forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15041 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
212f64d2f1
commit
9653976f05
36
doc/Makefile
36
doc/Makefile
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@ -29,33 +29,40 @@ help:
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@echo " clean-all to reset the entire build environment"
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@echo " clean-all to reset the entire build environment"
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||||||
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clean-all:
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clean-all:
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rm -rf $(BUILDDIR)/*
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rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
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clean:
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clean:
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rm -rf $(RSTDIR)
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rm -rf $(RSTDIR)
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txt2html: utils/txt2html/txt2html.exe
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html: $(OBJECTS)
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html: $(OBJECTS)
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@(\
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@(\
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source $(VENV)/bin/activate ;\
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. $(VENV)/bin/activate ;\
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cp -r src/* $(RSTDIR)/ ;\
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cp -r src/* $(RSTDIR)/ ;\
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sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
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sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
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deactivate ;\
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deactivate ;\
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)
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)
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@echo "Build finished. The HTML pages are in doc/html."
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@echo "Build finished. The HTML pages are in doc/html."
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pdf:
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pdf: utils/txt2html/txt2html.exe
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cd src; ../utils/txt2html/txt2html -b *.txt
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@(\
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cd src; htmldoc --title --toctitle "Table of Contents" --tocfooter ..i --toclevels 4 --header ... --footer ..1 --size letter --linkstyle plain --linkcolor blue -f Manual.pdf Manual.html Section_intro.html Section_start.html Section_commands.html Section_packages.html Section_accelerate.html Section_howto.html Section_example.html Section_perf.html Section_tools.html Section_modify.html Section_python.html Section_errors.html Section_history.html [a-z]*.html
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cd src; \
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cd src; mv Manual.pdf ..
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../utils/txt2html/txt2html.exe -b *.txt; \
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cd src; rm *.html
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htmldoc --batch ../lammps.book; \
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for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
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do grep -q $$s ../lammps.book || \
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echo doc file $$s missing in lammps.book; done; \
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rm *.html; \
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)
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txt2html:
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utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
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cd utils/txt2html; g++ -O txt2html.cpp -o txt2html
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g++ -O -Wall -o $@ $<
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$(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
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$(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
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@(\
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@(\
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mkdir -p $(RSTDIR) ; \
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mkdir -p $(RSTDIR) ; \
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source $(VENV)/bin/activate ;\
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. $(VENV)/bin/activate ;\
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txt2rst $< > $@ ;\
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txt2rst $< > $@ ;\
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deactivate ;\
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deactivate ;\
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)
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)
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@ -63,7 +70,7 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
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$(VENV):
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$(VENV):
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@( \
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@( \
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virtualenv -p $(PYTHON) $(VENV); \
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virtualenv -p $(PYTHON) $(VENV); \
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source $(VENV)/bin/activate; \
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. $(VENV)/bin/activate; \
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pip install Sphinx; \
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pip install Sphinx; \
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pip install sphinxcontrib-images; \
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pip install sphinxcontrib-images; \
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deactivate;\
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deactivate;\
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@ -71,9 +78,8 @@ $(VENV):
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$(TXT2RST): $(VENV)
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$(TXT2RST): $(VENV)
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@( \
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@( \
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source $(VENV)/bin/activate; \
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. $(VENV)/bin/activate; \
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pushd utils/converters;\
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(cd utils/converters;\
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python setup.py develop;\
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python setup.py develop);\
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popd;\
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deactivate;\
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deactivate;\
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)
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)
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@ -0,0 +1,526 @@
