forked from lijiext/lammps
Merge branch 'master' into fft
# Conflicts: # doc/txt/kspace_style.txt
This commit is contained in:
Axel Kohlmeyer
commit
2834965e98
46
doc/Makefile
46
doc/Makefile
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|
@ -31,7 +31,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
|
|||
SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt))
|
||||
OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)
|
||||
|
||||
.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check
|
||||
.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check style_check
|
||||
|
||||
# ------------------------------------------
|
||||
|
||||
|
|
@ -46,6 +46,7 @@ help:
|
|||
@echo " clean remove all intermediate RST files"
|
||||
@echo " clean-all reset the entire build environment"
|
||||
@echo " anchor_check scan for duplicate anchor labels"
|
||||
@echo " style_check check for complete and consistent style lists"
|
||||
@echo " spelling spell-check the manual"
|
||||
|
||||
# ------------------------------------------
|
||||
|
|
@ -69,6 +70,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
|
|||
echo "############################################" ;\
|
||||
rst_anchor_check src/*.rst ;\
|
||||
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
|
||||
python utils/check-styles.py -s ../src -d src ;\
|
||||
echo "############################################" ;\
|
||||
deactivate ;\
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||||
)
|
||||
|
|
@ -122,24 +124,27 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
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|||
cd ../../; \
|
||||
)
|
||||
@(\
|
||||
. $(VENV)/bin/activate ;\
|
||||
sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
|
||||
echo "############################################" ;\
|
||||
rst_anchor_check src/*.rst ;\
|
||||
echo "############################################" ;\
|
||||
deactivate ;\
|
||||
. $(VENV)/bin/activate ;\
|
||||
sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
|
||||
echo "############################################" ;\
|
||||
rst_anchor_check src/*.rst ;\
|
||||
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
|
||||
python utils/check-styles.py -s ../src -d src ;\
|
||||
echo "############################################" ;\
|
||||
deactivate ;\
|
||||
)
|
||||
@cd latex && \
|
||||
sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
|
||||
mv temp Makefile && \
|
||||
sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
|
||||
mv tmp.tex LAMMPS.tex && \
|
||||
sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
|
||||
mv tmp.tex LAMMPS.tex && \
|
||||
make && \
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||||
make && \
|
||||
mv LAMMPS.pdf ../Manual.pdf && \
|
||||
cd ../;
|
||||
sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
|
||||
mv temp Makefile && \
|
||||
sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
|
||||
mv tmp.tex LAMMPS.tex && \
|
||||
sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
|
||||
mv tmp.tex LAMMPS.tex && \
|
||||
make && \
|
||||
make && \
|
||||
make && \
|
||||
mv LAMMPS.pdf ../Manual.pdf && \
|
||||
cd ../;
|
||||
@rm -rf latex/_sources
|
||||
@rm -rf latex/PDF
|
||||
@rm -rf latex/USER
|
||||
|
|
@ -166,6 +171,13 @@ anchor_check : $(ANCHORCHECK)
|
|||
deactivate ;\
|
||||
)
|
||||
|
||||
style_check :
|
||||
@(\
|
||||
. $(VENV)/bin/activate ;\
|
||||
python utils/check-styles.py -s ../src -d src ;\
|
||||
deactivate ;\
|
||||
)
|
||||
|
||||
# ------------------------------------------
|
||||
|
||||
$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)
|
||||
|
|
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|||
|
|
@ -55,9 +55,9 @@ the doc dir.
|
|||
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
|
||||
make clean # remove intermediate RST files created by HTML build
|
||||
make clean-all # remove entire build folder and any cached data
|
||||
|
||||
make anchor\_check # check for duplicate anchor labels
|
||||
make spelling # spell-check the manual
|
||||
make anchor_check # check for duplicate anchor labels
|
||||
style_check # check for complete and consistent style lists
|
||||
make spelling # spell-check the manual
|
||||
|
||||
|
||||
----------
|
||||
|
|
|
|||
|
|
@ -100,6 +100,7 @@ accelerated styles exist.
|
|||
* :doc:`nonlinear <bond_nonlinear>` - nonlinear bond
|
||||
* :doc:`oxdna/fene <bond_oxdna>` - modified FENE bond suitable for DNA modeling
|
||||
* :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
|
||||
* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
|
||||
* :doc:`quartic <bond_quartic>` - breakable quartic bond
|
||||
* :doc:`table <bond_table>` - tabulated by bond length
|
||||
|
||||
|
|
|
|||
|
|
@ -64,16 +64,16 @@ with new settings). This is the same as if an "unfix" command were
|
|||
first performed on the old fix, except that the new fix is kept in the
|
||||
same order relative to the existing fixes as the old one originally
|
||||
was. Note that this operation also wipes out any additional changes
|
||||
made to the old fix via the :doc:`fix\_modify <fix_modify>` command.
|
||||
made to the old fix via the :doc:`fix_modify <fix_modify>` command.
|
||||
|
||||
The :doc:`fix modify <fix_modify>` command allows settings for some
|
||||
fixes to be reset. See the doc page for individual fixes for details.
|
||||
|
||||
Some fixes store an internal "state" which is written to binary
|
||||
restart files via the :doc:`restart <restart>` or
|
||||
:doc:`write\_restart <write_restart>` commands. This allows the fix to
|
||||
:doc:`write_restart <write_restart>` commands. This allows the fix to
|
||||
continue on with its calculations in a restarted simulation. See the
|
||||
:doc:`read\_restart <read_restart>` command for info on how to re-specify
|
||||
:doc:`read_restart <read_restart>` command for info on how to re-specify
|
||||
a fix in an input script that reads a restart file. See the doc pages
|
||||
for individual fixes for info on which ones can be restarted.
|
||||
|
||||
|
|
@ -133,7 +133,7 @@ various commands explain the details.
|
|||
|
||||
In LAMMPS, the values generated by a fix can be used in several ways:
|
||||
|
||||
* Global values can be output via the :doc:`thermo\_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
|
||||
* Global values can be output via the :doc:`thermo_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
|
||||
Or the values can be referenced in a :doc:`variable equal <variable>` or
|
||||
:doc:`variable atom <variable>` command.
|
||||
* Per-atom values can be output via the :doc:`dump custom <dump>` command.
|
||||
|
|
@ -257,6 +257,7 @@ accelerated styles exist.
|
|||
* :doc:`mvv/edpd <fix_mvv_dpd>` - constant energy DPD using the modified velocity-Verlet algorithm
|
||||
* :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
|
||||
* :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
|
||||
* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
|
||||
* :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
|
||||
* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
|
||||
* :doc:`nph/body <fix_nph_body>` - NPH for body particles
|
||||
|
|
@ -339,15 +340,16 @@ accelerated styles exist.
|
|||
* :doc:`rx <fix_rx>` -
|
||||
* :doc:`saed/vtk <fix_saed_vtk>` -
|
||||
* :doc:`setforce <fix_setforce>` - set the force on each atom
|
||||
* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
|
||||
* :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles
|
||||
* :doc:`shardlow <fix_shardlow>` - integration of DPD equations of motion using the Shardlow splitting
|
||||
* :doc:`smd <fix_smd>` - applied a steered MD force to a group
|
||||
* :doc:`smd/adjust\_dt <fix_smd_adjust_dt>` -
|
||||
* :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` -
|
||||
* :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>` -
|
||||
* :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` -
|
||||
* :doc:`smd/adjust_dt <fix_smd_adjust_dt>` -
|
||||
* :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>` -
|
||||
* :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>` -
|
||||
* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>` -
|
||||
* :doc:`smd/setvel <fix_smd_setvel>` -
|
||||
* :doc:`smd/wall\_surface <fix_smd_wall_surface>` -
|
||||
* :doc:`smd/wall_surface <fix_smd_wall_surface>` -
|
||||
* :doc:`spring <fix_spring>` - apply harmonic spring force to group of atoms
|
||||
* :doc:`spring/chunk <fix_spring_chunk>` - apply harmonic spring force to each chunk of atoms
|
||||
* :doc:`spring/rg <fix_spring_rg>` - spring on radius of gyration of group of atoms
|
||||
|
|
@ -399,7 +401,7 @@ individual fixes tell if it is part of a package.
|
|||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`unfix <unfix>`, :doc:`fix\_modify <fix_modify>`
|
||||
:doc:`unfix <unfix>`, :doc:`fix_modify <fix_modify>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
|
|
|||
|
|
@ -12,9 +12,9 @@ Syntax
|
|||
kspace_style style value
|
||||
|
||||
* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* 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/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos*
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
|
||||
*none* value = none
|
||||
*ewald* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
|
|
|
|||
|
|
@ -247,7 +247,9 @@ or *lj/coul* to change both to the same set of 3 values. The wt1,wt2,wt3
|
|||
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
|
||||
1-3, and 1-4 bond topology neighbors, respectively. The *special*
|
||||
keyword can only be used in conjunction with the *pair* keyword
|
||||
and has to directly follow it.
|
||||
and has to directly follow it. This option is not compatible with
|
||||
pair styles from the GPU or the USER-INTEL package and attempting
|
||||
it will cause an error.
|
||||
|
||||
.. note::
|
||||
|
||||
|
|
@ -278,10 +280,11 @@ and allows to selectively disable or enable processing of the various
|
|||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
You cannot use *shift* yes with *tail* yes, since those are
|
||||
conflicting options. You cannot use *tail* yes with 2d simulations.
|
||||
You cannot use *special* with pair styles from the GPU or
|
||||
USER-INTEL package.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ 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 :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
|
||||
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
|
||||
each pair of atom types, and are specified 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:`pair_coeff <pair_coeff>` command or read from a file by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
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
|
||||
corrections to Lennard-Jones potentials. Details on these options as
|
||||
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.
|
||||
|
||||
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
|
||||
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 :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
|
||||
reset. A new pair\_style command for these styles will wipe out all
|
||||
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
|
||||
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
|
||||
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/cut <pair_gauss>` - generalized Gaussian 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/hooke <pair_gran>` - granular potential with 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/stk <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/lps <pair_peri>` - peridynamic LPS 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:`smd/hertz <pair_smd_hertz>` -
|
||||
* :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:`smtbq <pair_smtbq>` -
|
||||
* :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
|
||||
:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`, or
|
||||
:doc:`read\_restart <read_restart>` commands.
|
||||
:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`, or
|
||||
:doc:`read_restart <read_restart>` commands.
|
||||
|
||||
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
|
||||
|
|
@ -338,9 +345,9 @@ individual pair potentials tell if it is part of a package.
|
|||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`,
|
||||
:doc:`pair\_modify <pair_modify>`, :doc:`kspace\_style <kspace_style>`,
|
||||
:doc:`dielectric <dielectric>`, :doc:`pair\_write <pair_write>`
|
||||
:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`,
|
||||
:doc:`pair_modify <pair_modify>`, :doc:`kspace_style <kspace_style>`,
|
||||
:doc:`dielectric <dielectric>`, :doc:`pair_write <pair_write>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
|
|
|||
|
|
@ -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 performs charge assignment and force interpolation
|
||||
calculations, along with the FFTs themselves, on the GPU or threaded
|
||||
using OpenMP.
|
||||
|
||||
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).
|
||||
|
|
@ -1,281 +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_modify command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_modify keyword values ... :pre
|
||||
|
||||
one or more keyword/value pairs may be listed :ulb,l
|
||||
keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner}
|
||||
or {tabinner/disp} or {tail} or {compute} or {nofdotr} :l
|
||||
{pair} values = sub-style N {special} which wt1 wt2 wt3
|
||||
or sub-style N {compute/tally} flag
|
||||
sub-style = sub-style of "pair hybrid"_pair_hybrid.html
|
||||
N = which instance of sub-style (only if sub-style is used multiple times)
|
||||
{special} which wt1 wt2 wt3 = override {special_bonds} settings (optional)
|
||||
which = {lj/coul} or {lj} or {coul}
|
||||
w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
|
||||
{compute/tally} flag = {yes} or {no}
|
||||
{mix} value = {geometric} or {arithmetic} or {sixthpower}
|
||||
{shift} value = {yes} or {no}
|
||||
{table} value = N
|
||||
2^N = # of values in table
|
||||
{table/disp} value = N
|
||||
2^N = # of values in table
|
||||
{tabinner} value = cutoff
|
||||
cutoff = inner cutoff at which to begin table (distance units)
|
||||
{tabinner/disp} value = cutoff
|
||||
cutoff = inner cutoff at which to begin table (distance units)
|
||||
{tail} value = {yes} or {no}
|
||||
{compute} value = {yes} or {no}
|
||||
{nofdotr} :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_modify shift yes mix geometric
|
||||
pair_modify tail yes
|
||||
pair_modify table 12
|
||||
pair_modify pair lj/cut compute no
|
||||
pair_modify pair tersoff compute/tally no
|
||||
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Modify the parameters of the currently defined pair style. Not all
|
||||
parameters are relevant to all pair styles.
|
||||
|
||||
If used, the {pair} keyword must appear first in the list of keywords.
|
||||
It can only be used with the "hybrid and
|
||||
hybrid/overlay"_pair_hybrid.html pair styles. It means that all the
|
||||
following parameters will only be modified for the specified
|
||||
sub-style. If the sub-style is defined multiple times, then an
|
||||
additional numeric argument {N} must also be specified, which is a
|
||||
number from 1 to M where M is the number of times the sub-style was
|
||||
listed in the "pair_style hybrid"_pair_hybrid.html command. The extra
|
||||
number indicates which instance of the sub-style the remaining
|
||||
keywords will be applied to. Note that if the {pair} keyword is not
|
||||
used, and the pair style is {hybrid} or {hybrid/overlay}, then all the
|
||||
specified keywords will be applied to all sub-styles.
|
||||
|
||||
The {special} and {compute/tally} keywords can [only] be used in
|
||||
conjunction with the {pair} keyword and must directly follow it.
|
||||
{special} allows to override the
|
||||
"special_bonds"_special_bonds.html settings for the specified sub-style.
|
||||
{compute/tally} allows to disable or enable registering
|
||||
"compute */tally"_compute_tally.html computes for a given sub-style.
|
||||
More details are given below.
|
||||
|
||||
The {mix} keyword affects pair coefficients for interactions between
|
||||
atoms of type I and J, when I != J and the coefficients are not
|
||||
explicitly set in the input script. Note that coefficients for I = J
|
||||
must be set explicitly, either in the input script via the
|
||||
"pair_coeff" command or in the "Pair Coeffs" section of the "data
|
||||
file"_read_data.html. For some pair styles it is not necessary to
|
||||
specify coefficients when I != J, since a "mixing" rule will create
|
||||
them from the I,I and J,J settings. The pair_modify {mix} value
|
||||
determines what formulas are used to compute the mixed coefficients.
|
||||
In each case, the cutoff distance is mixed the same way as sigma.
|
||||
|
||||
Note that not all pair styles support mixing. Also, some mix options
|
||||
are not available for certain pair styles. See the doc page for
|
||||
individual pair styles for those restrictions. Note also that the
|
||||
"pair_coeff"_pair_coeff.html command also can be to directly set
|
||||
coefficients for a specific I != J pairing, in which case no mixing is
|
||||
performed.
|
||||
|
||||
mix {geometric}
|
||||
|
||||
epsilon_ij = sqrt(epsilon_i * epsilon_j)
|
||||
sigma_ij = sqrt(sigma_i * sigma_j) :pre
|
||||
|
||||
mix {arithmetic}
|
||||
|
||||
epsilon_ij = sqrt(epsilon_i * epsilon_j)
|
||||
sigma_ij = (sigma_i + sigma_j) / 2 :pre
|
||||
|
||||
mix {sixthpower}
|
||||
|
||||
epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
|
||||
(sigma_i^6 + sigma_j^6)
|
||||
sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre
|
||||
|
||||
The {shift} keyword determines whether a Lennard-Jones potential is
|
||||
shifted at its cutoff to 0.0. If so, this adds an energy term to each
|
||||
pairwise interaction which will be included in the thermodynamic
|
||||
output, but does not affect pair forces or atom trajectories. See the
|
||||
doc page for individual pair styles to see which ones support this
|
||||
option.
|
||||
|
||||
The {table} and {table/disp} keywords apply to pair styles with a
|
||||
long-range Coulombic term or long-range dispersion term respectively;
|
||||
see the doc page for individual styles to see which potentials support
|
||||
these options. If N is non-zero, a table of length 2^N is
|
||||
pre-computed for forces and energies, which can shrink their
|
||||
computational cost by up to a factor of 2. The table is indexed via a
|
||||
bit-mapping technique "(Wolff)"_#Wolff1 and a linear interpolation is
|
||||
performed between adjacent table values. In our experiments with
|
||||
different table styles (lookup, linear, spline), this method typically
|
||||
gave the best performance in terms of speed and accuracy.
|
||||
|
||||
The choice of table length is a tradeoff in accuracy versus speed. A
|
||||
larger N yields more accurate force computations, but requires more
|
||||
memory which can slow down the computation due to cache misses. A
|
||||
reasonable value of N is between 8 and 16. The default value of 12
|
||||
(table of length 4096) gives approximately the same accuracy as the
|
||||
no-table (N = 0) option. For N = 0, forces and energies are computed
|
||||
directly, using a polynomial fit for the needed erfc() function
|
||||
evaluation, which is what earlier versions of LAMMPS did. Values
|
||||
greater than 16 typically slow down the simulation and will not
|
||||
improve accuracy; values from 1 to 8 give unreliable results.
|
||||
|
||||
The {tabinner} and {tabinner/disp} keywords set an inner cutoff above
|
||||
which the pairwise computation is done by table lookup (if tables are
|
||||
invoked), for the corresponding Coulombic and dispersion tables
|
||||
discussed with the {table} and {table/disp} keywords. The smaller the
|
||||
cutoff is set, the less accurate the table becomes (for a given number
|
||||
of table values), which can require use of larger tables. The default
|
||||
cutoff value is sqrt(2.0) distance units which means nearly all
|
||||
pairwise interactions are computed via table lookup for simulations
|
||||
with "real" units, but some close pairs may be computed directly
|
||||
(non-table) for simulations with "lj" units.
|
||||
|
||||
When the {tail} keyword is set to {yes}, certain pair styles will add
|
||||
a long-range VanderWaals tail "correction" to the energy and pressure.
|
||||
These corrections are bookkeeping terms which do not affect dynamics,
|
||||
unless a constant-pressure simulation is being performed. See the doc
|
||||
page for individual styles to see which support this option. These
|
||||
corrections are included in the calculation and printing of
|
||||
thermodynamic quantities (see the "thermo_style"_thermo_style.html
|
||||
command). Their effect will also be included in constant NPT or NPH
|
||||
simulations where the pressure influences the simulation box
|
||||
dimensions (e.g. the "fix npt"_fix_nh.html and "fix nph"_fix_nh.html
|
||||
commands). The formulas used for the long-range corrections come from
|
||||
equation 5 of "(Sun)"_#Sun.
|
||||
|
||||
NOTE: The tail correction terms are computed at the beginning of each
|
||||
run, using the current atom counts of each atom type. If atoms are
|
||||
deleted (or lost) or created during a simulation, e.g. via the "fix
|
||||
gcmc"_fix_gcmc.html command, the correction factors are not
|
||||
re-computed. If you expect the counts to change dramatically, you can
|
||||
break a run into a series of shorter runs so that the correction
|
||||
factors are re-computed more frequently.
|
||||
|
||||
Several additional assumptions are inherent in using tail corrections,
|
||||
including the following:
|
||||
|
||||
The simulated system is a 3d bulk homogeneous liquid. This option
|
||||
should not be used for systems that are non-liquid, 2d, have a slab
|
||||
geometry (only 2d periodic), or inhomogeneous. :ulb,l
|
||||
|
||||
G(r), the radial distribution function (rdf), is unity beyond the
|
||||
cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
|
||||
LJ fluid), and it is probably a good idea to verify this assumption by
|
||||
checking the rdf. The rdf is not exactly unity beyond the cutoff for
|
||||
each pair of interaction types, so the tail correction is necessarily
|
||||
an approximation. :l
|
||||
|
||||
The tail corrections are computed at the beginning of each simulation
|
||||
run. If the number of atoms changes during the run, e.g. due to atoms
|
||||
leaving the simulation domain, or use of the "fix gcmc"_fix_gcmc.html
|
||||
command, then the corrections are not updated to reflect the changed
|
||||
atom count. If this is a large effect in your simulation, you should
|
||||
break the long run into several short runs, so that the correction
|
||||
factors are re-computed multiple times.
|
||||
|
||||
Thermophysical properties obtained from calculations with this option
|
||||
enabled will not be thermodynamically consistent with the truncated
|
||||
force-field that was used. In other words, atoms do not feel any LJ
|
||||
pair interactions beyond the cutoff, but the energy and pressure
|
||||
reported by the simulation include an estimated contribution from
|
||||
those interactions. :l
|
||||
:ule
|
||||
|
||||
The {compute} keyword allows pairwise computations to be turned off,
|
||||
even though a "pair_style"_pair_style.html is defined. This is not
|
||||
useful for running a real simulation, but can be useful for debugging
|
||||
purposes or for performing a "rerun"_rerun.html simulation, when you
|
||||
only wish to compute partial forces that do not include the pairwise
|
||||
contribution.
|
||||
|
||||
Two examples are as follows. First, this option allows you to perform
|
||||
a simulation with "pair_style hybrid"_pair_hybrid.html with only a
|
||||
subset of the hybrid sub-styles enabled. Second, this option allows
|
||||
you to perform a simulation with only long-range interactions but no
|
||||
short-range pairwise interactions. Doing this by simply not defining
|
||||
a pair style will not work, because the
|
||||
"kspace_style"_kspace_style.html command requires a Kspace-compatible
|
||||
pair style be defined.
|
||||
|
||||
The {nofdotr} keyword allows to disable an optimization that computes
|
||||
the global stress tensor from the total forces and atom positions rather
|
||||
than from summing forces between individual pairs of atoms.
|
||||
|
||||
:line
|
||||
|
||||
The {special} keyword allows to override the 1-2, 1-3, and 1-4
|
||||
exclusion settings for individual sub-styles of a
|
||||
"hybrid pair style"_pair_hybrid.html. It requires 4 arguments similar
|
||||
to the "special_bonds"_special_bonds.html command, {which} and
|
||||
wt1,wt2,wt3. The {which} argument can be {lj} to change the
|
||||
Lennard-Jones settings, {coul} to change the Coulombic settings,
|
||||
or {lj/coul} to change both to the same set of 3 values. The wt1,wt2,wt3
|
||||
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
|
||||
1-3, and 1-4 bond topology neighbors, respectively. The {special}
|
||||
keyword can only be used in conjunction with the {pair} keyword
|
||||
and has to directly follow it.
|
||||
|
||||
NOTE: The global settings specified by the
|
||||
"special_bonds"_special_bonds.html command affect the construction of
|
||||
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
|
||||
exclude those pairs from the neighbor list entirely. Weights of 1.0
|
||||
store the neighbor with no weighting applied. Thus only global values
|
||||
different from exactly 0.0 or 1.0 can be overridden and an error is
|
||||
generated if the requested setting is not compatible with the global
|
||||
setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
|
||||
usually a sufficient workaround in this case without causing a
|
||||
significant error.
|
||||
|
||||
The {compute/tally} keyword takes exactly 1 argument ({no} or {yes}),
|
||||
and allows to selectively disable or enable processing of the various
|
||||
"compute */tally"_compute_tally.html styles for a given
|
||||
"pair hybrid or hybrid/overlay"_pair_hybrid.html sub-style.
|
||||
|
||||
NOTE: Any "pair_modify pair compute/tally" command must be issued
|
||||
[before] the corresponding compute style is defined.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
You cannot use {shift} yes with {tail} yes, since those are
|
||||
conflicting options. You cannot use {tail} yes with 2d simulations.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style"_pair_style.html, "pair_style hybrid"_pair_hybrid.html,
|
||||
pair_coeff"_pair_coeff.html, "thermo_style"_thermo_style.html,
|
||||
"compute */tally"_compute_tally.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are mix = geometric, shift = no, table = 12,
|
||||
tabinner = sqrt(2.0), tail = no, and compute = yes.
|
||||
|
||||
Note that some pair styles perform mixing, but only a certain style of
|
||||
mixing. See the doc pages for individual pair styles for details.
|
||||
|
||||
:line
|
||||
|
||||
:link(Wolff1)
|
||||
[(Wolff)] Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
|
||||
|
||||
:link(Sun)
|
||||
[(Sun)] Sun, J Phys Chem B, 102, 7338-7364 (1998).
|
||||
|
|
@ -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
|
||||
|
|
@ -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)
|
||||
|
||||
|
|
@ -42,7 +42,7 @@ def main():
|
|||
else:
|
||||
anchors[label] = [(filename, line_number+1)]
|
||||
|
||||
print("found %d anchor labels" % len(anchors))
|
||||
print("Found %d anchor labels" % len(anchors))
|
||||
|
||||
count = 0
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "math_special.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathSpecial;
|
||||
|
|
@ -68,6 +69,7 @@ PairBeckGPU::PairBeckGPU(LAMMPS *lmp) : PairBeck(lmp), gpu_mode(GPU_FORCE)
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -36,6 +36,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
|
@ -90,6 +91,7 @@ PairBornCoulLongCSGPU::PairBornCoulLongCSGPU(LAMMPS *lmp) :
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -36,6 +36,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
|
|
@ -85,6 +86,7 @@ PairBornCoulLongGPU::PairBornCoulLongGPU(LAMMPS *lmp) :
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
|
@ -78,6 +79,7 @@ PairBornCoulWolfCSGPU::PairBornCoulWolfCSGPU(LAMMPS *lmp) : PairBornCoulWolfCS(l
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
|
@ -76,6 +77,7 @@ PairBornCoulWolfGPU::PairBornCoulWolfGPU(LAMMPS *lmp) : PairBornCoulWolf(lmp),
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -71,6 +72,7 @@ PairBornGPU::PairBornGPU(LAMMPS *lmp) : PairBorn(lmp), gpu_mode(GPU_FORCE)
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -72,6 +73,7 @@ PairBuckCoulCutGPU::PairBuckCoulCutGPU(LAMMPS *lmp) : PairBuckCoulCut(lmp),
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
|
|
@ -81,6 +82,7 @@ PairBuckCoulLongGPU::PairBuckCoulLongGPU(LAMMPS *lmp) :
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -69,6 +70,7 @@ PairBuckGPU::PairBuckGPU(LAMMPS *lmp) : PairBuck(lmp), gpu_mode(GPU_FORCE)
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -69,6 +70,7 @@ PairColloidGPU::PairColloidGPU(LAMMPS *lmp) : PairColloid(lmp), gpu_mode(GPU_FOR
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -69,6 +70,7 @@ PairCoulCutGPU::PairCoulCutGPU(LAMMPS *lmp) : PairCoulCut(lmp), gpu_mode(GPU_FOR
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -70,6 +71,7 @@ PairCoulDebyeGPU::PairCoulDebyeGPU(LAMMPS *lmp) :
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define MY_PIS 1.77245385090551602729
|
||||
#define EWALD_F 1.12837917
|
||||
|
|
@ -81,6 +82,7 @@ PairCoulDSFGPU::PairCoulDSFGPU(LAMMPS *lmp) : PairCoulDSF(lmp),
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -83,6 +84,7 @@ PairCoulLongCSGPU::PairCoulLongCSGPU(LAMMPS *lmp) :
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
|
|
@ -78,6 +79,7 @@ PairCoulLongGPU::PairCoulLongGPU(LAMMPS *lmp) :
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -209,6 +210,7 @@ PairDPDGPU::PairDPDGPU(LAMMPS *lmp) : PairDPD(lmp), gpu_mode(GPU_FORCE)
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -212,6 +213,7 @@ PairDPDTstatGPU::PairDPDTstatGPU(LAMMPS *lmp) : PairDPDTstat(lmp),
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@
|
|||
#include "gpu_extra.h"
|
||||
#include "domain.h"
|
||||
#include "utils.h"
|
||||
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -72,6 +72,7 @@ PairEAMAlloyGPU::PairEAMAlloyGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -29,6 +29,7 @@
|
|||
#include "neigh_request.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "domain.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -70,6 +71,7 @@ PairEAMFSGPU::PairEAMFSGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -30,6 +30,7 @@
|
|||
#include "error.h"
|
||||
#include "neigh_request.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define MAXLINE 1024
|
||||
|
||||
|
|
@ -71,6 +72,7 @@ PairEAMGPU::PairEAMGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -66,6 +67,7 @@ PairGaussGPU::PairGaussGPU(LAMMPS *lmp) : PairGauss(lmp), gpu_mode(GPU_FORCE)
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -36,6 +36,7 @@
|
|||
#include "domain.h"
|
||||
#include "update.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -74,6 +75,7 @@ PairGayBerneGPU::PairGayBerneGPU(LAMMPS *lmp) : PairGayBerne(lmp),
|
|||
quat_nmax = 0;
|
||||
reinitflag = 0;
|
||||
quat = NULL;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -66,6 +67,7 @@ PairLJ96CutGPU::PairLJ96CutGPU(LAMMPS *lmp) : PairLJ96Cut(lmp), gpu_mode(GPU_FOR
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
|
|
@ -83,6 +84,7 @@ PairLJCharmmCoulLongGPU::PairLJCharmmCoulLongGPU(LAMMPS *lmp) :
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
|
|
@ -80,6 +81,7 @@ PairLJClass2CoulLongGPU::PairLJClass2CoulLongGPU(LAMMPS *lmp) :
|
|||
{
|
||||
cpu_time = 0.0;
|
||||
reinitflag = 0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -65,6 +66,7 @@ PairLJClass2GPU::PairLJClass2GPU(LAMMPS *lmp) : PairLJClass2(lmp), gpu_mode(GPU_
|
|||
{
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace PairLJCubicConstants;
|
||||
|
|
@ -70,6 +71,7 @@ PairLJCubicGPU::PairLJCubicGPU(LAMMPS *lmp) : PairLJCubic(lmp),
|
|||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
reinitflag = 0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -71,6 +72,7 @@ PairLJCutCoulCutGPU::PairLJCutCoulCutGPU(LAMMPS *lmp) : PairLJCutCoulCut(lmp), g
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -73,6 +74,7 @@ PairLJCutCoulDebyeGPU::PairLJCutCoulDebyeGPU(LAMMPS *lmp) :
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define MY_PIS 1.77245385090551602729
|
||||
#define EWALD_F 1.12837917
|
||||
|
|
@ -82,6 +83,7 @@ PairLJCutCoulDSFGPU::PairLJCutCoulDSFGPU(LAMMPS *lmp) : PairLJCutCoulDSF(lmp), g
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
|
|
@ -83,6 +84,7 @@ PairLJCutCoulLongGPU::PairLJCutCoulLongGPU(LAMMPS *lmp) :
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -72,6 +73,7 @@ PairLJCutCoulMSMGPU::PairLJCutCoulMSMGPU(LAMMPS *lmp) :
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -73,6 +74,7 @@ PairLJCutDipoleCutGPU::PairLJCutDipoleCutGPU(LAMMPS *lmp) : PairLJCutDipoleCut(l
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -36,6 +36,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
|
|
@ -84,6 +85,7 @@ PairLJCutDipoleLongGPU::PairLJCutDipoleLongGPU(LAMMPS *lmp) : PairLJCutDipoleLon
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -70,6 +71,7 @@ PairLJCutGPU::PairLJCutGPU(LAMMPS *lmp) : PairLJCut(lmp), gpu_mode(GPU_FORCE)
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -37,6 +37,7 @@
|
|||
#include "angle.h"
|
||||
#include "bond.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
|
|
@ -91,6 +92,7 @@ PairLJCutTIP4PLongGPU::PairLJCutTIP4PLongGPU(LAMMPS *lmp)
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
|
|
@ -83,6 +84,7 @@ PairLJExpandCoulLongGPU::PairLJExpandCoulLongGPU(LAMMPS *lmp) :
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -69,6 +70,7 @@ PairLJExpandGPU::PairLJExpandGPU(LAMMPS *lmp) : PairLJExpand(lmp), gpu_mode(GPU_
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -71,6 +72,7 @@ PairLJGromacsGPU::PairLJGromacsGPU(LAMMPS *lmp) :
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "kspace.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
|
|
@ -86,6 +87,7 @@ PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) :
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -71,6 +72,7 @@ PairLJSDKGPU::PairLJSDKGPU(LAMMPS *lmp) : PairLJSDK(lmp), gpu_mode(GPU_FORCE)
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -72,6 +73,7 @@ PairLJSFDipoleSFGPU::PairLJSFDipoleSFGPU(LAMMPS *lmp) : PairLJSFDipoleSF(lmp),
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -67,6 +68,7 @@ PairMIECutGPU::PairMIECutGPU(LAMMPS *lmp) : PairMIECut(lmp), gpu_mode(GPU_FORCE)
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -65,6 +66,7 @@ PairMorseGPU::PairMorseGPU(LAMMPS *lmp) : PairMorse(lmp), gpu_mode(GPU_FORCE)
|
|||
{
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -36,6 +36,7 @@
|
|||
#include "domain.h"
|
||||
#include "update.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -76,6 +77,7 @@ PairRESquaredGPU::PairRESquaredGPU(LAMMPS *lmp) : PairRESquared(lmp),
|
|||
error->all(FLERR,"Pair resquared/gpu requires atom style ellipsoid");
|
||||
quat_nmax = 0;
|
||||
quat = NULL;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "math_const.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -70,6 +71,7 @@ PairSoftGPU::PairSoftGPU(LAMMPS *lmp) : PairSoft(lmp), gpu_mode(GPU_FORCE)
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -32,6 +32,7 @@
|
|||
#include "error.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -72,6 +73,7 @@ PairSWGPU::PairSWGPU(LAMMPS *lmp) : PairSW(lmp), gpu_mode(GPU_FORCE)
|
|||
{
|
||||
cpu_time = 0.0;
|
||||
reinitflag = 0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
|
||||
cutghost = NULL;
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
#define LOOKUP 0
|
||||
#define LINEAR 1
|
||||
|
|
@ -73,6 +74,7 @@ PairTableGPU::PairTableGPU(LAMMPS *lmp) : PairTable(lmp),
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -32,6 +32,7 @@
|
|||
#include "error.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -76,6 +77,7 @@ extern double lmp_gpu_forces(double **f, double **tor, double *eatom,
|
|||
PairTersoffGPU::PairTersoffGPU(LAMMPS *lmp) : PairTersoff(lmp), gpu_mode(GPU_FORCE)
|
||||
{
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
|
||||
cutghost = NULL;
|
||||
|
|
|
|||
|
|
@ -32,6 +32,7 @@
|
|||
#include "error.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -69,6 +70,7 @@ PairTersoffMODGPU::PairTersoffMODGPU(LAMMPS *lmp) : PairTersoffMOD(lmp),
|
|||
gpu_mode(GPU_FORCE)
|
||||
{
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
|
||||
cutghost = NULL;
|
||||
|
|
|
|||
|
|
@ -32,6 +32,7 @@
|
|||
#include "error.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -77,6 +78,7 @@ PairTersoffZBLGPU::PairTersoffZBLGPU(LAMMPS *lmp) : PairTersoffZBL(lmp),
|
|||
gpu_mode(GPU_FORCE)
|
||||
{
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
|
||||
cutghost = NULL;
|
||||
|
|
|
|||
|
|
@ -36,6 +36,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -72,6 +73,7 @@ PairUFMGPU::PairUFMGPU(LAMMPS *lmp) : PairUFM(lmp), gpu_mode(GPU_FORCE)
|
|||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -32,6 +32,7 @@
|
|||
#include "error.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -73,6 +74,7 @@ PairVashishtaGPU::PairVashishtaGPU(LAMMPS *lmp) : PairVashishta(lmp), gpu_mode(G
|
|||
cpu_time = 0.0;
|
||||
reinitflag = 0;
|
||||
gpu_allocated = false;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
|
||||
cutghost = NULL;
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -68,6 +69,7 @@ PairYukawaColloidGPU::PairYukawaColloidGPU(LAMMPS *lmp) : PairYukawaColloid(lmp)
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -67,6 +68,7 @@ PairYukawaGPU::PairYukawaGPU(LAMMPS *lmp) : PairYukawa(lmp),
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@
|
|||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "gpu_extra.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -70,6 +71,7 @@ PairZBLGPU::PairZBLGPU(LAMMPS *lmp) : PairZBL(lmp), gpu_mode(GPU_FORCE)
|
|||
respa_enable = 0;
|
||||
reinitflag = 0;
|
||||
cpu_time = 0.0;
|
||||
suffix_flag |= Suffix::GPU;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ using namespace FixConst;
|
|||
|
||||
FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg),
|
||||
partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL),
|
||||
partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL),
|
||||
broken(NULL), copy(NULL), random(NULL)
|
||||
{
|
||||
if (narg < 6) error->all(FLERR,"Illegal fix bond/break command");
|
||||
|
|
|
|||
|
|
@ -226,7 +226,7 @@ void FixBondCreate::init()
|
|||
if (strcmp(modify->fix[i]->style,"bond/create") == 0) count++;
|
||||
if (strcmp(modify->fix[i]->style,"bond/break") == 0) count++;
|
||||
}
|
||||
if (count > 1 && me == 0)
|
||||
if (count > 1 && me == 0)
|
||||
error->warning(FLERR,"Fix bond/create is used multiple times "
|
||||
" or with fix bond/break - may not work as expected");
|
||||
|
||||
|
|
|
|||
|
|
@ -27,6 +27,7 @@
|
|||
#include "error.h"
|
||||
#include "respa.h"
|
||||
#include "utils.h"
|
||||
#include "suffix.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -919,6 +920,12 @@ void PairHybrid::modify_special(int m, int /*narg*/, char **arg)
|
|||
special[2] = force->numeric(FLERR,arg[2]);
|
||||
special[3] = force->numeric(FLERR,arg[3]);
|
||||
|
||||
// have to cast to PairHybrid to work around C++ access restriction
|
||||
|
||||
if (((PairHybrid *)styles[m])->suffix_flag & (Suffix::INTEL|Suffix::GPU))
|
||||
error->all(FLERR,"Pair_modify special is not compatible with "
|
||||
"suffix version of hybrid substyle");
|
||||
|
||||
if (strcmp(arg[0],"lj/coul") == 0) {
|
||||
if (!special_lj[m]) special_lj[m] = new double[4];
|
||||
if (!special_coul[m]) special_coul[m] = new double[4];
|
||||
|
|
|
|||
15
src/suffix.h
15
src/suffix.h
|
|
@ -16,13 +16,14 @@
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
namespace Suffix {
|
||||
static const int NONE = 0;
|
||||
static const int OPT = 1<<0;
|
||||
static const int GPU = 1<<1;
|
||||
static const int OMP = 1<<2;
|
||||
static const int INTEL = 1<<3;
|
||||
}
|
||||
enum Suffix {
|
||||
NONE = 0,
|
||||
OPT = 1<<0,
|
||||
GPU = 1<<1,
|
||||
OMP = 1<<2,
|
||||
INTEL = 1<<3,
|
||||
KOKKOS = 1<<4
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue