forked from lijiext/lammps
fix for ScaFaCoS library
This commit is contained in:
Rene Halver
parent
510834cb7b
commit
b259de95d2
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@ -119,7 +119,7 @@ option(ENABLE_ALL "Build all default packages" OFF)
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set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
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KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
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REAX REPLICA RIGID SHOCK SNAP SRD)
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set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
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set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE SCAFACOS
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USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO
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USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
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USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
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@ -150,11 +150,11 @@ pkg_depends(CORESHELL KSPACE)
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######################################################
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# packages with special compiler needs or external libs
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######################################################
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if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE)
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if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_SCAFACOS)
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enable_language(Fortran)
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endif()
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if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)
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if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_SCAFACOS)
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enable_language(C)
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endif()
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@ -313,6 +313,13 @@ if(PKG_LATTE)
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list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
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endif()
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if(PKG_SCAFACOS)
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FIND_PACKAGE(PkgConfig)
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PKG_CHECK_MODULES(SCAFACOS scafacos)
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include_directories(${SCAFACOS_INCLUDE_DIRS})
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list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
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endif()
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if(PKG_USER-MOLFILE)
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add_library(molfile INTERFACE)
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target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
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@ -0,0 +1,25 @@
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LAMMPS Description
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8 atoms
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2 atom types
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0.0000000000000000 2.000000000000000 xlo xhi
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0.0000000000000000 2.000000000000000 ylo yhi
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0.0000000000000000 2.000000000000000 zlo zhi
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Masses
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1 22.98976928
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2 35.45
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Atoms
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1 1 1 1.0 0.0 0.0 0.0
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2 1 2 -1.0 1.0 0.0 0.0
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3 1 2 -1.0 0.0 1.0 0.0
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4 1 1 1.0 1.0 1.0 0.0
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5 1 2 -1.0 0.0 0.0 1.0
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6 1 1 1.0 1.0 0.0 1.0
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7 1 1 1.0 0.0 1.0 1.0
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8 1 2 -1.0 1.0 1.0 1.0
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@ -0,0 +1,22 @@
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# Point dipoles in a 2d box
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units lj
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atom_style full
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read_data data.NaCl
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# need both mass settings due to hybrid atom style
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velocity all set 0.0 0.0 0.0 mom no
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pair_style zero 1.0
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pair_coeff * *
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neighbor 1.0 bin
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neigh_modify delay 0
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fix 1 all scafacos fmm
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timestep 0.005
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run 100
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@ -0,0 +1,67 @@
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# Install/unInstall package files in LAMMPS
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# mode = 0/1/2 for uninstall/install/update
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mode=$1
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# enforce using portable C locale
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LC_ALL=C
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export LC_ALL
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# arg1 = file, arg2 = file it depends on
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action () {
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if (test $mode = 0) then
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rm -f ../$1
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elif (! cmp -s $1 ../$1) then
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if (test -z "$2" || test -e ../$2) then
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cp $1 ..
