst rename to doc/src/pair_mgpt.rst diff --git a/doc/rst/pair_mie.rst b/doc/src/pair_mie.rst similarity index 100% rename from doc/rst/pair_mie.rst rename to doc/src/pair_mie.rst diff --git a/doc/rst/pair_mm3_switch3_coulgauss.rst b/doc/src/pair_mm3_switch3_coulgauss.rst similarity index 100% rename from doc/rst/pair_mm3_switch3_coulgauss.rst rename to doc/src/pair_mm3_switch3_coulgauss.rst diff --git a/doc/rst/pair_modify.rst b/doc/src/pair_modify.rst similarity index 100% rename from doc/rst/pair_modify.rst rename to doc/src/pair_modify.rst diff --git a/doc/rst/pair_momb.rst b/doc/src/pair_momb.rst similarity index 100% rename from doc/rst/pair_momb.rst rename to doc/src/pair_momb.rst diff --git a/doc/rst/pair_morse.rst b/doc/src/pair_morse.rst similarity index 100% rename from doc/rst/pair_morse.rst rename to doc/src/pair_morse.rst diff --git a/doc/rst/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst similarity index 100% rename from doc/rst/pair_multi_lucy.rst rename to doc/src/pair_multi_lucy.rst diff --git a/doc/rst/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst similarity index 100% rename from doc/rst/pair_multi_lucy_rx.rst rename to doc/src/pair_multi_lucy_rx.rst diff --git a/doc/rst/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst similarity index 100% rename from doc/rst/pair_nb3b_harmonic.rst rename to doc/src/pair_nb3b_harmonic.rst diff --git a/doc/rst/pair_nm.rst b/doc/src/pair_nm.rst similarity index 100% rename from doc/rst/pair_nm.rst rename to doc/src/pair_nm.rst diff --git a/doc/rst/pair_none.rst b/doc/src/pair_none.rst similarity index 100% rename from doc/rst/pair_none.rst rename to doc/src/pair_none.rst diff --git a/doc/rst/pair_oxdna.rst b/doc/src/pair_oxdna.rst similarity index 100% rename from doc/rst/pair_oxdna.rst rename to doc/src/pair_oxdna.rst diff --git a/doc/rst/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst similarity index 100% rename from doc/rst/pair_oxdna2.rst rename to doc/src/pair_oxdna2.rst diff --git a/doc/rst/pair_peri.rst b/doc/src/pair_peri.rst similarity index 100% rename from doc/rst/pair_peri.rst rename to doc/src/pair_peri.rst diff --git a/doc/rst/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst similarity index 100% rename from doc/rst/pair_polymorphic.rst rename to doc/src/pair_polymorphic.rst diff --git a/doc/rst/pair_python.rst b/doc/src/pair_python.rst similarity index 100% rename from doc/rst/pair_python.rst rename to doc/src/pair_python.rst diff --git a/doc/rst/pair_quip.rst b/doc/src/pair_quip.rst similarity index 100% rename from doc/rst/pair_quip.rst rename to doc/src/pair_quip.rst diff --git a/doc/rst/pair_reaxc.rst b/doc/src/pair_reaxc.rst similarity index 100% rename from doc/rst/pair_reaxc.rst rename to doc/src/pair_reaxc.rst diff --git a/doc/rst/pair_resquared.rst b/doc/src/pair_resquared.rst similarity index 100% rename from doc/rst/pair_resquared.rst rename to doc/src/pair_resquared.rst diff --git a/doc/rst/pair_sdk.rst b/doc/src/pair_sdk.rst similarity index 100% rename from doc/rst/pair_sdk.rst rename to doc/src/pair_sdk.rst diff --git a/doc/rst/pair_sdpd_taitwater_isothermal.rst b/doc/src/pair_sdpd_taitwater_isothermal.rst similarity index 100% rename from doc/rst/pair_sdpd_taitwater_isothermal.rst rename to doc/src/pair_sdpd_taitwater_isothermal.rst diff --git a/doc/rst/pair_smd_hertz.rst b/doc/src/pair_smd_hertz.rst similarity index 100% rename from doc/rst/pair_smd_hertz.rst rename to doc/src/pair_smd_hertz.rst diff --git a/doc/rst/pair_smd_tlsph.rst b/doc/src/pair_smd_tlsph.rst similarity index 100% rename from doc/rst/pair_smd_tlsph.rst rename to doc/src/pair_smd_tlsph.rst diff --git a/doc/rst/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst similarity index 100% rename from doc/rst/pair_smd_triangulated_surface.rst rename to doc/src/pair_smd_triangulated_surface.rst diff --git a/doc/rst/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst similarity index 100% rename from doc/rst/pair_smd_ulsph.rst rename to doc/src/pair_smd_ulsph.rst diff --git a/doc/rst/pair_smtbq.rst b/doc/src/pair_smtbq.rst similarity index 100% rename from doc/rst/pair_smtbq.rst rename to doc/src/pair_smtbq.rst diff --git a/doc/rst/pair_snap.rst b/doc/src/pair_snap.rst similarity index 100% rename from doc/rst/pair_snap.rst rename to doc/src/pair_snap.rst diff --git a/doc/rst/pair_soft.rst b/doc/src/pair_soft.rst similarity index 100% rename from doc/rst/pair_soft.rst rename to doc/src/pair_soft.rst diff --git a/doc/rst/pair_sph_heatconduction.rst b/doc/src/pair_sph_heatconduction.rst similarity index 100% rename from doc/rst/pair_sph_heatconduction.rst rename to doc/src/pair_sph_heatconduction.rst diff --git a/doc/rst/pair_sph_idealgas.rst b/doc/src/pair_sph_idealgas.rst similarity index 100% rename from doc/rst/pair_sph_idealgas.rst rename to doc/src/pair_sph_idealgas.rst diff --git a/doc/rst/pair_sph_lj.rst b/doc/src/pair_sph_lj.rst similarity index 100% rename from doc/rst/pair_sph_lj.rst rename to doc/src/pair_sph_lj.rst diff --git a/doc/rst/pair_sph_rhosum.rst b/doc/src/pair_sph_rhosum.rst similarity index 100% rename from doc/rst/pair_sph_rhosum.rst rename to doc/src/pair_sph_rhosum.rst diff --git a/doc/rst/pair_sph_taitwater.rst b/doc/src/pair_sph_taitwater.rst similarity index 100% rename from doc/rst/pair_sph_taitwater.rst rename to doc/src/pair_sph_taitwater.rst diff --git a/doc/rst/pair_sph_taitwater_morris.rst b/doc/src/pair_sph_taitwater_morris.rst similarity index 100% rename from doc/rst/pair_sph_taitwater_morris.rst rename to doc/src/pair_sph_taitwater_morris.rst diff --git a/doc/rst/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst similarity index 100% rename from doc/rst/pair_spin_dipole.rst rename to doc/src/pair_spin_dipole.rst diff --git a/doc/rst/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst similarity index 100% rename from doc/rst/pair_spin_dmi.rst rename to doc/src/pair_spin_dmi.rst diff --git a/doc/rst/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst similarity index 100% rename from doc/rst/pair_spin_exchange.rst rename to doc/src/pair_spin_exchange.rst diff --git a/doc/rst/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst similarity index 100% rename from doc/rst/pair_spin_magelec.rst rename to doc/src/pair_spin_magelec.rst diff --git a/doc/rst/pair_spin_neel.rst b/doc/src/pair_spin_neel.rst similarity index 100% rename from doc/rst/pair_spin_neel.rst rename to doc/src/pair_spin_neel.rst diff --git a/doc/rst/pair_srp.rst b/doc/src/pair_srp.rst similarity index 100% rename from doc/rst/pair_srp.rst rename to doc/src/pair_srp.rst diff --git a/doc/rst/pair_style.rst b/doc/src/pair_style.rst similarity index 100% rename from doc/rst/pair_style.rst rename to doc/src/pair_style.rst diff --git a/doc/rst/pair_sw.rst b/doc/src/pair_sw.rst similarity index 100% rename from doc/rst/pair_sw.rst rename to doc/src/pair_sw.rst diff --git a/doc/rst/pair_table.rst b/doc/src/pair_table.rst similarity index 100% rename from doc/rst/pair_table.rst rename to doc/src/pair_table.rst diff --git a/doc/rst/pair_table_rx.rst b/doc/src/pair_table_rx.rst similarity index 100% rename from doc/rst/pair_table_rx.rst rename to doc/src/pair_table_rx.rst diff --git a/doc/rst/pair_tersoff.rst b/doc/src/pair_tersoff.rst similarity index 100% rename from doc/rst/pair_tersoff.rst rename to doc/src/pair_tersoff.rst diff --git a/doc/rst/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst similarity index 100% rename from doc/rst/pair_tersoff_mod.rst rename to doc/src/pair_tersoff_mod.rst diff --git a/doc/rst/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst similarity index 100% rename from doc/rst/pair_tersoff_zbl.rst rename to doc/src/pair_tersoff_zbl.rst diff --git a/doc/rst/pair_thole.rst b/doc/src/pair_thole.rst similarity index 100% rename from doc/rst/pair_thole.rst rename to doc/src/pair_thole.rst diff --git a/doc/rst/pair_tri_lj.rst b/doc/src/pair_tri_lj.rst similarity index 100% rename from doc/rst/pair_tri_lj.rst rename to doc/src/pair_tri_lj.rst diff --git a/doc/rst/pair_ufm.rst b/doc/src/pair_ufm.rst similarity index 100% rename from doc/rst/pair_ufm.rst rename to doc/src/pair_ufm.rst diff --git a/doc/rst/pair_vashishta.rst b/doc/src/pair_vashishta.rst similarity index 100% rename from doc/rst/pair_vashishta.rst rename to doc/src/pair_vashishta.rst diff --git a/doc/rst/pair_write.rst b/doc/src/pair_write.rst similarity index 100% rename from doc/rst/pair_write.rst rename to doc/src/pair_write.rst diff --git a/doc/rst/pair_yukawa.rst b/doc/src/pair_yukawa.rst similarity index 100% rename from doc/rst/pair_yukawa.rst rename to doc/src/pair_yukawa.rst diff --git a/doc/rst/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst similarity index 100% rename from doc/rst/pair_yukawa_colloid.rst rename to doc/src/pair_yukawa_colloid.rst diff --git a/doc/rst/pair_zbl.rst b/doc/src/pair_zbl.rst similarity index 100% rename from doc/rst/pair_zbl.rst rename to doc/src/pair_zbl.rst diff --git a/doc/rst/pair_zero.rst b/doc/src/pair_zero.rst similarity index 100% rename from doc/rst/pair_zero.rst rename to doc/src/pair_zero.rst diff --git a/doc/src/pairs.rst b/doc/src/pairs.rst new file mode 100644 index 0000000000000000000000000000000000000000..4fdf2b2c692a7b7fc568edc76c8d0a1161205684 --- /dev/null +++ b/doc/src/pairs.rst @@ -0,0 +1,9 @@ +Pair Styles +########### + + +.. toctree:: + :maxdepth: 1 + :glob: + + pair_* diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt deleted file mode 100644 index 1f8f130e48d429feca355647902e16d28ec27437..0000000000000000000000000000000000000000 --- a/doc/src/pairs.txt +++ /dev/null @@ -1,131 +0,0 @@ -Pair Styles :h1 - - diff --git a/doc/rst/partition.rst b/doc/src/partition.rst similarity index 100% rename from doc/rst/partition.rst rename to doc/src/partition.rst diff --git a/doc/rst/prd.rst b/doc/src/prd.rst similarity index 100% rename from doc/rst/prd.rst rename to doc/src/prd.rst diff --git a/doc/rst/print.rst b/doc/src/print.rst similarity index 100% rename from doc/rst/print.rst rename to doc/src/print.rst diff --git a/doc/rst/processors.rst b/doc/src/processors.rst similarity index 100% rename from doc/rst/processors.rst rename to doc/src/processors.rst diff --git a/doc/rst/python.rst b/doc/src/python.rst similarity index 100% rename from doc/rst/python.rst rename to doc/src/python.rst diff --git a/doc/rst/quit.rst b/doc/src/quit.rst similarity index 100% rename from doc/rst/quit.rst rename to doc/src/quit.rst diff --git a/doc/rst/read_data.rst b/doc/src/read_data.rst similarity index 100% rename from doc/rst/read_data.rst rename to doc/src/read_data.rst diff --git a/doc/rst/read_dump.rst b/doc/src/read_dump.rst similarity index 100% rename from doc/rst/read_dump.rst rename to doc/src/read_dump.rst diff --git a/doc/rst/read_restart.rst b/doc/src/read_restart.rst similarity index 100% rename from doc/rst/read_restart.rst rename to doc/src/read_restart.rst diff --git a/doc/rst/region.rst b/doc/src/region.rst similarity index 100% rename from doc/rst/region.rst rename to doc/src/region.rst diff --git a/doc/rst/replicate.rst b/doc/src/replicate.rst similarity index 100% rename from doc/rst/replicate.rst rename to doc/src/replicate.rst diff --git a/doc/rst/rerun.rst b/doc/src/rerun.rst similarity index 100% rename from doc/rst/rerun.rst rename to doc/src/rerun.rst diff --git a/doc/rst/reset_ids.rst b/doc/src/reset_ids.rst similarity index 100% rename from doc/rst/reset_ids.rst rename to doc/src/reset_ids.rst diff --git a/doc/rst/reset_timestep.rst b/doc/src/reset_timestep.rst similarity index 100% rename from doc/rst/reset_timestep.rst rename to doc/src/reset_timestep.rst diff --git a/doc/rst/restart.rst b/doc/src/restart.rst similarity index 100% rename from doc/rst/restart.rst rename to doc/src/restart.rst diff --git a/doc/rst/run.rst b/doc/src/run.rst similarity index 100% rename from doc/rst/run.rst rename to doc/src/run.rst diff --git a/doc/rst/run_style.rst b/doc/src/run_style.rst similarity index 100% rename from doc/rst/run_style.rst rename to doc/src/run_style.rst diff --git a/doc/rst/server.rst b/doc/src/server.rst similarity index 100% rename from doc/rst/server.rst rename to doc/src/server.rst diff --git a/doc/rst/server_mc.rst b/doc/src/server_mc.rst similarity index 100% rename from doc/rst/server_mc.rst rename to doc/src/server_mc.rst diff --git a/doc/rst/server_md.rst b/doc/src/server_md.rst similarity index 100% rename from doc/rst/server_md.rst rename to doc/src/server_md.rst diff --git a/doc/rst/set.rst b/doc/src/set.rst similarity index 100% rename from doc/rst/set.rst rename to doc/src/set.rst diff --git a/doc/rst/shell.rst b/doc/src/shell.rst similarity index 100% rename from doc/rst/shell.rst rename to doc/src/shell.rst diff --git a/doc/rst/special_bonds.rst b/doc/src/special_bonds.rst similarity index 100% rename from doc/rst/special_bonds.rst rename to doc/src/special_bonds.rst diff --git a/doc/rst/suffix.rst b/doc/src/suffix.rst similarity index 100% rename from doc/rst/suffix.rst rename to doc/src/suffix.rst diff --git a/doc/rst/tad.rst b/doc/src/tad.rst similarity index 100% rename from doc/rst/tad.rst rename to doc/src/tad.rst diff --git a/doc/rst/temper.rst b/doc/src/temper.rst similarity index 100% rename from doc/rst/temper.rst rename to doc/src/temper.rst diff --git a/doc/rst/temper_grem.rst b/doc/src/temper_grem.rst similarity index 100% rename from doc/rst/temper_grem.rst rename to doc/src/temper_grem.rst diff --git a/doc/rst/temper_npt.rst b/doc/src/temper_npt.rst similarity index 100% rename from doc/rst/temper_npt.rst rename to doc/src/temper_npt.rst diff --git a/doc/rst/thermo.rst b/doc/src/thermo.rst similarity index 100% rename from doc/rst/thermo.rst rename to doc/src/thermo.rst diff --git a/doc/rst/thermo_modify.rst b/doc/src/thermo_modify.rst similarity index 100% rename from doc/rst/thermo_modify.rst rename to doc/src/thermo_modify.rst diff --git a/doc/rst/thermo_style.rst b/doc/src/thermo_style.rst similarity index 100% rename from doc/rst/thermo_style.rst rename to doc/src/thermo_style.rst diff --git a/doc/rst/third_order.rst b/doc/src/third_order.rst similarity index 100% rename from doc/rst/third_order.rst rename to doc/src/third_order.rst diff --git a/doc/rst/timer.rst b/doc/src/timer.rst similarity index 100% rename from doc/rst/timer.rst rename to doc/src/timer.rst diff --git a/doc/rst/timestep.rst b/doc/src/timestep.rst similarity index 100% rename from doc/rst/timestep.rst rename to doc/src/timestep.rst diff --git a/doc/rst/uncompute.rst b/doc/src/uncompute.rst similarity index 100% rename from doc/rst/uncompute.rst rename to doc/src/uncompute.rst diff --git a/doc/rst/undump.rst b/doc/src/undump.rst similarity index 100% rename from doc/rst/undump.rst rename to doc/src/undump.rst diff --git a/doc/rst/unfix.rst b/doc/src/unfix.rst similarity index 100% rename from doc/rst/unfix.rst rename to doc/src/unfix.rst diff --git a/doc/rst/units.rst b/doc/src/units.rst similarity index 100% rename from doc/rst/units.rst rename to doc/src/units.rst diff --git a/doc/rst/variable.rst b/doc/src/variable.rst similarity index 100% rename from doc/rst/variable.rst rename to doc/src/variable.rst diff --git a/doc/rst/velocity.rst b/doc/src/velocity.rst similarity index 100% rename from doc/rst/velocity.rst rename to doc/src/velocity.rst diff --git a/doc/rst/write_coeff.rst b/doc/src/write_coeff.rst similarity index 100% rename from doc/rst/write_coeff.rst rename to doc/src/write_coeff.rst diff --git a/doc/rst/write_data.rst b/doc/src/write_data.rst similarity index 100% rename from doc/rst/write_data.rst rename to doc/src/write_data.rst diff --git a/doc/rst/write_dump.rst b/doc/src/write_dump.rst similarity index 100% rename from doc/rst/write_dump.rst rename to doc/src/write_dump.rst diff --git a/doc/rst/write_restart.rst b/doc/src/write_restart.rst similarity index 100% rename from doc/rst/write_restart.rst rename to doc/src/write_restart.rst diff --git a/doc/src/Build.txt b/doc/txt/Build.txt similarity index 100% rename from doc/src/Build.txt rename to doc/txt/Build.txt diff --git a/doc/src/Build_basics.txt b/doc/txt/Build_basics.txt similarity index 100% rename from doc/src/Build_basics.txt rename to doc/txt/Build_basics.txt diff --git a/doc/src/Build_cmake.txt b/doc/txt/Build_cmake.txt similarity index 100% rename from doc/src/Build_cmake.txt rename to doc/txt/Build_cmake.txt diff --git a/doc/src/Build_development.txt b/doc/txt/Build_development.txt similarity index 100% rename from doc/src/Build_development.txt rename to doc/txt/Build_development.txt diff --git a/doc/src/Build_extras.txt b/doc/txt/Build_extras.txt similarity index 100% rename from doc/src/Build_extras.txt rename to doc/txt/Build_extras.txt diff --git a/doc/src/Build_link.txt b/doc/txt/Build_link.txt similarity index 100% rename from doc/src/Build_link.txt rename to doc/txt/Build_link.txt diff --git a/doc/src/Build_make.txt b/doc/txt/Build_make.txt similarity index 100% rename from doc/src/Build_make.txt rename to doc/txt/Build_make.txt diff --git a/doc/src/Build_package.txt b/doc/txt/Build_package.txt similarity index 100% rename from doc/src/Build_package.txt rename to doc/txt/Build_package.txt diff --git a/doc/src/Build_settings.txt b/doc/txt/Build_settings.txt similarity index 100% rename from doc/src/Build_settings.txt rename to doc/txt/Build_settings.txt diff --git a/doc/src/Build_windows.txt b/doc/txt/Build_windows.txt similarity index 100% rename from doc/src/Build_windows.txt rename to doc/txt/Build_windows.txt diff --git a/doc/src/Commands.txt b/doc/txt/Commands.txt similarity index 100% rename from doc/src/Commands.txt rename to doc/txt/Commands.txt diff --git a/doc/src/Commands_all.txt b/doc/txt/Commands_all.txt similarity index 100% rename from doc/src/Commands_all.txt rename to doc/txt/Commands_all.txt diff --git a/doc/src/Commands_bond.txt b/doc/txt/Commands_bond.txt similarity index 100% rename from doc/src/Commands_bond.txt rename to doc/txt/Commands_bond.txt diff --git a/doc/src/Commands_category.txt b/doc/txt/Commands_category.txt similarity index 100% rename from doc/src/Commands_category.txt rename to doc/txt/Commands_category.txt diff --git a/doc/src/Commands_compute.txt b/doc/txt/Commands_compute.txt similarity index 100% rename from doc/src/Commands_compute.txt rename to doc/txt/Commands_compute.txt diff --git a/doc/src/Commands_fix.txt b/doc/txt/Commands_fix.txt similarity index 100% rename from doc/src/Commands_fix.txt rename to doc/txt/Commands_fix.txt diff --git a/doc/src/Commands_input.txt b/doc/txt/Commands_input.txt similarity index 100% rename from doc/src/Commands_input.txt rename to doc/txt/Commands_input.txt diff --git a/doc/src/Commands_kspace.txt b/doc/txt/Commands_kspace.txt similarity index 100% rename from doc/src/Commands_kspace.txt rename to doc/txt/Commands_kspace.txt diff --git a/doc/src/Commands_pair.txt b/doc/txt/Commands_pair.txt similarity index 100% rename from doc/src/Commands_pair.txt rename to doc/txt/Commands_pair.txt diff --git a/doc/src/Commands_parse.txt b/doc/txt/Commands_parse.txt similarity index 100% rename from doc/src/Commands_parse.txt rename to doc/txt/Commands_parse.txt diff --git a/doc/src/Commands_removed.txt b/doc/txt/Commands_removed.txt similarity index 100% rename from doc/src/Commands_removed.txt rename to doc/txt/Commands_removed.txt diff --git a/doc/src/Commands_structure.txt b/doc/txt/Commands_structure.txt similarity index 100% rename from doc/src/Commands_structure.txt rename to doc/txt/Commands_structure.txt diff --git a/doc/src/Developer/.gitignore b/doc/txt/Developer/.gitignore similarity index 100% rename from doc/src/Developer/.gitignore rename to doc/txt/Developer/.gitignore diff --git a/doc/src/Developer/classes.fig b/doc/txt/Developer/classes.fig similarity index 100% rename from doc/src/Developer/classes.fig rename to doc/txt/Developer/classes.fig diff --git a/doc/src/Developer/classes.pdf b/doc/txt/Developer/classes.pdf similarity index 100% rename from doc/src/Developer/classes.pdf rename to doc/txt/Developer/classes.pdf diff --git a/doc/src/Developer/developer.tex b/doc/txt/Developer/developer.tex similarity index 100% rename from doc/src/Developer/developer.tex rename to doc/txt/Developer/developer.tex diff --git a/doc/src/Errors.txt b/doc/txt/Errors.txt similarity index 100% rename from doc/src/Errors.txt rename to doc/txt/Errors.txt diff --git a/doc/src/Errors_bugs.txt b/doc/txt/Errors_bugs.txt similarity index 100% rename from doc/src/Errors_bugs.txt rename to doc/txt/Errors_bugs.txt diff --git a/doc/src/Errors_common.txt b/doc/txt/Errors_common.txt similarity index 100% rename from doc/src/Errors_common.txt rename to doc/txt/Errors_common.txt diff --git a/doc/src/Errors_messages.txt b/doc/txt/Errors_messages.txt similarity index 100% rename from doc/src/Errors_messages.txt rename to doc/txt/Errors_messages.txt diff --git a/doc/src/Errors_warnings.txt b/doc/txt/Errors_warnings.txt similarity index 100% rename from doc/src/Errors_warnings.txt rename to doc/txt/Errors_warnings.txt diff --git a/doc/src/Examples.txt b/doc/txt/Examples.txt similarity index 100% rename from doc/src/Examples.txt rename to doc/txt/Examples.txt diff --git a/doc/src/Howto.txt b/doc/txt/Howto.txt similarity index 100% rename from doc/src/Howto.txt rename to doc/txt/Howto.txt diff --git a/doc/src/Howto_2d.txt b/doc/txt/Howto_2d.txt similarity index 100% rename from doc/src/Howto_2d.txt rename to doc/txt/Howto_2d.txt diff --git a/doc/src/Howto_barostat.txt b/doc/txt/Howto_barostat.txt similarity index 100% rename from doc/src/Howto_barostat.txt rename to doc/txt/Howto_barostat.txt diff --git a/doc/src/Howto_bash.txt b/doc/txt/Howto_bash.txt similarity index 100% rename from doc/src/Howto_bash.txt rename to doc/txt/Howto_bash.txt diff --git a/doc/src/Howto_bioFF.txt b/doc/txt/Howto_bioFF.txt similarity index 100% rename from doc/src/Howto_bioFF.txt rename to doc/txt/Howto_bioFF.txt diff --git a/doc/src/Howto_body.txt b/doc/txt/Howto_body.txt similarity index 100% rename from doc/src/Howto_body.txt rename to doc/txt/Howto_body.txt diff --git a/doc/src/Howto_chunk.txt b/doc/txt/Howto_chunk.txt similarity index 100% rename from doc/src/Howto_chunk.txt rename to doc/txt/Howto_chunk.txt diff --git a/doc/src/Howto_client_server.txt b/doc/txt/Howto_client_server.txt similarity index 100% rename from doc/src/Howto_client_server.txt rename to doc/txt/Howto_client_server.txt diff --git a/doc/src/Howto_coreshell.txt b/doc/txt/Howto_coreshell.txt similarity index 100% rename from doc/src/Howto_coreshell.txt rename to doc/txt/Howto_coreshell.txt diff --git a/doc/src/Howto_couple.txt b/doc/txt/Howto_couple.txt similarity index 100% rename from doc/src/Howto_couple.txt rename to doc/txt/Howto_couple.txt diff --git a/doc/src/Howto_diffusion.txt b/doc/txt/Howto_diffusion.txt similarity index 100% rename from doc/src/Howto_diffusion.txt rename to doc/txt/Howto_diffusion.txt diff --git a/doc/src/Howto_dispersion.txt b/doc/txt/Howto_dispersion.txt similarity index 100% rename from doc/src/Howto_dispersion.txt rename to doc/txt/Howto_dispersion.txt diff --git a/doc/src/Howto_drude.txt b/doc/txt/Howto_drude.txt similarity index 100% rename from doc/src/Howto_drude.txt rename to doc/txt/Howto_drude.txt diff --git a/doc/src/Howto_drude2.txt b/doc/txt/Howto_drude2.txt similarity index 100% rename from doc/src/Howto_drude2.txt rename to doc/txt/Howto_drude2.txt diff --git a/doc/src/Howto_elastic.txt b/doc/txt/Howto_elastic.txt similarity index 100% rename from doc/src/Howto_elastic.txt rename to doc/txt/Howto_elastic.txt diff --git a/doc/src/Howto_github.txt b/doc/txt/Howto_github.txt similarity index 100% rename from doc/src/Howto_github.txt rename to doc/txt/Howto_github.txt diff --git a/doc/src/Howto_granular.txt b/doc/txt/Howto_granular.txt similarity index 100% rename from doc/src/Howto_granular.txt rename to doc/txt/Howto_granular.txt diff --git a/doc/src/Howto_kappa.txt b/doc/txt/Howto_kappa.txt similarity index 100% rename from doc/src/Howto_kappa.txt rename to doc/txt/Howto_kappa.txt diff --git a/doc/src/Howto_library.txt b/doc/txt/Howto_library.txt similarity index 100% rename from doc/src/Howto_library.txt rename to doc/txt/Howto_library.txt diff --git a/doc/src/Howto_manifold.txt b/doc/txt/Howto_manifold.txt similarity index 100% rename from doc/src/Howto_manifold.txt rename to doc/txt/Howto_manifold.txt diff --git a/doc/src/Howto_multiple.txt b/doc/txt/Howto_multiple.txt similarity index 100% rename from doc/src/Howto_multiple.txt rename to doc/txt/Howto_multiple.txt diff --git a/doc/src/Howto_nemd.txt b/doc/txt/Howto_nemd.txt similarity index 100% rename from doc/src/Howto_nemd.txt rename to doc/txt/Howto_nemd.txt diff --git a/doc/src/Howto_output.txt b/doc/txt/Howto_output.txt similarity index 100% rename from doc/src/Howto_output.txt rename to doc/txt/Howto_output.txt diff --git a/doc/src/Howto_polarizable.txt b/doc/txt/Howto_polarizable.txt similarity index 100% rename from doc/src/Howto_polarizable.txt rename to doc/txt/Howto_polarizable.txt diff --git a/doc/src/Howto_pylammps.txt b/doc/txt/Howto_pylammps.txt similarity index 100% rename from doc/src/Howto_pylammps.txt rename to doc/txt/Howto_pylammps.txt diff --git a/doc/src/Howto_replica.txt b/doc/txt/Howto_replica.txt similarity index 100% rename from doc/src/Howto_replica.txt rename to doc/txt/Howto_replica.txt diff --git a/doc/src/Howto_restart.txt b/doc/txt/Howto_restart.txt similarity index 100% rename from doc/src/Howto_restart.txt rename to doc/txt/Howto_restart.txt diff --git a/doc/src/Howto_spc.txt b/doc/txt/Howto_spc.txt similarity index 100% rename from doc/src/Howto_spc.txt rename to doc/txt/Howto_spc.txt diff --git a/doc/src/Howto_spherical.txt b/doc/txt/Howto_spherical.txt similarity index 100% rename from doc/src/Howto_spherical.txt rename to doc/txt/Howto_spherical.txt diff --git a/doc/src/Howto_spins.txt b/doc/txt/Howto_spins.txt similarity index 100% rename from doc/src/Howto_spins.txt rename to doc/txt/Howto_spins.txt diff --git a/doc/src/Howto_temperature.txt b/doc/txt/Howto_temperature.txt similarity index 100% rename from doc/src/Howto_temperature.txt rename to doc/txt/Howto_temperature.txt diff --git a/doc/src/Howto_thermostat.txt b/doc/txt/Howto_thermostat.txt similarity index 100% rename from doc/src/Howto_thermostat.txt rename to doc/txt/Howto_thermostat.txt diff --git a/doc/src/Howto_tip3p.txt b/doc/txt/Howto_tip3p.txt similarity index 100% rename from doc/src/Howto_tip3p.txt rename to doc/txt/Howto_tip3p.txt diff --git a/doc/src/Howto_tip4p.txt b/doc/txt/Howto_tip4p.txt similarity index 100% rename from doc/src/Howto_tip4p.txt rename to doc/txt/Howto_tip4p.txt diff --git a/doc/src/Howto_triclinic.txt b/doc/txt/Howto_triclinic.txt similarity index 100% rename from doc/src/Howto_triclinic.txt rename to doc/txt/Howto_triclinic.txt diff --git a/doc/src/Howto_viscosity.txt b/doc/txt/Howto_viscosity.txt similarity index 100% rename from doc/src/Howto_viscosity.txt rename to doc/txt/Howto_viscosity.txt diff --git a/doc/src/Howto_viz.txt b/doc/txt/Howto_viz.txt similarity index 100% rename from doc/src/Howto_viz.txt rename to doc/txt/Howto_viz.txt diff --git a/doc/src/Howto_walls.txt b/doc/txt/Howto_walls.txt similarity index 100% rename from doc/src/Howto_walls.txt rename to doc/txt/Howto_walls.txt diff --git a/doc/src/Install.txt b/doc/txt/Install.txt similarity index 100% rename from doc/src/Install.txt rename to doc/txt/Install.txt diff --git a/doc/src/Install_git.txt b/doc/txt/Install_git.txt similarity index 100% rename from doc/src/Install_git.txt rename to doc/txt/Install_git.txt diff --git a/doc/src/Install_linux.txt b/doc/txt/Install_linux.txt similarity index 100% rename from doc/src/Install_linux.txt rename to doc/txt/Install_linux.txt diff --git a/doc/src/Install_mac.txt b/doc/txt/Install_mac.txt similarity index 100% rename from doc/src/Install_mac.txt rename to doc/txt/Install_mac.txt diff --git a/doc/src/Install_patch.txt b/doc/txt/Install_patch.txt similarity index 100% rename from doc/src/Install_patch.txt rename to doc/txt/Install_patch.txt diff --git a/doc/src/Install_svn.txt b/doc/txt/Install_svn.txt similarity index 100% rename from doc/src/Install_svn.txt rename to doc/txt/Install_svn.txt diff --git a/doc/src/Install_tarball.txt b/doc/txt/Install_tarball.txt similarity index 100% rename from doc/src/Install_tarball.txt rename to doc/txt/Install_tarball.txt diff --git a/doc/src/Install_windows.txt b/doc/txt/Install_windows.txt similarity index 100% rename from doc/src/Install_windows.txt rename to doc/txt/Install_windows.txt diff --git a/doc/src/Intro.txt b/doc/txt/Intro.txt similarity index 100% rename from doc/src/Intro.txt rename to doc/txt/Intro.txt diff --git a/doc/src/Intro_authors.txt b/doc/txt/Intro_authors.txt similarity index 100% rename from doc/src/Intro_authors.txt rename to doc/txt/Intro_authors.txt diff --git a/doc/src/Intro_features.txt b/doc/txt/Intro_features.txt similarity index 100% rename from doc/src/Intro_features.txt rename to doc/txt/Intro_features.txt diff --git a/doc/src/Intro_nonfeatures.txt b/doc/txt/Intro_nonfeatures.txt similarity index 100% rename from doc/src/Intro_nonfeatures.txt rename to doc/txt/Intro_nonfeatures.txt diff --git a/doc/src/Intro_opensource.txt b/doc/txt/Intro_opensource.txt similarity index 100% rename from doc/src/Intro_opensource.txt rename to doc/txt/Intro_opensource.txt diff --git a/doc/src/Intro_overview.txt b/doc/txt/Intro_overview.txt similarity index 100% rename from doc/src/Intro_overview.txt rename to doc/txt/Intro_overview.txt diff --git a/doc/src/Intro_website.txt b/doc/txt/Intro_website.txt similarity index 100% rename from doc/src/Intro_website.txt rename to doc/txt/Intro_website.txt diff --git a/doc/src/Manual_build.txt b/doc/txt/Manual_build.txt similarity index 100% rename from doc/src/Manual_build.txt rename to doc/txt/Manual_build.txt diff --git a/doc/src/Manual_version.txt b/doc/txt/Manual_version.txt similarity index 100% rename from doc/src/Manual_version.txt rename to doc/txt/Manual_version.txt diff --git a/doc/src/Modify.txt b/doc/txt/Modify.txt similarity index 100% rename from doc/src/Modify.txt rename to doc/txt/Modify.txt diff --git a/doc/src/Modify_atom.txt b/doc/txt/Modify_atom.txt similarity index 100% rename from doc/src/Modify_atom.txt rename to doc/txt/Modify_atom.txt diff --git a/doc/src/Modify_body.txt b/doc/txt/Modify_body.txt similarity index 100% rename from doc/src/Modify_body.txt rename to doc/txt/Modify_body.txt diff --git a/doc/src/Modify_bond.txt b/doc/txt/Modify_bond.txt similarity index 100% rename from doc/src/Modify_bond.txt rename to doc/txt/Modify_bond.txt diff --git a/doc/src/Modify_command.txt b/doc/txt/Modify_command.txt similarity index 100% rename from doc/src/Modify_command.txt rename to doc/txt/Modify_command.txt diff --git a/doc/src/Modify_compute.txt b/doc/txt/Modify_compute.txt similarity index 100% rename from doc/src/Modify_compute.txt rename to doc/txt/Modify_compute.txt diff --git a/doc/src/Modify_contribute.txt b/doc/txt/Modify_contribute.txt similarity index 100% rename from doc/src/Modify_contribute.txt rename to doc/txt/Modify_contribute.txt diff --git a/doc/src/Modify_dump.txt b/doc/txt/Modify_dump.txt similarity index 100% rename from doc/src/Modify_dump.txt rename to doc/txt/Modify_dump.txt diff --git a/doc/src/Modify_fix.txt b/doc/txt/Modify_fix.txt similarity index 100% rename from doc/src/Modify_fix.txt rename to doc/txt/Modify_fix.txt diff --git a/doc/src/Modify_kspace.txt b/doc/txt/Modify_kspace.txt similarity index 100% rename from doc/src/Modify_kspace.txt rename to doc/txt/Modify_kspace.txt diff --git a/doc/src/Modify_min.txt b/doc/txt/Modify_min.txt similarity index 100% rename from doc/src/Modify_min.txt rename to doc/txt/Modify_min.txt diff --git a/doc/src/Modify_overview.txt b/doc/txt/Modify_overview.txt similarity index 100% rename from doc/src/Modify_overview.txt rename to doc/txt/Modify_overview.txt diff --git a/doc/src/Modify_pair.txt b/doc/txt/Modify_pair.txt similarity index 100% rename from doc/src/Modify_pair.txt rename to doc/txt/Modify_pair.txt diff --git a/doc/src/Modify_region.txt b/doc/txt/Modify_region.txt similarity index 100% rename from doc/src/Modify_region.txt rename to doc/txt/Modify_region.txt diff --git a/doc/src/Modify_thermo.txt b/doc/txt/Modify_thermo.txt similarity index 100% rename from doc/src/Modify_thermo.txt rename to doc/txt/Modify_thermo.txt diff --git a/doc/src/Modify_variable.txt b/doc/txt/Modify_variable.txt similarity index 100% rename from doc/src/Modify_variable.txt rename to doc/txt/Modify_variable.txt diff --git a/doc/src/Packages.txt b/doc/txt/Packages.txt similarity index 100% rename from doc/src/Packages.txt rename to doc/txt/Packages.txt diff --git a/doc/src/Packages_details.txt b/doc/txt/Packages_details.txt similarity index 100% rename from doc/src/Packages_details.txt rename to doc/txt/Packages_details.txt diff --git a/doc/src/Packages_standard.txt b/doc/txt/Packages_standard.txt similarity index 100% rename from doc/src/Packages_standard.txt rename to doc/txt/Packages_standard.txt diff --git a/doc/src/Packages_user.txt b/doc/txt/Packages_user.txt similarity index 100% rename from doc/src/Packages_user.txt rename to doc/txt/Packages_user.txt diff --git a/doc/src/Python_call.txt b/doc/txt/Python_call.txt similarity index 100% rename from doc/src/Python_call.txt rename to doc/txt/Python_call.txt diff --git a/doc/src/Python_examples.txt b/doc/txt/Python_examples.txt similarity index 100% rename from doc/src/Python_examples.txt rename to doc/txt/Python_examples.txt diff --git