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#HTMLDOC 1.8.27
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-t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=1 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont helvetica --bodyfont times --headfootsize 11.0 --headfootfont helvetica --charset iso-8859-1 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow
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Manual.html
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Section_intro.html
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Section_start.html
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Section_commands.html
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Section_packages.html
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Section_accelerate.html
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accelerate_cuda.html
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accelerate_gpu.html
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accelerate_intel.html
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accelerate_kokkos.html
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accelerate_omp.html
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accelerate_opt.html
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Section_howto.html
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Section_example.html
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tutorial_drude.html
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Section_perf.html
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Section_tools.html
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Section_modify.html
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tutorial_github.html
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Section_python.html
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Section_errors.html
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Section_history.html
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balance.html
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box.html
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boundary.html
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change_box.html
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clear.html
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comm_style.html
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comm_modify.html
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create_atoms.html
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create_bonds.html
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create_box.html
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delete_atoms.html
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delete_bonds.html
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dielectric.html
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dimension.html
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displace_atoms.html
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echo.html
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group.html
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group2ndx.html
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if.html
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include.html
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info.html
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jump.html
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label.html
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lattice.html
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log.html
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mass.html
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minimize.html
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min_style.html
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min_modify.html
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molecule.html
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neb.html
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neighbor.html
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neigh_modify.html
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newton.html
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next.html
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package.html
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partition.html
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prd.html
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print.html
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processors.html
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python.html
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quit.html
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region.html
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replicate.html
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reset_timestep.html
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run.html
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run_style.html
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set.html
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shell.html
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special_bonds.html
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suffix.html
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tad.html
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temper.html
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thermo.html
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thermo_style.html
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thermo_modify.html
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timestep.html
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timer.html
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units.html
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variable.html
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velocity.html
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read_data.html
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write_data.html
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write_coeff.html
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restart.html
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read_restart.html
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write_restart.html
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dump.html
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undump.html
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dump_modify.html
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dump_custom_vtk.html
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dump_h5md.html
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dump_image.html
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dump_molfile.html
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rerun.html
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read_dump.html
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write_dump.html
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atom_style.html
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body.html
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atom_modify.html
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kspace_style.html
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kspace_modify.html
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fix.html
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unfix.html
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fix_modify.html
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fix_adapt.html
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fix_adapt_fep.html
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fix_addforce.html
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fix_addtorque.html
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fix_append_atoms.html
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fix_atc.html
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fix_atom_swap.html
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fix_ave_atom.html
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fix_ave_correlate.html
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fix_ave_correlate_long.html
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fix_ave_chunk.html
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fix_ave_histo.html
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fix_ave_spatial.html
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fix_ave_spatial_sphere.html
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fix_ave_time.html
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fix_aveforce.html
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fix_balance.html
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fix_bond_break.html
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fix_bond_create.html
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fix_bond_swap.html
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fix_box_relax.html
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fix_colvars.html
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fix_deform.html
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fix_deposit.html
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fix_drag.html
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fix_drude_transform.html
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fix_drude.html
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fix_eos_cv.html
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fix_eos_table.html
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fix_langevin_drude.html
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fix_dt_reset.html
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fix_efield.html
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fix_enforce2d.html
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fix_evaporate.html
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fix_external.html
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fix_freeze.html
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fix_gcmc.html
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fix_gld.html
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fix_gle.html
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fix_gravity.html
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fix_heat.html
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fix_imd.html
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fix_ipi.html
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fix_indent.html
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fix_langevin.html
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fix_langevin_eff.html
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fix_lb_fluid.html
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fix_lb_momentum.html
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fix_lb_pc.html
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fix_lb_rigid_pc_sphere.html
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fix_lb_viscous.html
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fix_lineforce.html
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fix_manifoldforce.html
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fix_nve_manifold_rattle.html
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fix_nvt_manifold_rattle.html
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manifolds.html
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fix_meso.html
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fix_meso_stationary.html
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fix_momentum.html
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fix_move.html
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fix_msst.html
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fix_neb.html
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fix_nh.html
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fix_nh_eff.html
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fix_nph_asphere.html
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fix_nph_body.html
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fix_nph_sphere.html
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fix_nphug.html
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fix_npt_asphere.html
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fix_npt_body.html
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fix_npt_sphere.html
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fix_nve.html
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fix_nve_eff.html
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fix_nve_asphere.html
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fix_nve_asphere_noforce.html
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fix_nve_body.html
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fix_nve_limit.html
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fix_nve_line.html
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fix_nve_noforce.html
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fix_nve_sphere.html
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fix_nve_tri.html
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fix_nvt_asphere.html
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fix_nvt_body.html
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fix_nvt_sllod.html
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fix_nvt_sllod_eff.html
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fix_nvt_sphere.html
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fix_oneway.html
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fix_orient_fcc.html
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fix_phonon.html
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fix_pimd.html
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fix_planeforce.html
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fix_poems.html
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fix_pour.html
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fix_press_berendsen.html
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fix_print.html
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fix_property_atom.html
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fix_qbmsst.html
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fix_qeq.html
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fix_qeq_comb.html
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fix_qeq_reax.html
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fix_qmmm.html
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fix_qtb.html
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fix_reaxc_bonds.html
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fix_reaxc_species.html
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fix_recenter.html
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fix_restrain.html
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fix_rigid.html
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fix_setforce.html
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fix_shake.html
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fix_saed_vtk.html
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fix_shardlow.html
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fix_smd.html
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fix_smd_adjust_dt.html
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fix_smd_integrate_tlsph.html
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fix_smd_integrate_ulsph.html
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fix_smd_move_triangulated_surface.html
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fix_smd_setvel.html
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fix_smd_tlsph_reference_configuration.html
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fix_smd_wall_surface.html
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fix_spring.html
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fix_spring_rg.html
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fix_spring_self.html
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fix_srd.html
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fix_store_force.html
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fix_store_state.html
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fix_temp_berendsen.html
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fix_temp_csvr.html
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fix_temp_rescale.html
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fix_temp_rescale_eff.html
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fix_tfmc.html
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fix_thermal_conductivity.html
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fix_ti_rs.html
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fix_ti_spring.html
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fix_tmd.html
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fix_tune_kspace.html
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fix_ttm.html
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fix_vector.html
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fix_viscosity.html
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fix_viscous.html
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fix_wall_gran.html
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fix_wall.html
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fix_wall_piston.html
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fix_wall_reflect.html
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fix_wall_region.html
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fix_wall_srd.html
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compute.html
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uncompute.html
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compute_modify.html
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compute_group_group.html
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compute_pair.html
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compute_angle.html
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compute_bond.html
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compute_dihedral.html
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compute_improper.html
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compute_pair_local.html
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compute_body_local.html
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compute_angle_local.html
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compute_dihedral_local.html
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compute_improper_local.html
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compute_property_local.html
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compute_chunk_atom.html
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compute_angmom_chunk.html
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compute_com_chunk.html
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compute_dipole_chunk.html
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compute_gyration_chunk.html
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compute_inertia_chunk.html
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compute_msd_chunk.html
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compute_omega_chunk.html
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compute_property_chunk.html
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compute_temp_chunk.html
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compute_torque_chunk.html
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compute_vcm_chunk.html
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compute_com.html
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compute_dpd.html
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compute_erotate_asphere.html
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compute_erotate_sphere.html
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||||||
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compute_erotate_rigid.html
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compute_event_displace.html
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compute_fep.html
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compute_gyration.html
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compute_heat_flux.html
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compute_ke.html
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compute_msd.html
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compute_pe.html
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compute_msd_nongauss.html
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compute_pressure.html
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compute_rdf.html
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compute_reduce.html
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compute_slice.html
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compute_saed.html
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compute_property_atom.html
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compute_ackland_atom.html
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compute_basal_atom.html
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compute_bond_local.html
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compute_centro_atom.html
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compute_cluster_atom.html
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compute_cna_atom.html
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compute_contact_atom.html
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|
compute_coord_atom.html
|
||||||
|
compute_damage_atom.html
|
||||||
|
compute_dilatation_atom.html
|
||||||
|
compute_displace_atom.html
|
||||||
|
compute_dpd_atom.html
|
||||||
|
compute_erotate_sphere_atom.html
|
||||||
|
compute_hexorder_atom.html
|
||||||
|
compute_ke_atom.html
|
||||||
|
compute_ke_eff.html
|
||||||
|
compute_ke_atom_eff.html
|
||||||
|
compute_ke_rigid.html
|
||||||
|
compute_meso_e_atom.html
|
||||||
|
compute_meso_rho_atom.html
|
||||||
|
compute_meso_t_atom.html
|
||||||
|
compute_orientorder_atom.html
|
||||||
|
compute_pe_atom.html
|
||||||
|
compute_plasticity_atom.html
|
||||||
|
compute_sna_atom.html
|
||||||
|
compute_stress_atom.html
|
||||||
|
compute_voronoi_atom.html
|
||||||
|
compute_xrd.html
|
||||||
|
compute_smd_contact_radius.html
|
||||||
|
compute_smd_damage.html
|
||||||
|
compute_smd_hourglass_error.html
|
||||||
|
compute_smd_internal_energy.html
|
||||||
|
compute_smd_plastic_strain_rate.html
|
||||||
|
compute_smd_plastic_strain.html
|
||||||
|
compute_smd_rho.html
|
||||||
|
compute_smd_tlsph_defgrad.html
|
||||||
|
compute_smd_tlsph_dt.html
|
||||||
|
compute_smd_tlsph_num_neighs.html
|
||||||
|
compute_smd_tlsph_shape.html
|
||||||
|
compute_smd_tlsph_strain_rate.html
|
||||||
|
compute_smd_tlsph_strain.html
|
||||||
|
compute_smd_tlsph_stress.html
|
||||||
|
compute_smd_triangle_mesh_vertices.html
|
||||||
|
compute_smd_ulsph_num_neighs.html
|
||||||
|
compute_smd_ulsph_strain_rate.html
|
||||||
|
compute_smd_ulsph_strain.html
|
||||||
|
compute_smd_ulsph_stress.html
|
||||||
|
compute_smd_vol.html
|
||||||
|
compute_tally.html
|
||||||
|
compute_temp.html
|
||||||
|
compute_temp_asphere.html
|
||||||
|
compute_temp_body.html
|
||||||
|
compute_temp_com.html
|
||||||
|
compute_temp_cs.html
|
||||||
|
compute_temp_deform.html
|
||||||
|
compute_temp_drude.html
|
||||||
|
compute_temp_partial.html
|
||||||
|
compute_temp_profile.html
|
||||||
|
compute_temp_ramp.html
|
||||||
|
compute_temp_region.html
|
||||||
|
compute_temp_rotate.html
|
||||||
|
compute_temp_sphere.html
|
||||||
|
compute_temp_eff.html
|
||||||
|
compute_temp_deform_eff.html
|
||||||
|
compute_temp_region_eff.html
|
||||||
|
compute_ti.html
|
||||||
|
compute_vacf.html
|
||||||
|
pair_style.html
|
||||||
|
pair_modify.html
|
||||||
|
pair_write.html
|
||||||
|
pair_none.html
|
||||||
|
pair_zero.html
|
||||||
|
pair_adp.html
|
||||||
|
pair_airebo.html
|
||||||
|
pair_awpmd.html
|
||||||
|
pair_beck.html
|
||||||
|
pair_body.html
|
||||||
|
pair_bop.html
|
||||||
|
pair_born.html
|
||||||
|
pair_brownian.html
|
||||||
|
pair_buck.html
|
||||||
|
pair_buck_long.html
|
||||||
|
pair_charmm.html
|
||||||
|
pair_class2.html
|
||||||
|
pair_coeff.html
|
||||||
|
pair_colloid.html
|
||||||
|
pair_comb.html
|
||||||
|
pair_coul.html
|
||||||
|
pair_coul_diel.html
|
||||||
|
pair_cs.html
|
||||||
|
pair_dipole.html
|
||||||
|
pair_dpd.html
|
||||||
|
pair_dpd_conservative.html
|
||||||
|
pair_dpd_fdt.html
|
||||||
|
pair_dsmc.html
|
||||||
|
pair_eam.html
|
||||||
|
pair_edip.html
|
||||||
|
pair_eff.html
|
||||||
|
pair_eim.html
|
||||||
|
pair_gauss.html
|
||||||
|
pair_gayberne.html
|
||||||
|
pair_gran.html
|
||||||
|
pair_gromacs.html
|
||||||
|
pair_hbond_dreiding.html
|
||||||
|
pair_hybrid.html
|
||||||
|
pair_kim.html
|
||||||
|
pair_lcbop.html
|
||||||
|
pair_list.html
|
||||||
|
pair_lj.html
|
||||||
|
pair_line_lj.html
|
||||||
|
pair_lj96.html
|
||||||
|
pair_lj_cubic.html
|
||||||
|
pair_lj_expand.html
|
||||||
|
pair_lj_long.html
|
||||||
|
pair_lj_sf.html
|
||||||
|
pair_lj_smooth.html
|
||||||
|
pair_lj_smooth_linear.html
|
||||||
|
pair_lj_soft.html
|
||||||
|
pair_lubricate.html
|
||||||
|
pair_lubricateU.html
|
||||||
|
pair_nb3b_harmonic.html
|
||||||
|
pair_mdf.html
|
||||||
|
pair_meam.html
|
||||||
|
pair_meam_spline.html
|
||||||
|
pair_meam_sw_spline.html
|
||||||
|
pair_mgpt.html
|
||||||
|
pair_mie.html
|
||||||
|
pair_morse.html
|
||||||
|
pair_nm.html
|
||||||
|
pair_peri.html
|
||||||
|
pair_polymorphic.html
|
||||||
|
pair_quip.html
|
||||||
|
pair_reax_c.html
|
||||||
|
pair_resquared.html
|
||||||
|
pair_sdk.html
|
||||||
|
pair_snap.html
|
||||||
|
pair_soft.html
|
||||||
|
pair_smd_hertz.html
|
||||||
|
pair_smd_tlsph.html
|
||||||
|
pair_smd_triangulated_surface.html
|
||||||
|
pair_smd_ulsph.html
|
||||||
|
pair_smtbq.html
|
||||||
|
pair_sph_heatconduction.html
|
||||||
|
pair_sph_idealgas.html
|
||||||
|
pair_sph_lj.html
|
||||||
|
pair_sph_rhosum.html
|
||||||
|
pair_sph_taitwater.html
|
||||||
|
pair_sph_taitwater_morris.html
|
||||||
|
pair_srp.html
|
||||||
|
pair_sw.html
|
||||||
|
pair_table.html
|
||||||
|
pair_tersoff.html
|
||||||
|
pair_tersoff_mod.html
|
||||||
|
pair_tersoff_zbl.html
|
||||||
|
pair_thole.html
|
||||||
|
pair_tri_lj.html
|
||||||
|
pair_vashishta.html
|
||||||
|
pair_yukawa.html
|
||||||
|
pair_yukawa_colloid.html
|
||||||
|
pair_zbl.html
|
||||||
|
bond_style.html
|
||||||
|
bond_write.html
|
||||||
|
bond_none.html
|
||||||
|
bond_zero.html
|
||||||
|
bond_class2.html
|
||||||
|
bond_coeff.html
|
||||||
|
bond_fene_expand.html
|
||||||
|
bond_fene.html
|
||||||
|
bond_harmonic.html
|
||||||
|
bond_harmonic_shift.html
|
||||||
|
bond_harmonic_shift_cut.html
|
||||||
|
bond_hybrid.html
|
||||||
|
bond_morse.html
|
||||||
|
bond_nonlinear.html
|
||||||
|
bond_quartic.html
|
||||||
|
bond_table.html
|
||||||
|
angle_style.html
|
||||||
|
angle_none.html
|
||||||
|
angle_zero.html
|
||||||
|
angle_charmm.html
|
||||||
|
angle_class2.html
|
||||||
|
angle_coeff.html
|
||||||
|
angle_cosine.html
|
||||||
|
angle_cosine_delta.html
|
||||||
|
angle_cosine_periodic.html
|
||||||
|
angle_cosine_shift.html
|
||||||
|
angle_cosine_shift_exp.html
|
||||||
|
angle_cosine_squared.html
|
||||||
|
angle_dipole.html
|
||||||
|
angle_fourier.html
|
||||||
|
angle_fourier_simple.html
|
||||||
|
angle_harmonic.html
|
||||||
|
angle_hybrid.html
|
||||||
|
angle_quartic.html
|
||||||
|
angle_sdk.html
|
||||||
|
angle_table.html
|
||||||
|
dihedral_style.html
|
||||||
|
dihedral_none.html
|
||||||
|
dihedral_zero.html
|
||||||
|
dihedral_charmm.html
|
||||||
|
dihedral_class2.html
|
||||||
|
dihedral_coeff.html
|
||||||
|
dihedral_cosine_shift_exp.html
|
||||||
|
dihedral_fourier.html
|
||||||
|
dihedral_harmonic.html
|
||||||
|
dihedral_helix.html
|
||||||
|
dihedral_hybrid.html
|
||||||
|
dihedral_multi_harmonic.html
|
||||||
|
dihedral_nharmonic.html
|
||||||
|
dihedral_opls.html
|
||||||
|
dihedral_quadratic.html
|
||||||
|
dihedral_table.html
|
||||||
|
improper_style.html
|
||||||
|
improper_none.html
|
||||||
|
improper_zero.html
|
||||||
|
improper_class2.html
|
||||||
|
improper_coeff.html
|
||||||
|
improper_cossq.html
|
||||||
|
improper_cvff.html
|
||||||
|
improper_distance.html
|
||||||
|
improper_fourier.html
|
||||||
|
improper_harmonic.html
|
||||||
|
improper_hybrid.html
|
||||||
|
improper_ring.html
|
||||||
|
improper_umbrella.html
|
||||||
|
|
@ -1309,7 +1309,7 @@ to output and the kind of data they operate on and produce:
|
||||||
"Dump file output"_#dump
|
"Dump file output"_#dump
|
||||||
"Fixes that write output files"_#fixoutput
|
"Fixes that write output files"_#fixoutput
|
||||||
"Computes that process output quantities"_#computeoutput
|
"Computes that process output quantities"_#computeoutput
|
||||||
"Fixes that process output quantities"_#fixoutput
|
"Fixes that process output quantities"_#fixprocoutput
|
||||||
"Computes that generate values to output"_#compute
|
"Computes that generate values to output"_#compute
|
||||||
"Fixes that generate values to output"_#fix
|
"Fixes that generate values to output"_#fix
|
||||||
"Variables that generate values to output"_#variable
|
"Variables that generate values to output"_#variable
|
||||||
|
|
@ -1477,7 +1477,7 @@ info, etc) and stores the values in a local vector or array. These
|
||||||
are produced as output values which can be used as input to other
|
are produced as output values which can be used as input to other
|
||||||
output commands.
|
output commands.
|
||||||
|
|
||||||
Fixes that process output quantities :h5,link(fixoutput)
|
Fixes that process output quantities :h5,link(fixprocoutput)
|
||||||
|
|
||||||
The "fix vector"_fix_vector.html command can create global vectors as
|
The "fix vector"_fix_vector.html command can create global vectors as
|
||||||
output from global scalars as input, accumulating them one element at
|
output from global scalars as input, accumulating them one element at
|
||||||
|
|
|
||||||
|
|
@ -70,6 +70,6 @@ section for more info on packages.
|
||||||
[Related commands:]
|
[Related commands:]
|
||||||
|
|
||||||
"angle_coeff"_angle_coeff.html,
|
"angle_coeff"_angle_coeff.html,
|
||||||
"angle_cosineshiftexp"_angle_cosineshiftexp.html
|
"angle_cosine_shift_exp"_angle_cosine_shift_exp.html
|
||||||
|
|
||||||
[Default:] none
|
[Default:] none
|
||||||
|
|
|
||||||
|
|
@ -82,7 +82,7 @@ section for more info on packages.