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if (test $mode = 2) then
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echo " updating src/$1"
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fi
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fi
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elif (test -n "$2") then
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if (test ! -e ../$2) then
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rm -f ../$1
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fi
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fi
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}
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# all package files with no dependencies
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for file in *.cpp *.h; do
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test -f ${file} && action $file
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done
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# edit 2 Makefile.package files to include/exclude package info
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if (test $1 = 1) then
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if (test -e ../Makefile.package) then
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sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package
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sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/scafacos/includelink |' ../Makefile.package
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sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/scafacos/liblink |' ../Makefile.package
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#sed -i -e 's|^PKG_LIB =[ \t]*|&-lscafacos |' ../Makefile.package
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sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(scafacos_SYSINC) |' ../Makefile.package
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sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(scafacos_SYSLIB) |' ../Makefile.package
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sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(scafacos_SYSPATH) |' ../Makefile.package
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fi
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if (test -e ../Makefile.package.settings) then
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sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings
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# multiline form needed for BSD sed on Macs
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sed -i -e '4 i \
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include ..\/..\/lib\/scafacos\/Makefile.lammps
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' ../Makefile.package.settings
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fi
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elif (test $1 = 0) then
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if (test -e ../Makefile.package) then
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sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package
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fi
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if (test -e ../Makefile.package.settings) then
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sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings
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fi
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fi
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@ -0,0 +1,488 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Rene Halver (JSC)
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------------------------------------------------------------------------- */
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#include <cstdio>
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#include <cstring>
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#include "fix_scafacos.h"
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#include "atom.h"
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#include "comm.h"
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#include "update.h"
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#include "neighbor.h"
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#include "domain.h"
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#include "force.h"
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#include "pair.h"
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#include "modify.h"
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#include "compute.h"
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#include "memory.h"
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#include "error.h"
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// ScaFaCoS library
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#include <iostream>
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#include <sstream>
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#include <string>
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#include "fcs.h"
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#include "universe.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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#define INVOKED_PERATOM 8
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/* ---------------------------------------------------------------------- */
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FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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// form of fix string:
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// fix <#> <group> scafacos <method> [ tolerance <type> <value> ]
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if (narg < 4) error->all(FLERR,"Illegal fix scafacos command");
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// read method from fix input
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method = arg[3];
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// check if fmm method was chosen
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fmm_chosen = !strcmp(method.c_str(),"fmm");
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int arg_index = 4;
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tolerance_set = false;
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while(arg_index < narg)
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{
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// check if tolerance option is set
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if (strcmp(arg[arg_index],"tolerance") == 0)
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{
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tolerance_set = true;
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++arg_index;
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if (strcmp(arg[arg_index],"energy") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
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else if (strcmp(arg[arg_index],"energy_rel") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
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else if (strcmp(arg[arg_index],"field") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
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else if (strcmp(arg[arg_index],"field_rel") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
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else if (strcmp(arg[arg_index],"potential") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
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else if (strcmp(arg[arg_index],"potential_rel") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
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else
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error->all(FLERR,"Illegal fix scafacos command");
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++arg_index;
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tolerance_value = atof(arg[arg_index]);
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++arg_index;
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}
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else
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error->all(FLERR,"Illegal fix scafacos command");
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}
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}
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/* ---------------------------------------------------------------------- */
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FixScafacos::~FixScafacos()
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{
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memory->destroy(pot);
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memory->destroy(field);
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}
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/* ---------------------------------------------------------------------- */
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int FixScafacos::setmask()
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{
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int mask = 0;
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//mask |= INITIAL_INTEGRATE;
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//mask |= FINAL_INTEGRATE;
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mask |= PRE_REVERSE;
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mask |= POST_FORCE;
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mask |= MIN_POST_FORCE;
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mask |= THERMO_ENERGY;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixScafacos::init()
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{
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// error checks
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if (domain->dimension == 2)
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error->all(FLERR,"Fix scafacos requires 3d problem");