a/doc/src/Python_head.txt b/doc/txt/Python_head.txt similarity index 100% rename from doc/src/Python_head.txt rename to doc/txt/Python_head.txt diff --git a/doc/src/Python_install.txt b/doc/txt/Python_install.txt similarity index 100% rename from doc/src/Python_install.txt rename to doc/txt/Python_install.txt diff --git a/doc/src/Python_library.txt b/doc/txt/Python_library.txt similarity index 100% rename from doc/src/Python_library.txt rename to doc/txt/Python_library.txt diff --git a/doc/src/Python_mpi.txt b/doc/txt/Python_mpi.txt similarity index 100% rename from doc/src/Python_mpi.txt rename to doc/txt/Python_mpi.txt diff --git a/doc/src/Python_overview.txt b/doc/txt/Python_overview.txt similarity index 100% rename from doc/src/Python_overview.txt rename to doc/txt/Python_overview.txt diff --git a/doc/src/Python_pylammps.txt b/doc/txt/Python_pylammps.txt similarity index 100% rename from doc/src/Python_pylammps.txt rename to doc/txt/Python_pylammps.txt diff --git a/doc/src/Python_run.txt b/doc/txt/Python_run.txt similarity index 100% rename from doc/src/Python_run.txt rename to doc/txt/Python_run.txt diff --git a/doc/src/Python_shlib.txt b/doc/txt/Python_shlib.txt similarity index 100% rename from doc/src/Python_shlib.txt rename to doc/txt/Python_shlib.txt diff --git a/doc/src/Python_test.txt b/doc/txt/Python_test.txt similarity index 100% rename from doc/src/Python_test.txt rename to doc/txt/Python_test.txt diff --git a/doc/src/Run_basics.txt b/doc/txt/Run_basics.txt similarity index 100% rename from doc/src/Run_basics.txt rename to doc/txt/Run_basics.txt diff --git a/doc/src/Run_head.txt b/doc/txt/Run_head.txt similarity index 100% rename from doc/src/Run_head.txt rename to doc/txt/Run_head.txt diff --git a/doc/src/Run_options.txt b/doc/txt/Run_options.txt similarity index 100% rename from doc/src/Run_options.txt rename to doc/txt/Run_options.txt diff --git a/doc/src/Run_output.txt b/doc/txt/Run_output.txt similarity index 100% rename from doc/src/Run_output.txt rename to doc/txt/Run_output.txt diff --git a/doc/src/Run_windows.txt b/doc/txt/Run_windows.txt similarity index 100% rename from doc/src/Run_windows.txt rename to doc/txt/Run_windows.txt diff --git a/doc/src/Speed.txt b/doc/txt/Speed.txt similarity index 100% rename from doc/src/Speed.txt rename to doc/txt/Speed.txt diff --git a/doc/src/Speed_bench.txt b/doc/txt/Speed_bench.txt similarity index 100% rename from doc/src/Speed_bench.txt rename to doc/txt/Speed_bench.txt diff --git a/doc/src/Speed_compare.txt b/doc/txt/Speed_compare.txt similarity index 100% rename from doc/src/Speed_compare.txt rename to doc/txt/Speed_compare.txt diff --git a/doc/src/Speed_gpu.txt b/doc/txt/Speed_gpu.txt similarity index 100% rename from doc/src/Speed_gpu.txt rename to doc/txt/Speed_gpu.txt diff --git a/doc/src/Speed_intel.txt b/doc/txt/Speed_intel.txt similarity index 100% rename from doc/src/Speed_intel.txt rename to doc/txt/Speed_intel.txt diff --git a/doc/src/Speed_kokkos.txt b/doc/txt/Speed_kokkos.txt similarity index 100% rename from doc/src/Speed_kokkos.txt rename to doc/txt/Speed_kokkos.txt diff --git a/doc/src/Speed_measure.txt b/doc/txt/Speed_measure.txt similarity index 100% rename from doc/src/Speed_measure.txt rename to doc/txt/Speed_measure.txt diff --git a/doc/src/Speed_omp.txt b/doc/txt/Speed_omp.txt similarity index 100% rename from doc/src/Speed_omp.txt rename to doc/txt/Speed_omp.txt diff --git a/doc/src/Speed_opt.txt b/doc/txt/Speed_opt.txt similarity index 100% rename from doc/src/Speed_opt.txt rename to doc/txt/Speed_opt.txt diff --git a/doc/src/Speed_packages.txt b/doc/txt/Speed_packages.txt similarity index 100% rename from doc/src/Speed_packages.txt rename to doc/txt/Speed_packages.txt diff --git a/doc/src/Speed_tips.txt b/doc/txt/Speed_tips.txt similarity index 100% rename from doc/src/Speed_tips.txt rename to doc/txt/Speed_tips.txt diff --git a/doc/src/Tools.txt b/doc/txt/Tools.txt similarity index 100% rename from doc/src/Tools.txt rename to doc/txt/Tools.txt diff --git a/doc/src/angle_charmm.txt b/doc/txt/angle_charmm.txt similarity index 100% rename from doc/src/angle_charmm.txt rename to doc/txt/angle_charmm.txt diff --git a/doc/src/angle_class2.txt b/doc/txt/angle_class2.txt similarity index 100% rename from doc/src/angle_class2.txt rename to doc/txt/angle_class2.txt diff --git a/doc/src/angle_coeff.txt b/doc/txt/angle_coeff.txt similarity index 100% rename from doc/src/angle_coeff.txt rename to doc/txt/angle_coeff.txt diff --git a/doc/src/angle_cosine.txt b/doc/txt/angle_cosine.txt similarity index 100% rename from doc/src/angle_cosine.txt rename to doc/txt/angle_cosine.txt diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/txt/angle_cosine_buck6d.txt similarity index 100% rename from doc/src/angle_cosine_buck6d.txt rename to doc/txt/angle_cosine_buck6d.txt diff --git a/doc/src/angle_cosine_delta.txt b/doc/txt/angle_cosine_delta.txt similarity index 100% rename from doc/src/angle_cosine_delta.txt rename to doc/txt/angle_cosine_delta.txt diff --git a/doc/src/angle_cosine_periodic.txt b/doc/txt/angle_cosine_periodic.txt similarity index 100% rename from doc/src/angle_cosine_periodic.txt rename to doc/txt/angle_cosine_periodic.txt diff --git a/doc/src/angle_cosine_shift.txt b/doc/txt/angle_cosine_shift.txt similarity index 100% rename from doc/src/angle_cosine_shift.txt rename to doc/txt/angle_cosine_shift.txt diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/txt/angle_cosine_shift_exp.txt similarity index 100% rename from doc/src/angle_cosine_shift_exp.txt rename to doc/txt/angle_cosine_shift_exp.txt diff --git a/doc/src/angle_cosine_squared.txt b/doc/txt/angle_cosine_squared.txt similarity index 100% rename from doc/src/angle_cosine_squared.txt rename to doc/txt/angle_cosine_squared.txt diff --git a/doc/src/angle_cross.txt b/doc/txt/angle_cross.txt similarity index 100% rename from doc/src/angle_cross.txt rename to doc/txt/angle_cross.txt diff --git a/doc/src/angle_dipole.txt b/doc/txt/angle_dipole.txt similarity index 100% rename from doc/src/angle_dipole.txt rename to doc/txt/angle_dipole.txt diff --git a/doc/src/angle_fourier.txt b/doc/txt/angle_fourier.txt similarity index 100% rename from doc/src/angle_fourier.txt rename to doc/txt/angle_fourier.txt diff --git a/doc/src/angle_fourier_simple.txt b/doc/txt/angle_fourier_simple.txt similarity index 100% rename from doc/src/angle_fourier_simple.txt rename to doc/txt/angle_fourier_simple.txt diff --git a/doc/src/angle_harmonic.txt b/doc/txt/angle_harmonic.txt similarity index 100% rename from doc/src/angle_harmonic.txt rename to doc/txt/angle_harmonic.txt diff --git a/doc/src/angle_hybrid.txt b/doc/txt/angle_hybrid.txt similarity index 100% rename from doc/src/angle_hybrid.txt rename to doc/txt/angle_hybrid.txt diff --git a/doc/src/angle_mm3.txt b/doc/txt/angle_mm3.txt similarity index 100% rename from doc/src/angle_mm3.txt rename to doc/txt/angle_mm3.txt diff --git a/doc/src/angle_none.txt b/doc/txt/angle_none.txt similarity index 100% rename from doc/src/angle_none.txt rename to doc/txt/angle_none.txt diff --git a/doc/src/angle_quartic.txt b/doc/txt/angle_quartic.txt similarity index 100% rename from doc/src/angle_quartic.txt rename to doc/txt/angle_quartic.txt diff --git a/doc/src/angle_sdk.txt b/doc/txt/angle_sdk.txt similarity index 100% rename from doc/src/angle_sdk.txt rename to doc/txt/angle_sdk.txt diff --git a/doc/src/angle_style.txt b/doc/txt/angle_style.txt similarity index 100% rename from doc/src/angle_style.txt rename to doc/txt/angle_style.txt diff --git a/doc/src/angle_table.txt b/doc/txt/angle_table.txt similarity index 100% rename from doc/src/angle_table.txt rename to doc/txt/angle_table.txt diff --git a/doc/src/angle_zero.txt b/doc/txt/angle_zero.txt similarity index 100% rename from doc/src/angle_zero.txt rename to doc/txt/angle_zero.txt diff --git a/doc/src/atom_modify.txt b/doc/txt/atom_modify.txt similarity index 100% rename from doc/src/atom_modify.txt rename to doc/txt/atom_modify.txt diff --git a/doc/src/atom_style.txt b/doc/txt/atom_style.txt similarity index 100% rename from doc/src/atom_style.txt rename to doc/txt/atom_style.txt diff --git a/doc/src/balance.txt b/doc/txt/balance.txt similarity index 100% rename from doc/src/balance.txt rename to doc/txt/balance.txt diff --git a/doc/src/bond_class2.txt b/doc/txt/bond_class2.txt similarity index 100% rename from doc/src/bond_class2.txt rename to doc/txt/bond_class2.txt diff --git a/doc/src/bond_coeff.txt b/doc/txt/bond_coeff.txt similarity index 100% rename from doc/src/bond_coeff.txt rename to doc/txt/bond_coeff.txt diff --git a/doc/src/bond_fene.txt b/doc/txt/bond_fene.txt similarity index 100% rename from doc/src/bond_fene.txt rename to doc/txt/bond_fene.txt diff --git a/doc/src/bond_fene_expand.txt b/doc/txt/bond_fene_expand.txt similarity index 100% rename from doc/src/bond_fene_expand.txt rename to doc/txt/bond_fene_expand.txt diff --git a/doc/src/bond_gromos.txt b/doc/txt/bond_gromos.txt similarity index 100% rename from doc/src/bond_gromos.txt rename to doc/txt/bond_gromos.txt diff --git a/doc/src/bond_harmonic.txt b/doc/txt/bond_harmonic.txt similarity index 100% rename from doc/src/bond_harmonic.txt rename to doc/txt/bond_harmonic.txt diff --git a/doc/src/bond_harmonic_shift.txt b/doc/txt/bond_harmonic_shift.txt similarity index 100% rename from doc/src/bond_harmonic_shift.txt rename to doc/txt/bond_harmonic_shift.txt diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/txt/bond_harmonic_shift_cut.txt similarity index 100% rename from doc/src/bond_harmonic_shift_cut.txt rename to doc/txt/bond_harmonic_shift_cut.txt diff --git a/doc/src/bond_hybrid.txt b/doc/txt/bond_hybrid.txt similarity index 100% rename from doc/src/bond_hybrid.txt rename to doc/txt/bond_hybrid.txt diff --git a/doc/src/bond_mm3.txt b/doc/txt/bond_mm3.txt similarity index 100% rename from doc/src/bond_mm3.txt rename to doc/txt/bond_mm3.txt diff --git a/doc/src/bond_morse.txt b/doc/txt/bond_morse.txt similarity index 100% rename from doc/src/bond_morse.txt rename to doc/txt/bond_morse.txt diff --git a/doc/src/bond_none.txt b/doc/txt/bond_none.txt similarity index 100% rename from doc/src/bond_none.txt rename to doc/txt/bond_none.txt diff --git a/doc/src/bond_nonlinear.txt b/doc/txt/bond_nonlinear.txt similarity index 100% rename from doc/src/bond_nonlinear.txt rename to doc/txt/bond_nonlinear.txt diff --git a/doc/src/bond_oxdna.txt b/doc/txt/bond_oxdna.txt similarity index 100% rename from doc/src/bond_oxdna.txt rename to doc/txt/bond_oxdna.txt diff --git a/doc/src/bond_quartic.txt b/doc/txt/bond_quartic.txt similarity index 100% rename from doc/src/bond_quartic.txt rename to doc/txt/bond_quartic.txt diff --git a/doc/src/bond_style.txt b/doc/txt/bond_style.txt similarity index 100% rename from doc/src/bond_style.txt rename to doc/txt/bond_style.txt diff --git a/doc/src/bond_table.txt b/doc/txt/bond_table.txt similarity index 100% rename from doc/src/bond_table.txt rename to doc/txt/bond_table.txt diff --git a/doc/src/bond_write.txt b/doc/txt/bond_write.txt similarity index 100% rename from doc/src/bond_write.txt rename to doc/txt/bond_write.txt diff --git a/doc/src/bond_zero.txt b/doc/txt/bond_zero.txt similarity index 100% rename from doc/src/bond_zero.txt rename to doc/txt/bond_zero.txt diff --git a/doc/src/boundary.txt b/doc/txt/boundary.txt similarity index 100% rename from doc/src/boundary.txt rename to doc/txt/boundary.txt diff --git a/doc/src/box.txt b/doc/txt/box.txt similarity index 100% rename from doc/src/box.txt rename to doc/txt/box.txt diff --git a/doc/src/change_box.txt b/doc/txt/change_box.txt similarity index 100% rename from doc/src/change_box.txt rename to doc/txt/change_box.txt diff --git a/doc/src/clear.txt b/doc/txt/clear.txt similarity index 100% rename from doc/src/clear.txt rename to doc/txt/clear.txt diff --git a/doc/src/comm_modify.txt b/doc/txt/comm_modify.txt similarity index 100% rename from doc/src/comm_modify.txt rename to doc/txt/comm_modify.txt diff --git a/doc/src/comm_style.txt b/doc/txt/comm_style.txt similarity index 100% rename from doc/src/comm_style.txt rename to doc/txt/comm_style.txt diff --git a/doc/src/commands_list.txt b/doc/txt/commands_list.txt similarity index 100% rename from doc/src/commands_list.txt rename to doc/txt/commands_list.txt diff --git a/doc/src/compute.txt b/doc/txt/compute.txt similarity index 100% rename from doc/src/compute.txt rename to doc/txt/compute.txt diff --git a/doc/src/compute_ackland_atom.txt b/doc/txt/compute_ackland_atom.txt similarity index 100% rename from doc/src/compute_ackland_atom.txt rename to doc/txt/compute_ackland_atom.txt diff --git a/doc/src/compute_adf.txt b/doc/txt/compute_adf.txt similarity index 100% rename from doc/src/compute_adf.txt rename to doc/txt/compute_adf.txt diff --git a/doc/src/compute_angle.txt b/doc/txt/compute_angle.txt similarity index 100% rename from doc/src/compute_angle.txt rename to doc/txt/compute_angle.txt diff --git a/doc/src/compute_angle_local.txt b/doc/txt/compute_angle_local.txt similarity index 100% rename from doc/src/compute_angle_local.txt rename to doc/txt/compute_angle_local.txt diff --git a/doc/src/compute_angmom_chunk.txt b/doc/txt/compute_angmom_chunk.txt similarity index 100% rename from doc/src/compute_angmom_chunk.txt rename to doc/txt/compute_angmom_chunk.txt diff --git a/doc/src/compute_basal_atom.txt b/doc/txt/compute_basal_atom.txt similarity index 100% rename from doc/src/compute_basal_atom.txt rename to doc/txt/compute_basal_atom.txt diff --git a/doc/src/compute_body_local.txt b/doc/txt/compute_body_local.txt similarity index 100% rename from doc/src/compute_body_local.txt rename to doc/txt/compute_body_local.txt diff --git a/doc/src/compute_bond.txt b/doc/txt/compute_bond.txt similarity index 100% rename from doc/src/compute_bond.txt rename to doc/txt/compute_bond.txt diff --git a/doc/src/compute_bond_local.txt b/doc/txt/compute_bond_local.txt similarity index 100% rename from doc/src/compute_bond_local.txt rename to doc/txt/compute_bond_local.txt diff --git a/doc/src/compute_centro_atom.txt b/doc/txt/compute_centro_atom.txt similarity index 100% rename from doc/src/compute_centro_atom.txt rename to doc/txt/compute_centro_atom.txt diff --git a/doc/src/compute_chunk_atom.txt b/doc/txt/compute_chunk_atom.txt similarity index 100% rename from doc/src/compute_chunk_atom.txt rename to doc/txt/compute_chunk_atom.txt diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/txt/compute_chunk_spread_atom.txt similarity index 100% rename from doc/src/compute_chunk_spread_atom.txt rename to doc/txt/compute_chunk_spread_atom.txt diff --git a/doc/src/compute_cluster_atom.txt b/doc/txt/compute_cluster_atom.txt similarity index 100% rename from doc/src/compute_cluster_atom.txt rename to doc/txt/compute_cluster_atom.txt diff --git a/doc/src/compute_cna_atom.txt b/doc/txt/compute_cna_atom.txt similarity index 100% rename from doc/src/compute_cna_atom.txt rename to doc/txt/compute_cna_atom.txt diff --git a/doc/src/compute_cnp_atom.txt b/doc/txt/compute_cnp_atom.txt similarity index 100% rename from doc/src/compute_cnp_atom.txt rename to doc/txt/compute_cnp_atom.txt diff --git a/doc/src/compute_com.txt b/doc/txt/compute_com.txt similarity index 100% rename from doc/src/compute_com.txt rename to doc/txt/compute_com.txt diff --git a/doc/src/compute_com_chunk.txt b/doc/txt/compute_com_chunk.txt similarity index 100% rename from doc/src/compute_com_chunk.txt rename to doc/txt/compute_com_chunk.txt diff --git a/doc/src/compute_contact_atom.txt b/doc/txt/compute_contact_atom.txt similarity index 100% rename from doc/src/compute_contact_atom.txt rename to doc/txt/compute_contact_atom.txt diff --git a/doc/src/compute_coord_atom.txt b/doc/txt/compute_coord_atom.txt similarity index 100% rename from doc/src/compute_coord_atom.txt rename to doc/txt/compute_coord_atom.txt diff --git a/doc/src/compute_damage_atom.txt b/doc/txt/compute_damage_atom.txt similarity index 100% rename from doc/src/compute_damage_atom.txt rename to doc/txt/compute_damage_atom.txt diff --git a/doc/src/compute_dihedral.txt b/doc/txt/compute_dihedral.txt similarity index 100% rename from doc/src/compute_dihedral.txt rename to doc/txt/compute_dihedral.txt diff --git a/doc/src/compute_dihedral_local.txt b/doc/txt/compute_dihedral_local.txt similarity index 100% rename from doc/src/compute_dihedral_local.txt rename to doc/txt/compute_dihedral_local.txt diff --git a/doc/src/compute_dilatation_atom.txt b/doc/txt/compute_dilatation_atom.txt similarity index 100% rename from doc/src/compute_dilatation_atom.txt rename to doc/txt/compute_dilatation_atom.txt diff --git a/doc/src/compute_dipole_chunk.txt b/doc/txt/compute_dipole_chunk.txt similarity index 100% rename from doc/src/compute_dipole_chunk.txt rename to doc/txt/compute_dipole_chunk.txt