From 82ba71c7620917d69d64f97f2c9dff618cff9f36 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 2 Oct 2012 23:18:29 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8875 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_accelerate.html | 3 +- doc/Section_accelerate.txt | 3 +- doc/Section_intro.html | 1 - doc/Section_intro.txt | 1 - doc/Section_packages.html | 35 ---------------- doc/Section_packages.txt | 35 ---------------- doc/kspace_style.html | 30 ++++++++++++++ doc/kspace_style.txt | 34 +++++++++++++++ doc/pair_charmm.html | 22 +++++----- doc/pair_charmm.txt | 22 +++++----- doc/pair_class2.html | 13 ++++-- doc/pair_class2.txt | 13 ++++-- doc/pair_lj.html | 21 ++++++---- doc/pair_lj.txt | 19 +++++---- doc/pair_lj_disp.html | 82 +++++++++++++++++++++++++++++-------- doc/pair_lj_disp.txt | 75 +++++++++++++++++++++++++++------ 16 files changed, 262 insertions(+), 147 deletions(-) diff --git a/doc/Section_accelerate.html b/doc/Section_accelerate.html index b4a3858f7b..a461cdf2df 100644 --- a/doc/Section_accelerate.html +++ b/doc/Section_accelerate.html @@ -98,7 +98,8 @@ simply trying them out.
  • processor mapping via processors numa command
  • load-balancing: balance and fix balance
  • processor command for layout -
  • OMP when lots of cores +
  • OMP when lots of cores +
  • proxy/OMP for PPPM
    diff --git a/doc/Section_accelerate.txt b/doc/Section_accelerate.txt index e0f57258d2..bfa7efaa3d 100644 --- a/doc/Section_accelerate.txt +++ b/doc/Section_accelerate.txt @@ -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 diff --git a/doc/Section_intro.html b/doc/Section_intro.html index 3ce8ad865a..1e9511b0d0 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -526,7 +526,6 @@ and efforts.
  • 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 diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index 360089c5ac..4a8a915578 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -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 diff --git a/doc/Section_packages.html b/doc/Section_packages.html index 37f6eae1f8..d3be2e15aa 100644 --- a/doc/Section_packages.html +++ b/doc/Section_packages.html @@ -109,7 +109,6 @@ E.g. "peptide" refers to the examples/peptide directory. USER-COLVARS collective variables Fiorin & Henin & Kohlmeyer (3) fix colvars USER/colvars colvars lib/colvars USER-CUDA NVIDIA GPU styles Christian Trott (U Tech Ilmenau) Section accelerate USER/cuda - lib/cuda USER-EFF electron force field Andres Jaramillo-Botero (Caltech) pair_style eff/cut USER/eff eff - -USER-EWALDN Ewald for 1/R^n Pieter in' t Veld (BASF) kspace_style - - - USER-MOLFILE VMD molfile plug-ins Axel Kohlmeyer (Temple U) dump molfile - - lib/molfile USER-OMP OpenMP threaded styles Axel Kohlmeyer (Temple U) Section accelerate - - - USER-REAXC C version of ReaxFF Metin Aktulga (LBNL) pair_style reaxc reax - - @@ -362,40 +361,6 @@ have questions.


    -

    USER-EWALDN package -

    -

    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. -

    -
    -

    USER-OMP package

    This package provides OpenMP multi-threading support and diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt index 06ec3fbe2c..bbd2d9d93b 100644 --- a/doc/Section_packages.txt +++ b/doc/Section_packages.txt @@ -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 diff --git a/doc/kspace_style.html b/doc/kspace_style.html index b95ed6e0a9..ba16ef97df 100644 --- a/doc/kspace_style.html +++ b/doc/kspace_style.html @@ -78,6 +78,36 @@ 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. +


    The pppm style invokes a particle-particle particle-mesh solver diff --git a/doc/kspace_style.txt b/doc/kspace_style.txt index 0d3b60dac2..396ca07e36 100644 --- a/doc/kspace_style.txt +++ b/doc/kspace_style.txt @@ -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 diff --git a/doc/pair_charmm.html b/doc/pair_charmm.html index d586bb4006..e5c842820f 100644 --- a/doc/pair_charmm.html +++ b/doc/pair_charmm.html @@ -31,7 +31,7 @@

    pair_style lj/charmm/coul/long/omp command

    -

    pair_style lj/charmm/coul/pppm/omp command +

    pair_style lj/charmm/coul/long/proxy/omp command

    Syntax:

    @@ -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).

    -

    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 +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 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 diff --git a/doc/pair_charmm.txt b/doc/pair_charmm.txt index fa46832205..926a244ae7 100644 --- a/doc/pair_charmm.txt +++ b/doc/pair_charmm.txt @@ -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 diff --git a/doc/pair_class2.html b/doc/pair_class2.html index 1f73c4daaf..e2ba876b00 100644 --- a/doc/pair_class2.html +++ b/doc/pair_class2.html @@ -31,7 +31,7 @@

    pair_style lj/class2/coul/long/omp command

    -

    pair_style lj/class2/coul/pppm/omp command +

    pair_style lj/class2/coul/long/proxy/omp command

    Syntax:

    @@ -75,8 +75,7 @@ pair_coeff 1 1 100.0 3.5 9.0

    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 -styles. +Coulombic term as described for the lj/cut pair styles.

    See (Sun) for a description of the COMPASS class2 force field.

    @@ -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.

    +

    Style lj/class2/coul/long/proxy/omp is a variant for use with +K-space style pppm/proxy 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. +


    If the pair_coeff command is not used to define coefficients for a diff --git a/doc/pair_class2.txt b/doc/pair_class2.txt index cc80ed5e68..1152954898 100644 --- a/doc/pair_class2.txt +++ b/doc/pair_class2.txt @@ -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 diff --git a/doc/pair_lj.html b/doc/pair_lj.html index 355e924eab..03c6104563 100644 --- a/doc/pair_lj.html +++ b/doc/pair_lj.html @@ -51,10 +51,14 @@

    pair_style lj/cut/coul/long/omp command

    +

    pair_style lj/cut/coul/long/proxy/omp command +

    pair_style lj/cut/coul/long/tip4p command

    pair_style lj/cut/coul/long/tip4p/omp command

    +

    pair_style lj/cut/coul/long/proxy/tip4p/omp command +

    pair_style lj/cut/coul/long/tip4p/opt command

    Syntax: @@ -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.

    -

    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 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 and pppm/tip4p/proxy, 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.


    diff --git a/doc/pair_lj.txt b/doc/pair_lj.txt index e87ffbcb0d..58a4c306d2 100644 --- a/doc/pair_lj.txt +++ b/doc/pair_lj.txt @@ -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 diff --git a/doc/pair_lj_disp.html b/doc/pair_lj_disp.html index f2042d5701..547df34dc2 100644 --- a/doc/pair_lj_disp.html +++ b/doc/pair_lj_disp.html @@ -13,24 +13,37 @@

    pair_style lj/disp/coul/long/omp command

    +

    pair_style lj/disp/coul/long/tip4p command +

    Syntax:

    -
    pair_style lj/disp/coul/long flag_lj flag_coul cutoff (cutoff2) 
    +
    pair_style style args 
     
    -
    • flag_lj = long or cut - -
        long = use Kspace long-range summation for the dispersion term 1/r^6
      -  cut = use a cutoff 
      -
      -
    • flag_coul = long or off - -
        long = use Kspace long-range summation for the Coulombic term 1/r
      -  off = omit the Coulombic term 
      -
      -
    • cutoff = global cutoff for LJ (and Coulombic if only 1 cutoff) (distance units) - -
    • cutoff2 = global cutoff for Coulombic (optional) (distance units) +
      • style = lj/disp/coul/long or lj/disp/coul/long/tip4p +
      • args = list of arguments for a particular style
      +
        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) 
      +

      Examples:

      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 
       
      +
      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 
      +

      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

      @@ -62,6 +80,29 @@ settings. The In 't Veld paper has more details on when i 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), 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 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 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 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. +


      Styles with a cuda, gpu, omp, or opt suffix are functionally @@ -162,7 +210,7 @@ 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 for more info. Note that the KSPACE package is installed by default. diff --git a/doc/pair_lj_disp.txt b/doc/pair_lj_disp.txt index 98cd1b4d9f..f02930cdc4 100644 --- a/doc/pair_lj_disp.txt +++ b/doc/pair_lj_disp.txt @@ -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.