|
||||||
[Related commands:]
|
[Related commands:]
|
||||||
|
|
||||||
"angle_coeff"_angle_coeff.html,
|
"angle_coeff"_angle_coeff.html,
|
||||||
"angle_cosineshift"_angle_cosineshift.html,
|
"angle_cosine_shift"_angle_cosine_shift.html,
|
||||||
"dihedral_cosineshift"_dihedral_cosineshift.html
|
"dihedral_cosine_shift_exp"_dihedral_cosine_shift_exp.html
|
||||||
|
|
||||||
[Default:] none
|
[Default:] none
|
||||||
|
|
|
||||||
|
|
@ -92,7 +92,7 @@ more instructions on how to use the accelerated styles effectively.
|
||||||
[Restrictions:]
|
[Restrictions:]
|
||||||
|
|
||||||
This angle style can only be used if LAMMPS was built with the
|
This angle style can only be used if LAMMPS was built with the
|
||||||
USER-MISC package. See the "Making LAMMPS"_Section_start.html#2_3
|
USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_2_3
|
||||||
section for more info on packages.
|
section for more info on packages.
|
||||||
|
|
||||||
NOTE: In the "Angles" section of the data file, the atom ID 'j'
|
NOTE: In the "Angles" section of the data file, the atom ID 'j'
|
||||||
|
|
|
||||||
|
|
@ -73,6 +73,6 @@ section for more info on packages.
|
||||||
|
|
||||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
|
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
|
||||||
"bond_harmonic"_bond_harmonic.html,
|
"bond_harmonic"_bond_harmonic.html,
|
||||||
"bond_harmonicshift"_bond_harmonicshift.html
|
"bond_harmonic_shift"_bond_harmonic_shift.html
|
||||||
|
|
||||||
[Default:] none
|
[Default:] none
|
||||||
|
|
|
||||||
|
|
@ -81,6 +81,6 @@ section for more info on packages.
|
||||||
[Related commands:]
|
[Related commands:]
|
||||||
|
|
||||||
"dihedral_coeff"_dihedral_coeff.html,
|
"dihedral_coeff"_dihedral_coeff.html,
|
||||||
"angle_cosineshiftexp"_angle_cosineshiftexp.html
|
"angle_cosine_shift_exp"_angle_cosine_shift_exp.html
|
||||||
|
|
||||||
[Default:] none
|
[Default:] none
|
||||||
|
|
|
||||||
|
|
@ -248,7 +248,7 @@ N timesteps.
|
||||||
If the keyword {trilinear} is used, the trilinear stencil is used to
|
If the keyword {trilinear} is used, the trilinear stencil is used to
|
||||||
interpolate the particle nodes onto the fluid mesh. By default, the
|
interpolate the particle nodes onto the fluid mesh. By default, the
|
||||||
immersed boundary method, Peskin stencil is used. Both of these
|
immersed boundary method, Peskin stencil is used. Both of these
|
||||||
interpolation methods are described in "Mackay et al."_#Mfluid-ackay.
|
interpolation methods are described in "Mackay et al."_#fluid-Mackay.
|
||||||
|
|
||||||
If the keyword {D3Q19} is used, the 19 velocity (D3Q19) lattice is
|
If the keyword {D3Q19} is used, the 19 velocity (D3Q19) lattice is
|
||||||
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
|
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
|
||||||
|
|
@ -299,7 +299,7 @@ is written to the main LAMMPS "binary restart files"_restart.html.
|
||||||
|
|
||||||
None of the "fix_modify"_fix_modify.html options are relevant to this
|
None of the "fix_modify"_fix_modify.html options are relevant to this
|
||||||
fix. No global or per-atom quantities are stored by this fix for
|
fix. No global or per-atom quantities are stored by this fix for
|
||||||
access by various "output commands"_Section_howto.html#4_15. No
|
access by various "output commands"_Section_howto.html#howto_15. No
|
||||||
parameter of this fix can be used with the {start/stop} keywords of
|
parameter of this fix can be used with the {start/stop} keywords of
|
||||||
the "run"_run.html command. This fix is not invoked during "energy
|
the "run"_run.html command. This fix is not invoked during "energy
|
||||||
minimization"_minimize.html.
|
minimization"_minimize.html.
|
||||||
|
|
|
||||||
|
|
@ -31,7 +31,7 @@ fix vf vacancy ti/rs 10.0 70000 50000 function 2 :pre
|
||||||
This fix allows you to compute the free energy temperature dependence
|
This fix allows you to compute the free energy temperature dependence
|
||||||
by performing a thermodynamic integration procedure known as
|
by performing a thermodynamic integration procedure known as
|
||||||
Reversible Scaling "(de Koning99,"_#deKoning99 "de
|
Reversible Scaling "(de Koning99,"_#deKoning99 "de
|
||||||
Koning00a)"_#deKoning00a". The thermodynamic integration is performed
|
Koning00a)"_#deKoning00a. The thermodynamic integration is performed
|
||||||
using the nonequilibrium method of Adiabatic Switching
|
using the nonequilibrium method of Adiabatic Switching
|
||||||
"(Watanabe,"_#Watanabe "de Koning96)"_#deKoning96.
|
"(Watanabe,"_#Watanabe "de Koning96)"_#deKoning96.
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -235,7 +235,7 @@ In the second stage of NEB, the replica with the highest energy
|
||||||
is selected and the inter-replica forces on it are converted to a
|
is selected and the inter-replica forces on it are converted to a
|
||||||
force that drives its atom coordinates to the top or saddle point of
|
force that drives its atom coordinates to the top or saddle point of
|
||||||
the barrier, via the barrier-climbing calculation described in
|
the barrier, via the barrier-climbing calculation described in
|
||||||
"(Henkelman2)"_#Hinkelman2. As before, the other replicas rearrange
|
"(Henkelman2)"_#Henkelman2. As before, the other replicas rearrange
|
||||||
themselves along the MEP so as to be roughly equally spaced.
|
themselves along the MEP so as to be roughly equally spaced.
|
||||||
|
|
||||||
When both stages are complete, if the NEB calculation was successful,
|
When both stages are complete, if the NEB calculation was successful,
|
||||||
|
|
|
||||||
|
|
@ -105,7 +105,7 @@ This pair style can only be used via the {pair} keyword of the
|
||||||
|
|
||||||
This style is part of the BODY package. It is only enabled if LAMMPS
|
This style is part of the BODY package. It is only enabled if LAMMPS
|
||||||
was built with that package. See the "Making
|
was built with that package. See the "Making
|
||||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
LAMMPS"_Section_start.html#start_2_3 section for more info.
|
||||||
|
|
||||||
Defining particles to be bodies so they participate in body/body or
|
Defining particles to be bodies so they participate in body/body or
|
||||||
body/particle interactions requires the use of the "atom_style
|
body/particle interactions requires the use of the "atom_style
|
||||||
|
|
|
||||||
|
|
@ -94,7 +94,7 @@ the "mass"_mass.html command to specify them. Note that for BOP
|
||||||
potentials with hydrogen, you will likely want to set the mass of H
|
potentials with hydrogen, you will likely want to set the mass of H
|
||||||
atoms to be 10x or 20x larger to avoid having to use a tiny timestep.
|
atoms to be 10x or 20x larger to avoid having to use a tiny timestep.
|
||||||
You can do this by using the "mass"_mass.html command after using the
|
You can do this by using the "mass"_mass.html command after using the
|
||||||
"pair_coeff"_doc/pair_coeff.html command to read the BOP potential
|
"pair_coeff"_pair_coeff.html command to read the BOP potential
|
||||||
file.
|
file.
|
||||||
|
|
||||||
One option can be specified as a keyword with the pair_style command.
|
One option can be specified as a keyword with the pair_style command.
|
||||||
|
|
@ -392,15 +392,15 @@ non-tabulated potential file, a_0 is non-zero.
|
||||||
|
|
||||||
:line
|
:line
|
||||||
|
|
||||||
:link(Pettofor_1)
|
:link(Pettifor_1)
|
||||||
[(Pettifor_1)] D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487
|
[(Pettifor_1)] D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487
|
||||||
(1999).
|
(1999).
|
||||||
|
|
||||||
:link(Pettofor_2)
|
:link(Pettifor_2)
|
||||||
[(Pettifor_2)] D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84,
|
[(Pettifor_2)] D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84,
|
||||||
4124 (2000).
|
4124 (2000).
|
||||||
|
|
||||||
:link(Pettofor_3)
|
:link(Pettifor_3)
|
||||||
[(Pettifor_3)] D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103
|
[(Pettifor_3)] D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103
|
||||||
(2002).
|
(2002).
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -88,7 +88,7 @@ This pair style can only be used via the {pair} keyword of the
|
||||||
|
|
||||||
This style is part of the "user-misc" package. It is only enabled
|
This style is part of the "user-misc" package. It is only enabled
|
||||||
if LAMMPS was built with that package. See the "Making
|
if LAMMPS was built with that package. See the "Making
|
||||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
LAMMPS"_Section_start.html#start_2_3 section for more info.
|
||||||
|
|
||||||
[Related commands:]
|
[Related commands:]
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -144,7 +144,7 @@ thermo_style custom step temp epair v_occ :pre
|
||||||
|
|
||||||
The {gauss/cut} style is part of the "user-misc" package. It is only
|
The {gauss/cut} style is part of the "user-misc" package. It is only
|
||||||
enabled if LAMMPS is build with that package. See the "Making of
|
enabled if LAMMPS is build with that package. See the "Making of
|
||||||
LAMMPS"_Section_start.html#3 section for more info.
|
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||||
|
|
||||||
[Related commands:]
|
[Related commands:]
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -131,7 +131,7 @@ with the nearest image.
|
||||||
|
|
||||||
This style is part of the USER-MISC package. It is only enabled if
|
This style is part of the USER-MISC package. It is only enabled if
|
||||||
LAMMPS is build with that package. See the "Making of
|
LAMMPS is build with that package. See the "Making of
|
||||||
LAMMPS"_Section_start.html#3 section for more info.
|
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||||
|
|
||||||
[Related commands:]
|
[Related commands:]
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -192,7 +192,7 @@ This pair style can only be used via the {pair} keyword of the
|
||||||
|
|
||||||
These styles are part of the COLLOID package. They are only enabled
|
These styles are part of the COLLOID package. They are only enabled
|
||||||
if LAMMPS was built with that package. See the "Making
|
if LAMMPS was built with that package. See the "Making
|
||||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
LAMMPS"_Section_start.html#start_2_3 section for more info.
|
||||||
|
|
||||||
Only spherical monodisperse particles are allowed for pair_style
|
Only spherical monodisperse particles are allowed for pair_style
|
||||||
lubricate.
|
lubricate.
|
||||||
|
|
|
||||||
|
|
@ -180,7 +180,7 @@ This pair style can only be used via the {pair} keyword of the
|
||||||
|
|
||||||
These styles are part of the COLLOID package. They are only enabled
|
These styles are part of the COLLOID package. They are only enabled
|
||||||
if LAMMPS was built with that package. See the "Making
|
if LAMMPS was built with that package. See the "Making
|
||||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
LAMMPS"_Section_start.html#start_2_3 section for more info.
|
||||||
|
|
||||||
Currently, these pair styles assume that all other types of
|
Currently, these pair styles assume that all other types of
|
||||||
forces/torques on the particles have been already been computed when
|
forces/torques on the particles have been already been computed when
|
||||||
|
|
|
||||||
|
|
@ -296,7 +296,7 @@ a3 = attrac, astar >= 0 :pre
|
||||||
|
|
||||||
Most published MEAM parameter sets use the default values attrac=repulse=0.
|
Most published MEAM parameter sets use the default values attrac=repulse=0.
|
||||||
Setting repuls=attrac=delta corresponds to the form used in several
|
Setting repuls=attrac=delta corresponds to the form used in several
|
||||||
recent published MEAM parameter sets, such as "(Vallone)"_#Vallone
|
recent published MEAM parameter sets, such as "(Valone)"_#Valone
|
||||||
|
|
||||||
NOTE: The default form of the erose expression in LAMMPS was corrected
|
NOTE: The default form of the erose expression in LAMMPS was corrected
|
||||||
in March 2009. The current version is correct, but may show different
|
in March 2009. The current version is correct, but may show different
|
||||||
|
|
|
||||||
|
|
@ -180,7 +180,7 @@ Divided line :ul
|
||||||
|
|
||||||
7) Charge initialization mode:
|
7) Charge initialization mode:
|
||||||
|
|
||||||
Keyword ({QInitMode}) and initial oxygen charge ({Q<sub>init</sub>}). If keyword = 'true', all oxygen charges are initially set equal to {Q<sub>init</sub>}. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create_atom"#create_atom command or the charge specified in the file structure using "read_data"_#read_data.html command.
|
Keyword ({QInitMode}) and initial oxygen charge ({Q<sub>init</sub>}). If keyword = 'true', all oxygen charges are initially set equal to {Q<sub>init</sub>}. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create_atom"#create_atom command or the charge specified in the file structure using "read_data"_read_data.html command.
|
||||||
Divided line :ul
|
Divided line :ul
|
||||||
|
|
||||||
8) Mode for the electronegativity equalization (Qeq) :
|
8) Mode for the electronegativity equalization (Qeq) :
|
||||||
|
|
@ -229,7 +229,7 @@ This pair style requires the "newton"_newton.html setting to be "on"
|
||||||
for pair interactions.
|
for pair interactions.
|
||||||
|
|
||||||
The SMTB-Q potential files provided with LAMMPS (see the potentials
|
The SMTB-Q potential files provided with LAMMPS (see the potentials
|
||||||
directory) are parameterized for metal "units"_unit.html.
|
directory) are parameterized for metal "units"_units.html.
|
||||||
|
|
||||||
:line
|
:line
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -74,6 +74,6 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
||||||
|
|
||||||
:line
|
:line
|
||||||
|
|
||||||
:link(Monoghan)
|
:link(Monaghan)
|
||||||
[(Monaghan)] Monaghan and Gingold, Journal of Computational Physics,
|
[(Monaghan)] Monaghan and Gingold, Journal of Computational Physics,
|
||||||
52, 374-389 (1983).
|
52, 374-389 (1983).
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue