Merge branch 'master' into fix-dummy

sync with latest whitespace changes

doc/Makefile

@@ -1,11 +1,12 @@
 # Makefile for LAMMPS documentation
 
 SHELL         = /bin/bash
-BUILDDIR      = ${PWD}
+BUILDDIR      = ${CURDIR}
-RSTDIR        = $(BUILDDIR)/rst
+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))
+SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt))
-OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
+OBJECTS=$(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 ;\
+		rst_anchor_check src/*.rst ;\
-		env LC_ALL=C grep -n '[^ -~]' src/*.txt ;\
+		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 ;\
 	)
 

doc/rst/angles.rst

@@ -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
-

doc/rst/bonds.rst

@@ -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
-

doc/rst/computes.rst

@@ -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
-

doc/rst/dihedrals.rst

@@ -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
-

doc/rst/fixes.rst

@@ -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
-

doc/rst/impropers.rst

@@ -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
-

doc/rst/pairs.rst

@@ -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
-

doc/src/Build_extras.rst

@@ -1254,11 +1254,11 @@ lib/quip/README file for details on how to do this.
 
 .. parsed-literal::
 
-   -D QUIP_LIBRARIES=path     # path to libquip.a (only needed if a custom location)
+   -D QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location)
 
 CMake will not download and build the QUIP library.  But once you have
 done that, a CMake build of LAMMPS with "-D PKG\_USER-QUIP=yes" should
-work.  Set QUIP\_LIBRARIES if CMake cannot find the QUIP library.
+work.  Set QUIP\_LIBRARY if CMake cannot find the QUIP library.
 
 **Traditional make**\ :
 

doc/src/Manual.rst

@@ -1,8 +1,8 @@
 LAMMPS Documentation
 ####################
 
-30 Oct 2019 version
+|version| version
-*******************
+*****************
 
 :doc:`What is a LAMMPS version? <Manual_version>`
 

doc/src/Manual.txt

@@ -1,124 +0,0 @@
-<!-- HTML_ONLY -->
-<HEAD>
-<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="30 Oct 2019 version">
-<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
-<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
-</HEAD>
-
-<BODY>
-
-<H1></H1>
-
-<!-- END_HTML_ONLY -->
-
-"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.
-
-<!-- RST
-
-.. toctree::
-   :maxdepth: 2
-   :numbered: 3
-   :caption: User Documentation
-   :name: userdoc
-   :includehidden:
-
-   Intro
-   Install
-   Build
-   Run_head
-   Commands
-   Packages
-   Speed
-   Howto
-   Examples
-   Tools
-   Modify
-   Python_head
-   Errors
-   Manual_build
-
-.. toctree::
-   :caption: Index
-   :name: index
-   :hidden:
-
-   commands_list
-   fixes
-   computes
-   pairs
-   bonds
-   angles
-   dihedrals
-   impropers
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`search`
-
-END_RST -->
-
-<!-- HTML_ONLY -->
-"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
-
-<!-- END_HTML_ONLY -->
-
-</BODY>