Commit f2795f26 authored by Steve Plimpton's avatar Steve Plimpton
Browse files

Merge branch 'master' into fix-dummy 

sync with latest whitespace changes
parents 6af726e5 bb18adc7

doc/Makefile

+12 −13
Original line number Diff line number Diff line 
# 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 ;\

	)
@@ -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

deleted100644 → 0
+0 −29
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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

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+0 −24
Original line number Diff line number Diff line 
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

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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

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+0 −39
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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

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