Loading doc/Makefile +12 −1 Original line number Diff line number Diff line Loading @@ -22,7 +22,7 @@ endif SOURCES=$(wildcard src/*.txt) OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) .PHONY: help clean-all clean epub html pdf old venv spelling .PHONY: help clean-all clean epub html pdf old venv spelling anchor_check # ------------------------------------------ Loading @@ -36,6 +36,7 @@ help: @echo " clean remove all intermediate RST files" @echo " clean-all reset the entire build environment" @echo " txt2html build txt2html tool" @echo " anchor_check scan for duplicate anchor labels" # ------------------------------------------ Loading @@ -54,6 +55,9 @@ html: $(OBJECTS) . $(VENV)/bin/activate ;\ cp -r src/* $(RSTDIR)/ ;\ sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\ echo "############################################" ;\ doc_anchor_check src/*.txt ;\ echo "############################################" ;\ deactivate ;\ ) -rm html/searchindex.js Loading Loading @@ -127,6 +131,13 @@ fetch: txt2html: utils/txt2html/txt2html.exe anchor_check : $(TXT2RST) @(\ . $(VENV)/bin/activate ;\ doc_anchor_check src/*.txt ;\ deactivate ;\ ) # ------------------------------------------ utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp Loading doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="10 Mar 2017 version"> <META NAME="docnumber" CONTENT="17 Mar 2017 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> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 10 Mar 2017 version :c,h4 17 Mar 2017 version :c,h4 Version info: :h4 Loading doc/src/Section_commands.txt +1 −0 Original line number Diff line number Diff line Loading @@ -687,6 +687,7 @@ package"_Section_start.html#start_3. "eos/cv"_fix_eos_cv.html, "eos/table"_fix_eos_table.html, "eos/table/rx"_fix_eos_table_rx.html, "filter/corotate"_fix_filter_corotate.html, "flow/gauss"_fix_flow_gauss.html, "gle"_fix_gle.html, "grem"_fix_grem.html, Loading doc/src/fix_filter_corotate.txt 0 → 100644 +87 −0 Original line number Diff line number Diff line "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line fix filter/corotate command :h3 [Syntax:] fix ID group-ID filter/corotate keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l one or more constraint/value pairs are appended :l constraint = {b} or {a} or {t} or {m} :l {b} values = one or more bond types {a} values = one or more angle types {t} values = one or more atom types {m} value = one or more mass values :pre :ule [Examples:] timestep 8 run_style respa 3 2 8 bond 1 pair 2 kspace 3 fix cor all filter/corotate m 1.0 :pre fix cor all filter/corotate b 4 19 a 3 5 2 :pre [Description:] This fix implements a corotational filter for a mollified impulse method. In biomolecular simulations, it allows the usage of larger timesteps for long-range electrostatic interactions. For details, see "(Fath)"_#Fath2017. When using "run_style respa"_run_style.html for a biomolecular simulation with high-frequency covalent bonds, the outer time-step is restricted to below ~ 4fs due to resonance problems. This fix filters the outer stage of the respa and thus a larger (outer) time-step can be used. Since in large biomolecular simulations the computation of the long-range electrostatic contributions poses a major bottleneck, this can significantly accelerate the simulation. The filter computes a cluster decomposition of the molecular structure following the criteria indicated by the options a, b, t and m. This process is similar to the approach in "fix shake"_fix_shake.html, however, the clusters are not kept contrained. Instead, the position is slightly modified only for the computation of long-range forces. A good cluster decomposition constitutes in building clusters which contain the fastest covalent bonds inside clusters. If the clusters are chosen suitably, the "run_style respa"_run_style.html is stable for outer time-steps of at least 8fs. :line [Restart, fix_modify, output, run start/stop, minimize info:] No information about these fixes is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to these fixes. No global or per-atom quantities are stored by these fixes for access by various "output commands"_Section_howto.html#howto_15. No parameter of these fixes can be used with the {start/stop} keywords of the "run"_run.html command. These fixes are not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. Currently, it does not support "molecule templates"_molecule.html. [Related commands:] [Default:] none :line :link(Fath2017) [(Fath)] Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017). doc/src/fix_qeq_reax.txt +3 −3 Original line number Diff line number Diff line Loading @@ -36,7 +36,7 @@ uses charges on each atom. The "fix qeq/comb"_fix_qeq_comb.html command should be used to perform charge equilibration with the "COMB potential"_pair_comb.html. For more technical details about the charge equilibration performed by fix qeq/reax, see the "(Aktulga)"_#Aktulga paper. "(Aktulga)"_#qeq-Aktulga paper. The QEq method minimizes the electrostatic energy of the system by adjusting the partial charge on individual atoms based on interactions Loading Loading @@ -119,6 +119,6 @@ be used for periodic cell dimensions less than 10 angstroms. :link(Nakano) [(Nakano)] Nakano, Computer Physics Communications, 104, 59-69 (1997). :link(Aktulga) (Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, :link(qeq-Aktulga) [(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012). Loading
doc/Makefile +12 −1 Original line number Diff line number Diff line Loading @@ -22,7 +22,7 @@ endif SOURCES=$(wildcard src/*.txt) OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) .PHONY: help clean-all clean epub html pdf old venv spelling .PHONY: help clean-all clean epub html pdf old venv spelling anchor_check # ------------------------------------------ Loading @@ -36,6 +36,7 @@ help: @echo " clean remove all intermediate RST files" @echo " clean-all reset the entire build environment" @echo " txt2html build txt2html tool" @echo " anchor_check scan for duplicate anchor labels" # ------------------------------------------ Loading @@ -54,6 +55,9 @@ html: $(OBJECTS) . $(VENV)/bin/activate ;\ cp -r src/* $(RSTDIR)/ ;\ sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\ echo "############################################" ;\ doc_anchor_check src/*.txt ;\ echo "############################################" ;\ deactivate ;\ ) -rm html/searchindex.js Loading Loading @@ -127,6 +131,13 @@ fetch: txt2html: utils/txt2html/txt2html.exe anchor_check : $(TXT2RST) @(\ . $(VENV)/bin/activate ;\ doc_anchor_check src/*.txt ;\ deactivate ;\ ) # ------------------------------------------ utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp Loading
doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="10 Mar 2017 version"> <META NAME="docnumber" CONTENT="17 Mar 2017 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> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 10 Mar 2017 version :c,h4 17 Mar 2017 version :c,h4 Version info: :h4 Loading
doc/src/Section_commands.txt +1 −0 Original line number Diff line number Diff line Loading @@ -687,6 +687,7 @@ package"_Section_start.html#start_3. "eos/cv"_fix_eos_cv.html, "eos/table"_fix_eos_table.html, "eos/table/rx"_fix_eos_table_rx.html, "filter/corotate"_fix_filter_corotate.html, "flow/gauss"_fix_flow_gauss.html, "gle"_fix_gle.html, "grem"_fix_grem.html, Loading
doc/src/fix_filter_corotate.txt 0 → 100644 +87 −0 Original line number Diff line number Diff line "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line fix filter/corotate command :h3 [Syntax:] fix ID group-ID filter/corotate keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l one or more constraint/value pairs are appended :l constraint = {b} or {a} or {t} or {m} :l {b} values = one or more bond types {a} values = one or more angle types {t} values = one or more atom types {m} value = one or more mass values :pre :ule [Examples:] timestep 8 run_style respa 3 2 8 bond 1 pair 2 kspace 3 fix cor all filter/corotate m 1.0 :pre fix cor all filter/corotate b 4 19 a 3 5 2 :pre [Description:] This fix implements a corotational filter for a mollified impulse method. In biomolecular simulations, it allows the usage of larger timesteps for long-range electrostatic interactions. For details, see "(Fath)"_#Fath2017. When using "run_style respa"_run_style.html for a biomolecular simulation with high-frequency covalent bonds, the outer time-step is restricted to below ~ 4fs due to resonance problems. This fix filters the outer stage of the respa and thus a larger (outer) time-step can be used. Since in large biomolecular simulations the computation of the long-range electrostatic contributions poses a major bottleneck, this can significantly accelerate the simulation. The filter computes a cluster decomposition of the molecular structure following the criteria indicated by the options a, b, t and m. This process is similar to the approach in "fix shake"_fix_shake.html, however, the clusters are not kept contrained. Instead, the position is slightly modified only for the computation of long-range forces. A good cluster decomposition constitutes in building clusters which contain the fastest covalent bonds inside clusters. If the clusters are chosen suitably, the "run_style respa"_run_style.html is stable for outer time-steps of at least 8fs. :line [Restart, fix_modify, output, run start/stop, minimize info:] No information about these fixes is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to these fixes. No global or per-atom quantities are stored by these fixes for access by various "output commands"_Section_howto.html#howto_15. No parameter of these fixes can be used with the {start/stop} keywords of the "run"_run.html command. These fixes are not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. Currently, it does not support "molecule templates"_molecule.html. [Related commands:] [Default:] none :line :link(Fath2017) [(Fath)] Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).
doc/src/fix_qeq_reax.txt +3 −3 Original line number Diff line number Diff line Loading @@ -36,7 +36,7 @@ uses charges on each atom. The "fix qeq/comb"_fix_qeq_comb.html command should be used to perform charge equilibration with the "COMB potential"_pair_comb.html. For more technical details about the charge equilibration performed by fix qeq/reax, see the "(Aktulga)"_#Aktulga paper. "(Aktulga)"_#qeq-Aktulga paper. The QEq method minimizes the electrostatic energy of the system by adjusting the partial charge on individual atoms based on interactions Loading Loading @@ -119,6 +119,6 @@ be used for periodic cell dimensions less than 10 angstroms. :link(Nakano) [(Nakano)] Nakano, Computer Physics Communications, 104, 59-69 (1997). :link(Aktulga) (Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, :link(qeq-Aktulga) [(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012).
