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Merge pull request #1832 from akohlmey/doc-styles-check 

Check style command lists against existing styles in sources
This commit is contained in:
Axel Kohlmeyer 2020-01-13 10:38:26 -05:00 committed by GitHub
parent eed85bb676 64e72b1cd5
commit 6813ab4c9c
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GPG Key ID: 4AEE18F83AFDEB23
12 changed files with 314 additions and 881 deletions
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46
doc/Makefile
View File

@ -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 ;\
) )
@ -122,24 +124,27 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
cd ../../; \ cd ../../; \
) )
@(\ @(\
. $(VENV)/bin/activate ;\ . $(VENV)/bin/activate ;\
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 ;\
echo "############################################" ;\ env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
deactivate ;\ python utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
) )
@cd latex && \ @cd latex && \
sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \ sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
mv temp Makefile && \ mv temp Makefile && \
sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \ sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
mv tmp.tex LAMMPS.tex && \ mv tmp.tex LAMMPS.tex && \
sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \ sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
mv tmp.tex LAMMPS.tex && \ mv tmp.tex LAMMPS.tex && \
make && \ make && \
make && \ make && \
mv LAMMPS.pdf ../Manual.pdf && \ make && \
cd ../; mv LAMMPS.pdf ../Manual.pdf && \
cd ../;
@rm -rf latex/_sources @rm -rf latex/_sources
@rm -rf latex/PDF @rm -rf latex/PDF
@rm -rf latex/USER @rm -rf latex/USER
@ -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)

6
doc/src/Manual_build.rst
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@ -55,9 +55,9 @@ 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
---------- ----------

1
doc/src/bond_style.rst
View File

@ -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

22
doc/src/fix.rst
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@ -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
* :doc:`smd <fix_smd>` - applied a steered MD force to a group * :doc:`smd <fix_smd>` - applied a steered MD force to a group
* :doc:`smd/adjust\_dt <fix_smd_adjust_dt>` - * :doc:`smd/adjust_dt <fix_smd_adjust_dt>` -
* :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` - * :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>` -
* :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>` - * :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>` -
* :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` - * :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>` -
* :doc:`smd/setvel <fix_smd_setvel>` - * :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 <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/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 * :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 Related commands
"""""""""""""""" """"""""""""""""
:doc:`unfix <unfix>`, :doc:`fix\_modify <fix_modify>` :doc:`unfix <unfix>`, :doc:`fix_modify <fix_modify>`
**Default:** none **Default:** none

33
doc/src/pair_style.rst
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@ -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.
@ -170,6 +170,7 @@ accelerated styles exist.
* :doc:`gauss <pair_gauss>` - Gaussian potential * :doc:`gauss <pair_gauss>` - Gaussian potential
* :doc:`gauss/cut <pair_gauss>` - generalized Gaussian potential * :doc:`gauss/cut <pair_gauss>` - generalized Gaussian potential
* :doc:`gayberne <pair_gayberne>` - Gay-Berne ellipsoidal potential * :doc:`gayberne <pair_gayberne>` - Gay-Berne ellipsoidal potential
* :doc:`granular <pair_granular>` - Generalized granular potential
* :doc:`gran/hertz/history <pair_gran>` - granular potential with Hertzian interactions * :doc:`gran/hertz/history <pair_gran>` - granular potential with Hertzian interactions
* :doc:`gran/hooke <pair_gran>` - granular potential with history effects * :doc:`gran/hooke <pair_gran>` - granular potential with history effects
* :doc:`gran/hooke/history <pair_gran>` - granular potential without history effects * :doc:`gran/hooke/history <pair_gran>` - granular potential without history effects
@ -267,6 +268,12 @@ accelerated styles exist.
* :doc:`oxdna2/hbond <pair_oxdna2>` - * :doc:`oxdna2/hbond <pair_oxdna2>` -
* :doc:`oxdna2/stk <pair_oxdna2>` - * :doc:`oxdna2/stk <pair_oxdna2>` -
* :doc:`oxdna2/xstk <pair_oxdna2>` - * :doc:`oxdna2/xstk <pair_oxdna2>` -
* :doc:`oxrna2/coaxstk <pair_oxrna2>` -
* :doc:`oxrna2/dh <pair_oxrna2>` -
* :doc:`oxrna2/excv <pair_oxrna2>` -
* :doc:`oxrna2/hbond <pair_oxrna2>` -
* :doc:`oxrna2/stk <pair_oxrna2>` -
* :doc:`oxrna2/xstk <pair_oxrna2>` -
* :doc:`peri/eps <pair_peri>` - peridynamic EPS potential * :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
* :doc:`peri/lps <pair_peri>` - peridynamic LPS potential * :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
* :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential * :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
@ -280,7 +287,7 @@ accelerated styles exist.
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
* :doc:`smd/hertz <pair_smd_hertz>` - * :doc:`smd/hertz <pair_smd_hertz>` -
* :doc:`smd/tlsph <pair_smd_tlsph>` - * :doc:`smd/tlsph <pair_smd_tlsph>` -
* :doc:`smd/tri\_surface <pair_smd_triangulated_surface>` - * :doc:`smd/tri_surface <pair_smd_triangulated_surface>` -
* :doc:`smd/ulsph <pair_smd_ulsph>` - * :doc:`smd/ulsph <pair_smd_ulsph>` -
* :doc:`smtbq <pair_smtbq>` - * :doc:`smtbq <pair_smtbq>` -
* :doc:`snap <pair_snap>` - SNAP quantum-accurate potential * :doc:`snap <pair_snap>` - SNAP quantum-accurate potential
@ -328,8 +335,8 @@ Restrictions
This command must be used before any coefficients are set by the This command must be used before any coefficients are set by the
:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`, or :doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`, or
:doc:`read\_restart <read_restart>` commands. :doc:`read_restart <read_restart>` commands.
Some pair styles are part of specific packages. They are only enabled Some pair styles are part of specific packages. They are only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. The doc pages for if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. The doc pages for
@ -338,9 +345,9 @@ individual pair potentials tell if it is part of a package.
