Merge branch 'master' into fft (2834965e) · Commits · 郑智淋 / lammps

doc/Makefile

+29 −17

Original line number	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 $(TXTDIR)/.txt))
		OBJECTS=$(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-all reset the entire build environment"
		@echo " anchor_check scan for duplicate anchor labels"
		@echo " style_check check for complete and consistent style lists"
		@echo " spelling spell-check the manual"

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

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

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

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

doc/src/Manual_build.rst

+3 −3

Original line number	Diff line number	Diff line
		@@ -55,8 +55,8 @@ the doc dir.
		make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
		make clean # remove intermediate RST files created by HTML build
		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

doc/src/bond_style.rst

+1 −0

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

doc/src/fix.rst

+12 −10

Original line number	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
		same order relative to the existing fixes as the old one originally
		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
		fixes to be reset. See the doc page for individual fixes for details.

		Some fixes store an internal "state" which is written to binary
		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
		: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
		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:

		* 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
		:doc:`variable atom <variable>` 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/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/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/asphere <fix_nph_asphere>` - NPH for aspherical particles
		* :doc:`nph/body <fix_nph_body>` - NPH for body particles
		@@ -339,15 +340,16 @@ accelerated styles exist.
		* :doc:`rx <fix_rx>` -
		* :doc:`saed/vtk <fix_saed_vtk>` -
		* :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:`shardlow <fix_shardlow>` - integration of DPD equations of motion using the Shardlow splitting
		* :doc:`smd <fix_smd>` - applied a steered MD force to a group
		* :doc:`smd/adjust\_dt <fix_smd_adjust_dt>` -
		* :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` -
		* :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>` -
		* :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` -
		* :doc:`smd/adjust_dt <fix_smd_adjust_dt>` -
		* :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>` -
		* :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>` -
		* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>` -
		* :doc:`smd/setvel <fix_smd_setvel>` -
		* :doc:`smd/wall\_surface <fix_smd_wall_surface>` -
		* :doc:`smd/wall_surface <fix_smd_wall_surface>` -
		* :doc:`spring <fix_spring>` - apply harmonic spring force to group of atoms
		* :doc:`spring/chunk <fix_spring_chunk>` - apply harmonic spring force to each chunk of atoms
		* :doc:`spring/rg <fix_spring_rg>` - spring on radius of gyration of group of atoms
		@@ -399,7 +401,7 @@ individual fixes tell if it is part of a package.
		Related commands
		""""""""""""""""

		:doc:`unfix <unfix>`, :doc:`fix\_modify <fix_modify>`
		:doc:`unfix <unfix>`, :doc:`fix_modify <fix_modify>`

		Default: none

doc/src/pair_modify.rst

+5 −2

Original line number	Diff line number	Diff line
		@@ -247,7 +247,9 @@ or lj/coul to change both to the same set of 3 values. The wt1,wt2,wt3
		values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
		1-3, and 1-4 bond topology neighbors, respectively. The special
		keyword can only be used in conjunction with the pair keyword
		and has to directly follow it.
		and has to directly follow it. This option is not compatible with
		pair styles from the GPU or the USER-INTEL package and attempting
		it will cause an error.

		.. note::

		@@ -278,10 +280,11 @@ and allows to selectively disable or enable processing of the various

		Restrictions
		""""""""""""
		none

		You cannot use shift yes with tail yes, since those are
		conflicting options. You cannot use tail yes with 2d simulations.
		You cannot use special with pair styles from the GPU or
		USER-INTEL package.

		Related commands
		""""""""""""""""

Admin message