diff --git a/doc/src/compute_displace_atom.txt b/doc/txt/compute_displace_atom.txt similarity index 100% rename from doc/src/compute_displace_atom.txt rename to doc/txt/compute_displace_atom.txt diff --git a/doc/src/compute_dpd.txt b/doc/txt/compute_dpd.txt similarity index 100% rename from doc/src/compute_dpd.txt rename to doc/txt/compute_dpd.txt diff --git a/doc/src/compute_dpd_atom.txt b/doc/txt/compute_dpd_atom.txt similarity index 100% rename from doc/src/compute_dpd_atom.txt rename to doc/txt/compute_dpd_atom.txt diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/txt/compute_edpd_temp_atom.txt similarity index 100% rename from doc/src/compute_edpd_temp_atom.txt rename to doc/txt/compute_edpd_temp_atom.txt diff --git a/doc/src/compute_entropy_atom.txt b/doc/txt/compute_entropy_atom.txt similarity index 100% rename from doc/src/compute_entropy_atom.txt rename to doc/txt/compute_entropy_atom.txt diff --git a/doc/src/compute_erotate_asphere.txt b/doc/txt/compute_erotate_asphere.txt similarity index 100% rename from doc/src/compute_erotate_asphere.txt rename to doc/txt/compute_erotate_asphere.txt diff --git a/doc/src/compute_erotate_rigid.txt b/doc/txt/compute_erotate_rigid.txt similarity index 100% rename from doc/src/compute_erotate_rigid.txt rename to doc/txt/compute_erotate_rigid.txt diff --git a/doc/src/compute_erotate_sphere.txt b/doc/txt/compute_erotate_sphere.txt similarity index 100% rename from doc/src/compute_erotate_sphere.txt rename to doc/txt/compute_erotate_sphere.txt diff --git a/doc/src/compute_erotate_sphere_atom.txt b/doc/txt/compute_erotate_sphere_atom.txt similarity index 100% rename from doc/src/compute_erotate_sphere_atom.txt rename to doc/txt/compute_erotate_sphere_atom.txt diff --git a/doc/src/compute_event_displace.txt b/doc/txt/compute_event_displace.txt similarity index 100% rename from doc/src/compute_event_displace.txt rename to doc/txt/compute_event_displace.txt diff --git a/doc/src/compute_fep.txt b/doc/txt/compute_fep.txt similarity index 100% rename from doc/src/compute_fep.txt rename to doc/txt/compute_fep.txt diff --git a/doc/src/compute_global_atom.txt b/doc/txt/compute_global_atom.txt similarity index 100% rename from doc/src/compute_global_atom.txt rename to doc/txt/compute_global_atom.txt diff --git a/doc/src/compute_group_group.txt b/doc/txt/compute_group_group.txt similarity index 100% rename from doc/src/compute_group_group.txt rename to doc/txt/compute_group_group.txt diff --git a/doc/src/compute_gyration.txt b/doc/txt/compute_gyration.txt similarity index 100% rename from doc/src/compute_gyration.txt rename to doc/txt/compute_gyration.txt diff --git a/doc/src/compute_gyration_chunk.txt b/doc/txt/compute_gyration_chunk.txt similarity index 100% rename from doc/src/compute_gyration_chunk.txt rename to doc/txt/compute_gyration_chunk.txt diff --git a/doc/src/compute_gyration_shape.txt b/doc/txt/compute_gyration_shape.txt similarity index 100% rename from doc/src/compute_gyration_shape.txt rename to doc/txt/compute_gyration_shape.txt diff --git a/doc/src/compute_heat_flux.txt b/doc/txt/compute_heat_flux.txt similarity index 100% rename from doc/src/compute_heat_flux.txt rename to doc/txt/compute_heat_flux.txt diff --git a/doc/src/compute_hexorder_atom.txt b/doc/txt/compute_hexorder_atom.txt similarity index 100% rename from doc/src/compute_hexorder_atom.txt rename to doc/txt/compute_hexorder_atom.txt diff --git a/doc/src/compute_hma.txt b/doc/txt/compute_hma.txt similarity index 100% rename from doc/src/compute_hma.txt rename to doc/txt/compute_hma.txt diff --git a/doc/src/compute_improper.txt b/doc/txt/compute_improper.txt similarity index 100% rename from doc/src/compute_improper.txt rename to doc/txt/compute_improper.txt diff --git a/doc/src/compute_improper_local.txt b/doc/txt/compute_improper_local.txt similarity index 100% rename from doc/src/compute_improper_local.txt rename to doc/txt/compute_improper_local.txt diff --git a/doc/src/compute_inertia_chunk.txt b/doc/txt/compute_inertia_chunk.txt similarity index 100% rename from doc/src/compute_inertia_chunk.txt rename to doc/txt/compute_inertia_chunk.txt diff --git a/doc/src/compute_ke.txt b/doc/txt/compute_ke.txt similarity index 100% rename from doc/src/compute_ke.txt rename to doc/txt/compute_ke.txt diff --git a/doc/src/compute_ke_atom.txt b/doc/txt/compute_ke_atom.txt similarity index 100% rename from doc/src/compute_ke_atom.txt rename to doc/txt/compute_ke_atom.txt diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/txt/compute_ke_atom_eff.txt similarity index 100% rename from doc/src/compute_ke_atom_eff.txt rename to doc/txt/compute_ke_atom_eff.txt diff --git a/doc/src/compute_ke_eff.txt b/doc/txt/compute_ke_eff.txt similarity index 100% rename from doc/src/compute_ke_eff.txt rename to doc/txt/compute_ke_eff.txt diff --git a/doc/src/compute_ke_rigid.txt b/doc/txt/compute_ke_rigid.txt similarity index 100% rename from doc/src/compute_ke_rigid.txt rename to doc/txt/compute_ke_rigid.txt diff --git a/doc/src/compute_meso_e_atom.txt b/doc/txt/compute_meso_e_atom.txt similarity index 100% rename from doc/src/compute_meso_e_atom.txt rename to doc/txt/compute_meso_e_atom.txt diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/txt/compute_meso_rho_atom.txt similarity index 100% rename from doc/src/compute_meso_rho_atom.txt rename to doc/txt/compute_meso_rho_atom.txt diff --git a/doc/src/compute_meso_t_atom.txt b/doc/txt/compute_meso_t_atom.txt similarity index 100% rename from doc/src/compute_meso_t_atom.txt rename to doc/txt/compute_meso_t_atom.txt diff --git a/doc/src/compute_modify.txt b/doc/txt/compute_modify.txt similarity index 100% rename from doc/src/compute_modify.txt rename to doc/txt/compute_modify.txt diff --git a/doc/src/compute_momentum.txt b/doc/txt/compute_momentum.txt similarity index 100% rename from doc/src/compute_momentum.txt rename to doc/txt/compute_momentum.txt diff --git a/doc/src/compute_msd.txt b/doc/txt/compute_msd.txt similarity index 100% rename from doc/src/compute_msd.txt rename to doc/txt/compute_msd.txt diff --git a/doc/src/compute_msd_chunk.txt b/doc/txt/compute_msd_chunk.txt similarity index 100% rename from doc/src/compute_msd_chunk.txt rename to doc/txt/compute_msd_chunk.txt diff --git a/doc/src/compute_msd_nongauss.txt b/doc/txt/compute_msd_nongauss.txt similarity index 100% rename from doc/src/compute_msd_nongauss.txt rename to doc/txt/compute_msd_nongauss.txt diff --git a/doc/src/compute_omega_chunk.txt b/doc/txt/compute_omega_chunk.txt similarity index 100% rename from doc/src/compute_omega_chunk.txt rename to doc/txt/compute_omega_chunk.txt diff --git a/doc/src/compute_orientorder_atom.txt b/doc/txt/compute_orientorder_atom.txt similarity index 100% rename from doc/src/compute_orientorder_atom.txt rename to doc/txt/compute_orientorder_atom.txt diff --git a/doc/src/compute_pair.txt b/doc/txt/compute_pair.txt similarity index 100% rename from doc/src/compute_pair.txt rename to doc/txt/compute_pair.txt diff --git a/doc/src/compute_pair_local.txt b/doc/txt/compute_pair_local.txt similarity index 100% rename from doc/src/compute_pair_local.txt rename to doc/txt/compute_pair_local.txt diff --git a/doc/src/compute_pe.txt b/doc/txt/compute_pe.txt similarity index 100% rename from doc/src/compute_pe.txt rename to doc/txt/compute_pe.txt diff --git a/doc/src/compute_pe_atom.txt b/doc/txt/compute_pe_atom.txt similarity index 100% rename from doc/src/compute_pe_atom.txt rename to doc/txt/compute_pe_atom.txt diff --git a/doc/src/compute_plasticity_atom.txt b/doc/txt/compute_plasticity_atom.txt similarity index 100% rename from doc/src/compute_plasticity_atom.txt rename to doc/txt/compute_plasticity_atom.txt diff --git a/doc/src/compute_pressure.txt b/doc/txt/compute_pressure.txt similarity index 100% rename from doc/src/compute_pressure.txt rename to doc/txt/compute_pressure.txt diff --git a/doc/src/compute_pressure_cylinder.txt b/doc/txt/compute_pressure_cylinder.txt similarity index 100% rename from doc/src/compute_pressure_cylinder.txt rename to doc/txt/compute_pressure_cylinder.txt diff --git a/doc/src/compute_pressure_uef.txt b/doc/txt/compute_pressure_uef.txt similarity index 100% rename from doc/src/compute_pressure_uef.txt rename to doc/txt/compute_pressure_uef.txt diff --git a/doc/src/compute_property_atom.txt b/doc/txt/compute_property_atom.txt similarity index 100% rename from doc/src/compute_property_atom.txt rename to doc/txt/compute_property_atom.txt diff --git a/doc/src/compute_property_chunk.txt b/doc/txt/compute_property_chunk.txt similarity index 100% rename from doc/src/compute_property_chunk.txt rename to doc/txt/compute_property_chunk.txt diff --git a/doc/src/compute_property_local.txt b/doc/txt/compute_property_local.txt similarity index 100% rename from doc/src/compute_property_local.txt rename to doc/txt/compute_property_local.txt diff --git a/doc/src/compute_ptm_atom.txt b/doc/txt/compute_ptm_atom.txt similarity index 100% rename from doc/src/compute_ptm_atom.txt rename to doc/txt/compute_ptm_atom.txt diff --git a/doc/src/compute_rdf.txt b/doc/txt/compute_rdf.txt similarity index 100% rename from doc/src/compute_rdf.txt rename to doc/txt/compute_rdf.txt diff --git a/doc/src/compute_reduce.txt b/doc/txt/compute_reduce.txt similarity index 100% rename from doc/src/compute_reduce.txt rename to doc/txt/compute_reduce.txt diff --git a/doc/src/compute_reduce_chunk.txt b/doc/txt/compute_reduce_chunk.txt similarity index 100% rename from doc/src/compute_reduce_chunk.txt rename to doc/txt/compute_reduce_chunk.txt diff --git a/doc/src/compute_rigid_local.txt b/doc/txt/compute_rigid_local.txt similarity index 100% rename from doc/src/compute_rigid_local.txt rename to doc/txt/compute_rigid_local.txt diff --git a/doc/src/compute_saed.txt b/doc/txt/compute_saed.txt similarity index 100% rename from doc/src/compute_saed.txt rename to doc/txt/compute_saed.txt diff --git a/doc/src/compute_slice.txt b/doc/txt/compute_slice.txt similarity index 100% rename from doc/src/compute_slice.txt rename to doc/txt/compute_slice.txt diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/txt/compute_smd_contact_radius.txt similarity index 100% rename from doc/src/compute_smd_contact_radius.txt rename to doc/txt/compute_smd_contact_radius.txt diff --git a/doc/src/compute_smd_damage.txt b/doc/txt/compute_smd_damage.txt similarity index 100% rename from doc/src/compute_smd_damage.txt rename to doc/txt/compute_smd_damage.txt diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/txt/compute_smd_hourglass_error.txt similarity index 100% rename from doc/src/compute_smd_hourglass_error.txt rename to doc/txt/compute_smd_hourglass_error.txt diff --git a/doc/src/compute_smd_internal_energy.txt b/doc/txt/compute_smd_internal_energy.txt similarity index 100% rename from doc/src/compute_smd_internal_energy.txt rename to doc/txt/compute_smd_internal_energy.txt diff --git a/doc/src/compute_smd_plastic_strain.txt b/doc/txt/compute_smd_plastic_strain.txt similarity index 100% rename from doc/src/compute_smd_plastic_strain.txt rename to doc/txt/compute_smd_plastic_strain.txt diff --git a/doc/src/compute_smd_plastic_strain_rate.txt b/doc/txt/compute_smd_plastic_strain_rate.txt similarity index 100% rename from doc/src/compute_smd_plastic_strain_rate.txt rename to doc/txt/compute_smd_plastic_strain_rate.txt diff --git a/doc/src/compute_smd_rho.txt b/doc/txt/compute_smd_rho.txt similarity index 100% rename from doc/src/compute_smd_rho.txt rename to doc/txt/compute_smd_rho.txt diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/txt/compute_smd_tlsph_defgrad.txt similarity index 100% rename from doc/src/compute_smd_tlsph_defgrad.txt rename to doc/txt/compute_smd_tlsph_defgrad.txt diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/txt/compute_smd_tlsph_dt.txt similarity index 100% rename from doc/src/compute_smd_tlsph_dt.txt rename to doc/txt/compute_smd_tlsph_dt.txt diff --git a/doc/src/compute_smd_tlsph_num_neighs.txt b/doc/txt/compute_smd_tlsph_num_neighs.txt similarity index 100% rename from doc/src/compute_smd_tlsph_num_neighs.txt rename to doc/txt/compute_smd_tlsph_num_neighs.txt diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/txt/compute_smd_tlsph_shape.txt similarity index 100% rename from doc/src/compute_smd_tlsph_shape.txt rename to doc/txt/compute_smd_tlsph_shape.txt diff --git a/doc/src/compute_smd_tlsph_strain.txt b/doc/txt/compute_smd_tlsph_strain.txt similarity index 100% rename from doc/src/compute_smd_tlsph_strain.txt rename to doc/txt/compute_smd_tlsph_strain.txt diff --git a/doc/src/compute_smd_tlsph_strain_rate.txt b/doc/txt/compute_smd_tlsph_strain_rate.txt similarity index 100% rename from doc/src/compute_smd_tlsph_strain_rate.txt rename to doc/txt/compute_smd_tlsph_strain_rate.txt diff --git a/doc/src/compute_smd_tlsph_stress.txt b/doc/txt/compute_smd_tlsph_stress.txt similarity index 100% rename from doc/src/compute_smd_tlsph_stress.txt rename to doc/txt/compute_smd_tlsph_stress.txt diff --git a/doc/src/compute_smd_triangle_vertices.txt b/doc/txt/compute_smd_triangle_vertices.txt similarity index 100% rename from doc/src/compute_smd_triangle_vertices.txt rename to doc/txt/compute_smd_triangle_vertices.txt diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/txt/compute_smd_ulsph_num_neighs.txt similarity index 100% rename from doc/src/compute_smd_ulsph_num_neighs.txt rename to doc/txt/compute_smd_ulsph_num_neighs.txt diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/txt/compute_smd_ulsph_strain.txt similarity index 100% rename from doc/src/compute_smd_ulsph_strain.txt rename to doc/txt/compute_smd_ulsph_strain.txt diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/txt/compute_smd_ulsph_strain_rate.txt similarity index 100% rename from doc/src/compute_smd_ulsph_strain_rate.txt rename to doc/txt/compute_smd_ulsph_strain_rate.txt diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/txt/compute_smd_ulsph_stress.txt similarity index 100% rename from doc/src/compute_smd_ulsph_stress.txt rename to doc/txt/compute_smd_ulsph_stress.txt diff --git a/doc/src/compute_smd_vol.txt b/doc/txt/compute_smd_vol.txt similarity index 100% rename from doc/src/compute_smd_vol.txt rename to doc/txt/compute_smd_vol.txt diff --git a/doc/src/compute_sna_atom.txt b/doc/txt/compute_sna_atom.txt similarity index 100% rename from doc/src/compute_sna_atom.txt rename to doc/txt/compute_sna_atom.txt diff --git a/doc/src/compute_spin.txt b/doc/txt/compute_spin.txt similarity index 100% rename from doc/src/compute_spin.txt rename to doc/txt/compute_spin.txt diff --git a/doc/src/compute_stress_atom.txt b/doc/txt/compute_stress_atom.txt similarity index 100% rename from doc/src/compute_stress_atom.txt rename to doc/txt/compute_stress_atom.txt diff --git a/doc/src/compute_stress_mop.txt b/doc/txt/compute_stress_mop.txt similarity index 100% rename from doc/src/compute_stress_mop.txt rename to doc/txt/compute_stress_mop.txt diff --git a/doc/src/compute_tally.txt b/doc/txt/compute_tally.txt similarity index 100% rename from doc/src/compute_tally.txt rename to doc/txt/compute_tally.txt diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/txt/compute_tdpd_cc_atom.txt similarity index 100% rename from doc/src/compute_tdpd_cc_atom.txt rename to doc/txt/compute_tdpd_cc_atom.txt diff --git a/doc/src/compute_temp.txt b/doc/txt/compute_temp.txt similarity index 100% rename from doc/src/compute_temp.txt rename to doc/txt/compute_temp.txt diff --git a/doc/src/compute_temp_asphere.txt b/doc/txt/compute_temp_asphere.txt similarity index 100% rename from doc/src/compute_temp_asphere.txt rename to doc/txt/compute_temp_asphere.txt diff --git a/doc/src/compute_temp_body.txt b/doc/txt/compute_temp_body.txt similarity index 100% rename from doc/src/compute_temp_body.txt rename to doc/txt/compute_temp_body.txt diff --git a/doc/src/compute_temp_chunk.txt b/doc/txt/compute_temp_chunk.txt similarity index 100% rename from doc/src/compute_temp_chunk.txt rename to doc/txt/compute_temp_chunk.txt diff --git a/doc/src/compute_temp_com.txt b/doc/txt/compute_temp_com.txt similarity index 100% rename from doc/src/compute_temp_com.txt rename to doc/txt/compute_temp_com.txt diff --git a/doc/src/compute_temp_cs.txt b/doc/txt/compute_temp_cs.txt similarity index 100% rename from doc/src/compute_temp_cs.txt rename to doc/txt/compute_temp_cs.txt diff --git a/doc/src/compute_temp_deform.txt b/doc/txt/compute_temp_deform.txt similarity index 100% rename from doc/src/compute_temp_deform.txt rename to doc/txt/compute_temp_deform.txt diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/txt/compute_temp_deform_eff.txt similarity index 100% rename from doc/src/compute_temp_deform_eff.txt rename to doc/txt/compute_temp_deform_eff.txt diff --git a/doc/src/compute_temp_drude.txt b/doc/txt/compute_temp_drude.txt similarity index 100% rename from doc/src/compute_temp_drude.txt rename to doc/txt/compute_temp_drude.txt diff --git a/doc/src/compute_temp_eff.txt b/doc/txt/compute_temp_eff.txt similarity index 100% rename from doc/src/compute_temp_eff.txt rename to doc/txt/compute_temp_eff.txt diff --git a/doc/src/compute_temp_partial.txt b/doc/txt/compute_temp_partial.txt similarity index 100% rename from doc/src/compute_temp_partial.txt rename to doc/txt/compute_temp_partial.txt diff --git a/doc/src/compute_temp_profile.txt b/doc/txt/compute_temp_profile.txt similarity index 100% rename from doc/src/compute_temp_profile.txt rename to doc/txt/compute_temp_profile.txt diff --git a/doc/src/compute_temp_ramp.txt b/doc/txt/compute_temp_ramp.txt similarity index 100% rename from doc/src/compute_temp_ramp.txt rename to doc/txt/compute_temp_ramp.txt diff --git a/doc/src/compute_temp_region.txt b/doc/txt/compute_temp_region.txt similarity index 100% rename from doc/src/compute_temp_region.txt rename to doc/txt/compute_temp_region.txt diff --git a/doc/src/compute_temp_region_eff.txt b/doc/txt/compute_temp_region_eff.txt similarity index 100% rename from doc/src/compute_temp_region_eff.txt rename to doc/txt/compute_temp_region_eff.txt diff --git a/doc/src/compute_temp_rotate.txt b/doc/txt/compute_temp_rotate.txt similarity index 100% rename from doc/src/compute_temp_rotate.txt rename to doc/txt/compute_temp_rotate.txt diff --git a/doc/src/compute_temp_sphere.txt b/doc/txt/compute_temp_sphere.txt similarity index 100% rename from doc/src/compute_temp_sphere.txt rename to doc/txt/compute_temp_sphere.txt diff --git a/doc/src/compute_temp_uef.txt b/doc/txt/compute_temp_uef.txt similarity index 100% rename from doc/src/compute_temp_uef.txt rename to doc/txt/compute_temp_uef.txt diff --git a/doc/src/compute_ti.txt b/doc/txt/compute_ti.txt similarity index 100% rename from doc/src/compute_ti.txt rename to doc/txt/compute_ti.txt diff --git a/doc/src/compute_torque_chunk.txt b/doc/txt/compute_torque_chunk.txt similarity index 100% rename from doc/src/compute_torque_chunk.txt rename to doc/txt/compute_torque_chunk.txt diff --git a/doc/src/compute_vacf.txt b/doc/txt/compute_vacf.txt similarity index 100% rename from doc/src/compute_vacf.txt rename to doc/txt/compute_vacf.txt diff --git a/doc/src/compute_vcm_chunk.txt b/doc/txt/compute_vcm_chunk.txt similarity index 100% rename from doc/src/compute_vcm_chunk.txt rename to doc/txt/compute_vcm_chunk.txt diff --git a/doc/src/compute_voronoi_atom.txt b/doc/txt/compute_voronoi_atom.txt similarity index 100% rename from doc/src/compute_voronoi_atom.txt rename to doc/txt/compute_voronoi_atom.txt diff --git a/doc/src/compute_xrd.txt b/doc/txt/compute_xrd.txt similarity index 100% rename from doc/src/compute_xrd.txt rename to doc/txt/compute_xrd.txt diff --git a/doc/src/computes.txt b/doc/txt/computes.txt similarity index 100% rename from doc/src/computes.txt rename to doc/txt/computes.txt diff --git a/doc/src/create_atoms.txt b/doc/txt/create_atoms.txt similarity index 100% rename from doc/src/create_atoms.txt rename to doc/txt/create_atoms.txt diff --git a/doc/src/create_bonds.txt b/doc/txt/create_bonds.txt similarity index 100% rename from doc/src/create_bonds.txt rename to doc/txt/create_bonds.txt diff --git a/doc/src/create_box.txt b/doc/txt/create_box.txt similarity index 100% rename from doc/src/create_box.txt rename to doc/txt/create_box.txt diff --git a/doc/src/delete_atoms.txt b/doc/txt/delete_atoms.txt similarity index 100% rename from doc/src/delete_atoms.txt rename to doc/txt/delete_atoms.txt diff --git a/doc/src/delete_bonds.txt b/doc/txt/delete_bonds.txt similarity index 100% rename from doc/src/delete_bonds.txt rename to doc/txt/delete_bonds.txt diff --git a/doc/src/dielectric.txt b/doc/txt/dielectric.txt similarity index 100% rename from doc/src/dielectric.txt rename to doc/txt/dielectric.txt diff --git a/doc/src/dihedral_charmm.txt b/doc/txt/dihedral_charmm.txt similarity index 100% rename from doc/src/dihedral_charmm.txt rename to doc/txt/dihedral_charmm.txt diff --git a/doc/src/dihedral_class2.txt b/doc/txt/dihedral_class2.txt similarity index 100% rename from doc/src/dihedral_class2.txt rename to doc/txt/dihedral_class2.txt diff --git a/doc/src/dihedral_coeff.txt b/doc/txt/dihedral_coeff.txt similarity index 100% rename from doc/src/dihedral_coeff.txt rename to doc/txt/dihedral_coeff.txt diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/txt/dihedral_cosine_shift_exp.txt similarity index 100% rename from doc/src/dihedral_cosine_shift_exp.txt rename to doc/txt/dihedral_cosine_shift_exp.txt diff --git a/doc/src/dihedral_fourier.txt b/doc/txt/dihedral_fourier.txt similarity index 100% rename from doc/src/dihedral_fourier.txt rename to doc/txt/dihedral_fourier.txt diff --git a/doc/src/dihedral_harmonic.txt b/doc/txt/dihedral_harmonic.txt similarity index 100% rename from doc/src/dihedral_harmonic.txt rename to doc/txt/dihedral_harmonic.txt diff --git a/doc/src/dihedral_helix.txt b/doc/txt/dihedral_helix.txt similarity index 100% rename from doc/src/dihedral_helix.txt rename to doc/txt/dihedral_helix.txt diff --git a/doc/src/dihedral_hybrid.txt b/doc/txt/dihedral_hybrid.txt similarity index 100% rename from doc/src/dihedral_hybrid.txt rename to doc/txt/dihedral_hybrid.txt diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/txt/dihedral_multi_harmonic.txt similarity index 100% rename from doc/src/dihedral_multi_harmonic.txt rename to doc/txt/dihedral_multi_harmonic.txt diff --git a/doc/src/dihedral_nharmonic.txt b/doc/txt/dihedral_nharmonic.txt similarity index 100% rename from doc/src/dihedral_nharmonic.txt rename to doc/txt/dihedral_nharmonic.txt diff --git a/doc/src/dihedral_none.txt b/doc/txt/dihedral_none.txt similarity index 100% rename from doc/src/dihedral_none.txt rename to doc/txt/dihedral_none.txt diff --git a/doc/src/dihedral_opls.txt b/doc/txt/dihedral_opls.txt similarity index 100% rename from doc/src/dihedral_opls.txt rename to doc/txt/dihedral_opls.txt diff --git a/doc/src/dihedral_quadratic.txt b/doc/txt/dihedral_quadratic.txt similarity index 100% rename from doc/src/dihedral_quadratic.txt rename to doc/txt/dihedral_quadratic.txt diff --git a/doc/src/dihedral_spherical.txt b/doc/txt/dihedral_spherical.txt similarity index 100% rename from doc/src/dihedral_spherical.txt rename to doc/txt/dihedral_spherical.txt diff --git a/doc/src/dihedral_style.txt b/doc/txt/dihedral_style.txt similarity index 100% rename from doc/src/dihedral_style.txt rename to doc/txt/dihedral_style.txt diff --git a/doc/src/dihedral_table.txt b/doc/txt/dihedral_table.txt similarity index 100% rename from doc/src/dihedral_table.txt rename to doc/txt/dihedral_table.txt diff --git a/doc/src/dihedral_table_cut.txt b/doc/txt/dihedral_table_cut.txt similarity index 100% rename from doc/src/dihedral_table_cut.txt rename to doc/txt/dihedral_table_cut.txt diff --git a/doc/src/dihedral_zero.txt b/doc/txt/dihedral_zero.txt similarity index 100% rename from doc/src/dihedral_zero.txt rename to doc/txt/dihedral_zero.txt diff --git a/doc/src/dimension.txt b/doc/txt/dimension.txt similarity index 100% rename from doc/src/dimension.txt rename to doc/txt/dimension.txt diff --git a/doc/src/displace_atoms.txt b/doc/txt/displace_atoms.txt similarity index 100% rename from doc/src/displace_atoms.txt rename to doc/txt/displace_atoms.txt diff --git a/doc/src/dump.txt b/doc/txt/dump.txt similarity index 100% rename from doc/src/dump.txt rename to doc/txt/dump.txt diff --git a/doc/src/dump_adios.txt b/doc/txt/dump_adios.txt similarity index 100% rename from doc/src/dump_adios.txt rename to doc/txt/dump_adios.txt diff --git a/doc/src/dump_cfg_uef.txt b/doc/txt/dump_cfg_uef.txt similarity index 100% rename from doc/src/dump_cfg_uef.txt rename to doc/txt/dump_cfg_uef.txt diff --git a/doc/src/dump_h5md.txt b/doc/txt/dump_h5md.txt similarity index 100% rename from doc/src/dump_h5md.txt rename to doc/txt/dump_h5md.txt diff --git a/doc/src/dump_image.txt b/doc/txt/dump_image.txt similarity index 100% rename from doc/src/dump_image.txt rename to doc/txt/dump_image.txt diff --git a/doc/src/dump_modify.txt b/doc/txt/dump_modify.txt similarity index 100% rename from doc/src/dump_modify.txt rename to doc/txt/dump_modify.txt diff --git a/doc/src/dump_molfile.txt b/doc/txt/dump_molfile.txt similarity index 100% rename from doc/src/dump_molfile.txt rename to doc/txt/dump_molfile.txt diff --git a/doc/src/dump_netcdf.txt b/doc/txt/dump_netcdf.txt similarity index 100% rename from doc/src/dump_netcdf.txt rename to doc/txt/dump_netcdf.txt diff --git a/doc/src/dump_vtk.txt b/doc/txt/dump_vtk.txt similarity index 100% rename from doc/src/dump_vtk.txt rename to doc/txt/dump_vtk.txt diff --git a/doc/src/dynamical_matrix.txt b/doc/txt/dynamical_matrix.txt similarity index 100% rename from doc/src/dynamical_matrix.txt rename to doc/txt/dynamical_matrix.txt diff --git a/doc/src/echo.txt b/doc/txt/echo.txt similarity index 100% rename from doc/src/echo.txt rename to doc/txt/echo.txt diff --git a/doc/src/fix.txt b/doc/txt/fix.txt similarity index 100% rename from doc/src/fix.txt rename to doc/txt/fix.txt diff --git a/doc/src/fix_adapt.txt b/doc/txt/fix_adapt.txt similarity index 100% rename from doc/src/fix_adapt.txt rename to doc/txt/fix_adapt.txt diff --git a/doc/src/fix_adapt_fep.txt b/doc/txt/fix_adapt_fep.txt similarity index 100% rename from doc/src/fix_adapt_fep.txt rename to doc/txt/fix_adapt_fep.txt diff --git a/doc/src/fix_addforce.txt b/doc/txt/fix_addforce.txt similarity index 100% rename from doc/src/fix_addforce.txt rename to doc/txt/fix_addforce.txt diff --git a/doc/src/fix_addtorque.txt b/doc/txt/fix_addtorque.txt similarity index 100% rename from doc/src/fix_addtorque.txt rename to doc/txt/fix_addtorque.txt diff --git a/doc/src/fix_append_atoms.txt b/doc/txt/fix_append_atoms.txt similarity index 100% rename from doc/src/fix_append_atoms.txt rename to doc/txt/fix_append_atoms.txt diff --git a/doc/src/fix_atc.txt b/doc/txt/fix_atc.txt similarity index 100% rename from doc/src/fix_atc.txt rename to doc/txt/fix_atc.txt diff --git a/doc/src/fix_atom_swap.txt b/doc/txt/fix_atom_swap.txt similarity index 100% rename from doc/src/fix_atom_swap.txt rename to doc/txt/fix_atom_swap.txt diff --git a/doc/src/fix_ave_atom.txt b/doc/txt/fix_ave_atom.txt similarity index 100% rename from doc/src/fix_ave_atom.txt rename to doc/txt/fix_ave_atom.txt diff --git a/doc/src/fix_ave_chunk.txt b/doc/txt/fix_ave_chunk.txt similarity index 100% rename from doc/src/fix_ave_chunk.txt rename to doc/txt/fix_ave_chunk.txt diff --git a/doc/src/fix_ave_correlate.txt b/doc/txt/fix_ave_correlate.txt similarity index 100% rename from doc/src/fix_ave_correlate.txt rename to doc/txt/fix_ave_correlate.txt diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/txt/fix_ave_correlate_long.txt similarity index 100% rename from doc/src/fix_ave_correlate_long.txt rename to doc/txt/fix_ave_correlate_long.txt diff --git a/doc/src/fix_ave_histo.txt b/doc/txt/fix_ave_histo.txt similarity index 100% rename from doc/src/fix_ave_histo.txt rename to doc/txt/fix_ave_histo.txt diff --git a/doc/src/fix_ave_time.txt b/doc/txt/fix_ave_time.txt similarity index 100% rename from doc/src/fix_ave_time.txt rename to doc/txt/fix_ave_time.txt diff --git a/doc/src/fix_aveforce.txt b/doc/txt/fix_aveforce.txt similarity index 100% rename from doc/src/fix_aveforce.txt rename to doc/txt/fix_aveforce.txt diff --git a/doc/src/fix_balance.txt b/doc/txt/fix_balance.txt similarity index 100% rename from doc/src/fix_balance.txt rename to doc/txt/fix_balance.txt diff --git a/doc/src/fix_bocs.txt b/doc/txt/fix_bocs.txt similarity index 100% rename from doc/src/fix_bocs.txt rename to doc/txt/fix_bocs.txt diff --git a/doc/src/fix_bond_break.txt b/doc/txt/fix_bond_break.txt similarity index 100% rename from doc/src/fix_bond_break.txt rename to doc/txt/fix_bond_break.txt diff --git a/doc/src/fix_bond_create.txt b/doc/txt/fix_bond_create.txt similarity index 100% rename from doc/src/fix_bond_create.txt rename to doc/txt/fix_bond_create.txt diff --git a/doc/src/fix_bond_react.txt b/doc/txt/fix_bond_react.txt similarity index 100% rename from doc/src/fix_bond_react.txt rename to doc/txt/fix_bond_react.txt diff --git a/doc/src/fix_bond_swap.txt b/doc/txt/fix_bond_swap.txt similarity index 100% rename from doc/src/fix_bond_swap.txt rename to doc/txt/fix_bond_swap.txt diff --git a/doc/src/fix_box_relax.txt b/doc/txt/fix_box_relax.txt similarity index 100% rename from doc/src/fix_box_relax.txt rename to doc/txt/fix_box_relax.txt diff --git a/doc/src/fix_client_md.txt b/doc/txt/fix_client_md.txt similarity index 100% rename from doc/src/fix_client_md.txt rename to doc/txt/fix_client_md.txt diff --git a/doc/src/fix_cmap.txt b/doc/txt/fix_cmap.txt similarity index 100% rename from doc/src/fix_cmap.txt rename to doc/txt/fix_cmap.txt diff --git a/doc/src/fix_colvars.txt b/doc/txt/fix_colvars.txt similarity index 100% rename from doc/src/fix_colvars.txt rename to doc/txt/fix_colvars.txt diff --git a/doc/src/fix_controller.txt b/doc/txt/fix_controller.txt similarity index 100% rename from doc/src/fix_controller.txt rename to doc/txt/fix_controller.txt diff --git a/doc/src/fix_deform.txt b/doc/txt/fix_deform.txt similarity index 100% rename from doc/src/fix_deform.txt rename to doc/txt/fix_deform.txt diff --git a/doc/src/fix_deposit.txt b/doc/txt/fix_deposit.txt similarity index 100% rename from doc/src/fix_deposit.txt rename to doc/txt/fix_deposit.txt diff --git a/doc/src/fix_dpd_energy.txt b/doc/txt/fix_dpd_energy.txt similarity index 100% rename from doc/src/fix_dpd_energy.txt rename to doc/txt/fix_dpd_energy.txt diff --git a/doc/src/fix_dpd_source.txt b/doc/txt/fix_dpd_source.txt similarity index 100% rename from doc/src/fix_dpd_source.txt rename to doc/txt/fix_dpd_source.txt diff --git a/doc/src/fix_drag.txt b/doc/txt/fix_drag.txt similarity index 100% rename from doc/src/fix_drag.txt rename to doc/txt/fix_drag.txt diff --git a/doc/src/fix_drude.txt b/doc/txt/fix_drude.txt similarity index 100% rename from doc/src/fix_drude.txt rename to doc/txt/fix_drude.txt diff --git a/doc/src/fix_drude_transform.txt b/doc/txt/fix_drude_transform.txt similarity index 100% rename from doc/src/fix_drude_transform.txt rename to doc/txt/fix_drude_transform.txt diff --git a/doc/src/fix_dt_reset.txt b/doc/txt/fix_dt_reset.txt similarity index 100% rename from doc/src/fix_dt_reset.txt rename to doc/txt/fix_dt_reset.txt diff --git a/doc/src/fix_efield.txt b/doc/txt/fix_efield.txt similarity index 100% rename from doc/src/fix_efield.txt rename to doc/txt/fix_efield.txt diff --git a/doc/src/fix_ehex.txt b/doc/txt/fix_ehex.txt similarity index 100% rename from doc/src/fix_ehex.txt rename to doc/txt/fix_ehex.txt diff --git a/doc/src/fix_electron_stopping.txt b/doc/txt/fix_electron_stopping.txt similarity index 100% rename from doc/src/fix_electron_stopping.txt rename to doc/txt/fix_electron_stopping.txt diff --git a/doc/src/fix_enforce2d.txt b/doc/txt/fix_enforce2d.txt similarity index 100% rename from doc/src/fix_enforce2d.txt rename to doc/txt/fix_enforce2d.txt diff --git a/doc/src/fix_eos_cv.txt b/doc/txt/fix_eos_cv.txt similarity index 100% rename from doc/src/fix_eos_cv.txt rename to doc/txt/fix_eos_cv.txt diff --git a/doc/src/fix_eos_table.txt b/doc/txt/fix_eos_table.txt similarity index 100% rename from doc/src/fix_eos_table.txt rename to doc/txt/fix_eos_table.txt diff --git a/doc/src/fix_eos_table_rx.txt b/doc/txt/fix_eos_table_rx.txt similarity index 100% rename from doc/src/fix_eos_table_rx.txt rename to doc/txt/fix_eos_table_rx.txt diff --git a/doc/src/fix_evaporate.txt b/doc/txt/fix_evaporate.txt similarity index 100% rename from doc/src/fix_evaporate.txt rename to doc/txt/fix_evaporate.txt diff --git a/doc/src/fix_external.txt b/doc/txt/fix_external.txt similarity index 100% rename from doc/src/fix_external.txt rename to doc/txt/fix_external.txt diff --git a/doc/src/fix_ffl.txt b/doc/txt/fix_ffl.txt similarity index 100% rename from doc/src/fix_ffl.txt rename to doc/txt/fix_ffl.txt diff --git a/doc/src/fix_filter_corotate.txt b/doc/txt/fix_filter_corotate.txt similarity index 100% rename from doc/src/fix_filter_corotate.txt rename to doc/txt/fix_filter_corotate.txt diff --git a/doc/src/fix_flow_gauss.txt b/doc/txt/fix_flow_gauss.txt similarity index 100% rename from doc/src/fix_flow_gauss.txt rename to doc/txt/fix_flow_gauss.txt diff --git a/doc/src/fix_freeze.txt b/doc/txt/fix_freeze.txt similarity index 100% rename from doc/src/fix_freeze.txt rename to doc/txt/fix_freeze.txt diff --git a/doc/src/fix_gcmc.txt b/doc/txt/fix_gcmc.txt similarity index 100% rename from doc/src/fix_gcmc.txt rename to doc/txt/fix_gcmc.txt diff --git a/doc/src/fix_gld.txt b/doc/txt/fix_gld.txt similarity index 100% rename from doc/src/fix_gld.txt rename to doc/txt/fix_gld.txt diff --git a/doc/src/fix_gle.txt b/doc/txt/fix_gle.txt similarity index 100% rename from doc/src/fix_gle.txt rename to doc/txt/fix_gle.txt diff --git a/doc/src/fix_gravity.txt b/doc/txt/fix_gravity.txt similarity index 100% rename from doc/src/fix_gravity.txt rename to doc/txt/fix_gravity.txt diff --git a/doc/src/fix_grem.txt b/doc/txt/fix_grem.txt similarity index 100% rename from doc/src/fix_grem.txt rename to doc/txt/fix_grem.txt diff --git a/doc/src/fix_halt.txt b/doc/txt/fix_halt.txt similarity index 100% rename from doc/src/fix_halt.txt rename to doc/txt/fix_halt.txt diff --git a/doc/src/fix_heat.txt b/doc/txt/fix_heat.txt similarity index 100% rename from doc/src/fix_heat.txt rename to doc/txt/fix_heat.txt diff --git a/doc/src/fix_hyper_global.txt b/doc/txt/fix_hyper_global.txt similarity index 100% rename from doc/src/fix_hyper_global.txt rename to doc/txt/fix_hyper_global.txt diff --git a/doc/src/fix_hyper_local.txt b/doc/txt/fix_hyper_local.txt similarity index 100% rename from doc/src/fix_hyper_local.txt rename to doc/txt/fix_hyper_local.txt diff --git a/doc/src/fix_imd.txt b/doc/txt/fix_imd.txt similarity index 100% rename from doc/src/fix_imd.txt rename to doc/txt/fix_imd.txt diff --git a/doc/src/fix_indent.txt b/doc/txt/fix_indent.txt similarity index 100% rename from doc/src/fix_indent.txt rename to doc/txt/fix_indent.txt diff --git a/doc/src/fix_ipi.txt b/doc/txt/fix_ipi.txt similarity index 100% rename from doc/src/fix_ipi.txt rename to doc/txt/fix_ipi.txt diff --git a/doc/src/fix_langevin.txt b/doc/txt/fix_langevin.txt similarity index 100% rename from doc/src/fix_langevin.txt rename to doc/txt/fix_langevin.txt diff --git a/doc/src/fix_langevin_drude.txt b/doc/txt/fix_langevin_drude.txt similarity index 100% rename from doc/src/fix_langevin_drude.txt rename to doc/txt/fix_langevin_drude.txt diff --git a/doc/src/fix_langevin_eff.txt b/doc/txt/fix_langevin_eff.txt similarity index 100% rename from doc/src/fix_langevin_eff.txt rename to doc/txt/fix_langevin_eff.txt diff --git a/doc/src/fix_langevin_spin.txt b/doc/txt/fix_langevin_spin.txt similarity index 100% rename from doc/src/fix_langevin_spin.txt rename to doc/txt/fix_langevin_spin.txt diff --git a/doc/src/fix_latte.txt b/doc/txt/fix_latte.txt similarity index 100% rename from doc/src/fix_latte.txt rename to doc/txt/fix_latte.txt diff --git a/doc/src/fix_lb_fluid.txt b/doc/txt/fix_lb_fluid.txt similarity index 100% rename from doc/src/fix_lb_fluid.txt rename to doc/txt/fix_lb_fluid.txt diff --git a/doc/src/fix_lb_momentum.txt b/doc/txt/fix_lb_momentum.txt similarity index 100% rename from doc/src/fix_lb_momentum.txt rename to doc/txt/fix_lb_momentum.txt diff --git a/doc/src/fix_lb_pc.txt b/doc/txt/fix_lb_pc.txt similarity index 100% rename from doc/src/fix_lb_pc.txt rename to doc/txt/fix_lb_pc.txt diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/txt/fix_lb_rigid_pc_sphere.txt similarity index 100% rename from doc/src/fix_lb_rigid_pc_sphere.txt rename to doc/txt/fix_lb_rigid_pc_sphere.txt diff --git a/doc/src/fix_lb_viscous.txt b/doc/txt/fix_lb_viscous.txt similarity index 100% rename from doc/src/fix_lb_viscous.txt rename to doc/txt/fix_lb_viscous.txt diff --git a/doc/src/fix_lineforce.txt b/doc/txt/fix_lineforce.txt similarity index 100% rename from doc/src/fix_lineforce.txt rename to doc/txt/fix_lineforce.txt diff --git a/doc/src/fix_manifoldforce.txt b/doc/txt/fix_manifoldforce.txt similarity index 100% rename from doc/src/fix_manifoldforce.txt rename to doc/txt/fix_manifoldforce.txt diff --git a/doc/src/fix_meso.txt b/doc/txt/fix_meso.txt similarity index 100% rename from doc/src/fix_meso.txt rename to doc/txt/fix_meso.txt diff --git a/doc/src/fix_meso_move.txt b/doc/txt/fix_meso_move.txt similarity index 100% rename from doc/src/fix_meso_move.txt rename to doc/txt/fix_meso_move.txt diff --git a/doc/src/fix_meso_stationary.txt b/doc/txt/fix_meso_stationary.txt similarity index 100% rename from doc/src/fix_meso_stationary.txt rename to doc/txt/fix_meso_stationary.txt diff --git a/doc/src/fix_modify.txt b/doc/txt/fix_modify.txt similarity index 100% rename from doc/src/fix_modify.txt rename to doc/txt/fix_modify.txt diff --git a/doc/src/fix_momentum.txt b/doc/txt/fix_momentum.txt similarity index 100% rename from doc/src/fix_momentum.txt rename to doc/txt/fix_momentum.txt diff --git a/doc/src/fix_move.txt b/doc/txt/fix_move.txt similarity index 100% rename from doc/src/fix_move.txt rename to doc/txt/fix_move.txt diff --git a/doc/src/fix_mscg.txt b/doc/txt/fix_mscg.txt similarity index 100% rename from doc/src/fix_mscg.txt rename to doc/txt/fix_mscg.txt diff --git a/doc/src/fix_msst.txt b/doc/txt/fix_msst.txt similarity index 100% rename from doc/src/fix_msst.txt rename to doc/txt/fix_msst.txt diff --git a/doc/src/fix_mvv_dpd.txt b/doc/txt/fix_mvv_dpd.txt similarity index 100% rename from doc/src/fix_mvv_dpd.txt rename to doc/txt/fix_mvv_dpd.txt diff --git a/doc/src/fix_neb.txt b/doc/txt/fix_neb.txt similarity index 100% rename from doc/src/fix_neb.txt rename to doc/txt/fix_neb.txt diff --git a/doc/src/fix_neb_spin.txt b/doc/txt/fix_neb_spin.txt similarity index 100% rename from doc/src/fix_neb_spin.txt rename to doc/txt/fix_neb_spin.txt diff --git a/doc/src/fix_nh.txt b/doc/txt/fix_nh.txt similarity index 100% rename from doc/src/fix_nh.txt rename to doc/txt/fix_nh.txt diff --git a/doc/src/fix_nh_eff.txt b/doc/txt/fix_nh_eff.txt similarity index 100% rename from doc/src/fix_nh_eff.txt rename to doc/txt/fix_nh_eff.txt diff --git a/doc/src/fix_nh_uef.txt b/doc/txt/fix_nh_uef.txt similarity index 100% rename from doc/src/fix_nh_uef.txt rename to doc/txt/fix_nh_uef.txt diff --git a/doc/src/fix_nph_asphere.txt b/doc/txt/fix_nph_asphere.txt similarity index 100% rename from doc/src/fix_nph_asphere.txt rename to doc/txt/fix_nph_asphere.txt diff --git a/doc/src/fix_nph_body.txt b/doc/txt/fix_nph_body.txt similarity index 100% rename from doc/src/fix_nph_body.txt rename to doc/txt/fix_nph_body.txt diff --git a/doc/src/fix_nph_sphere.txt b/doc/txt/fix_nph_sphere.txt similarity index 100% rename from doc/src/fix_nph_sphere.txt rename to doc/txt/fix_nph_sphere.txt diff --git a/doc/src/fix_nphug.txt b/doc/txt/fix_nphug.txt similarity index 100% rename from doc/src/fix_nphug.txt rename to doc/txt/fix_nphug.txt diff --git a/doc/src/fix_npt_asphere.txt b/doc/txt/fix_npt_asphere.txt similarity index 100% rename from doc/src/fix_npt_asphere.txt rename to doc/txt/fix_npt_asphere.txt diff --git a/doc/src/fix_npt_body.txt b/doc/txt/fix_npt_body.txt similarity index 100% rename from doc/src/fix_npt_body.txt rename to doc/txt/fix_npt_body.txt diff --git a/doc/src/fix_npt_sphere.txt b/doc/txt/fix_npt_sphere.txt similarity index 100% rename from doc/src/fix_npt_sphere.txt rename to doc/txt/fix_npt_sphere.txt diff --git a/doc/src/fix_nve.txt b/doc/txt/fix_nve.txt similarity index 100% rename from doc/src/fix_nve.txt rename to doc/txt/fix_nve.txt diff --git a/doc/src/fix_nve_asphere.txt b/doc/txt/fix_nve_asphere.txt similarity index 100% rename from doc/src/fix_nve_asphere.txt rename to doc/txt/fix_nve_asphere.txt diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/txt/fix_nve_asphere_noforce.txt similarity index 100% rename from doc/src/fix_nve_asphere_noforce.txt rename to doc/txt/fix_nve_asphere_noforce.txt diff --git a/doc/src/fix_nve_awpmd.txt b/doc/txt/fix_nve_awpmd.txt similarity index 100% rename from doc/src/fix_nve_awpmd.txt rename to doc/txt/fix_nve_awpmd.txt diff --git a/doc/src/fix_nve_body.txt b/doc/txt/fix_nve_body.txt similarity index 100% rename from doc/src/fix_nve_body.txt rename to doc/txt/fix_nve_body.txt diff --git a/doc/src/fix_nve_dot.txt b/doc/txt/fix_nve_dot.txt similarity index 100% rename from doc/src/fix_nve_dot.txt rename to doc/txt/fix_nve_dot.txt diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/txt/fix_nve_dotc_langevin.txt similarity index 100% rename from doc/src/fix_nve_dotc_langevin.txt rename to doc/txt/fix_nve_dotc_langevin.txt diff --git a/doc/src/fix_nve_eff.txt b/doc/txt/fix_nve_eff.txt similarity index 100% rename from doc/src/fix_nve_eff.txt rename to doc/txt/fix_nve_eff.txt diff --git a/doc/src/fix_nve_limit.txt b/doc/txt/fix_nve_limit.txt similarity index 100% rename from doc/src/fix_nve_limit.txt rename to doc/txt/fix_nve_limit.txt diff --git a/doc/src/fix_nve_line.txt b/doc/txt/fix_nve_line.txt similarity index 100% rename from doc/src/fix_nve_line.txt rename to doc/txt/fix_nve_line.txt diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/txt/fix_nve_manifold_rattle.txt similarity index 100% rename from doc/src/fix_nve_manifold_rattle.txt rename to doc/txt/fix_nve_manifold_rattle.txt diff --git a/doc/src/fix_nve_noforce.txt b/doc/txt/fix_nve_noforce.txt similarity index 100% rename from doc/src/fix_nve_noforce.txt rename to doc/txt/fix_nve_noforce.txt diff --git a/doc/src/fix_nve_sphere.txt b/doc/txt/fix_nve_sphere.txt similarity index 100% rename from doc/src/fix_nve_sphere.txt rename to doc/txt/fix_nve_sphere.txt diff --git a/doc/src/fix_nve_spin.txt b/doc/txt/fix_nve_spin.txt similarity index 100% rename from doc/src/fix_nve_spin.txt rename to doc/txt/fix_nve_spin.txt diff --git a/doc/src/fix_nve_tri.txt b/doc/txt/fix_nve_tri.txt similarity index 100% rename from doc/src/fix_nve_tri.txt rename to doc/txt/fix_nve_tri.txt diff --git a/doc/src/fix_nvk.txt b/doc/txt/fix_nvk.txt similarity index 100% rename from doc/src/fix_nvk.txt rename to doc/txt/fix_nvk.txt diff --git a/doc/src/fix_nvt_asphere.txt b/doc/txt/fix_nvt_asphere.txt similarity index 100% rename from doc/src/fix_nvt_asphere.txt rename to doc/txt/fix_nvt_asphere.txt diff --git a/doc/src/fix_nvt_body.txt b/doc/txt/fix_nvt_body.txt similarity index 100% rename from doc/src/fix_nvt_body.txt rename to doc/txt/fix_nvt_body.txt diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/txt/fix_nvt_manifold_rattle.txt similarity index 100% rename from doc/src/fix_nvt_manifold_rattle.txt rename to doc/txt/fix_nvt_manifold_rattle.txt diff --git a/doc/src/fix_nvt_sllod.txt b/doc/txt/fix_nvt_sllod.txt similarity index 100% rename from doc/src/fix_nvt_sllod.txt rename to doc/txt/fix_nvt_sllod.txt diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/txt/fix_nvt_sllod_eff.txt similarity index 100% rename from doc/src/fix_nvt_sllod_eff.txt rename to doc/txt/fix_nvt_sllod_eff.txt diff --git a/doc/src/fix_nvt_sphere.txt b/doc/txt/fix_nvt_sphere.txt similarity index 100% rename from doc/src/fix_nvt_sphere.txt rename to doc/txt/fix_nvt_sphere.txt diff --git a/doc/src/fix_oneway.txt b/doc/txt/fix_oneway.txt similarity index 100% rename from doc/src/fix_oneway.txt rename to doc/txt/fix_oneway.txt diff --git a/doc/src/fix_orient.txt b/doc/txt/fix_orient.txt similarity index 100% rename from doc/src/fix_orient.txt rename to doc/txt/fix_orient.txt diff --git a/doc/src/fix_phonon.txt b/doc/txt/fix_phonon.txt similarity index 100% rename from doc/src/fix_phonon.txt rename to doc/txt/fix_phonon.txt diff --git a/doc/src/fix_pimd.txt b/doc/txt/fix_pimd.txt similarity index 100% rename from doc/src/fix_pimd.txt rename to doc/txt/fix_pimd.txt diff --git a/doc/src/fix_planeforce.txt b/doc/txt/fix_planeforce.txt similarity index 100% rename from doc/src/fix_planeforce.txt rename to doc/txt/fix_planeforce.txt diff --git a/doc/src/fix_plumed.txt b/doc/txt/fix_plumed.txt similarity index 100% rename from doc/src/fix_plumed.txt rename to doc/txt/fix_plumed.txt diff --git a/doc/src/fix_poems.txt b/doc/txt/fix_poems.txt similarity index 100% rename from doc/src/fix_poems.txt rename to doc/txt/fix_poems.txt diff --git a/doc/src/fix_pour.txt b/doc/txt/fix_pour.txt similarity index 100% rename from doc/src/fix_pour.txt rename to doc/txt/fix_pour.txt diff --git a/doc/src/fix_precession_spin.txt b/doc/txt/fix_precession_spin.txt similarity index 100% rename from doc/src/fix_precession_spin.txt rename to doc/txt/fix_precession_spin.txt diff --git a/doc/src/fix_press_berendsen.txt b/doc/txt/fix_press_berendsen.txt similarity index 100% rename from doc/src/fix_press_berendsen.txt rename to doc/txt/fix_press_berendsen.txt diff --git a/doc/src/fix_print.txt b/doc/txt/fix_print.txt similarity index 100% rename from doc/src/fix_print.txt rename to doc/txt/fix_print.txt diff --git a/doc/src/fix_property_atom.txt b/doc/txt/fix_property_atom.txt similarity index 100% rename from doc/src/fix_property_atom.txt rename to doc/txt/fix_property_atom.txt diff --git a/doc/src/fix_python_invoke.txt b/doc/txt/fix_python_invoke.txt similarity index 100% rename from doc/src/fix_python_invoke.txt rename to doc/txt/fix_python_invoke.txt diff --git a/doc/src/fix_python_move.txt b/doc/txt/fix_python_move.txt similarity index 100% rename from doc/src/fix_python_move.txt rename to doc/txt/fix_python_move.txt diff --git a/doc/src/fix_qbmsst.txt b/doc/txt/fix_qbmsst.txt similarity index 100% rename from doc/src/fix_qbmsst.txt rename to doc/txt/fix_qbmsst.txt diff --git a/doc/src/fix_qeq.txt b/doc/txt/fix_qeq.txt similarity index 100% rename from doc/src/fix_qeq.txt rename to doc/txt/fix_qeq.txt diff --git a/doc/src/fix_qeq_comb.txt b/doc/txt/fix_qeq_comb.txt similarity index 100% rename from doc/src/fix_qeq_comb.txt rename to doc/txt/fix_qeq_comb.txt diff --git a/doc/src/fix_qeq_reax.txt b/doc/txt/fix_qeq_reax.txt similarity index 100% rename from doc/src/fix_qeq_reax.txt rename to doc/txt/fix_qeq_reax.txt diff --git a/doc/src/fix_qmmm.txt b/doc/txt/fix_qmmm.txt similarity index 100% rename from doc/src/fix_qmmm.txt rename to doc/txt/fix_qmmm.txt diff --git a/doc/src/fix_qtb.txt b/doc/txt/fix_qtb.txt similarity index 100% rename from doc/src/fix_qtb.txt rename to doc/txt/fix_qtb.txt diff --git a/doc/src/fix_reaxc_bonds.txt b/doc/txt/fix_reaxc_bonds.txt similarity index 100% rename from doc/src/fix_reaxc_bonds.txt rename to doc/txt/fix_reaxc_bonds.txt diff --git a/doc/src/fix_reaxc_species.txt b/doc/txt/fix_reaxc_species.txt similarity index 100% rename from doc/src/fix_reaxc_species.txt rename to doc/txt/fix_reaxc_species.txt diff --git a/doc/src/fix_recenter.txt b/doc/txt/fix_recenter.txt similarity index 100% rename from doc/src/fix_recenter.txt rename to doc/txt/fix_recenter.txt diff --git a/doc/src/fix_restrain.txt b/doc/txt/fix_restrain.txt similarity index 100% rename from doc/src/fix_restrain.txt rename to doc/txt/fix_restrain.txt diff --git a/doc/src/fix_rhok.txt b/doc/txt/fix_rhok.txt similarity index 100% rename from doc/src/fix_rhok.txt rename to doc/txt/fix_rhok.txt diff --git a/doc/src/fix_rigid.txt b/doc/txt/fix_rigid.txt similarity index 100% rename from doc/src/fix_rigid.txt rename to doc/txt/fix_rigid.txt diff --git a/doc/src/fix_rigid_meso.txt b/doc/txt/fix_rigid_meso.txt similarity index 100% rename from doc/src/fix_rigid_meso.txt rename to doc/txt/fix_rigid_meso.txt diff --git a/doc/src/fix_rx.txt b/doc/txt/fix_rx.txt similarity index 100% rename from doc/src/fix_rx.txt rename to doc/txt/fix_rx.txt diff --git a/doc/src/fix_saed_vtk.txt b/doc/txt/fix_saed_vtk.txt similarity index 100% rename from doc/src/fix_saed_vtk.txt rename to doc/txt/fix_saed_vtk.txt diff --git a/doc/src/fix_setforce.txt b/doc/txt/fix_setforce.txt similarity index 100% rename from doc/src/fix_setforce.txt rename to doc/txt/fix_setforce.txt diff --git a/doc/src/fix_shake.txt b/doc/txt/fix_shake.txt similarity index 100% rename from doc/src/fix_shake.txt rename to doc/txt/fix_shake.txt diff --git a/doc/src/fix_shardlow.txt b/doc/txt/fix_shardlow.txt similarity index 100% rename from doc/src/fix_shardlow.txt rename to doc/txt/fix_shardlow.txt diff --git a/doc/src/fix_smd.txt b/doc/txt/fix_smd.txt similarity index 100% rename from doc/src/fix_smd.txt rename to doc/txt/fix_smd.txt diff --git a/doc/src/fix_smd_adjust_dt.txt b/doc/txt/fix_smd_adjust_dt.txt similarity index 100% rename from doc/src/fix_smd_adjust_dt.txt rename to doc/txt/fix_smd_adjust_dt.txt diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/txt/fix_smd_integrate_tlsph.txt similarity index 100% rename from doc/src/fix_smd_integrate_tlsph.txt rename to doc/txt/fix_smd_integrate_tlsph.txt diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/txt/fix_smd_integrate_ulsph.txt similarity index 100% rename from doc/src/fix_smd_integrate_ulsph.txt rename to doc/txt/fix_smd_integrate_ulsph.txt diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/txt/fix_smd_move_triangulated_surface.txt similarity index 100% rename from doc/src/fix_smd_move_triangulated_surface.txt rename to doc/txt/fix_smd_move_triangulated_surface.txt diff --git a/doc/src/fix_smd_setvel.txt b/doc/txt/fix_smd_setvel.txt similarity index 100% rename from doc/src/fix_smd_setvel.txt rename to doc/txt/fix_smd_setvel.txt diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/txt/fix_smd_wall_surface.txt similarity index 100% rename from doc/src/fix_smd_wall_surface.txt rename to doc/txt/fix_smd_wall_surface.txt diff --git a/doc/src/fix_spring.txt b/doc/txt/fix_spring.txt similarity index 100% rename from doc/src/fix_spring.txt rename to doc/txt/fix_spring.txt diff --git a/doc/src/fix_spring_chunk.txt b/doc/txt/fix_spring_chunk.txt similarity index 100% rename from doc/src/fix_spring_chunk.txt rename to doc/txt/fix_spring_chunk.txt diff --git a/doc/src/fix_spring_rg.txt b/doc/txt/fix_spring_rg.txt similarity index 100% rename from doc/src/fix_spring_rg.txt rename to doc/txt/fix_spring_rg.txt diff --git a/doc/src/fix_spring_self.txt b/doc/txt/fix_spring_self.txt similarity index 100% rename from doc/src/fix_spring_self.txt rename to doc/txt/fix_spring_self.txt diff --git a/doc/src/fix_srd.txt b/doc/txt/fix_srd.txt similarity index 100% rename from doc/src/fix_srd.txt rename to doc/txt/fix_srd.txt diff --git a/doc/src/fix_store_force.txt b/doc/txt/fix_store_force.txt similarity index 100% rename from doc/src/fix_store_force.txt rename to doc/txt/fix_store_force.txt diff --git a/doc/src/fix_store_state.txt b/doc/txt/fix_store_state.txt similarity index 100% rename from doc/src/fix_store_state.txt rename to doc/txt/fix_store_state.txt diff --git a/doc/src/fix_temp_berendsen.txt b/doc/txt/fix_temp_berendsen.txt similarity index 100% rename from doc/src/fix_temp_berendsen.txt rename to doc/txt/fix_temp_berendsen.txt diff --git a/doc/src/fix_temp_csvr.txt b/doc/txt/fix_temp_csvr.txt similarity index 100% rename from doc/src/fix_temp_csvr.txt rename to doc/txt/fix_temp_csvr.txt diff --git a/doc/src/fix_temp_rescale.txt b/doc/txt/fix_temp_rescale.txt similarity index 100% rename from doc/src/fix_temp_rescale.txt rename to doc/txt/fix_temp_rescale.txt diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/txt/fix_temp_rescale_eff.txt similarity index 100% rename from doc/src/fix_temp_rescale_eff.txt rename to doc/txt/fix_temp_rescale_eff.txt diff --git a/doc/src/fix_tfmc.txt b/doc/txt/fix_tfmc.txt similarity index 100% rename from doc/src/fix_tfmc.txt rename to doc/txt/fix_tfmc.txt diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/txt/fix_thermal_conductivity.txt similarity index 100% rename from doc/src/fix_thermal_conductivity.txt rename to doc/txt/fix_thermal_conductivity.txt diff --git a/doc/src/fix_ti_spring.txt b/doc/txt/fix_ti_spring.txt similarity index 100% rename from doc/src/fix_ti_spring.txt rename to doc/txt/fix_ti_spring.txt diff --git a/doc/src/fix_tmd.txt b/doc/txt/fix_tmd.txt similarity index 100% rename from doc/src/fix_tmd.txt rename to doc/txt/fix_tmd.txt diff --git a/doc/src/fix_ttm.txt b/doc/txt/fix_ttm.txt similarity index 100% rename from doc/src/fix_ttm.txt rename to doc/txt/fix_ttm.txt diff --git a/doc/src/fix_tune_kspace.txt b/doc/txt/fix_tune_kspace.txt similarity index 100% rename from doc/src/fix_tune_kspace.txt rename to doc/txt/fix_tune_kspace.txt diff --git a/doc/src/fix_vector.txt b/doc/txt/fix_vector.txt similarity index 100% rename from doc/src/fix_vector.txt rename to doc/txt/fix_vector.txt diff --git a/doc/src/fix_viscosity.txt b/doc/txt/fix_viscosity.txt similarity index 100% rename from doc/src/fix_viscosity.txt rename to doc/txt/fix_viscosity.txt diff --git a/doc/src/fix_viscous.txt b/doc/txt/fix_viscous.txt similarity index 100% rename from doc/src/fix_viscous.txt rename to doc/txt/fix_viscous.txt diff --git a/doc/src/fix_wall.txt b/doc/txt/fix_wall.txt similarity index 100% rename from doc/src/fix_wall.txt rename to doc/txt/fix_wall.txt diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/txt/fix_wall_body_polygon.txt similarity index 100% rename from doc/src/fix_wall_body_polygon.txt rename to doc/txt/fix_wall_body_polygon.txt diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/txt/fix_wall_body_polyhedron.txt similarity index 100% rename from doc/src/fix_wall_body_polyhedron.txt rename to doc/txt/fix_wall_body_polyhedron.txt diff --git a/doc/src/fix_wall_ees.txt b/doc/txt/fix_wall_ees.txt similarity index 100% rename from doc/src/fix_wall_ees.txt rename to doc/txt/fix_wall_ees.txt diff --git a/doc/src/fix_wall_gran.txt b/doc/txt/fix_wall_gran.txt similarity index 100% rename from doc/src/fix_wall_gran.txt rename to doc/txt/fix_wall_gran.txt diff --git a/doc/src/fix_wall_gran_region.txt b/doc/txt/fix_wall_gran_region.txt similarity index 100% rename from doc/src/fix_wall_gran_region.txt rename to doc/txt/fix_wall_gran_region.txt diff --git a/doc/src/fix_wall_piston.txt b/doc/txt/fix_wall_piston.txt similarity index 100% rename from doc/src/fix_wall_piston.txt rename to doc/txt/fix_wall_piston.txt diff --git a/doc/src/fix_wall_reflect.txt b/doc/txt/fix_wall_reflect.txt similarity index 100% rename from doc/src/fix_wall_reflect.txt rename to doc/txt/fix_wall_reflect.txt diff --git a/doc/src/fix_wall_region.txt b/doc/txt/fix_wall_region.txt similarity index 100% rename from doc/src/fix_wall_region.txt rename to doc/txt/fix_wall_region.txt diff --git a/doc/src/fix_wall_srd.txt b/doc/txt/fix_wall_srd.txt similarity index 100% rename from doc/src/fix_wall_srd.txt rename to doc/txt/fix_wall_srd.txt diff --git a/doc/src/group.txt b/doc/txt/group.txt similarity index 100% rename from doc/src/group.txt rename to doc/txt/group.txt diff --git a/doc/src/group2ndx.txt b/doc/txt/group2ndx.txt similarity index 100% rename from doc/src/group2ndx.txt rename to doc/txt/group2ndx.txt diff --git a/doc/src/hyper.txt b/doc/txt/hyper.txt similarity index 100% rename from doc/src/hyper.txt rename to doc/txt/hyper.txt diff --git a/doc/src/if.txt b/doc/txt/if.txt similarity index 100% rename from doc/src/if.txt rename to doc/txt/if.txt diff --git a/doc/src/improper_class2.txt b/doc/txt/improper_class2.txt similarity index 100% rename from doc/src/improper_class2.txt rename to doc/txt/improper_class2.txt diff --git a/doc/src/improper_coeff.txt b/doc/txt/improper_coeff.txt similarity index 100% rename from doc/src/improper_coeff.txt rename to doc/txt/improper_coeff.txt diff --git a/doc/src/improper_cossq.txt b/doc/txt/improper_cossq.txt similarity index 100% rename from doc/src/improper_cossq.txt rename to doc/txt/improper_cossq.txt diff --git a/doc/src/improper_cvff.txt b/doc/txt/improper_cvff.txt similarity index 100% rename from doc/src/improper_cvff.txt rename to doc/txt/improper_cvff.txt diff --git a/doc/src/improper_distance.txt b/doc/txt/improper_distance.txt similarity index 100% rename from doc/src/improper_distance.txt rename to doc/txt/improper_distance.txt diff --git a/doc/src/improper_distharm.txt b/doc/txt/improper_distharm.txt similarity index 100% rename from doc/src/improper_distharm.txt rename to doc/txt/improper_distharm.txt diff --git a/doc/src/improper_fourier.txt b/doc/txt/improper_fourier.txt similarity index 100% rename from doc/src/improper_fourier.txt rename to doc/txt/improper_fourier.txt diff --git a/doc/src/improper_harmonic.txt b/doc/txt/improper_harmonic.txt similarity index 100% rename from doc/src/improper_harmonic.txt rename to doc/txt/improper_harmonic.txt diff --git a/doc/src/improper_hybrid.txt b/doc/txt/improper_hybrid.txt similarity index 100% rename from doc/src/improper_hybrid.txt rename to doc/txt/improper_hybrid.txt diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/txt/improper_inversion_harmonic.txt similarity index 100% rename from doc/src/improper_inversion_harmonic.txt rename to doc/txt/improper_inversion_harmonic.txt diff --git a/doc/src/improper_none.txt b/doc/txt/improper_none.txt similarity index 100% rename from doc/src/improper_none.txt rename to doc/txt/improper_none.txt diff --git a/doc/src/improper_ring.txt b/doc/txt/improper_ring.txt similarity index 100% rename from doc/src/improper_ring.txt rename to doc/txt/improper_ring.txt diff --git a/doc/src/improper_sqdistharm.txt b/doc/txt/improper_sqdistharm.txt similarity index 100% rename from doc/src/improper_sqdistharm.txt rename to doc/txt/improper_sqdistharm.txt diff --git a/doc/src/improper_style.txt b/doc/txt/improper_style.txt similarity index 100% rename from doc/src/improper_style.txt rename to doc/txt/improper_style.txt diff --git a/doc/src/improper_umbrella.txt b/doc/txt/improper_umbrella.txt similarity index 100% rename from doc/src/improper_umbrella.txt rename to doc/txt/improper_umbrella.txt diff --git a/doc/src/improper_zero.txt b/doc/txt/improper_zero.txt similarity index 100% rename from doc/src/improper_zero.txt rename to doc/txt/improper_zero.txt diff --git a/doc/src/impropers.txt b/doc/txt/impropers.txt similarity index 100% rename from doc/src/impropers.txt rename to doc/txt/impropers.txt diff --git a/doc/src/include.txt b/doc/txt/include.txt similarity index 100% rename from doc/src/include.txt rename to doc/txt/include.txt diff --git a/doc/src/info.txt b/doc/txt/info.txt similarity index 100% rename from doc/src/info.txt rename to doc/txt/info.txt diff --git a/doc/src/jump.txt b/doc/txt/jump.txt similarity index 100% rename from doc/src/jump.txt rename to doc/txt/jump.txt diff --git a/doc/src/kim_commands.txt b/doc/txt/kim_commands.txt similarity index 100% rename from doc/src/kim_commands.txt rename to doc/txt/kim_commands.txt diff --git a/doc/src/kspace_modify.txt b/doc/txt/kspace_modify.txt similarity index 100% rename from doc/src/kspace_modify.txt rename to doc/txt/kspace_modify.txt diff --git a/doc/src/kspace_style.txt b/doc/txt/kspace_style.txt similarity index 100% rename from doc/src/kspace_style.txt rename to doc/txt/kspace_style.txt diff --git a/doc/src/label.txt b/doc/txt/label.txt similarity index 100% rename from doc/src/label.txt rename to doc/txt/label.txt diff --git a/doc/src/lammps.book b/doc/txt/lammps.book similarity index 100% rename from doc/src/lammps.book rename to doc/txt/lammps.book diff --git a/doc/src/lammps_commands.txt b/doc/txt/lammps_commands.txt similarity index 100% rename from doc/src/lammps_commands.txt rename to doc/txt/lammps_commands.txt diff --git a/doc/src/lammps_commands_angle.txt b/doc/txt/lammps_commands_angle.txt similarity index 100% rename from doc/src/lammps_commands_angle.txt rename to doc/txt/lammps_commands_angle.txt diff --git a/doc/src/lammps_commands_atc.txt b/doc/txt/lammps_commands_atc.txt similarity index 100% rename from doc/src/lammps_commands_atc.txt rename to doc/txt/lammps_commands_atc.txt diff --git a/doc/src/lammps_commands_bond.txt b/doc/txt/lammps_commands_bond.txt similarity index 100% rename from doc/src/lammps_commands_bond.txt rename to doc/txt/lammps_commands_bond.txt diff --git a/doc/src/lammps_commands_compute.txt b/doc/txt/lammps_commands_compute.txt similarity index 100% rename from doc/src/lammps_commands_compute.txt rename to doc/txt/lammps_commands_compute.txt diff --git a/doc/src/lammps_commands_dihedral.txt b/doc/txt/lammps_commands_dihedral.txt similarity index 100% rename from doc/src/lammps_commands_dihedral.txt rename to doc/txt/lammps_commands_dihedral.txt diff --git a/doc/src/lammps_commands_fix.txt b/doc/txt/lammps_commands_fix.txt similarity index 100% rename from doc/src/lammps_commands_fix.txt rename to doc/txt/lammps_commands_fix.txt diff --git a/doc/src/lammps_commands_improper.txt b/doc/txt/lammps_commands_improper.txt similarity index 100% rename from doc/src/lammps_commands_improper.txt rename to doc/txt/lammps_commands_improper.txt diff --git a/doc/src/lammps_commands_kspace.txt b/doc/txt/lammps_commands_kspace.txt similarity index 100% rename from doc/src/lammps_commands_kspace.txt rename to doc/txt/lammps_commands_kspace.txt diff --git a/doc/src/lammps_commands_pair.txt b/doc/txt/lammps_commands_pair.txt similarity index 100% rename from doc/src/lammps_commands_pair.txt rename to doc/txt/lammps_commands_pair.txt diff --git a/doc/src/lattice.txt b/doc/txt/lattice.txt similarity index 100% rename from doc/src/lattice.txt rename to doc/txt/lattice.txt diff --git a/doc/src/log.txt b/doc/txt/log.txt similarity index 100% rename from doc/src/log.txt rename to doc/txt/log.txt diff --git a/doc/src/mass.txt b/doc/txt/mass.txt similarity index 100% rename from doc/src/mass.txt rename to doc/txt/mass.txt diff --git a/doc/src/message.txt b/doc/txt/message.txt similarity index 100% rename from doc/src/message.txt rename to doc/txt/message.txt diff --git a/doc/src/min_modify.txt b/doc/txt/min_modify.txt similarity index 100% rename from doc/src/min_modify.txt rename to doc/txt/min_modify.txt diff --git a/doc/src/min_spin.txt b/doc/txt/min_spin.txt similarity index 100% rename from doc/src/min_spin.txt rename to doc/txt/min_spin.txt diff --git a/doc/src/min_style.txt b/doc/txt/min_style.txt similarity index 100% rename from doc/src/min_style.txt rename to doc/txt/min_style.txt diff --git a/doc/src/minimize.txt b/doc/txt/minimize.txt similarity index 100% rename from doc/src/minimize.txt rename to doc/txt/minimize.txt diff --git a/doc/src/molecule.txt b/doc/txt/molecule.txt similarity index 100% rename from doc/src/molecule.txt rename to doc/txt/molecule.txt diff --git a/doc/src/neb.txt b/doc/txt/neb.txt similarity index 100% rename from doc/src/neb.txt rename to doc/txt/neb.txt diff --git a/doc/src/neb_spin.txt b/doc/txt/neb_spin.txt similarity index 100% rename from doc/src/neb_spin.txt rename to doc/txt/neb_spin.txt diff --git a/doc/src/neigh_modify.txt b/doc/txt/neigh_modify.txt similarity index 100% rename from doc/src/neigh_modify.txt rename to doc/txt/neigh_modify.txt diff --git a/doc/src/neighbor.txt b/doc/txt/neighbor.txt similarity index 100% rename from doc/src/neighbor.txt rename to doc/txt/neighbor.txt diff --git a/doc/src/newton.txt b/doc/txt/newton.txt similarity index 100% rename from doc/src/newton.txt rename to doc/txt/newton.txt diff --git a/doc/src/next.txt b/doc/txt/next.txt similarity index 100% rename from doc/src/next.txt rename to doc/txt/next.txt diff --git a/doc/src/package.txt b/doc/txt/package.txt similarity index 100% rename from doc/src/package.txt rename to doc/txt/package.txt diff --git a/doc/src/pair_adp.txt b/doc/txt/pair_adp.txt similarity index 100% rename from doc/src/pair_adp.txt rename to doc/txt/pair_adp.txt diff --git a/doc/src/pair_agni.txt b/doc/txt/pair_agni.txt similarity index 100% rename from doc/src/pair_agni.txt rename to doc/txt/pair_agni.txt diff --git a/doc/src/pair_airebo.txt b/doc/txt/pair_airebo.txt similarity index 100% rename from doc/src/pair_airebo.txt rename to doc/txt/pair_airebo.txt diff --git a/doc/src/pair_atm.txt b/doc/txt/pair_atm.txt similarity index 100% rename from doc/src/pair_atm.txt rename to doc/txt/pair_atm.txt diff --git a/doc/src/pair_awpmd.txt b/doc/txt/pair_awpmd.txt similarity index 100% rename from doc/src/pair_awpmd.txt rename to doc/txt/pair_awpmd.txt diff --git a/doc/src/pair_beck.txt b/doc/txt/pair_beck.txt similarity index 100% rename from doc/src/pair_beck.txt rename to doc/txt/pair_beck.txt diff --git a/doc/src/pair_body_nparticle.txt b/doc/txt/pair_body_nparticle.txt similarity index 100% rename from doc/src/pair_body_nparticle.txt rename to doc/txt/pair_body_nparticle.txt diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/txt/pair_body_rounded_polygon.txt similarity index 100% rename from doc/src/pair_body_rounded_polygon.txt rename to doc/txt/pair_body_rounded_polygon.txt diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/txt/pair_body_rounded_polyhedron.txt similarity index 100% rename from doc/src/pair_body_rounded_polyhedron.txt rename to doc/txt/pair_body_rounded_polyhedron.txt diff --git a/doc/src/pair_bop.txt b/doc/txt/pair_bop.txt similarity index 100% rename from doc/src/pair_bop.txt rename to doc/txt/pair_bop.txt diff --git a/doc/src/pair_born.txt b/doc/txt/pair_born.txt similarity index 100% rename from doc/src/pair_born.txt rename to doc/txt/pair_born.txt diff --git a/doc/src/pair_brownian.txt b/doc/txt/pair_brownian.txt similarity index 100% rename from doc/src/pair_brownian.txt rename to doc/txt/pair_brownian.txt diff --git a/doc/src/pair_buck.txt b/doc/txt/pair_buck.txt similarity index 100% rename from doc/src/pair_buck.txt rename to doc/txt/pair_buck.txt diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/txt/pair_buck6d_coul_gauss.txt similarity index 100% rename from doc/src/pair_buck6d_coul_gauss.txt rename to doc/txt/pair_buck6d_coul_gauss.txt diff --git a/doc/src/pair_buck_long.txt b/doc/txt/pair_buck_long.txt similarity index 100% rename from doc/src/pair_buck_long.txt rename to doc/txt/pair_buck_long.txt diff --git a/doc/src/pair_charmm.txt b/doc/txt/pair_charmm.txt similarity index 100% rename from doc/src/pair_charmm.txt rename to doc/txt/pair_charmm.txt diff --git a/doc/src/pair_class2.txt b/doc/txt/pair_class2.txt similarity index 100% rename from doc/src/pair_class2.txt rename to doc/txt/pair_class2.txt diff --git a/doc/src/pair_coeff.txt b/doc/txt/pair_coeff.txt similarity index 100% rename from doc/src/pair_coeff.txt rename to doc/txt/pair_coeff.txt diff --git a/doc/src/pair_colloid.txt b/doc/txt/pair_colloid.txt similarity index 100% rename from doc/src/pair_colloid.txt rename to doc/txt/pair_colloid.txt diff --git a/doc/src/pair_comb.txt b/doc/txt/pair_comb.txt similarity index 100% rename from doc/src/pair_comb.txt rename to doc/txt/pair_comb.txt diff --git a/doc/src/pair_cosine_squared.txt b/doc/txt/pair_cosine_squared.txt similarity index 100% rename from doc/src/pair_cosine_squared.txt rename to doc/txt/pair_cosine_squared.txt diff --git a/doc/src/pair_coul.txt b/doc/txt/pair_coul.txt similarity index 100% rename from doc/src/pair_coul.txt rename to doc/txt/pair_coul.txt diff --git a/doc/src/pair_coul_diel.txt b/doc/txt/pair_coul_diel.txt similarity index 100% rename from doc/src/pair_coul_diel.txt rename to doc/txt/pair_coul_diel.txt diff --git a/doc/src/pair_coul_shield.txt b/doc/txt/pair_coul_shield.txt similarity index 100% rename from doc/src/pair_coul_shield.txt rename to doc/txt/pair_coul_shield.txt diff --git a/doc/src/pair_cs.txt b/doc/txt/pair_cs.txt similarity index 100% rename from doc/src/pair_cs.txt rename to doc/txt/pair_cs.txt diff --git a/doc/src/pair_dipole.txt b/doc/txt/pair_dipole.txt similarity index 100% rename from doc/src/pair_dipole.txt rename to doc/txt/pair_dipole.txt diff --git a/doc/src/pair_dpd.txt b/doc/txt/pair_dpd.txt similarity index 100% rename from doc/src/pair_dpd.txt rename to doc/txt/pair_dpd.txt diff --git a/doc/src/pair_dpd_fdt.txt b/doc/txt/pair_dpd_fdt.txt similarity index 100% rename from doc/src/pair_dpd_fdt.txt rename to doc/txt/pair_dpd_fdt.txt diff --git a/doc/src/pair_drip.txt b/doc/txt/pair_drip.txt similarity index 100% rename from doc/src/pair_drip.txt rename to doc/txt/pair_drip.txt diff --git a/doc/src/pair_dsmc.txt b/doc/txt/pair_dsmc.txt similarity index 100% rename from doc/src/pair_dsmc.txt rename to doc/txt/pair_dsmc.txt diff --git a/doc/src/pair_e3b.txt b/doc/txt/pair_e3b.txt similarity index 100% rename from doc/src/pair_e3b.txt rename to doc/txt/pair_e3b.txt diff --git a/doc/src/pair_eam.txt b/doc/txt/pair_eam.txt similarity index 100% rename from doc/src/pair_eam.txt rename to doc/txt/pair_eam.txt diff --git a/doc/src/pair_edip.txt b/doc/txt/pair_edip.txt similarity index 100% rename from doc/src/pair_edip.txt rename to doc/txt/pair_edip.txt diff --git a/doc/src/pair_eff.txt b/doc/txt/pair_eff.txt similarity index 100% rename from doc/src/pair_eff.txt rename to doc/txt/pair_eff.txt diff --git a/doc/src/pair_eim.txt b/doc/txt/pair_eim.txt similarity index 100% rename from doc/src/pair_eim.txt rename to doc/txt/pair_eim.txt diff --git a/doc/src/pair_exp6_rx.txt b/doc/txt/pair_exp6_rx.txt similarity index 100% rename from doc/src/pair_exp6_rx.txt rename to doc/txt/pair_exp6_rx.txt diff --git a/doc/src/pair_extep.txt b/doc/txt/pair_extep.txt similarity index 100% rename from doc/src/pair_extep.txt rename to doc/txt/pair_extep.txt diff --git a/doc/src/pair_fep_soft.txt b/doc/txt/pair_fep_soft.txt similarity index 100% rename from doc/src/pair_fep_soft.txt rename to doc/txt/pair_fep_soft.txt diff --git a/doc/src/pair_gauss.txt b/doc/txt/pair_gauss.txt similarity index 100% rename from doc/src/pair_gauss.txt rename to doc/txt/pair_gauss.txt diff --git a/doc/src/pair_gayberne.txt b/doc/txt/pair_gayberne.txt similarity index 100% rename from doc/src/pair_gayberne.txt rename to doc/txt/pair_gayberne.txt diff --git a/doc/src/pair_gran.txt b/doc/txt/pair_gran.txt similarity index 100% rename from doc/src/pair_gran.txt rename to doc/txt/pair_gran.txt diff --git a/doc/src/pair_granular.txt b/doc/txt/pair_granular.txt similarity index 100% rename from doc/src/pair_granular.txt rename to doc/txt/pair_granular.txt diff --git a/doc/src/pair_gromacs.txt b/doc/txt/pair_gromacs.txt similarity index 100% rename from doc/src/pair_gromacs.txt rename to doc/txt/pair_gromacs.txt diff --git a/doc/src/pair_gw.txt b/doc/txt/pair_gw.txt similarity index 100% rename from doc/src/pair_gw.txt rename to doc/txt/pair_gw.txt diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/txt/pair_hbond_dreiding.txt similarity index 100% rename from doc/src/pair_hbond_dreiding.txt rename to doc/txt/pair_hbond_dreiding.txt diff --git a/doc/src/pair_hybrid.txt b/doc/txt/pair_hybrid.txt similarity index 100% rename from doc/src/pair_hybrid.txt rename to doc/txt/pair_hybrid.txt diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/txt/pair_ilp_graphene_hbn.txt similarity index 100% rename from doc/src/pair_ilp_graphene_hbn.txt rename to doc/txt/pair_ilp_graphene_hbn.txt diff --git a/doc/src/pair_kim.txt b/doc/txt/pair_kim.txt similarity index 100% rename from doc/src/pair_kim.txt rename to doc/txt/pair_kim.txt diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/txt/pair_kolmogorov_crespi_full.txt similarity index 100% rename from doc/src/pair_kolmogorov_crespi_full.txt rename to doc/txt/pair_kolmogorov_crespi_full.txt diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/txt/pair_kolmogorov_crespi_z.txt similarity index 100% rename from doc/src/pair_kolmogorov_crespi_z.txt rename to doc/txt/pair_kolmogorov_crespi_z.txt diff --git a/doc/src/pair_lcbop.txt b/doc/txt/pair_lcbop.txt similarity index 100% rename from doc/src/pair_lcbop.txt rename to doc/txt/pair_lcbop.txt diff --git a/doc/src/pair_lebedeva_z.txt b/doc/txt/pair_lebedeva_z.txt similarity index 100% rename from doc/src/pair_lebedeva_z.txt rename to doc/txt/pair_lebedeva_z.txt diff --git a/doc/src/pair_line_lj.txt b/doc/txt/pair_line_lj.txt similarity index 100% rename from doc/src/pair_line_lj.txt rename to doc/txt/pair_line_lj.txt diff --git a/doc/src/pair_list.txt b/doc/txt/pair_list.txt similarity index 100% rename from doc/src/pair_list.txt rename to doc/txt/pair_list.txt diff --git a/doc/src/pair_lj.txt b/doc/txt/pair_lj.txt similarity index 100% rename from doc/src/pair_lj.txt rename to doc/txt/pair_lj.txt diff --git a/doc/src/pair_lj96.txt b/doc/txt/pair_lj96.txt similarity index 100% rename from doc/src/pair_lj96.txt rename to doc/txt/pair_lj96.txt diff --git a/doc/src/pair_lj_cubic.txt b/doc/txt/pair_lj_cubic.txt similarity index 100% rename from doc/src/pair_lj_cubic.txt rename to doc/txt/pair_lj_cubic.txt diff --git a/doc/src/pair_lj_expand.txt b/doc/txt/pair_lj_expand.txt similarity index 100% rename from doc/src/pair_lj_expand.txt rename to doc/txt/pair_lj_expand.txt diff --git a/doc/src/pair_lj_long.txt b/doc/txt/pair_lj_long.txt similarity index 100% rename from doc/src/pair_lj_long.txt rename to doc/txt/pair_lj_long.txt diff --git a/doc/src/pair_lj_smooth.txt b/doc/txt/pair_lj_smooth.txt similarity index 100% rename from doc/src/pair_lj_smooth.txt rename to doc/txt/pair_lj_smooth.txt diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/txt/pair_lj_smooth_linear.txt similarity index 100% rename from doc/src/pair_lj_smooth_linear.txt rename to doc/txt/pair_lj_smooth_linear.txt diff --git a/doc/src/pair_lj_switch3_coulgauss.txt b/doc/txt/pair_lj_switch3_coulgauss.txt similarity index 100% rename from doc/src/pair_lj_switch3_coulgauss.txt rename to doc/txt/pair_lj_switch3_coulgauss.txt diff --git a/doc/src/pair_local_density.txt b/doc/txt/pair_local_density.txt similarity index 100% rename from doc/src/pair_local_density.txt rename to doc/txt/pair_local_density.txt diff --git a/doc/src/pair_lubricate.txt b/doc/txt/pair_lubricate.txt similarity index 100% rename from doc/src/pair_lubricate.txt rename to doc/txt/pair_lubricate.txt diff --git a/doc/src/pair_lubricateU.txt b/doc/txt/pair_lubricateU.txt similarity index 100% rename from doc/src/pair_lubricateU.txt rename to doc/txt/pair_lubricateU.txt diff --git a/doc/src/pair_mdf.txt b/doc/txt/pair_mdf.txt similarity index 100% rename from doc/src/pair_mdf.txt rename to doc/txt/pair_mdf.txt diff --git a/doc/src/pair_meam_spline.txt b/doc/txt/pair_meam_spline.txt similarity index 100% rename from doc/src/pair_meam_spline.txt rename to doc/txt/pair_meam_spline.txt diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/txt/pair_meam_sw_spline.txt similarity index 100% rename from doc/src/pair_meam_sw_spline.txt rename to doc/txt/pair_meam_sw_spline.txt diff --git a/doc/src/pair_meamc.txt b/doc/txt/pair_meamc.txt similarity index 100% rename from doc/src/pair_meamc.txt rename to doc/txt/pair_meamc.txt diff --git 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 doc/txt/pair_reaxc.txt diff --git a/doc/src/pair_resquared.txt b/doc/txt/pair_resquared.txt similarity index 100% rename from doc/src/pair_resquared.txt rename to doc/txt/pair_resquared.txt diff --git a/doc/src/pair_sdk.txt b/doc/txt/pair_sdk.txt similarity index 100% rename from doc/src/pair_sdk.txt rename to doc/txt/pair_sdk.txt diff --git a/doc/src/pair_sdpd_taitwater_isothermal.txt b/doc/txt/pair_sdpd_taitwater_isothermal.txt similarity index 100% rename from doc/src/pair_sdpd_taitwater_isothermal.txt rename to doc/txt/pair_sdpd_taitwater_isothermal.txt diff --git a/doc/src/pair_smd_hertz.txt b/doc/txt/pair_smd_hertz.txt similarity index 100% rename from doc/src/pair_smd_hertz.txt rename to doc/txt/pair_smd_hertz.txt diff --git a/doc/src/pair_smd_tlsph.txt b/doc/txt/pair_smd_tlsph.txt similarity index 100% rename from doc/src/pair_smd_tlsph.txt rename to doc/txt/pair_smd_tlsph.txt diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/txt/pair_smd_triangulated_surface.txt 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 doc/txt/pair_style.txt diff --git a/doc/src/pair_sw.txt b/doc/txt/pair_sw.txt similarity index 100% rename from doc/src/pair_sw.txt rename to doc/txt/pair_sw.txt diff --git a/doc/src/pair_table.txt b/doc/txt/pair_table.txt similarity index 100% rename from doc/src/pair_table.txt rename to doc/txt/pair_table.txt diff --git a/doc/src/pair_table_rx.txt b/doc/txt/pair_table_rx.txt similarity index 100% rename from doc/src/pair_table_rx.txt rename to doc/txt/pair_table_rx.txt diff --git a/doc/src/pair_tersoff.txt b/doc/txt/pair_tersoff.txt similarity index 100% rename from doc/src/pair_tersoff.txt rename to doc/txt/pair_tersoff.txt diff --git a/doc/src/pair_tersoff_mod.txt b/doc/txt/pair_tersoff_mod.txt similarity index 100% rename from doc/src/pair_tersoff_mod.txt rename to doc/txt/pair_tersoff_mod.txt diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/txt/pair_tersoff_zbl.txt similarity index 100% rename from doc/src/pair_tersoff_zbl.txt rename to doc/txt/pair_tersoff_zbl.txt diff --git a/doc/src/pair_thole.txt b/doc/txt/pair_thole.txt similarity index 100% rename from doc/src/pair_thole.txt rename to doc/txt/pair_thole.txt diff --git a/doc/src/pair_tri_lj.txt b/doc/txt/pair_tri_lj.txt similarity index 100% rename from doc/src/pair_tri_lj.txt rename to doc/txt/pair_tri_lj.txt diff --git a/doc/src/pair_ufm.txt b/doc/txt/pair_ufm.txt similarity index 100% rename from doc/src/pair_ufm.txt rename to doc/txt/pair_ufm.txt diff --git a/doc/src/pair_vashishta.txt b/doc/txt/pair_vashishta.txt similarity index 100% rename from doc/src/pair_vashishta.txt rename to doc/txt/pair_vashishta.txt diff --git a/doc/src/pair_write.txt b/doc/txt/pair_write.txt similarity index 100% rename from doc/src/pair_write.txt rename to doc/txt/pair_write.txt diff --git a/doc/src/pair_yukawa.txt b/doc/txt/pair_yukawa.txt similarity index 100% rename from doc/src/pair_yukawa.txt rename to doc/txt/pair_yukawa.txt diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/txt/pair_yukawa_colloid.txt similarity index 100% rename from doc/src/pair_yukawa_colloid.txt rename to doc/txt/pair_yukawa_colloid.txt diff --git a/doc/src/pair_zbl.txt b/doc/txt/pair_zbl.txt similarity index 100% rename from doc/src/pair_zbl.txt rename to doc/txt/pair_zbl.txt diff --git a/doc/src/pair_zero.txt b/doc/txt/pair_zero.txt similarity index 100% rename from doc/src/pair_zero.txt rename to doc/txt/pair_zero.txt diff --git a/doc/src/partition.txt b/doc/txt/partition.txt similarity index 100% rename from doc/src/partition.txt rename to doc/txt/partition.txt diff --git a/doc/src/prd.txt b/doc/txt/prd.txt similarity index 100% rename from doc/src/prd.txt rename to doc/txt/prd.txt diff --git a/doc/src/print.txt b/doc/txt/print.txt similarity index 100% rename from doc/src/print.txt rename to doc/txt/print.txt diff --git a/doc/src/processors.txt b/doc/txt/processors.txt similarity index 100% rename from doc/src/processors.txt rename to doc/txt/processors.txt diff --git a/doc/src/python.txt b/doc/txt/python.txt similarity index 100% rename from doc/src/python.txt rename to doc/txt/python.txt diff --git a/doc/src/quit.txt b/doc/txt/quit.txt similarity index 100% rename from doc/src/quit.txt rename to doc/txt/quit.txt diff --git a/doc/src/read_data.txt b/doc/txt/read_data.txt similarity index 100% rename from doc/src/read_data.txt rename to doc/txt/read_data.txt diff --git a/doc/src/read_dump.txt b/doc/txt/read_dump.txt similarity index 100% rename from doc/src/read_dump.txt rename to doc/txt/read_dump.txt diff --git a/doc/src/read_restart.txt b/doc/txt/read_restart.txt similarity index 100% rename from doc/src/read_restart.txt rename to doc/txt/read_restart.txt diff --git a/doc/src/region.txt b/doc/txt/region.txt similarity index 100% rename from doc/src/region.txt rename to doc/txt/region.txt diff --git a/doc/src/replicate.txt b/doc/txt/replicate.txt similarity index 100% rename from doc/src/replicate.txt rename to doc/txt/replicate.txt diff --git a/doc/src/rerun.txt b/doc/txt/rerun.txt similarity index 100% rename from doc/src/rerun.txt rename to doc/txt/rerun.txt diff --git a/doc/src/reset_ids.txt b/doc/txt/reset_ids.txt similarity index 100% rename from doc/src/reset_ids.txt rename to doc/txt/reset_ids.txt diff --git a/doc/src/reset_timestep.txt b/doc/txt/reset_timestep.txt similarity index 100% rename from doc/src/reset_timestep.txt rename to doc/txt/reset_timestep.txt diff --git a/doc/src/restart.txt b/doc/txt/restart.txt similarity index 100% rename from doc/src/restart.txt rename to doc/txt/restart.txt diff --git a/doc/src/run.txt b/doc/txt/run.txt similarity index 100% rename from doc/src/run.txt rename to doc/txt/run.txt diff --git a/doc/src/run_style.txt b/doc/txt/run_style.txt similarity index 100% rename from doc/src/run_style.txt rename to doc/txt/run_style.txt diff --git a/doc/src/server.txt b/doc/txt/server.txt similarity index 100% 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 doc/src/tad.txt rename to doc/txt/tad.txt diff --git a/doc/src/temper.txt b/doc/txt/temper.txt similarity index 100% rename from doc/src/temper.txt rename to doc/txt/temper.txt diff --git a/doc/src/temper_grem.txt b/doc/txt/temper_grem.txt similarity index 100% rename from doc/src/temper_grem.txt rename to doc/txt/temper_grem.txt diff --git a/doc/src/temper_npt.txt b/doc/txt/temper_npt.txt similarity index 100% rename from doc/src/temper_npt.txt rename to doc/txt/temper_npt.txt diff --git a/doc/src/thermo.txt b/doc/txt/thermo.txt similarity index 100% rename from doc/src/thermo.txt rename to doc/txt/thermo.txt diff --git a/doc/src/thermo_modify.txt b/doc/txt/thermo_modify.txt similarity index 100% rename from doc/src/thermo_modify.txt rename to doc/txt/thermo_modify.txt diff --git a/doc/src/thermo_style.txt b/doc/txt/thermo_style.txt similarity index 100% rename from doc/src/thermo_style.txt rename to doc/txt/thermo_style.txt diff --git a/doc/src/third_order.txt 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 diff --git a/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py new file mode 100644 index 0000000000000000000000000000000000000000..353eed8b6e197f7519bbbe8f90d405d87708f766 --- /dev/null +++ b/doc/utils/converters/lammpsdoc/eqImg2mathjaxInline.py @@ -0,0 +1,255 @@ +#! /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 shutil +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') + +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"] + +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: + # 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 + 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: + 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. ' + modifiedRstFolder) + 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() + print(parsed_args) + + 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, + # files from both original and modified folders + # zombie modifications + if len(parsed_args.files) > 1: + 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) + except Exception as e: + print(e) + sys.exit(1) + + for filename in parsed_args.files: + print("filename: %s" % filename) + 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 0000000000000000000000000000000000000000..9c097e7d0e596187da3449843b46fb6bb0efbec5 --- /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 f4656a7f697cc6e0dd7235ac873b2201a0d299d2..d85669bcc1097c41d1fc5084d2f80d2e689249e8 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 '] }, )