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`, :doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`,
:doc:`pair\_modify <pair_modify>`, :doc:`kspace\_style <kspace_style>`, :doc:`pair_modify <pair_modify>`, :doc:`kspace_style <kspace_style>`,
:doc:`dielectric <dielectric>`, :doc:`pair\_write <pair_write>` :doc:`dielectric <dielectric>`, :doc:`pair_write <pair_write>`
Default Default
""""""" """""""

495
doc/txt/kspace_style.txt
View File

@ -1,495 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
kspace_style command :h3
[Syntax:]
kspace_style style value :pre
style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} or {scafacos} :ulb,l
{none} value = none
{ewald} value = accuracy
accuracy = desired relative error in forces
{ewald/disp} value = accuracy
accuracy = desired relative error in forces
{ewald/omp} value = accuracy
accuracy = desired relative error in forces
{ewald/dipole} value = accuracy
accuracy = desired relative error in forces
{ewald/dipole/spin} value = accuracy
accuracy = desired relative error in forces
{pppm} value = accuracy
accuracy = desired relative error in forces
{pppm/cg} values = accuracy (smallq)
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units)
{pppm/disp} value = accuracy
accuracy = desired relative error in forces
{pppm/tip4p} value = accuracy
accuracy = desired relative error in forces
{pppm/disp/tip4p} value = accuracy
accuracy = desired relative error in forces
{pppm/gpu} value = accuracy
accuracy = desired relative error in forces
{pppm/intel} value = accuracy
accuracy = desired relative error in forces
{pppm/kk} value = accuracy
accuracy = desired relative error in forces
{pppm/omp} value = accuracy
accuracy = desired relative error in forces
{pppm/cg/omp} value = accuracy
accuracy = desired relative error in forces
{pppm/disp/intel} value = accuracy
accuracy = desired relative error in forces
{pppm/tip4p/omp} value = accuracy
accuracy = desired relative error in forces
{pppm/stagger} value = accuracy
accuracy = desired relative error in forces
{pppm/dipole} value = accuracy
accuracy = desired relative error in forces
{pppm/dipole/spin} value = accuracy
accuracy = desired relative error in forces
{msm} value = accuracy
accuracy = desired relative error in forces
{msm/cg} value = accuracy (smallq)
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units)
{msm/omp} value = accuracy
accuracy = desired relative error in forces
{msm/cg/omp} value = accuracy (smallq)
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units)
{scafacos} values = method accuracy
method = fmm or p2nfft or p3m or ewald or direct
accuracy = desired relative error in forces :pre
:ule
[Examples:]
kspace_style pppm 1.0e-4
kspace_style pppm/cg 1.0e-5 1.0e-6
kspace style msm 1.0e-4
kspace style scafacos fmm 1.0e-4
kspace_style none :pre
[Description:]
Define a long-range solver for LAMMPS to use each timestep to compute
long-range Coulombic interactions or long-range 1/r^6 interactions.
Most of the long-range solvers perform their computation in K-space,
hence the name of this command.
When such a solver is used in conjunction with an appropriate pair
style, the cutoff for Coulombic or 1/r^N interactions is effectively
infinite. If the Coulombic case, this means each charge in the system
interacts with charges in an infinite array of periodic images of the
simulation domain.
Note that using a long-range solver requires use of a matching "pair
style"_pair_style.html to perform consistent short-range pairwise
calculations. This means that the name of the pair style contains a
matching keyword to the name of the KSpace style, as in this table:
Pair style : KSpace style
coul/long : ewald or pppm
coul/msm : msm
lj/long or buck/long : disp (for dispersion)
tip4p/long : tip4p :tb(s=:,ea=c)
:line
The {ewald} style performs a standard Ewald summation as described in
any solid-state physics text.
The {ewald/disp} style adds a long-range dispersion sum option for
1/r^6 potentials and is useful for simulation of interfaces
"(Veld)"_#Veld. It also performs standard Coulombic Ewald summations,
but in a more efficient manner than the {ewald} style. The 1/r^6
capability means that Lennard-Jones or Buckingham potentials can be
used without a cutoff, i.e. they become full long-range potentials.
The {ewald/disp} style can also be used with point-dipoles, see
"(Toukmaji)"_#Toukmaji.
The {ewald/dipole} style adds long-range standard Ewald summations
for dipole-dipole interactions, see "(Toukmaji)"_#Toukmaji.
The {ewald/dipole/spin} style adds long-range standard Ewald
summations for magnetic dipole-dipole interactions between
magnetic spins.
:line
The {pppm} style invokes a particle-particle particle-mesh solver
"(Hockney)"_#Hockney which maps atom charge to a 3d mesh, uses 3d FFTs
to solve Poisson's equation on the mesh, then interpolates electric
fields on the mesh points back to the atoms. It is closely related to
the particle-mesh Ewald technique (PME) "(Darden)"_#Darden used in
AMBER and CHARMM. The cost of traditional Ewald summation scales as
N^(3/2) where N is the number of atoms in the system. The PPPM solver
scales as Nlog(N) due to the FFTs, so it is almost always a faster
choice "(Pollock)"_#Pollock.
The {pppm/cg} style is identical to the {pppm} style except that it
has an optimization for systems where most particles are uncharged.
Similarly the {msm/cg} style implements the same optimization for {msm}.
The optional {smallq} argument defines the cutoff for the absolute
charge value which determines whether a particle is considered charged
or not. Its default value is 1.0e-5.
The {pppm/dipole} style invokes a particle-particle particle-mesh solver
for dipole-dipole interactions, following the method of "(Cerda)"_#Cerda2008.
The {pppm/dipole/spin} style invokes a particle-particle particle-mesh solver
for magnetic dipole-dipole interactions between magnetic spins.
The {pppm/tip4p} style is identical to the {pppm} style except that it
adds a charge at the massless 4th site in each TIP4P water molecule.
It should be used with "pair styles"_pair_style.html with a
{tip4p/long} in their style name.
The {pppm/stagger} style performs calculations using two different
meshes, one shifted slightly with respect to the other. This can
reduce force aliasing errors and increase the accuracy of the method
for a given mesh size. Or a coarser mesh can be used for the same
target accuracy, which saves CPU time. However, there is a trade-off
since FFTs on two meshes are now performed which increases the
computation required. See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov,
and "(Hockney)"_#Hockney for details of the method.
For high relative accuracy, using staggered PPPM allows the mesh size
to be reduced by a factor of 2 in each dimension as compared to
regular PPPM (for the same target accuracy). This can give up to a 4x
speedup in the KSpace time (8x less mesh points, 2x more expensive).
However, for low relative accuracy, the staggered PPPM mesh size may
be essentially the same as for regular PPPM, which means the method
will be up to 2x slower in the KSpace time (simply 2x more expensive).
For more details and timings, see the "Speed tips"_Speed_tips.html doc
page.
NOTE: Using {pppm/stagger} may not give the same increase in the
accuracy of energy and pressure as it does in forces, so some caution
must be used if energy and/or pressure are quantities of interest,
such as when using a barostat.
:line
The {pppm/disp} and {pppm/disp/tip4p} styles add a mesh-based long-range
dispersion sum option for 1/r^6 potentials "(Isele-Holder)"_#Isele-Holder2012,
similar to the {ewald/disp} style. The 1/r^6 capability means
that Lennard-Jones or Buckingham potentials can be used without a cutoff,
i.e. they become full long-range potentials.
For these styles, you will possibly want to adjust the default choice
of parameters by using the "kspace_modify"_kspace_modify.html command.
This can be done by either choosing the Ewald and grid parameters, or
by specifying separate accuracies for the real and kspace
calculations. When not making any settings, the simulation will stop
with an error message. Further information on the influence of the
parameters and how to choose them is described in
"(Isele-Holder)"_#Isele-Holder2012,
"(Isele-Holder2)"_#Isele-Holder2013 and the "Howto
dispersion"_Howto_dispersion.html doc page.
:line
NOTE: All of the PPPM styles can be used with single-precision FFTs by
using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
lo-level Makefile. This setting also changes some of the PPPM
operations (e.g. mapping charge to mesh and interpolating electric
fields to particles) to be performed in single precision. This option
can speed-up long-range calculations, particularly in parallel or on
GPUs. The use of the -DFFT_SINGLE flag is discussed on the "Build
settings"_Build_settings.html doc page. MSM does not currently support
the -DFFT_SINGLE compiler switch.
:line
The {msm} style invokes a multi-level summation method MSM solver,
"(Hardy)"_#Hardy2006 or "(Hardy2)"_#Hardy2009, which maps atom charge
to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser
meshes on which direct Coulomb solvers are done. This method does not
use FFTs and scales as N. It may therefore be faster than the other
K-space solvers for relatively large problems when running on large
core counts. MSM can also be used for non-periodic boundary conditions
and for mixed periodic and non-periodic boundaries.
MSM is most competitive versus Ewald and PPPM when only relatively
low accuracy forces, about 1e-4 relative error or less accurate,
are needed. Note that use of a larger Coulombic cutoff (i.e. 15
angstroms instead of 10 angstroms) provides better MSM accuracy for
both the real space and grid computed forces.
Currently calculation of the full pressure tensor in MSM is expensive.
Using the "kspace_modify"_kspace_modify.html {pressure/scalar yes}
command provides a less expensive way to compute the scalar pressure
(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
to run an isotropic barostat. If the full pressure tensor is needed,
then calculating the pressure at every timestep or using a fixed
pressure simulation with MSM will cause the code to run slower.
:line
The {scafacos} style is a wrapper on the "ScaFaCoS Coulomb solver
library"_http://www.scafacos.de which provides a variety of solver
methods which can be used with LAMMPS. The paper by "(Who)"_#Who2012
gives an overview of ScaFaCoS.
ScaFaCoS was developed by a consortium of German research facilities
with a BMBF (German Ministry of Science and Education) funded project
in 2009-2012. Participants of the consortium were the Universities of
Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
Forschungszentrum Juelich.
The library is available for download at "http://scafacos.de" or can
be cloned from the git-repository
"git://github.com/scafacos/scafacos.git".
In order to use this KSpace style, you must download and build the
ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package
installed package which links LAMMPS to the ScaFaCoS library.
See details on "this page"_Section_packages.html#USER-SCAFACOS.
NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all
Coulombic interactions, both short- and long-range. Thus you should
NOT use a Coulombic pair style when using kspace_style scafacos. This
also means the total Coulombic energy (short- and long-range) will be
tallied for "thermodynamic output"_thermo_style.html command as part
of the {elong} keyword; the {ecoul} keyword will be zero.
NOTE: See the current restriction below about use of ScaFaCoS in
LAMMPS with molecular charged systems or the TIP4P water model.
The specified {method} determines which ScaFaCoS algorithm is used.
These are the ScaFaCoS methods currently available from LAMMPS:
{fmm} = Fast Multi-Pole method
{p2nfft} = FFT-based Coulomb solver
{ewald} = Ewald summation
{direct} = direct O(N^2) summation
{p3m} = PPPM :ul
We plan to support additional ScaFaCoS solvers from LAMMPS in the
future. For an overview of the included solvers, refer to
"(Sutmann)"_#Sutmann2013
The specified {accuracy} is similar to the accuracy setting for other
LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret
it in different ways for different methods it supports. Within the
ScaFaCoS library the {accuracy} is treated as a tolerance level
(either absolute or relative) for the chosen quantity, where the
quantity can be either the Columic field values, the per-atom Columic
energy or the total Columic energy. To select from these options, see
the "kspace_modify scafacos accuracy"_kspace_modify.html doc page.
The "kspace_modify scafacos"_kspace_modify.html command also explains
other ScaFaCoS options currently exposed to LAMMPS.
:line
The specified {accuracy} determines the relative RMS error in per-atom
forces calculated by the long-range solver. It is set as a
dimensionless number, relative to the force that two unit point
charges (e.g. 2 monovalent ions) exert on each other at a distance of
1 Angstrom. This reference value was chosen as representative of the
magnitude of electrostatic forces in atomic systems. Thus an accuracy
value of 1.0e-4 means that the RMS error will be a factor of 10000
smaller than the reference force.
