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 
 
    
-