Merge pull request #1832 from akohlmey/doc-styles-check (6813ab4c) · Commits · 郑智淋 / lammps

doc/Makefile

+29 −17

Original line number	Original line	Diff line number	Diff line
	@@ -31,7 +31,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
	SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/.txt))		SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/.txt))
	OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)		OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)

	.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check		.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check style_check

	# ------------------------------------------		# ------------------------------------------

	@@ -46,6 +46,7 @@ help:
	@echo " clean remove all intermediate RST files"		@echo " clean remove all intermediate RST files"
	@echo " clean-all reset the entire build environment"		@echo " clean-all reset the entire build environment"
	@echo " anchor_check scan for duplicate anchor labels"		@echo " anchor_check scan for duplicate anchor labels"
			@echo " style_check check for complete and consistent style lists"
	@echo " spelling spell-check the manual"		@echo " spelling spell-check the manual"

	# ------------------------------------------		# ------------------------------------------
	@@ -69,6 +70,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
	echo "############################################" ;\		echo "############################################" ;\
	rst_anchor_check src/*.rst ;\		rst_anchor_check src/*.rst ;\
	env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
			python utils/check-styles.py -s ../src -d src ;\
	echo "############################################" ;\		echo "############################################" ;\
	deactivate ;\		deactivate ;\
	)		)
	@@ -126,6 +128,8 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
	sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\		sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
	echo "############################################" ;\		echo "############################################" ;\
	rst_anchor_check src/*.rst ;\		rst_anchor_check src/*.rst ;\
			env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
			python utils/check-styles.py -s ../src -d src ;\
	echo "############################################" ;\		echo "############################################" ;\
	deactivate ;\		deactivate ;\
	)		)
	@@ -138,6 +142,7 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
	mv tmp.tex LAMMPS.tex && \		mv tmp.tex LAMMPS.tex && \
	make && \		make && \
	make && \		make && \
			make && \
	mv LAMMPS.pdf ../Manual.pdf && \		mv LAMMPS.pdf ../Manual.pdf && \
	cd ../;		cd ../;
	@rm -rf latex/_sources		@rm -rf latex/_sources
	@@ -166,6 +171,13 @@ anchor_check : $(ANCHORCHECK)
	deactivate ;\		deactivate ;\
	)		)

			style_check :
			@(\
			. $(VENV)/bin/activate ;\
			python utils/check-styles.py -s ../src -d src ;\
			deactivate ;\
			)

	# ------------------------------------------		# ------------------------------------------

	$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)		$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)

doc/src/Manual_build.rst

+3 −3

Original line number	Original line	Diff line number	Diff line
	@@ -55,8 +55,8 @@ the doc dir.
	make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert		make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
	make clean # remove intermediate RST files created by HTML build		make clean # remove intermediate RST files created by HTML build
	make clean-all # remove entire build folder and any cached data		make clean-all # remove entire build folder and any cached data
			make anchor_check # check for duplicate anchor labels
	make anchor\_check # check for duplicate anchor labels		style_check # check for complete and consistent style lists
	make spelling # spell-check the manual		make spelling # spell-check the manual

doc/src/bond_style.rst

+1 −0

Original line number	Original line	Diff line number	Diff line
	@@ -100,6 +100,7 @@ accelerated styles exist.
	* :doc:`nonlinear <bond_nonlinear>` - nonlinear bond		* :doc:`nonlinear <bond_nonlinear>` - nonlinear bond
	* :doc:`oxdna/fene <bond_oxdna>` - modified FENE bond suitable for DNA modeling		* :doc:`oxdna/fene <bond_oxdna>` - modified FENE bond suitable for DNA modeling
	* :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles		* :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
			* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
	* :doc:`quartic <bond_quartic>` - breakable quartic bond		* :doc:`quartic <bond_quartic>` - breakable quartic bond
	* :doc:`table <bond_table>` - tabulated by bond length		* :doc:`table <bond_table>` - tabulated by bond length

doc/src/fix.rst

+12 −10

doc/src/pair_style.rst

+20 −13

Original line number	Original line	Diff line number	Diff line
	@@ -64,16 +64,16 @@ with new settings). This is the same as if an "unfix" command were
	first performed on the old fix, except that the new fix is kept in the		first performed on the old fix, except that the new fix is kept in the
	same order relative to the existing fixes as the old one originally		same order relative to the existing fixes as the old one originally
	was. Note that this operation also wipes out any additional changes		was. Note that this operation also wipes out any additional changes
	made to the old fix via the :doc:`fix\_modify <fix_modify>` command.		made to the old fix via the :doc:`fix_modify <fix_modify>` command.

	The :doc:`fix modify <fix_modify>` command allows settings for some		The :doc:`fix modify <fix_modify>` command allows settings for some
	fixes to be reset. See the doc page for individual fixes for details.		fixes to be reset. See the doc page for individual fixes for details.

	Some fixes store an internal "state" which is written to binary		Some fixes store an internal "state" which is written to binary
	restart files via the :doc:`restart <restart>` or		restart files via the :doc:`restart <restart>` or
	:doc:`write\_restart <write_restart>` commands. This allows the fix to		:doc:`write_restart <write_restart>` commands. This allows the fix to
	continue on with its calculations in a restarted simulation. See the		continue on with its calculations in a restarted simulation. See the
	:doc:`read\_restart <read_restart>` command for info on how to re-specify		:doc:`read_restart <read_restart>` command for info on how to re-specify
	a fix in an input script that reads a restart file. See the doc pages		a fix in an input script that reads a restart file. See the doc pages
	for individual fixes for info on which ones can be restarted.		for individual fixes for info on which ones can be restarted.

	@@ -133,7 +133,7 @@ various commands explain the details.

	In LAMMPS, the values generated by a fix can be used in several ways:		In LAMMPS, the values generated by a fix can be used in several ways:

	* Global values can be output via the :doc:`thermo\_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.		* Global values can be output via the :doc:`thermo_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
	Or the values can be referenced in a :doc:`variable equal <variable>` or		Or the values can be referenced in a :doc:`variable equal <variable>` or
	:doc:`variable atom <variable>` command.		:doc:`variable atom <variable>` command.
	* Per-atom values can be output via the :doc:`dump custom <dump>` command.		* Per-atom values can be output via the :doc:`dump custom <dump>` command.
	@@ -257,6 +257,7 @@ accelerated styles exist.
	* :doc:`mvv/edpd <fix_mvv_dpd>` - constant energy DPD using the modified velocity-Verlet algorithm		* :doc:`mvv/edpd <fix_mvv_dpd>` - constant energy DPD using the modified velocity-Verlet algorithm
	* :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm		* :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
	* :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces		* :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
			* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
	* :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover		* :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
	* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles		* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
	* :doc:`nph/body <fix_nph_body>` - NPH for body particles		* :doc:`nph/body <fix_nph_body>` - NPH for body particles
	@@ -339,15 +340,16 @@ accelerated styles exist.
	* :doc:`rx <fix_rx>` -		* :doc:`rx <fix_rx>` -
	* :doc:`saed/vtk <fix_saed_vtk>` -		* :doc:`saed/vtk <fix_saed_vtk>` -
	* :doc:`setforce <fix_setforce>` - set the force on each atom		* :doc:`setforce <fix_setforce>` - set the force on each atom
			* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
	* :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles		* :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles
	* :doc:`shardlow <fix_shardlow>` - integration of DPD equations of motion using the Shardlow splitting		* :doc:`shardlow <fix_shardlow>` - integration of DPD equations of motion using the Shardlow splitting

Original line number	Original line	Diff line number	Diff line
	@@ -32,7 +32,7 @@ Description
	Set the formula(s) LAMMPS uses to compute pairwise interactions. In		Set the formula(s) LAMMPS uses to compute pairwise interactions. In
	LAMMPS, pair potentials are defined between pairs of atoms that are		LAMMPS, pair potentials are defined between pairs of atoms that are
	within a cutoff distance and the set of active interactions typically		within a cutoff distance and the set of active interactions typically
	changes over time. See the :doc:`bond\_style <bond_style>` command to		changes over time. See the :doc:`bond_style <bond_style>` command to
	define potentials between pairs of bonded atoms, which typically		define potentials between pairs of bonded atoms, which typically
	remain in place for the duration of a simulation.		remain in place for the duration of a simulation.

	@@ -48,11 +48,11 @@ different pair potentials can be setup using the hybrid pair style.

	The coefficients associated with a pair style are typically set for		The coefficients associated with a pair style are typically set for
	each pair of atom types, and are specified by the		each pair of atom types, and are specified by the
	:doc:`pair\_coeff <pair_coeff>` command or read from a file by the		:doc:`pair_coeff <pair_coeff>` command or read from a file by the
	:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`		:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
	commands.		commands.

	The :doc:`pair\_modify <pair_modify>` command sets options for mixing of		The :doc:`pair_modify <pair_modify>` command sets options for mixing of
	type I-J interaction coefficients and adding energy offsets or tail		type I-J interaction coefficients and adding energy offsets or tail
	corrections to Lennard-Jones potentials. Details on these options as		corrections to Lennard-Jones potentials. Details on these options as
	they pertain to individual potentials are described on the doc page		they pertain to individual potentials are described on the doc page
	@@ -70,11 +70,11 @@ cutoffs for all pairs of atom types. The distance(s) can be smaller
	or larger than the dimensions of the simulation box.		or larger than the dimensions of the simulation box.

	Typically, the global cutoff value can be overridden for a specific		Typically, the global cutoff value can be overridden for a specific
	pair of atom types by the :doc:`pair\_coeff <pair_coeff>` command. The		pair of atom types by the :doc:`pair_coeff <pair_coeff>` command. The
	pair style settings (including global cutoffs) can be changed by a		pair style settings (including global cutoffs) can be changed by a
	subsequent pair\_style command using the same style. This will reset		subsequent pair\_style command using the same style. This will reset
	the cutoffs for all atom type pairs, including those previously set		the cutoffs for all atom type pairs, including those previously set
	explicitly by a :doc:`pair\_coeff <pair_coeff>` command. The exceptions		explicitly by a :doc:`pair_coeff <pair_coeff>` command. The exceptions
	to this are that pair\_style table and hybrid settings cannot be		to this are that pair\_style table and hybrid settings cannot be
	reset. A new pair\_style command for these styles will wipe out all		reset. A new pair\_style command for these styles will wipe out all
	previously specified pair\_coeff values.		previously specified pair\_coeff values.
	@@ -88,7 +88,7 @@ also listed in more compact form on the :doc:`Commands pair <Commands_pair>` doc

	Click on the style to display the formula it computes, any additional		Click on the style to display the formula it computes, any additional
	arguments specified in the pair\_style command, and coefficients		arguments specified in the pair\_style command, and coefficients
	specified by the associated :doc:`pair\_coeff <pair_coeff>` command.		specified by the associated :doc:`pair_coeff <pair_coeff>` command.

	There are also additional accelerated pair styles included in the		There are also additional accelerated pair styles included in the
	LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.		LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.

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