The accuracy setting is used in conjunction with the pairwise cutoff
to determine the number of K-space vectors for style {ewald} or the
grid size for style {pppm} or {msm}.
Note that style {pppm} only computes the grid size at the beginning of
a simulation, so if the length or triclinic tilt of the simulation
cell increases dramatically during the course of the simulation, the
accuracy of the simulation may degrade. Likewise, if the
"kspace_modify slab"_kspace_modify.html option is used with
shrink-wrap boundaries in the z-dimension, and the box size changes
dramatically in z. For example, for a triclinic system with all three
tilt factors set to the maximum limit, the PPPM grid should be
increased roughly by a factor of 1.5 in the y direction and 2.0 in the
z direction as compared to the same system using a cubic orthogonal
simulation cell. One way to handle this issue if you have a long
simulation where the box size changes dramatically, is to break it
into shorter simulations (multiple "run"_run.html commands). This
works because the grid size is re-computed at the beginning of each
run. Another way to ensure the described accuracy requirement is met
is to run a short simulation at the maximum expected tilt or length,
note the required grid size, and then use the
"kspace_modify"_kspace_modify.html {mesh} command to manually set the
PPPM grid size to this value for the long run. The simulation then
will be "too accurate" for some portion of the run.
RMS force errors in real space for {ewald} and {pppm} are estimated
using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as
equation 9 of "(Petersen)"_#Petersen. RMS force errors in K-space for
{ewald} are estimated using equation 11 of "(Petersen)"_#Petersen,
which is similar to equation 32 of "(Kolafa)"_#Kolafa. RMS force
errors in K-space for {pppm} are estimated using equation 38 of
"(Deserno)"_#Deserno. RMS force errors for {msm} are estimated
using ideas from chapter 3 of "(Hardy)"_#Hardy2006, with equation 3.197
of particular note. When using {msm} with non-periodic boundary
conditions, it is expected that the error estimation will be too
pessimistic. RMS force errors for dipoles when using {ewald/disp}
or {ewald/dipole} are estimated using equations 33 and 46 of
"(Wang)"_#Wang. The RMS force errors for {pppm/dipole} are estimated
using the equations in "(Cerda)"_#Cerda2008.
See the "kspace_modify"_kspace_modify.html command for additional
options of the K-space solvers that can be set, including a {force}
option for setting an absolute RMS error in forces, as opposed to a
relative RMS error.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
More specifically, the {pppm/gpu} style performs charge assignment and
force interpolation calculations on the GPU. These processes are
performed either in single or double precision, depending on whether
the -DFFT_SINGLE setting was specified in your lo-level Makefile, as
discussed above. The FFTs themselves are still calculated on the CPU.
If {pppm/gpu} is used with a GPU-enabled pair style, part of the PPPM
calculation can be performed concurrently on the GPU while other
calculations for non-bonded and bonded force calculation are performed
on the CPU.
The {pppm/kk} style also performs charge assignment and force
interpolation calculations on the GPU while the FFTs themselves are
calculated on the CPU in non-threaded mode.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP, and OPT packages respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
Note that the long-range electrostatic solvers in LAMMPS assume conducting
metal (tinfoil) boundary conditions for both charge and dipole
interactions. Vacuum boundary conditions are not currently supported.
The {ewald/disp}, {ewald}, {pppm}, and {msm} styles support
non-orthogonal (triclinic symmetry) simulation boxes. However,
triclinic simulation cells may not yet be supported by suffix versions
of these styles.
All of the kspace styles are part of the KSPACE package. They are
only enabled if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
For MSM, a simulation must be 3d and one can use any combination of
periodic, non-periodic, or shrink-wrapped boundaries (specified using
the "boundary"_boundary.html command).
For Ewald and PPPM, a simulation must be 3d and periodic in all
dimensions. The only exception is if the slab option is set with
"kspace_modify"_kspace_modify.html, in which case the xy dimensions
must be periodic and the z dimension must be non-periodic.
The scafacos KSpace style will only be enabled if LAMMPS is built with
the USER-SCAFACOS package. See the "Build package"_Build_package.html
doc page for more info.
The use of ScaFaCos in LAMMPS does not yet support molecular charged
systems where the short-range Coulombic interactions between atoms in
the same bond/angle/dihedral are weighted by the
"special_bonds"_special_bonds.html command. Likewise it does not
support the "TIP4P water style" where a fictitious charge site is
introduced in each water molecule.
Finally, the methods {p3m} and {ewald} do not support computing the
virial, so this contribution is not included.
[Related commands:]
"kspace_modify"_kspace_modify.html, "pair_style
lj/cut/coul/long"_pair_lj.html, "pair_style
lj/charmm/coul/long"_pair_charmm.html, "pair_style
lj/long/coul/long"_pair_lj_long.html, "pair_style
buck/coul/long"_pair_buck.html
[Default:]
kspace_style none :pre
:line
:link(Darden)
[(Darden)] Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
:link(Deserno)
[(Deserno)] Deserno and Holm, J Chem Phys, 109, 7694 (1998).
:link(Hockney)
[(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles,
Adam Hilger, NY (1989).
:link(Kolafa)
[(Kolafa)] Kolafa and Perram, Molecular Simulation, 9, 351 (1992).
:link(Petersen)
[(Petersen)] Petersen, J Chem Phys, 103, 3668 (1995).
:link(Wang)
[(Wang)] Wang and Holm, J Chem Phys, 115, 6277 (2001).
:link(Pollock)
[(Pollock)] Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
:link(Cerutti)
[(Cerutti)] Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory
and Computation 5, 2322 (2009)
:link(Neelov)
[(Neelov)] Neelov, Holm, J Chem Phys 132, 234103 (2010)
:link(Veld)
[(Veld)] In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
:link(Toukmaji)
[(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
10913 (2000).
:link(Isele-Holder2012)
[(Isele-Holder)] Isele-Holder, Mitchell, Ismail, J Chem Phys, 137,
174107 (2012).
:link(Isele-Holder2013)
[(Isele-Holder2)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail,
J Chem Theory Comput 9, 5412 (2013).
:link(Hardy2006)
[(Hardy)] David Hardy thesis: Multilevel Summation for the Fast
Evaluation of Forces for the Simulation of Biomolecules, University of
Illinois at Urbana-Champaign, (2006).
:link(Hardy2009)
[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing, 35, 164-177
(2009).
:link(Sutmann2013)
[(Sutmann)] Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
:link(Cerda2008)
[(Cerda)] Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
:link(Who2012)
[(Who)] Who, Author2, Author3, J of Long Range Solvers, 35, 164-177
(2012).

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@ -1,338 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
pair_style command :h3
[Syntax:]
pair_style style args :pre
style = one of the styles from the list below
args = arguments used by a particular style :ul
[Examples:]
pair_style lj/cut 2.5
pair_style eam/alloy
pair_style hybrid lj/charmm/coul/long 10.0 eam
pair_style table linear 1000
pair_style none :pre
[Description:]
Set the formula(s) LAMMPS uses to compute pairwise interactions. In
LAMMPS, pair potentials are defined between pairs of atoms that are
within a cutoff distance and the set of active interactions typically
changes over time. See the "bond_style"_bond_style.html command to
define potentials between pairs of bonded atoms, which typically
remain in place for the duration of a simulation.
In LAMMPS, pairwise force fields encompass a variety of interactions,
some of which include many-body effects, e.g. EAM, Stillinger-Weber,
Tersoff, REBO potentials. They are still classified as "pairwise"
potentials because the set of interacting atoms changes with time
(unlike molecular bonds) and thus a neighbor list is used to find
nearby interacting atoms.
Hybrid models where specified pairs of atom types interact via
different pair potentials can be setup using the {hybrid} pair style.
The coefficients associated with a pair style are typically set for
each pair of atom types, and are specified by the
"pair_coeff"_pair_coeff.html command or read from a file by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands.
The "pair_modify"_pair_modify.html command sets options for mixing of
type I-J interaction coefficients and adding energy offsets or tail
corrections to Lennard-Jones potentials. Details on these options as
they pertain to individual potentials are described on the doc page
for the potential. Likewise, info on whether the potential
information is stored in a "restart file"_write_restart.html is listed
on the potential doc page.
In the formulas listed for each pair style, {E} is the energy of a
pairwise interaction between two atoms separated by a distance {r}.
The force between the atoms is the negative derivative of this
expression.
If the pair_style command has a cutoff argument, it sets global
cutoffs for all pairs of atom types. The distance(s) can be smaller
or larger than the dimensions of the simulation box.
Typically, the global cutoff value can be overridden for a specific
pair of atom types by the "pair_coeff"_pair_coeff.html command. The
pair style settings (including global cutoffs) can be changed by a
subsequent pair_style command using the same style. This will reset
the cutoffs for all atom type pairs, including those previously set
explicitly by a "pair_coeff"_pair_coeff.html command. The exceptions
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
previously specified pair_coeff values.
:line
Here is an alphabetic list of pair styles defined in LAMMPS. They are
also listed in more compact form on the "Commands
pair"_Commands_pair.html doc page.
Click on the style to display the formula it computes, any additional
arguments specified in the pair_style command, and coefficients
specified by the associated "pair_coeff"_pair_coeff.html command.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands pair"_Commands_pair.html
doc page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
"none"_pair_none.html - turn off pairwise interactions
"hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
"hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions
"zero"_pair_zero.html - neighbor list but no interactions :ul
"adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
"agni"_pair_agni.html - machine learned potential mapping atomic environment to forces
"airebo"_pair_airebo.html - AIREBO potential of Stuart
"airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
"atm"_pair_atm.html - Axilrod-Teller-Muto potential
"awpmd/cut"_pair_awpmd.html - Antisymmetrized Wave Packet MD potential for atoms and electrons
"beck"_pair_beck.html - Beck potential
"body/nparticle"_pair_body_nparticle.html - interactions between body particles
"body/rounded/polygon"_pair_body_rounded_polygon.html - granular-style 2d polygon potential
"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - granular-style 3d polyhedron potential
"bop"_pair_bop.html - BOP potential of Pettifor
"born"_pair_born.html - Born-Mayer-Huggins potential
"born/coul/dsf"_pair_born.html - Born with damped-shifted-force model
"born/coul/dsf/cs"_pair_cs.html - Born with damped-shifted-force and core/shell model
"born/coul/long"_pair_born.html - Born with long-range Coulombics
"born/coul/long/cs"_pair_cs.html - Born with long-range Coulombics and core/shell
"born/coul/msm"_pair_born.html - Born with long-range MSM Coulombics
"born/coul/wolf"_pair_born.html - Born with Wolf potential for Coulombics
"born/coul/wolf/cs"_pair_cs.html - Born with Wolf potential for Coulombics and core/shell model
"brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics
"brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity
"buck"_pair_buck.html - Buckingham potential
"buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb
"buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics
"buck/coul/long/cs"_pair_cs.html - Buckingham with long-range Coulombics and core/shell
"buck/coul/msm"_pair_buck.html - Buckingham with long-range MSM Coulombics
"buck/long/coul/long"_pair_buck_long.html - long-range Buckingham with long-range Coulombics
"buck/mdf"_pair_mdf.html - Buckingham with a taper function
"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with damped-shift-force model
"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with long-range Coulombics
"colloid"_pair_colloid.html - integrated colloidal potential
"comb"_pair_comb.html - charge-optimized many-body (COMB) potential
"comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential
"cosine/squared"_pair_cosine_squared.html - Cooke-Kremer-Deserno membrane model potential
"coul/cut"_pair_coul.html - cutoff Coulombic potential
"coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core
"coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
"coul/diel"_pair_coul_diel.html - Coulomb potential with dielectric permittivity
"coul/dsf"_pair_coul.html - Coulombics with damped-shifted-force model
"coul/long"_pair_coul.html - long-range Coulombic potential
"coul/long/cs"_pair_cs.html - long-range Coulombic potential and core/shell
"coul/long/soft"_pair_fep_soft.html - long-range Coulombic potential with a soft core
"coul/msm"_pair_coul.html - long-range MSM Coulombics
"coul/shield"_pair_coul_shield.html - Coulombics for boron nitride for use with "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html potential
"coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals
"coul/wolf"_pair_coul.html - Coulombics via Wolf potential
"coul/wolf/cs"_pair_cs.html - ditto with core/shell adjustments
"dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
"dpd/fdt"_pair_dpd_fdt.html - DPD for constant temperature and pressure
"dpd/fdt/energy"_pair_dpd_fdt.html - DPD for constant energy and enthalpy
"dpd/tstat"_pair_dpd.html - pair-wise DPD thermostatting
"dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC)
"e3b"_pair_e3b.html - Explicit-three body (E3B) water model
"drip"_pair_drip.html - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
"eam"_pair_eam.html - embedded atom method (EAM)
"eam/alloy"_pair_eam.html - alloy EAM
"eam/cd"_pair_eam.html - concentration-dependent EAM
"eam/cd/old"_pair_eam.html - older two-site model for concentration-dependent EAM
"eam/fs"_pair_eam.html - Finnis-Sinclair EAM
"edip"_pair_edip.html - three-body EDIP potential
"edip/multi"_pair_edip.html - multi-element EDIP potential
"edpd"_pair_meso.html - eDPD particle interactions
"eff/cut"_pair_eff.html - electron force field with a cutoff
"eim"_pair_eim.html - embedded ion method (EIM)
"exp6/rx"_pair_exp6_rx.html - reactive DPD potential
"extep"_pair_extep.html - extended Tersoff potential
"gauss"_pair_gauss.html - Gaussian potential
"gauss/cut"_pair_gauss.html - generalized Gaussian potential
"gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
"gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions
"gran/hooke"_pair_gran.html - granular potential with history effects
"gran/hooke/history"_pair_gran.html - granular potential without history effects
"gw"_pair_gw.html - Gao-Weber potential
"gw/zbl"_pair_gw.html - Gao-Weber potential with a repulsive ZBL core
"hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential
"hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential
"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - registry-dependent interlayer potential (ILP)
"kim"_pair_kim.html - interface to potentials provided by KIM project
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis
"lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
"lebedeva/z"_pair_lebedeva_z.html - Lebedeva interlayer potential for graphene with normals along z-axis
"lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function
"line/lj"_pair_line_lj.html - LJ potential between line segments
"list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file
"lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
"lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
"lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
"lj/charmm/coul/long/soft"_pair_fep_soft.html - CHARMM with long-range Coulomb and a soft core
"lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics
"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html - CHARMM with force switching and shifting
"lj/charmmfsw/coul/long"_pair_charmm.html - CHARMM with force switching and long-rnage Coulombics
"lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
"lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
"lj/class2/coul/cut/soft"_pair_fep_soft.html - COMPASS with cutoff Coulomb with a soft core
"lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
"lj/class2/coul/long/soft"_pair_fep_soft.html - COMPASS with long-range Coulomb with a soft core
"lj/class2/soft"_pair_fep_soft.html - COMPASS (class 2) force field with no Coulomb with a soft core
"lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point
"lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
"lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
"lj/cut/coul/cut/soft"_pair_fep_soft.html - LJ with cutoff Coulomb with a soft core
"lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
"lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces
"lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics
"lj/cut/coul/long/cs"_pair_cs.html - ditto with core/shell adjustments
"lj/cut/coul/long/soft"_pair_fep_soft.html - LJ with long-range Coulombics with a soft core
"lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics
"lj/cut/coul/wolf"_pair_lj.html - LJ with Coulombics via Wolf potential
"lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff
"lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald
"lj/cut/soft"_pair_fep_soft.html - LJ with a soft core
"lj/cut/thole/long"_pair_thole.html - LJ with Coulombics with thole damping
"lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water
"lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
"lj/cut/tip4p/long/soft"_pair_fep_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core
"lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
"lj/expand/coul/long"_pair_lj_expand.html - Lennard-Jones for variable size particles with long-range Coulombics
"lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
"lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
"lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics
"lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles
"lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulombics for TIP4P water
"lj/mdf"_pair_mdf.html - LJ potential with a taper function
"lj/sdk"_pair_sdk.html - LJ for SDK coarse-graining
"lj/sdk/coul/long"_pair_sdk.html - LJ for SDK coarse-graining with long-range Coulombics
"lj/sdk/coul/msm"_pair_sdk.html - LJ for SDK coarse-graining with long-range Coulombics via MSM
"lj/sf/dipole/sf"_pair_dipole.html - LJ with dipole interaction with shifted forces
"lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed LJ potential
"lj/switch3/coulgauss"_pair_lj_switch3_coulgauss - smoothed LJ vdW potential with Gaussian electrostatics
"lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
"local/density"_pair_local_density.html - generalized basic local density potential
"lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
"lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity
"lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics
"lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
"mdpd"_pair_meso.html - mDPD particle interactions
"mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density
"meam/c"_pair_meamc.html - modified embedded atom method (MEAM) in C
"meam/spline"_pair_meam_spline.html - splined version of MEAM
"meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term
"mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential
"mie/cut"_pair_mie.html - Mie potential
"mm3/switch3/coulgauss"_pair_mm3_switch3_coulgauss - smoothed MM3 vdW potential with Gaussian electrostatics
"momb"_pair_momb.html - Many-Body Metal-Organic (MOMB) force field
"morse"_pair_morse.html - Morse potential
"morse/smooth/linear"_pair_morse.html - linear smoothed Morse potential
"morse/soft"_pair_morse.html - Morse potential with a soft core
"multi/lucy"_pair_multi_lucy.html - DPD potential with density-dependent force
"multi/lucy/rx"_pair_multi_lucy_rx.html - reactive DPD potential with density-dependent force
"nb3b/harmonic"_pair_nb3b_harmonic.html - non-bonded 3-body harmonic potential
"nm/cut"_pair_nm.html - N-M potential
"nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb
"nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics
"oxdna/coaxstk"_pair_oxdna.html -
"oxdna/excv"_pair_oxdna.html -
"oxdna/hbond"_pair_oxdna.html -
"oxdna/stk"_pair_oxdna.html -
"oxdna/xstk"_pair_oxdna.html -
"oxdna2/coaxstk"_pair_oxdna2.html -
"oxdna2/dh"_pair_oxdna2.html -
"oxdna2/excv"_pair_oxdna2.html -
"oxdna2/hbond"_pair_oxdna2.html -
"oxdna2/stk"_pair_oxdna2.html -
"oxdna2/xstk"_pair_oxdna2.html -
"peri/eps"_pair_peri.html - peridynamic EPS potential
"peri/lps"_pair_peri.html - peridynamic LPS potential
"peri/pmb"_pair_peri.html - peridynamic PMB potential
"peri/ves"_pair_peri.html - peridynamic VES potential
"polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
"python"_pair_python.html -
"quip"_pair_quip.html -
"reax/c"_pair_reaxc.html - ReaxFF potential in C
"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html - smoothed dissipative particle dynamics for water at isothermal conditions
"smd/hertz"_pair_smd_hertz.html -
"smd/tlsph"_pair_smd_tlsph.html -
"smd/tri_surface"_pair_smd_triangulated_surface.html -
"smd/ulsph"_pair_smd_ulsph.html -
"smtbq"_pair_smtbq.html -
"snap"_pair_snap.html - SNAP quantum-accurate potential
"soft"_pair_soft.html - Soft (cosine) potential
"sph/heatconduction"_pair_sph_heatconduction.html -
"sph/idealgas"_pair_sph_idealgas.html -
"sph/lj"_pair_sph_lj.html -
"sph/rhosum"_pair_sph_rhosum.html -
"sph/taitwater"_pair_sph_taitwater.html -
"sph/taitwater/morris"_pair_sph_taitwater_morris.html -
"spin/dipole/cut"_pair_spin_dipole.html -
"spin/dipole/long"_pair_spin_dipole.html -
"spin/dmi"_pair_spin_dmi.html -
"spin/exchange"_pair_spin_exchange.html -
"spin/magelec"_pair_spin_magelec.html -
"spin/neel"_pair_spin_neel.html -
"srp"_pair_srp.html -
"sw"_pair_sw.html - Stillinger-Weber 3-body potential
"table"_pair_table.html - tabulated pair potential
"table/rx"_pair_table_rx.html -
"tdpd"_pair_meso.html - tDPD particle interactions
"tersoff"_pair_tersoff.html - Tersoff 3-body potential
"tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential
"tersoff/mod/c"_pair_tersoff_mod.html -
"tersoff/table"_pair_tersoff.html -
"tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential
"thole"_pair_thole.html - Coulomb interactions with thole damping
"tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ
"tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ
"tip4p/long/soft"_pair_fep_soft.html -
"tri/lj"_pair_tri_lj.html - LJ potential between triangles
"ufm"_pair_ufm.html -
"vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential
"vashishta/table"_pair_vashishta.html -
"yukawa"_pair_yukawa.html - Yukawa potential
"yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles
"zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul
:line
[Restrictions:]
This command must be used before any coefficients are set by the
"pair_coeff"_pair_coeff.html, "read_data"_read_data.html, or
"read_restart"_read_restart.html commands.
Some pair styles are part of specific packages. They are only enabled
if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info. The doc pages for
individual pair potentials tell if it is part of a package.
[Related commands:]
"pair_coeff"_pair_coeff.html, "read_data"_read_data.html,
"pair_modify"_pair_modify.html, "kspace_style"_kspace_style.html,
"dielectric"_dielectric.html, "pair_write"_pair_write.html
[Default:]
pair_style none :pre

244
doc/utils/check-styles.py Executable file
View File

@ -0,0 +1,244 @@
#!/usr/bin/env python3
from __future__ import print_function
from glob import glob
from argparse import ArgumentParser
import os, re, sys
parser = ArgumentParser(prog='check-styles.py',
description="Check style table completeness")
parser.add_argument("-v", "--verbose",
action='store_const',
const=True, default=False,
help="Enable verbose output")
parser.add_argument("-d", "--doc",
help="Path to LAMMPS documentation sources")
parser.add_argument("-s", "--src",
help="Path to LAMMPS sources")
args = parser.parse_args()
verbose = args.verbose
src = args.src
doc = args.doc
if not args.src or not args.doc:
parser.print_help()
sys.exit(1)
if not os.path.isdir(src):
sys.exit("LAMMPS source path %s does not exist" % src)
if not os.path.isdir(doc):
sys.exit("LAMMPS documentation source path %s does not exist" % doc)
headers = glob(os.path.join(src, '*', '*.h'))
headers += glob(os.path.join(src, '*.h'))
angle = {}
atom = {}
body = {}
bond = {}
command = {}
compute = {}
dihedral = {}
dump = {}
fix = {}
improper = {}
integrate = {}
kspace = {}
minimize = {}
pair = {}
reader = {}
region = {}
upper = re.compile("[A-Z]+")
gpu = re.compile("(.+)/gpu$")
intel = re.compile("(.+)/intel$")
kokkos = re.compile("(.+)/kk$")
kokkos_skip = re.compile("(.+)/kk/(host|device)$")
omp = re.compile("(.+)/omp$")
opt = re.compile("(.+)/opt$")
removed = re.compile("(.+)Deprecated$")
def register_style(list,style,info):
if style in list.keys():
list[style]['gpu'] += info['gpu']
list[style]['intel'] += info['intel']
list[style]['kokkos'] += info['kokkos']
list[style]['omp'] += info['omp']
list[style]['opt'] += info['opt']
list[style]['removed'] += info['removed']
else:
list[style] = info
def add_suffix(list,style):
suffix = ""
if list[style]['gpu']:
suffix += 'g'
if list[style]['intel']:
suffix += 'i'
if list[style]['kokkos']:
suffix += 'k'
if list[style]['omp']:
suffix += 'o'
if list[style]['opt']:
suffix += 't'
if suffix:
return style + ' (' + suffix + ')'
else:
return style
def check_style(file,dir,pattern,list,name,suffix=False,skip=()):
f = os.path.join(dir, file)
fp = open(f)
text = fp.read()
fp.close()
matches = re.findall(pattern,text,re.MULTILINE)
counter = 0
for c in list.keys():
# known undocumented aliases we need to skip
if c in skip: continue
s = c
if suffix: s = add_suffix(list,c)
if not s in matches:
if not list[c]['removed']:
print("%s style entry %s" % (name,s),
"is missing or incomplete in %s" % file)
counter += 1
return counter
for h in headers:
if verbose: print("Checking ", h)
fp = open(h)
text = fp.read()
fp.close()
matches = re.findall("(.+)Style\((.+),(.+)\)",text,re.MULTILINE)
for m in matches:
# skip over internal styles w/o explicit documentation
style = m[1]
if upper.match(style):
continue
# detect, process, and flag suffix styles:
info = { 'kokkos': 0, 'gpu': 0, 'intel': 0, \
'omp': 0, 'opt': 0, 'removed': 0 }
suffix = kokkos_skip.match(style)
if suffix:
continue
suffix = gpu.match(style)
if suffix:
style = suffix.groups()[0]
info['gpu'] = 1
suffix = intel.match(style)
if suffix:
style = suffix.groups()[0]
info['intel'] = 1
suffix = kokkos.match(style)
if suffix:
style = suffix.groups()[0]
info['kokkos'] = 1
suffix = omp.match(style)
if suffix:
style = suffix.groups()[0]
info['omp'] = 1
suffix = opt.match(style)
if suffix:
style = suffix.groups()[0]
info['opt'] = 1
deprecated = removed.match(m[2])
if deprecated:
info['removed'] = 1
# register style and suffix flags
if m[0] == 'Angle':
register_style(angle,style,info)
elif m[0] == 'Atom':
register_style(atom,style,info)
elif m[0] == 'Body':
register_style(body,style,info)
elif m[0] == 'Bond':
register_style(bond,style,info)
elif m[0] == 'Command':
register_style(command,style,info)
elif m[0] == 'Compute':
register_style(compute,style,info)
elif m[0] == 'Dihedral':
register_style(dihedral,style,info)
elif m[0] == 'Dump':
register_style(dump,style,info)
elif m[0] == 'Fix':
register_style(fix,style,info)
elif m[0] == 'Improper':
register_style(improper,style,info)
elif m[0] == 'Integrate':
register_style(integrate,style,info)
elif m[0] == 'KSpace':
register_style(kspace,style,info)
elif m[0] == 'Minimize':
register_style(minimize,style,info)
elif m[0] == 'Pair':
register_style(pair,style,info)
elif m[0] == 'Reader':
register_style(reader,style,info)
elif m[0] == 'Region':
register_style(region,style,info)
else:
print("Skipping over: ",m)
print("""Parsed style names w/o suffixes from C++ tree in %s:
Angle styles: %3d Atom styles: %3d
Body styles: %3d Bond styles: %3d
Command styles: %3d Compute styles: %3d
Dihedral styles: %3d Dump styles: %3d
Fix styles: %3d Improper styles: %3d
Integrate styles: %3d Kspace styles: %3d
Minimize styles: %3d Pair styles: %3d
Reader styles: %3d Region styles: %3d""" \
% (src, len(angle), len(atom), len(body), len(bond), \
len(command), len(compute), len(dihedral), len(dump), \
len(fix), len(improper), len(integrate), len(kspace), \
len(minimize), len(pair), len(reader), len(region)))
counter = 0
counter += check_style('Commands_all.rst',doc,":doc:`(.+) <.+>`",
command,'Command',suffix=False)
counter += check_style('Commands_compute.rst',doc,":doc:`(.+) <compute.+>`",
compute,'Compute',suffix=True)
counter += check_style('compute.rst',doc,":doc:`(.+) <compute.+>` -",
compute,'Compute',suffix=False)
counter += check_style('Commands_fix.rst',doc,":doc:`(.+) <fix.+>`",
fix,'Fix',skip=('python'),suffix=True)
counter += check_style('fix.rst',doc,":doc:`(.+) <fix.+>` -",
fix,'Fix',skip=('python'),suffix=False)
counter += check_style('Commands_pair.rst',doc,":doc:`(.+) <pair.+>`",
pair,'Pair',skip=('meam','lj/sf'),suffix=True)
counter += check_style('pair_style.rst',doc,":doc:`(.+) <pair.+>` -",
pair,'Pair',skip=('meam','lj/sf'),suffix=False)
counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <bond.+>`",
bond,'Bond',suffix=True)
counter += check_style('bond_style.rst',doc,":doc:`(.+) <bond.+>` -",
bond,'Bond',suffix=False)
counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <angle.+>`",
angle,'Angle',suffix=True)
counter += check_style('angle_style.rst',doc,":doc:`(.+) <angle.+>` -",
angle,'Angle',suffix=False)
counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <dihedral.+>`",
dihedral,'Dihedral',suffix=True)
counter += check_style('dihedral_style.rst',doc,":doc:`(.+) <dihedral.+>` -",
dihedral,'Dihedral',suffix=False)
counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <improper.+>`",
improper,'Improper',suffix=True)
counter += check_style('improper_style.rst',doc,":doc:`(.+) <improper.+>` -",
improper,'Improper',suffix=False)
counter += check_style('Commands_kspace.rst',doc,":doc:`(.+) <kspace_style>`",
kspace,'KSpace',suffix=True)
if counter:
print("Found %d issue(s) with style lists" % counter)

2
doc/utils/converters/lammpsdoc/rst_anchor_check.py
View File

@ -42,7 +42,7 @@ def main():
else: else:
anchors[label] = [(filename, line_number+1)] anchors[label] = [(filename, line_number+1)]
print("found %d anchor labels" % len(anchors)) print("Found %d anchor labels" % len(anchors))
count = 0 count = 0