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rank = comm->me;
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int nlocal = 0;
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int proc_grid[3] = {comm->procgrid[0], comm->procgrid[1], comm->procgrid[2]};
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int myloc[3] = {comm->myloc[0], comm->myloc[1], comm->myloc[2]};
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// call ScaFaCoS init
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// TODO: check if universe->uworld is a good idea for computations
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result = fcs_init(&fcs,method.c_str(),universe->uworld);
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if (!check_result(result, rank)) return;
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setup_handle();
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nlocal = atom -> nlocal;
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// get particle data
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x = &atom->x[0][0];
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q = atom->q;
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if (tolerance_set)
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{
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result = fcs_set_tolerance(fcs,tolerance_type,tolerance_value);
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if (!check_result(result, rank)) return;
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}
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// print out parameters within handle
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if (rank == 0) fcs_print_parameters(fcs);
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// call the tuning routine (needs to be redone, if critical system parameters should change)
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result = fcs_tune(fcs,nlocal,x,q);
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if (!check_result(result, rank)) return;
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// allocate arrays larger in order to avoid fast reallocation due to fluctuations
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local_array_size = (int)(1.25 * (double)nlocal);
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// allocate new result arrays
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memory->create(pot,local_array_size,"scafacos:potential");
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memory->create(field,local_array_size*3,"scafacos:field");
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// set result vectors to zero
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for ( int i = 0; i < local_array_size; ++i)
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{
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pot[i] = 0.0;
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field[3*i] = field[3*i+1] = field[3*i+2] = 0.0;
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixScafacos::init_list(int id, NeighList *ptr)
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{
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}
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/* ---------------------------------------------------------------------- */
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void FixScafacos::setup(int vflag)
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{
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post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixScafacos::min_setup(int vflag)
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{
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post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixScafacos::setup_pre_reverse(int eflag, int vflag)
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{
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pre_reverse(eflag,vflag);
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}
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/* ----------------------------------------------------------------------
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integrate electronic degrees of freedom
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------------------------------------------------------------------------- */
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void FixScafacos::initial_integrate(int vflag) {}
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/* ----------------------------------------------------------------------
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store eflag, so can use it in post_force to tally per-atom energies
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------------------------------------------------------------------------- */
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void FixScafacos::pre_reverse(int eflag, int vflag)
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{
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int eflag_caller = eflag;
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}
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/* ---------------------------------------------------------------------- */
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void FixScafacos::post_force(int vflag)
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{
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int nlocal;
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nlocal = atom->nlocal;
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x = &atom->x[0][0];
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q = atom->q;
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// check if box has changed since the last call of fcs_tune, if yes, call fcs_tune
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if (box_has_changed())
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{
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setup_handle();
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// print out parameters within handle
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if (rank == 0)
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{
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std::cout << " updated ScaFaCoS handle: " << std::endl;
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fcs_print_parameters(fcs);
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}
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// call the tuning routine (needs to be redone, if critical system parameters should change)
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result = fcs_tune(fcs,nlocal,x,q);
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if (!check_result(result, rank)) return;
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}
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/*
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if (fmm_chosen && phantom_particle)
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for (int i = 0; i < nlocal; ++i)
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{
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std::cout << rank << " " << i << " " << x[3*i] << " " << x[3*i+1] << " " << x[3*i+2] << " " << q[i] << std::endl;
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}
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*/
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// check if arrays for potentials and field are still large enough for the number of particles on process
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if (nlocal > local_array_size)
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{
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// allocate arrays larger in order to avoid fast reallocation due to fluctuations
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local_array_size = (int)(1.25 * (double)nlocal);
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// destroy old result arrays
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memory->destroy(pot);
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memory->destroy(field);
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// allocate result arrays
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memory->create(pot,local_array_size,"scafacos:potential");
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memory->create(field,3*local_array_size,"scafacos:field");
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}
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// set result vectors to zero
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for ( int i = 0; i < nlocal; ++i)
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{
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pot[i] = 0.0;
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field[3*i] = field[3*i+1] = field[3*i+2] = 0.0;
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}
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// compute Coulomb
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fcs_run(fcs, nlocal, x, q, field, pot);
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if(!check_result(result,rank)) return;
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double E_coul_loc = 0.0;
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// no reduction required (?)
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//double E_coul = 0.0;
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for (int i = 0; i < atom->nlocal; ++i)
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{
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//std::cout << atom->f[i][0] << " " << field[3*i] << " " << q[i] << std::endl;
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atom->f[i][0] += field[3*i] * q[i];
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atom->f[i][1] += field[3*i+1] * q[i];
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atom->f[i][2] += field[3*i+2] * q[i];
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E_coul_loc += 0.5 * q[i] * pot[i];
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}
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// not required (?)
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// MPI_ALLREDUCE(&E_coul_loc, &E_coul, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
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force->pair->eng_coul += E_coul_loc;
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}
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/* ---------------------------------------------------------------------- */
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void FixScafacos::min_post_force(int vflag)
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{
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post_force(vflag);
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}
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/* ----------------------------------------------------------------------
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integrate electronic degrees of freedom
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------------------------------------------------------------------------- */
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void FixScafacos::final_integrate() {}
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/* ---------------------------------------------------------------------- */
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void FixScafacos::reset_dt()
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{
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//dtv = update->dt;
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//dtf = 0.5 * update->dt * force->ftm2v;
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}
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/* ----------------------------------------------------------------------
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DFTB energy from LATTE
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------------------------------------------------------------------------- */
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double FixScafacos::compute_scalar()
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{
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}
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|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixScafacos::memory_usage()
|
||||
{
|
||||
double bytes = 0.0;
|
||||
bytes += local_array_size * sizeof(double);
|
||||
bytes += local_array_size * 3 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
setup of ScaFaCoS handle with common parameters
|
||||
------------------------------------------------------------------------- */
|
||||
void FixScafacos::setup_handle()
|
||||
{
|
||||
// store periodicity
|
||||
periodicity[0] = domain->xperiodic;
|
||||
periodicity[1] = domain->yperiodic;
|
||||
periodicity[2] = domain->zperiodic;
|
||||
|
||||
// store offset of the system
|
||||
offset[0] = domain->boundary[0][0];
|
||||
offset[1] = domain->boundary[1][0];
|
||||
offset[2] = domain->boundary[2][0];
|
||||
|
||||
// calculate box vectors
|
||||
box_x[0] = domain->prd[0];
|
||||
box_x[1] = box_x[2] = 0.0;
|
||||
|
||||
box_y[1] = domain->prd[1];
|
||||
box_y[0] = box_y[2] = 0.0;
|
||||
|
||||
box_z[2] = domain->prd[2];
|
||||
box_z[1] = box_z[0] = 0.0;
|
||||
|
||||
total_particles = atom->natoms;
|
||||
|
||||
// TODO: for now disable short-range calculations within LAMMPS
|
||||
near_field_flag = 0;
|
||||
|
||||
// enter all parameters required to ScaFaCoS handle
|
||||
result = fcs_set_box_a(fcs, box_x);
|
||||
if (!check_result(result, rank)) return;
|
||||
|
||||
result = fcs_set_box_b(fcs, box_y);
|
||||
if (!check_result(result, rank)) return;
|
||||
|
||||
result = fcs_set_box_c(fcs, box_z);
|
||||
if (!check_result(result, rank)) return;
|
||||
|
||||
result = fcs_set_box_origin(fcs, offset);
|
||||
if (!check_result(result, rank)) return;
|
||||
|
||||
result = fcs_set_periodicity(fcs, periodicity);
|
||||
if (!check_result(result, rank)) return;
|
||||
|
||||
result = fcs_set_near_field_flag(fcs, near_field_flag);
|
||||
if (!check_result(result, rank)) return;
|
||||
|
||||
result = fcs_set_total_particles(fcs, atom->natoms);
|
||||
if (!check_result(result, rank)) return;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check if box parameters changed, requiring a new call to fcs_tune
|
||||
------------------------------------------------------------------------- */
|
||||
bool FixScafacos::box_has_changed()
|
||||
{
|
||||
bool changed = false;
|
||||
|
||||
double n_periodicity[3];
|
||||
double n_offset[3];
|
||||
double n_box_x[3];
|
||||
double n_box_y[3];
|
||||
double n_box_z[3];
|
||||
|
||||
int n_total_particles;
|
||||
|
||||
// store periodicity
|
||||
n_periodicity[0] = domain->xperiodic;
|
||||
n_periodicity[1] = domain->yperiodic;
|
||||
n_periodicity[2] = domain->zperiodic;
|
||||
|
||||
// store offset of the system
|
||||
n_offset[0] = domain->boundary[0][0];
|
||||
n_offset[1] = domain->boundary[1][0];
|
||||
n_offset[2] = domain->boundary[2][0];
|
||||
|
||||
// calculate box vectors
|
||||
n_box_x[0] = domain->prd[0];
|
||||
n_box_x[1] = n_box_x[2] = 0.0;
|
||||
|
||||
n_box_y[1] = domain->prd[1];
|
||||
n_box_y[0] = n_box_y[2] = 0.0;
|
||||
|
||||
n_box_z[2] = domain->prd[2];
|
||||
n_box_z[1] = n_box_z[0] = 0.0;
|
||||
|
||||
n_total_particles = atom->natoms;
|
||||
|
||||
changed = changed ||
|
||||
( n_periodicity[0] != periodicity[0] ) ||
|
||||
( n_periodicity[1] != periodicity[1] ) ||
|
||||
( n_periodicity[2] != periodicity[2] ) ||
|
||||
( n_offset[0] != offset[0] ) ||
|
||||
( n_offset[1] != offset[1] ) ||
|
||||
( n_offset[2] != offset[2] ) ||
|
||||
( n_box_x[0] != box_x[0] ) ||
|
||||
( n_box_x[1] != box_x[1] ) ||
|
||||
( n_box_x[2] != box_x[2] ) ||
|
||||
( n_box_y[0] != box_y[0] ) ||
|
||||
( n_box_y[1] != box_y[1] ) ||
|
||||
( n_box_y[2] != box_y[2] ) ||
|
||||
( n_box_z[0] != box_z[0] ) ||
|
||||
( n_box_z[1] != box_z[1] ) ||
|
||||
( n_box_z[2] != box_z[2] ) ||
|
||||
( n_total_particles != total_particles );
|
||||
/*
|
||||
if (changed)
|
||||
{
|
||||
std::cout << rank << " " << "n_per_x : per_x" << n_periodicity[0] << " " << periodicity[0] << std::endl;
|
||||
std::cout << rank << " " << "n_per_y : per_y" << n_periodicity[1] << " " << periodicity[1] << std::endl;
|
||||
std::cout << rank << " " << "n_per_z : per_z" << n_periodicity[2] << " " << periodicity[2] << std::endl;
|
||||
std::cout << rank << " " << "n_off_x : off_x" << n_offset[0] << " " << offset[0] << std::endl;
|
||||
std::cout << rank << " " << "n_off_y : off_y" << n_offset[1] << " " << offset[1] << std::endl;
|
||||
std::cout << rank << " " << "n_off_z : off_z" << n_offset[2] << " " << offset[2] << std::endl;
|
||||
std::cout << rank << " " << "n_bx_x : bx_x" << n_box_x[0] << " " << box_x[0] << std::endl;
|
||||
std::cout << rank << " " << "n_bx_y : bx_y" << n_box_x[1] << " " << box_x[1] << std::endl;
|
||||
std::cout << rank << " " << "n_bx_z : bx_z" << n_box_x[2] << " " << box_x[2] << std::endl;
|
||||
std::cout << rank << " " << "n_by_x : by_x" << n_box_y[0] << " " << box_y[0] << std::endl;
|
||||
std::cout << rank << " " << "n_by_y : by_y" << n_box_y[1] << " " << box_y[1] << std::endl;
|
||||
std::cout << rank << " " << "n_by_z : by_z" << n_box_y[2] << " " << box_y[2] << std::endl;
|
||||
std::cout << rank << " " << "n_bz_x : bz_x" << n_box_z[0] << " " << box_z[0] << std::endl;
|
||||
std::cout << rank << " " << "n_bz_y : bz_y" << n_box_z[1] << " " << box_z[1] << std::endl;
|
||||
std::cout << rank << " " << "n_bz_z : bz_z" << n_box_z[2] << " " << box_z[2] << std::endl;
|
||||
std::cout << rank << " " << "n_total : total" << n_total_particles << " " << total_particles << std::endl;
|
||||
}
|
||||
*/
|
||||
return changed;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check of ScaFaCoS result
|
||||
------------------------------------------------------------------------- */
|
||||
bool FixScafacos::check_result(FCSResult result, int comm_rank)
|
||||
{
|
||||
if (result)
|
||||
{
|
||||
std::cout << "ScaFaCoS ERROR: Caught error on task " << comm_rank << "!" << std::endl;
|
||||
std::string err_msg;
|
||||
std::stringstream ss;
|
||||
|
||||
ss << fcs_result_get_function(result) << "\n" << fcs_result_get_message(result) << "\n";
|
||||
err_msg = ss.str();
|
||||
|
||||
error -> all(FLERR, err_msg.c_str());
|
||||
fcs_result_destroy(result);
|
||||
}
|
||||
return true;
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,164 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(scafacos,FixScafacos)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_SCAFACOS_H
|
||||
#define LMP_FIX_SCAFACOS_H
|
||||
|
||||
#include "fix.h"
|
||||
#include "fcs.h"
|
||||
#include <string>
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixScafacos : public Fix {
|
||||
public:
|
||||
FixScafacos(class LAMMPS *, int, char **);
|
||||
virtual ~FixScafacos();
|
||||
int setmask();
|
||||
void init();
|
||||
void init_list(int, NeighList*);
|
||||
void setup(int);
|
||||
void min_setup(int);
|
||||
void setup_pre_reverse(int, int);
|
||||
void initial_integrate(int);
|
||||
void pre_reverse(int, int);
|
||||
void post_force(int);
|
||||
void min_post_force(int);
|
||||
void final_integrate();
|
||||
void reset_dt();
|
||||
double compute_scalar();
|
||||
double memory_usage();
|
||||
|
||||
protected:
|
||||
std::string method;
|
||||
|
||||
// MPI rank
|
||||
int rank;
|
||||
|
||||
// source arrays for positions and charges
|
||||
double *x, *q;
|
||||
// result arrays for potentials and field
|
||||
double *pot, *field;
|
||||
|
||||
// box vectors for each dimension
|
||||
fcs_float box_x[3], box_y[3], box_z[3];
|
||||
// offset of the box from the origin
|
||||
fcs_float offset[3];
|
||||
|
||||
// periodicity of the system
|
||||
fcs_int periodicity[3];
|
||||
|
||||
// ScaFaCoS handle
|
||||
FCS fcs;
|
||||
|
||||
// ScaFaCoS result variable
|
||||
FCSResult result;
|
||||
|
||||
// function to check results
|
||||
bool check_result(FCSResult, int);
|
||||
|
||||
// function to set up handle with common parameters
|
||||
void setup_handle();
|
||||
|
||||
// function to check if the box parameters changed, so that a new tuning step is required
|
||||
bool box_has_changed();
|
||||
|
||||
// store total number of particles (to check if tune needs to be called again)
|
||||
fcs_int total_particles;
|
||||
|
||||
// store number of local particles (to be able to readjust the size of result arrays, when needed)
|
||||
int local_array_size;
|
||||
|
||||
// should the near field calculations be computed by LAMMPS?
|
||||
fcs_int near_field_flag;
|
||||
|
||||
// type of accuracy chosen (if customized)
|
||||
fcs_int tolerance_type;
|
||||
|
||||
// value of tolerance
|
||||
fcs_float tolerance_value;
|
||||
|
||||
// is tolerance set?
|
||||
bool tolerance_set;
|
||||
|
||||
// check if fmm is chosen (ghost particles, since the implementation needs at least 1 particle on each process!)
|
||||
bool fmm_chosen;
|
||||
|
||||
// FMM: fmm particle array size
|
||||
int fmm_array_size;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Must use units metal with fix latte command
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Fix latte currently runs only in serial
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: LAMMPS is linked against incompatible LATTE library
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Fix latte does not yet support a LAMMPS calculation of a Coulomb potential
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Could not find fix latte compute ID
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Fix latte compute ID does not compute pe/atom
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Fix latte requires 3d problem
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Fix latte cannot compute Coulomb potential
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Fix latte requires 3d simulation
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
W: Fix latte should come after all other integration fixes
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Internal LATTE problem
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue