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3
doc/Section_accelerate.html
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@ -98,7 +98,8 @@ simply trying them out.
<LI>processor mapping via processors numa command
<LI>load-balancing: balance and fix balance
<LI>processor command for layout
<LI>OMP when lots of cores
<LI>OMP when lots of cores
<LI>proxy/OMP for PPPM
</UL>
<HR>

3
doc/Section_accelerate.txt
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@ -94,7 +94,8 @@ verlet/split
processor mapping via processors numa command
load-balancing: balance and fix balance
processor command for layout
OMP when lots of cores :ul
OMP when lots of cores
proxy/OMP for PPPM :ul
:line

1
doc/Section_intro.html
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@ -526,7 +526,6 @@ and efforts.
<LI>Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
<LI>Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package
<LI>Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
<LI>Pieter in' t Veld (BASF), pieter.intveld at basf.com, USER-EWALDN package for 1/r^N long-range solvers
<LI>Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
<LI>Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
<LI>Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package

1
doc/Section_intro.txt
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@ -512,7 +512,6 @@ Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package f
Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package
Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
Pieter in' t Veld (BASF), pieter.intveld at basf.com, USER-EWALDN package for 1/r^N long-range solvers
Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package :ul

35
doc/Section_packages.html
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@ -109,7 +109,6 @@ E.g. "peptide" refers to the examples/peptide directory.
<TR ALIGN="center"><TD >USER-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (3)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</TD></TR>
<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "Section_accelerate.html#acc_7">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-EWALDN</TD><TD > Ewald for 1/R^n</TD><TD > Pieter in' t Veld (BASF)</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-MOLFILE</TD><TD > <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molfile plug-ins</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump_molfile.html">dump molfile</A></TD><TD > -</TD><TD > -</TD><TD > lib/molfile</TD></TR>
<TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "Section_accelerate.html#acc_5">Section accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
@ -362,40 +361,6 @@ have questions.
</P>
<HR>
<H4>USER-EWALDN package
</H4>
<P>This package implements 3 commands which can be used in a LAMMPS input
script: pair_style lj/coul, pair_style buck/coul, and kspace_style
ewald/n.
</P>
<P>The "kspace_style ewald/n" command is similar to standard Ewald for
charges, but also enables the Lennard-Jones interaction, or any 1/r^N
interaction to be of infinite extent, instead of being cutoff. LAMMPS
pair potentials for long-range Coulombic interactions, such as
lj/cut/coul/long can be used with ewald/n. The two new pair_style
commands provide the modifications for the short-range LJ and
Buckingham interactions that can also be used with ewald/n.
</P>
<P>Two other advantages of kspace_style ewald/n are that
</P>
<P>a) it can be used with non-orthogonal (triclinic symmetry) simulation
boxes
</P>
<P>b) it can include long-range summations not just for Coulombic
interactions (1/r), but also for dispersion interactions (1/r^6) and
dipole interactions (1/r^3).
</P>
<P>Neither of these options is currently possible for other kspace styles
such as PPPM and ewald.
</P>
<P>See the doc pages for these commands for details.
</P>
<P>The person who created these files is Pieter in' t Veld while at
Sandia. He is now at BASF (pieter.intveld at basf.com). Contact him
directly if you have questions.
</P>
<HR>
<H4>USER-OMP package
</H4>
<P>This package provides OpenMP multi-threading support and

35
doc/Section_packages.txt
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@ -101,7 +101,6 @@ USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sd
USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_Section_accelerate.html#acc_7, USER/cuda, -, lib/cuda
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-EWALDN, Ewald for 1/R^n, Pieter in' t Veld (BASF), "kspace_style"_kspace_style.html, -, -, -
USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, lib/molfile
USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_Section_accelerate.html#acc_5, -, -, -
USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
@ -349,40 +348,6 @@ have questions.
:line
USER-EWALDN package :h4
This package implements 3 commands which can be used in a LAMMPS input
script: pair_style lj/coul, pair_style buck/coul, and kspace_style
ewald/n.
The "kspace_style ewald/n" command is similar to standard Ewald for
charges, but also enables the Lennard-Jones interaction, or any 1/r^N
interaction to be of infinite extent, instead of being cutoff. LAMMPS
pair potentials for long-range Coulombic interactions, such as
lj/cut/coul/long can be used with ewald/n. The two new pair_style
commands provide the modifications for the short-range LJ and
Buckingham interactions that can also be used with ewald/n.
Two other advantages of kspace_style ewald/n are that
a) it can be used with non-orthogonal (triclinic symmetry) simulation
boxes
b) it can include long-range summations not just for Coulombic
interactions (1/r), but also for dispersion interactions (1/r^6) and
dipole interactions (1/r^3).
Neither of these options is currently possible for other kspace styles
such as PPPM and ewald.
See the doc pages for these commands for details.
The person who created these files is Pieter in' t Veld while at
Sandia. He is now at BASF (pieter.intveld at basf.com). Contact him
directly if you have questions.
:line
USER-OMP package :h4
This package provides OpenMP multi-threading support and

30
doc/kspace_style.html
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@ -78,6 +78,36 @@ long-range potentials.
<P>Currently, only the <I>ewald/n</I> style can be used with non-orthogonal
(triclinic symmetry) simulation boxes.
</P>
<P>This package implements 3 commands which can be used in a LAMMPS input
script: pair_style lj/coul, pair_style buck/coul, and kspace_style
ewald/n.
</P>
<P>The "kspace_style ewald/n" command is similar to standard Ewald for
charges, but also enables the Lennard-Jones interaction, or any 1/r^N
interaction to be of infinite extent, instead of being cutoff. LAMMPS
pair potentials for long-range Coulombic interactions, such as
lj/cut/coul/long can be used with ewald/n. The two new pair_style
commands provide the modifications for the short-range LJ and
Buckingham interactions that can also be used with ewald/n.
</P>
<P>Two other advantages of kspace_style ewald/n are that
</P>
<P>a) it can be used with non-orthogonal (triclinic symmetry) simulation
boxes
</P>
<P>b) it can include long-range summations not just for Coulombic
interactions (1/r), but also for dispersion interactions (1/r^6) and
dipole interactions (1/r^3).
</P>
<P>Neither of these options is currently possible for other kspace styles
such as PPPM and ewald.
</P>
<P>See the doc pages for these commands for details.
</P>
<P>The person who created these files is Pieter in' t Veld while at
Sandia. He is now at BASF (pieter.intveld at basf.com). Contact him
directly if you have questions.
</P>
<HR>
<P>The <I>pppm</I> style invokes a particle-particle particle-mesh solver

34
doc/kspace_style.txt
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@ -73,6 +73,40 @@ long-range potentials.
Currently, only the {ewald/n} style can be used with non-orthogonal
(triclinic symmetry) simulation boxes.
This package implements 3 commands which can be used in a LAMMPS input
script: pair_style lj/coul, pair_style buck/coul, and kspace_style
ewald/n.
The "kspace_style ewald/n" command is similar to standard Ewald for
charges, but also enables the Lennard-Jones interaction, or any 1/r^N
interaction to be of infinite extent, instead of being cutoff. LAMMPS
pair potentials for long-range Coulombic interactions, such as
lj/cut/coul/long can be used with ewald/n. The two new pair_style
commands provide the modifications for the short-range LJ and
Buckingham interactions that can also be used with ewald/n.
Two other advantages of kspace_style ewald/n are that
a) it can be used with non-orthogonal (triclinic symmetry) simulation
boxes
b) it can include long-range summations not just for Coulombic
interactions (1/r), but also for dispersion interactions (1/r^6) and
dipole interactions (1/r^3).
Neither of these options is currently possible for other kspace styles
such as PPPM and ewald.
See the doc pages for these commands for details.
The person who created these files is Pieter in' t Veld while at
Sandia. He is now at BASF (pieter.intveld at basf.com). Contact him
directly if you have questions.
:line
The {pppm} style invokes a particle-particle particle-mesh solver

22
doc/pair_charmm.html
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@ -31,7 +31,7 @@
</H3>
<H3>pair_style lj/charmm/coul/long/omp command
</H3>
<H3>pair_style lj/charmm/coul/pppm/omp command
<H3>pair_style lj/charmm/coul/long/proxy/omp command
</H3>
<P><B>Syntax:</B>
</P>
@ -93,18 +93,18 @@ which is a simple model for an implicit solvent with additional
screening. It is designed for use in a simulation of an unsolvated
biomolecule (no explicit water molecules).
</P>
<P>Styles <I>lj/charmm/coul/long</I> and <I>lj/charmm/coul/pppm/omp</I> compute
the same formulas as style <I>lj/charmm/coul/charmm</I> except that an
additional damping factor is applied to the Coulombic term, as in
<P>Styles <I>lj/charmm/coul/long</I> and <I>lj/charmm/coul/long/proxy/omp</I>
compute the same formulas as style <I>lj/charmm/coul/charmm</I> except that
an additional damping factor is applied to the Coulombic term, as in
the discussion for pair style <I>lj/cut/coul/long</I>. Only one Coulombic
cutoff is specified for <I>lj/charmm/coul/long</I>; if only 2 arguments
are used in the pair_style command, then the outer LJ cutoff is
used as the single Coulombic cutoff. Style <I>lj/charmm/coul/pppm/omp</I>
is a variant for use with K-space style <A HREF = "kspace_style.html"><I>pppm/proxy</I></A>
cutoff is specified for <I>lj/charmm/coul/long</I>; if only 2 arguments are
used in the pair_style command, then the outer LJ cutoff is used as
the single Coulombic cutoff. Style <I>lj/charmm/coul/long/proxy/omp</I> is
a variant for use with K-space style <A HREF = "kspace_style.html"><I>pppm/proxy</I></A>
and OpenMP multi-threading and will perform the corresponding
reciprocal space calculation concurrently with the pair calculation
in a separate thread. For certain parallel setups, this may have
a performance benefit over performing k-space style and pair style
reciprocal space calculation concurrently with the pair calculation in
a separate thread. For certain parallel setups, this may have a
performance benefit over performing k-space style and pair style
separately and one after the other.
</P>
<P>The following coefficients must be defined for each pair of atoms

22
doc/pair_charmm.txt
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@ -17,7 +17,7 @@ pair_style lj/charmm/coul/long/cuda command :h3
pair_style lj/charmm/coul/long/gpu command :h3
pair_style lj/charmm/coul/long/opt command :h3
pair_style lj/charmm/coul/long/omp command :h3
pair_style lj/charmm/coul/pppm/omp command :h3
pair_style lj/charmm/coul/long/proxy/omp command :h3
[Syntax:]
@ -78,18 +78,18 @@ which is a simple model for an implicit solvent with additional
screening. It is designed for use in a simulation of an unsolvated
biomolecule (no explicit water molecules).
Styles {lj/charmm/coul/long} and {lj/charmm/coul/pppm/omp} compute
the same formulas as style {lj/charmm/coul/charmm} except that an
additional damping factor is applied to the Coulombic term, as in
Styles {lj/charmm/coul/long} and {lj/charmm/coul/long/proxy/omp}
compute the same formulas as style {lj/charmm/coul/charmm} except that
an additional damping factor is applied to the Coulombic term, as in
the discussion for pair style {lj/cut/coul/long}. Only one Coulombic
cutoff is specified for {lj/charmm/coul/long}; if only 2 arguments
are used in the pair_style command, then the outer LJ cutoff is
used as the single Coulombic cutoff. Style {lj/charmm/coul/pppm/omp}
is a variant for use with K-space style "{pppm/proxy}"_kspace_style.html
cutoff is specified for {lj/charmm/coul/long}; if only 2 arguments are
used in the pair_style command, then the outer LJ cutoff is used as
the single Coulombic cutoff. Style {lj/charmm/coul/long/proxy/omp} is
a variant for use with K-space style "{pppm/proxy}"_kspace_style.html
and OpenMP multi-threading and will perform the corresponding
reciprocal space calculation concurrently with the pair calculation
in a separate thread. For certain parallel setups, this may have
a performance benefit over performing k-space style and pair style
reciprocal space calculation concurrently with the pair calculation in
a separate thread. For certain parallel setups, this may have a
performance benefit over performing k-space style and pair style
separately and one after the other.
The following coefficients must be defined for each pair of atoms

13
doc/pair_class2.html
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@ -31,7 +31,7 @@
</H3>
<H3>pair_style lj/class2/coul/long/omp command
</H3>
<H3>pair_style lj/class2/coul/pppm/omp command
<H3>pair_style lj/class2/coul/long/proxy/omp command
</H3>
<P><B>Syntax:</B>
</P>
@ -75,8 +75,7 @@ pair_coeff 1 1 100.0 3.5 9.0
<P>Rc is the cutoff.
</P>
<P>The <I>lj/class2/coul/cut</I> and <I>lj/class2/coul/long</I> styles add a
Coulombic term as described for the <A HREF = "pair_lj.html">lj/cut</A> pair
styles.
Coulombic term as described for the <A HREF = "pair_lj.html">lj/cut</A> pair styles.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
@ -104,6 +103,14 @@ since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
</P>
<P>Style <I>lj/class2/coul/long/proxy/omp</I> is a variant for use with
K-space style <A HREF = "kspace_style.html"><I>pppm/proxy</I></A> and OpenMP
multi-threading and will perform the corresponding reciprocal space
calculation concurrently with the pair calculation in a separate
thread. For certain parallel setups, this may have a performance
benefit over performing k-space style and pair style separately and
one after the other.
</P>
<HR>
<P>If the pair_coeff command is not used to define coefficients for a

13
doc/pair_class2.txt
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@ -17,7 +17,7 @@ pair_style lj/class2/coul/long command :h3
pair_style lj/class2/coul/long/cuda command :h3
pair_style lj/class2/coul/long/gpu command :h3
pair_style lj/class2/coul/long/omp command :h3
pair_style lj/class2/coul/pppm/omp command :h3
pair_style lj/class2/coul/long/proxy/omp command :h3
[Syntax:]
@ -60,8 +60,7 @@ The {lj/class2} styles compute a 6/9 Lennard-Jones potential given by
Rc is the cutoff.
The {lj/class2/coul/cut} and {lj/class2/coul/long} styles add a
Coulombic term as described for the "lj/cut"_pair_lj.html pair
styles.
Coulombic term as described for the "lj/cut"_pair_lj.html pair styles.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
@ -89,6 +88,14 @@ since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
Style {lj/class2/coul/long/proxy/omp} is a variant for use with
K-space style "{pppm/proxy}"_kspace_style.html and OpenMP
multi-threading and will perform the corresponding reciprocal space
calculation concurrently with the pair calculation in a separate
thread. For certain parallel setups, this may have a performance
benefit over performing k-space style and pair style separately and
one after the other.
:line
If the pair_coeff command is not used to define coefficients for a

21
doc/pair_lj.html
View File

@ -51,10 +51,14 @@
</H3>
<H3>pair_style lj/cut/coul/long/omp command
</H3>
<H3>pair_style lj/cut/coul/long/proxy/omp command
</H3>
<H3>pair_style lj/cut/coul/long/tip4p command
</H3>
<H3>pair_style lj/cut/coul/long/tip4p/omp command
</H3>
<H3>pair_style lj/cut/coul/long/proxy/tip4p/omp command
</H3>
<H3>pair_style lj/cut/coul/long/tip4p/opt command
</H3>
<P><B>Syntax:</B>
@ -223,15 +227,16 @@ can be specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
</P>
<P>Styles <I>lj/cut/coul/pppm/omp</I> and <I>lj/cut/coul/pppm/tip4p/omp</I>
are variants of <I>lj/cut/coul/long/omp</I> and <I>lj/cut/coul/long/tip4p/omp</I>
for use with k-space styles <A HREF = "kspace_style.html"><I>pppm/proxy</I></A> and
<P>Styles <I>lj/cut/coul/long/proxy/omp</I> and
<I>lj/cut/coul/long/proxy/tip4p/omp</I> are variants of
<I>lj/cut/coul/long/omp</I> and <I>lj/cut/coul/long/tip4p/omp</I> for use with
k-space styles <A HREF = "kspace_style.html"><I>pppm/proxy</I></A> and
<A HREF = "kspace_style.html"><I>pppm/tip4p/proxy</I></A>, respectively and OpenMP
multi-threading and will perform the corresponding reciprocal
space calculation concurrently with the pair calculation
in a separate thread. For certain parallel setups, this may have
a performance benefit over performing k-space style and pair style
separately and one after the other.
multi-threading and will perform the corresponding reciprocal space
calculation concurrently with the pair calculation in a separate
thread. For certain parallel setups, this may have a performance
benefit over performing k-space style and pair style separately and
one after the other.
</P>
<HR>

19
doc/pair_lj.txt
View File

@ -27,8 +27,10 @@ pair_style lj/cut/coul/long/cuda command :h3
pair_style lj/cut/coul/long/gpu command :h3
pair_style lj/cut/coul/long/opt command :h3
pair_style lj/cut/coul/long/omp command :h3
pair_style lj/cut/coul/long/proxy/omp command :h3
pair_style lj/cut/coul/long/tip4p command :h3
pair_style lj/cut/coul/long/tip4p/omp command :h3
pair_style lj/cut/coul/long/proxy/tip4p/omp command :h3
pair_style lj/cut/coul/long/tip4p/opt command :h3
[Syntax:]
@ -196,15 +198,16 @@ can be specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
Styles {lj/cut/coul/pppm/omp} and {lj/cut/coul/pppm/tip4p/omp}
are variants of {lj/cut/coul/long/omp} and {lj/cut/coul/long/tip4p/omp}
for use with k-space styles "{pppm/proxy}"_kspace_style.html and
Styles {lj/cut/coul/long/proxy/omp} and
{lj/cut/coul/long/proxy/tip4p/omp} are variants of
{lj/cut/coul/long/omp} and {lj/cut/coul/long/tip4p/omp} for use with
k-space styles "{pppm/proxy}"_kspace_style.html and
"{pppm/tip4p/proxy}"_kspace_style.html, respectively and OpenMP
multi-threading and will perform the corresponding reciprocal
space calculation concurrently with the pair calculation
in a separate thread. For certain parallel setups, this may have
a performance benefit over performing k-space style and pair style
separately and one after the other.
multi-threading and will perform the corresponding reciprocal space
calculation concurrently with the pair calculation in a separate
thread. For certain parallel setups, this may have a performance
benefit over performing k-space style and pair style separately and
one after the other.
:line

82
doc/pair_lj_disp.html
View File

@ -13,24 +13,37 @@
</H3>
<H3>pair_style lj/disp/coul/long/omp command
</H3>
<H3>pair_style lj/disp/coul/long/tip4p command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj/disp/coul/long flag_lj flag_coul cutoff (cutoff2)
<PRE>pair_style style args
</PRE>
<UL><LI>flag_lj = <I>long</I> or <I>cut</I>
<PRE> <I>long</I> = use Kspace long-range summation for the dispersion term 1/r^6
<I>cut</I> = use a cutoff
</PRE>
<LI>flag_coul = <I>long</I> or <I>off</I>
<PRE> <I>long</I> = use Kspace long-range summation for the Coulombic term 1/r
<I>off</I> = omit the Coulombic term
</PRE>
<LI>cutoff = global cutoff for LJ (and Coulombic if only 1 cutoff) (distance units)
<LI>cutoff2 = global cutoff for Coulombic (optional) (distance units)
<UL><LI>style = <I>lj/disp/coul/long</I> or <I>lj/disp/coul/long/tip4p</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>lj/disp/coul/long</I> args = flag_lj flag_coul cutoff (cutoff2)
flag_lj = <I>long</I> or <I>cut</I>
<I>long</I> = use Kspace long-range summation for dispersion 1/r^6 term
<I>cut</I> = use a cutoff
flag_coul = <I>long</I> or <I>off</I>
<I>long</I> = use Kspace long-range summation for Coulombic 1/r term
<I>off</I> = omit Coulombic term
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/long/tip4p</I> args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
flag_lj = <I>long</I> or <I>cut</I>
<I>long</I> = use Kspace long-range summation for dispersion 1/r^6 term
<I>cut</I> = use a cutoff
flag_coul = <I>long</I> or <I>off</I>
<I>long</I> = use Kspace long-range summation for Coulombic 1/r term
<I>off</I> = omit Coulombic term
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/disp/coul/long cut off 2.5
@ -39,9 +52,14 @@ pair_style lj/disp/coul/long long long 2.5 4.0
pair_coeff * * 1 1
pair_coeff 1 1 1 3 4
</PRE>
<PRE>pair_style lj/disp/coul/long/tip4p long long 1 2 7 8 0.15 12.0
pair_style lj/disp/coul/long/tip4p long long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj/disp/coul/long</I> style computes the standard 12/6 Lennard-Jones and
<P>Style <I>lj/disp/coul/long</I> computes the standard 12/6 Lennard-Jones and
Coulombic potentials, given by
</P>
<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
@ -62,6 +80,29 @@ settings. The <A HREF = "#Veld">In 't Veld</A> paper has more details on when i
appropriate to include long-range 1/r^6 interactions, using this
potential.
</P>
<P>Style <I>lj/cut/coul/long/tip4p</I> implements the TIP4P water model of
<A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
angle. The atomic types of the oxygen and hydrogen atoms, the bond
and angle types for OH and HOH interactions, and the distance to the
massless charge site are specified as pair_style arguments.
</P>
<P>IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
IDs for the O and 2 H atoms must be consecutive, with the O atom
first. This is to enable LAMMPS to "find" the 2 H atoms associated
with each O atom. For example, if the atom ID of an O atom in a TIP4P
water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
</P>
<P>See the <A HREF = "Section_howto.html#howto_8">howto section</A> for more
information on how to use the TIP4P pair style. Note that the
neighobr list cutoff for Coulomb interactions is effectively extended
by a distance 2*qdist when using the TIP4P pair style, to account for
the offset distance of the fictitious charges on O atoms in water
molecules. Thus it is typically best in an efficiency sense to use a
LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the
neighbor list. This leads to slightly larger cost for the long-range
calculation, so you can test the trade-off for your model.
</P>
<P>If <I>flag_lj</I> is set to <I>long</I>, no cutoff is used on the LJ 1/r^6
dispersion term. The long-range portion is calculated by using the
<A HREF = "kspace_style.html">kspace_style ewald/n</A> command. The specified LJ
@ -99,12 +140,19 @@ LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. Note that if you are using <I>flag_lj</I> set to <I>long</I>, you
type pair.
</P>
<P>Note that if you are using <I>flag_lj</I> set to <I>long</I>, you
cannot specify a LJ cutoff for an atom type pair, since only one
global LJ cutoff is allowed. Similarly, if you are using <I>flag_coul</I>
set to <I>long</I>, you cannot specify a Coulombic cutoff for an atom type
pair, since only one global Coulombic cutoff is allowed.
</P>
<P>For <I>lj/disp/coul/long/tip4p</I> only the LJ cutoff can be specified
since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
@ -162,7 +210,7 @@ details.
<P><B>Restrictions:</B>
</P>
<P>This style is part of the KSPACE package. It is only enabled if
<P>These styles are part of the KSPACE package. They are only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info. Note that
the KSPACE package is installed by default.

75
doc/pair_lj_disp.txt
View File

@ -8,19 +8,35 @@
pair_style lj/disp/coul/long command :h3
pair_style lj/disp/coul/long/omp command :h3
pair_style lj/disp/coul/long/tip4p command :h3
[Syntax:]
pair_style lj/disp/coul/long flag_lj flag_coul cutoff (cutoff2) :pre
pair_style style args :pre
flag_lj = {long} or {cut} :ulb,l
{long} = use Kspace long-range summation for the dispersion term 1/r^6
{cut} = use a cutoff :pre
flag_coul = {long} or {off} :l
{long} = use Kspace long-range summation for the Coulombic term 1/r
{off} = omit the Coulombic term :pre
cutoff = global cutoff for LJ (and Coulombic if only 1 cutoff) (distance units) :l
cutoff2 = global cutoff for Coulombic (optional) (distance units) :l,ule
style = {lj/disp/coul/long} or {lj/disp/coul/long/tip4p}
args = list of arguments for a particular style :ul
{lj/disp/coul/long} args = flag_lj flag_coul cutoff (cutoff2)
flag_lj = {long} or {cut}
{long} = use Kspace long-range summation for dispersion 1/r^6 term
{cut} = use a cutoff
flag_coul = {long} or {off}
{long} = use Kspace long-range summation for Coulombic 1/r term
{off} = omit Coulombic term
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/long/tip4p} args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
flag_lj = {long} or {cut}
{long} = use Kspace long-range summation for dispersion 1/r^6 term
{cut} = use a cutoff
flag_coul = {long} or {off}
{long} = use Kspace long-range summation for Coulombic 1/r term
{off} = omit Coulombic term
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
[Examples:]
@ -30,9 +46,14 @@ pair_style lj/disp/coul/long long long 2.5 4.0
pair_coeff * * 1 1
pair_coeff 1 1 1 3 4 :pre
pair_style lj/disp/coul/long/tip4p long long 1 2 7 8 0.15 12.0
pair_style lj/disp/coul/long/tip4p long long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
[Description:]
The {lj/disp/coul/long} style computes the standard 12/6 Lennard-Jones and
Style {lj/disp/coul/long} computes the standard 12/6 Lennard-Jones and
Coulombic potentials, given by
:c,image(Eqs/pair_lj.jpg)
@ -53,6 +74,29 @@ settings. The "In 't Veld"_#Veld paper has more details on when it is
appropriate to include long-range 1/r^6 interactions, using this
potential.
Style {lj/cut/coul/long/tip4p} implements the TIP4P water model of
"(Jorgensen)"_#Jorgensen, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
angle. The atomic types of the oxygen and hydrogen atoms, the bond
and angle types for OH and HOH interactions, and the distance to the
massless charge site are specified as pair_style arguments.
IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
IDs for the O and 2 H atoms must be consecutive, with the O atom
first. This is to enable LAMMPS to "find" the 2 H atoms associated
with each O atom. For example, if the atom ID of an O atom in a TIP4P
water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the "howto section"_Section_howto.html#howto_8 for more
information on how to use the TIP4P pair style. Note that the
neighobr list cutoff for Coulomb interactions is effectively extended
by a distance 2*qdist when using the TIP4P pair style, to account for
the offset distance of the fictitious charges on O atoms in water
molecules. Thus it is typically best in an efficiency sense to use a
LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the
neighbor list. This leads to slightly larger cost for the long-range
calculation, so you can test the trade-off for your model.
If {flag_lj} is set to {long}, no cutoff is used on the LJ 1/r^6
dispersion term. The long-range portion is calculated by using the
"kspace_style ewald/n"_kspace_style.html command. The specified LJ
@ -90,12 +134,19 @@ LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. Note that if you are using {flag_lj} set to {long}, you
type pair.
Note that if you are using {flag_lj} set to {long}, you
cannot specify a LJ cutoff for an atom type pair, since only one
global LJ cutoff is allowed. Similarly, if you are using {flag_coul}
set to {long}, you cannot specify a Coulombic cutoff for an atom type
pair, since only one global Coulombic cutoff is allowed.
For {lj/disp/coul/long/tip4p} only the LJ cutoff can be specified
since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
:line
Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
@ -153,7 +204,7 @@ details.
[Restrictions:]
This style is part of the KSPACE package. It is only enabled if
These styles are part of the KSPACE package. They are only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info. Note that
the KSPACE package is installed by default.