first version of fix ave/grid
This commit is contained in:
Steve Plimpton
@ -291,7 +291,7 @@ void DumpGrid::init_style()
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}
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}
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} else {
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} else {
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if (field2source[0] == COMPUTE) {
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if (field2source[i] == COMPUTE) {
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icompute = compute[field2index[i]];
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icompute = compute[field2index[i]];
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grid3d = (Grid3d *) icompute->get_grid_by_index(field2grid[i]);
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grid3d = (Grid3d *) icompute->get_grid_by_index(field2grid[i]);
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} else {
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} else {
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@ -760,10 +760,10 @@ int DumpGrid::parse_fields(int narg, char **arg)
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if (argi.get_dim() == 0 && ncol)
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if (argi.get_dim() == 0 && ncol)
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error->all(FLERR,"Dump grid compute {} data {} is not per-grid vector",
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error->all(FLERR,"Dump grid compute {} data {} is not per-grid vector",
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idcompute,dname);
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idcompute,dname);
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if (argi.get_dim() > 0 && ncol == 0)
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if (argi.get_dim() && ncol == 0)
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error->all(FLERR,"Dump grid compute {} data {} is not per-grid array",
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error->all(FLERR,"Dump grid compute {} data {} is not per-grid array",
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idcompute,dname);
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idcompute,dname);
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if (argi.get_dim() > 0 && argi.get_index1() > ncol)
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if (argi.get_dim() && argi.get_index1() > ncol)
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error->all(FLERR,
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error->all(FLERR,
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"Dump grid compute {} array {} is accessed out-of-range",
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"Dump grid compute {} array {} is accessed out-of-range",
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idcompute,dname);
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idcompute,dname);
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@ -798,7 +798,9 @@ int DumpGrid::parse_fields(int narg, char **arg)
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if (ifix->pergrid_flag == 0)
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if (ifix->pergrid_flag == 0)
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error->all(FLERR,"Dump grid fix {} does not compute per-grid info",
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error->all(FLERR,"Dump grid fix {} does not compute per-grid info",
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idfix);
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idfix);
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if (update->ntimestep % ifix->pergrid_freq)
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error->all(FLERR,"Fix for dump grid not computed at compatible time");
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int dim;
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int dim;
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int igrid = ifix->get_grid_by_name(gname,dim);
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int igrid = ifix->get_grid_by_name(gname,dim);
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if (igrid < 0)
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if (igrid < 0)
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@ -961,7 +963,7 @@ int DumpGrid::modify_param(int narg, char **arg)
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double DumpGrid::memory_usage()
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double DumpGrid::memory_usage()
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{
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{
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double bytes = Dump::memory_usage();
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double bytes = Dump::memory_usage();
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//NOTE: restre if use choose
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//NOTE: restore if use choose
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//bytes += memory->usage(choose,maxlocal);
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//bytes += memory->usage(choose,maxlocal);
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//bytes += memory->usage(dchoose,maxlocal);
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//bytes += memory->usage(dchoose,maxlocal);
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//bytes += memory->usage(clist,maxlocal);
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//bytes += memory->usage(clist,maxlocal);
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@ -100,7 +100,8 @@ class Fix : protected Pointers {
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int local_freq; // frequency local data is available at
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int local_freq; // frequency local data is available at
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int pergrid_flag; // 0/1 if per-grid data is stored
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int pergrid_flag; // 0/1 if per-grid data is stored
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int pergrid_freq; // frequency per-grid data is available at
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int extscalar; // 0/1 if global scalar is intensive/extensive
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int extscalar; // 0/1 if global scalar is intensive/extensive
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int extvector; // 0/1/-1 if global vector is all int/ext/extlist
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int extvector; // 0/1/-1 if global vector is all int/ext/extlist
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int *extlist; // list of 0/1 int/ext for each vec component
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int *extlist; // list of 0/1 int/ext for each vec component
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765
src/fix_ave_grid.cpp
Normal file
765
src/fix_ave_grid.cpp
Normal file
@ -0,0 +1,765 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, 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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#include "fix_ave_grid.h"
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#include "arg_info.h"
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#include "atom.h"
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#include "compute.h"
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#include "domain.h"
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#include "error.h"
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#include "grid2d.h"
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#include "grid3d.h"
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#include "input.h"
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#include "memory.h"
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#include "modify.h"
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#include "update.h"
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#include "variable.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace FixConst;
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enum{SAMPLE,ALL};
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enum{NOSCALE,ATOM};
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enum{ONE,RUNNING,WINDOW};
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/* ---------------------------------------------------------------------- */
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FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg),
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which(nullptr), argindex(nullptr), ids(nullptr),
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value2index(nullptr), value2grid(nullptr), value2data(nullptr),
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grid2d(nullptr), grid3d(nullptr),
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vec2d(nullptr), array2d(nullptr), vec3d(nullptr), array3d(nullptr)
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{
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if (narg < 10) error->all(FLERR,"Illegal fix ave/grid command");
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pergrid_flag = 1;
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nevery = utils::inumeric(FLERR,arg[3],false,lmp);
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nrepeat = utils::inumeric(FLERR,arg[4],false,lmp);
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pergrid_freq = utils::inumeric(FLERR,arg[5],false,lmp);
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time_depend = 1;
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// NOTE: test for Dxyz as well
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nx = utils::inumeric(FLERR,arg[6],false,lmp);
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ny = utils::inumeric(FLERR,arg[7],false,lmp);
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nz = utils::inumeric(FLERR,arg[8],false,lmp);
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// expand args if any have wildcard character "*"
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// this can reset nvalues
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int expand = 0;
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char **earg;
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int nargnew = utils::expand_args(FLERR,nvalues,&arg[9],1,earg,lmp);
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if (earg != &arg[9]) expand = 1;
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arg = earg;
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// parse values
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which = new int[nvalues];
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argindex = new int[nvalues];
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ids = new char*[nvalues];
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value2index = new int[nvalues];
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value2grid = new int[nvalues];
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value2data = new int[nvalues];
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modeatom = modegrid = 0;
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int iarg = 0;
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while (iarg < nargnew) {
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ids[nvalues] = nullptr;
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if (strcmp(arg[iarg],"vx") == 0) {
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which[nvalues] = ArgInfo::V;
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argindex[nvalues++] = 0;
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modeatom = 1;
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} else if (strcmp(arg[iarg],"vy") == 0) {
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which[nvalues] = ArgInfo::V;
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argindex[nvalues++] = 1;
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modeatom = 1;
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} else if (strcmp(arg[iarg],"vz") == 0) {
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which[nvalues] = ArgInfo::V;
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argindex[nvalues++] = 2;
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modeatom = 1;
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} else if (strcmp(arg[iarg],"fx") == 0) {
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which[nvalues] = ArgInfo::F;
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argindex[nvalues++] = 0;
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modeatom = 1;
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} else if (strcmp(arg[iarg],"fy") == 0) {
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which[nvalues] = ArgInfo::F;
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argindex[nvalues++] = 1;
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modeatom = 1;
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} else if (strcmp(arg[iarg],"fz") == 0) {
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which[nvalues] = ArgInfo::F;
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argindex[nvalues++] = 2;
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modeatom = 1;
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} else if (strcmp(arg[iarg],"density/number") == 0) {
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which[nvalues] = ArgInfo::DENSITY_NUMBER;
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argindex[nvalues++] = 0;
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modeatom = 1;
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} else if (strcmp(arg[iarg],"density/mass") == 0) {
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which[nvalues] = ArgInfo::DENSITY_MASS;
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argindex[nvalues++] = 0;
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modeatom = 1;
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} else if (strcmp(arg[iarg],"mass") == 0) {
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which[nvalues] = ArgInfo::MASS;
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argindex[nvalues++] = 0;
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modeatom = 1;
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} else if (strcmp(arg[iarg],"temp") == 0) {
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which[nvalues] = ArgInfo::TEMPERATURE;
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argindex[nvalues++] = 0;
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modeatom = 1;
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} else {
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ArgInfo argi(arg[iarg]);
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if (argi.get_type() == ArgInfo::NONE) break;
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if ((argi.get_type() == ArgInfo::UNKNOWN) || (argi.get_dim() > 1))
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error->all(FLERR,"Invalid fix ave/grid command");
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which[nvalues] = argi.get_type();
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argindex[nvalues] = argi.get_index1();
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ids[nvalues] = argi.copy_name();
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if (strchr(ids[nvalues],':')) modegrid = 1;
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else modeatom = 1;
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if (modegrid && which[nvalues] == ArgInfo::VARIABLE)
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error->all(FLERR,"Fix ave/grid cannot use variable for grid info");
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nvalues++;
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}
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iarg++;
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}
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if (nvalues == 0) error->all(FLERR,"No values in fix ave/grid command");
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if (modeatom && modegrid)
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error->all(FLERR,"Fix ave/grid cannot operate on per-atom and "
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"per-grid values");
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// optional args
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normflag = ALL;
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scaleflag = ATOM;
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ave = ONE;
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nwindow = 0;
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while (iarg < nargnew) {
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if (strcmp(arg[iarg],"norm") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/grid command");
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if (strcmp(arg[iarg+1],"all") == 0) {
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normflag = ALL;
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scaleflag = ATOM;
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} else if (strcmp(arg[iarg+1],"sample") == 0) {
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normflag = SAMPLE;
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scaleflag = ATOM;
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} else if (strcmp(arg[iarg+1],"none") == 0) {
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normflag = SAMPLE;
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scaleflag = NOSCALE;
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} else error->all(FLERR,"Illegal fix ave/grid command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"ave") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/grid command");
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if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
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else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
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else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
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else error->all(FLERR,"Illegal fix ave/grid command");
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if (ave == WINDOW) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/grid command");
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nwindow = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
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if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/grid command");
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}
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iarg += 2;
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if (ave == WINDOW) iarg++;
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}
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}
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// if wildcard expansion occurred, free earg memory from exapnd_args()
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if (expand) {
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for (int i = 0; i < nvalues; i++) delete [] earg[i];
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memory->sfree(earg);
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}
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// setup and error check
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// for fix inputs, check that fix frequency is acceptable
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dimension = domain->dimension;
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if (nevery <= 0 || nrepeat <= 0 || pergrid_freq <= 0)
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error->all(FLERR,"Illegal fix ave/grid command");
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if (pergrid_freq % nevery || nrepeat*nevery > pergrid_freq)
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error->all(FLERR,"Illegal fix ave/grid command");
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if (nx < 1 || ny < 1 || nz < 1)
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error->all(FLERR,"Invalid fix ave/grid grid size");
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if (dimension == 2 && nz != 1)
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error->all(FLERR,"Fix ave/grid grid Nz must be 1 for 2d simulation");
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// error checks for ATOM mode
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if (modeatom) {
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == ArgInfo::COMPUTE) {
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int icompute = modify->find_compute(ids[i]);
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if (icompute < 0)
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error->all(FLERR,"Compute ID for fix ave/grid does not exist");
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if (modify->compute[icompute]->peratom_flag == 0)
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error->all(FLERR,
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"Fix ave/atom compute does not calculate per-atom values");
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if (argindex[i] == 0 &&
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modify->compute[icompute]->size_peratom_cols != 0)
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error->all(FLERR,"Fix ave/atom compute does not "
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"calculate a per-atom vector");
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if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
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error->all(FLERR,"Fix ave/atom compute does not "
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"calculate a per-atom array");
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if (argindex[i] &&
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argindex[i] > modify->compute[icompute]->size_peratom_cols)
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error->all(FLERR,"Fix ave/atom compute array is accessed out-of-range");
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} else if (which[i] == ArgInfo::FIX) {
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int ifix = modify->find_fix(ids[i]);
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if (ifix < 0)
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error->all(FLERR,"Fix ID for fix ave/atom does not exist");
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if (modify->fix[ifix]->peratom_flag == 0)
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error->all(FLERR,"Fix ave/atom fix does not calculate per-atom values");
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if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0)
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error->all(FLERR,
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"Fix ave/atom fix does not calculate a per-atom vector");
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if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
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error->all(FLERR,
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"Fix ave/atom fix does not calculate a per-atom array");
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if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
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error->all(FLERR,"Fix ave/atom fix array is accessed out-of-range");
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if (nevery % modify->fix[ifix]->peratom_freq)
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error->all(FLERR,
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"Fix for fix ave/atom not computed at compatible time");
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} else if (which[i] == ArgInfo::VARIABLE) {
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int ivariable = input->variable->find(ids[i]);
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if (ivariable < 0)
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error->all(FLERR,"Variable name for fix ave/atom does not exist");
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if (input->variable->atomstyle(ivariable) == 0)
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error->all(FLERR,"Fix ave/atom variable is not atom-style variable");
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}
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}
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}
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// setup and error checks for GRID mode
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if (modegrid) {
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == ArgInfo::COMPUTE) {
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char *idcompute,*gname,*dname;
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utils::grid_parse(FLERR,ids[i],idcompute,gname,dname,error);
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Compute *icompute = modify->get_compute_by_id(idcompute);
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if (!icompute)
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error->all(FLERR,"Could not find fix ave/grid compute ID: {}",
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idcompute);
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if (icompute->pergrid_flag == 0)
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error->all(FLERR,
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|
"Fix ave/grid compute {} does not compute per-grid info",
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|
idcompute);
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|
|
||||||
|
int dim;
|
||||||
|
int igrid = icompute->get_grid_by_name(gname,dim);
|
||||||
|
if (igrid < 0)
|
||||||
|
error->all(FLERR,
|
||||||
|
"Fix ave/grid compute {} does not recognize grid name {}",
|
||||||
|
idcompute,gname);
|
||||||
|
|
||||||
|
int ncol;
|
||||||
|
int idata = icompute->get_griddata_by_name(igrid,dname,ncol);
|
||||||
|
if (idata < 0)
|
||||||
|
error->all(FLERR,
|
||||||
|
"Fix ave/grid compute {} does not recognize data name {}",
|
||||||
|
idcompute,dname);
|
||||||
|
|
||||||
|
if (argindex[i] == 0 && ncol)
|
||||||
|
error->all(FLERR,
|
||||||
|
"Fix ave/grid compute {} data {} is not per-grid vector",
|
||||||
|
idcompute,dname);
|
||||||
|
if (argindex[i] && ncol == 0)
|
||||||
|
error->all(FLERR,
|
||||||
|
"Fix ave/grid compute {} data {} is not per-grid array",
|
||||||
|
idcompute,dname);
|
||||||
|
if (argindex[i] && argindex[i] > ncol)
|
||||||
|
error->all(FLERR,
|
||||||
|
"Fix ave/grid compute {} array {} is accessed out-of-range",
|
||||||
|
idcompute,dname);
|
||||||
|
|
||||||
|
value2grid[iarg] = igrid;
|
||||||
|
value2data[iarg] = idata;
|
||||||
|
|
||||||
|
delete [] idcompute;
|
||||||
|
delete [] gname;
|
||||||
|
delete [] dname;
|
||||||
|
|
||||||
|
} else if (which[i] == ArgInfo::FIX) {
|
||||||
|
|
||||||
|
char *idfix,*gname,*dname;
|
||||||
|
utils::grid_parse(FLERR,ids[i],idfix,gname,dname,error);
|
||||||
|
|
||||||
|
Fix *ifix = modify->get_fix_by_id(idfix);
|
||||||
|
if (!ifix) error->all(FLERR,"Could not find fix ave/grid fix ID: {}",
|
||||||
|
idfix);
|
||||||
|
if (ifix->pergrid_flag == 0)
|
||||||
|
error->all(FLERR,"Fix ave/grid fix {} does not compute per-grid info",
|
||||||
|
idfix);
|
||||||
|
if (nevery % ifix->pergrid_freq)
|
||||||
|
error->all(FLERR,
|
||||||
|
"Fix for fix grid/atom not computed at compatible time");
|
||||||
|
|
||||||
|
int dim;
|
||||||
|
int igrid = ifix->get_grid_by_name(gname,dim);
|
||||||
|
if (igrid < 0)
|
||||||
|
error->all(FLERR,
|
||||||
|
"Fix ave/grid compute {} does not recognize grid name {}",
|
||||||
|
idfix,gname);
|
||||||
|
|
||||||
|
int ncol;
|
||||||
|
int idata = ifix->get_griddata_by_name(igrid,dname,ncol);
|
||||||
|
if (idata < 0)
|
||||||
|
error->all(FLERR,
|
||||||
|
"Fix ave/grid compute {} does not recognize data name {}",
|
||||||
|
idfix,dname);
|
||||||
|
|
||||||
|
if (argindex[i] == 0 && ncol)
|
||||||
|
error->all(FLERR,
|
||||||
|
"Fix ave/grid compute {} data {} is not per-grid vector",
|
||||||
|
idfix,dname);
|
||||||
|
if (argindex[i] && ncol == 0)
|
||||||
|
error->all(FLERR,
|
||||||
|
"Fix ave/grid compute {} data {} is not per-grid array",
|
||||||
|
idfix,dname);
|
||||||
|
if (argindex[i] && argindex[i] > ncol)
|
||||||
|
error->all(FLERR,
|
||||||
|
"Fix ave/grid compute {} array {} is accessed out-of-range",
|
||||||
|
idfix,dname);
|
||||||
|
|
||||||
|
value2grid[iarg] = igrid;
|
||||||
|
value2data[iarg] = idata;
|
||||||
|
|
||||||
|
delete [] idfix;
|
||||||
|
delete [] gname;
|
||||||
|
delete [] dname;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// instantiate the Grid class and allocate per-grid memory
|
||||||
|
// NOTE: need to extend ghost grid for ATOM mode ?
|
||||||
|
|
||||||
|
if (dimension == 2) {
|
||||||
|
grid2d = new Grid2d(lmp, world, nx, ny, 0, 0.0, 0.0,
|
||||||
|
nxlo_in, nxhi_in, nylo_in, nyhi_in,
|
||||||
|
nxlo_out, nxhi_out, nylo_out, nyhi_out);
|
||||||
|
if (nvalues == 1)
|
||||||
|
memory->create2d_offset(vec2d, nylo_out, nyhi_out, nxlo_out, nxhi_out,
|
||||||
|
"fix_ave/grid:vec2d");
|
||||||
|
else
|
||||||
|
memory->create3d_offset_last(array2d, nylo_out, nyhi_out, nxlo_out,
|
||||||
|
nxhi_out, nvalues, "fix_ave/grid:array2d");
|
||||||
|
ngridout = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1);
|
||||||
|
|
||||||
|
} else {
|
||||||
|
grid3d = new Grid3d(lmp, world, nx, ny, nz, 0, 0.0, 0.0,
|
||||||
|
nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in,
|
||||||
|
nxlo_out, nxhi_out, nylo_out, nyhi_out,
|
||||||
|
nzlo_out, nzhi_out);
|
||||||
|
if (nvalues == 1)
|
||||||
|
memory->create3d_offset(vec3d, nzlo_out, nzhi_out, nylo_out,
|
||||||
|
nyhi_out, nxlo_out,
|
||||||
|
nxhi_out, "fix_ave/grid:vec3d");
|
||||||
|
else
|
||||||
|
memory->create4d_offset_last(array3d, nzlo_out, nzhi_out, nylo_out,
|
||||||
|
nyhi_out, nxlo_out,
|
||||||
|
nxhi_out, nvalues, "fix_ave/grid:array3d");
|
||||||
|
ngridout = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1) *
|
||||||
|
(nzhi_out - nzlo_out + 1);
|
||||||
|
}
|
||||||
|
|
||||||
|
// zero the array since dump may access it on timestep 0
|
||||||
|
// zero the array since a variable may access it before first run
|
||||||
|
|
||||||
|
/*
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
for (int i = 0; i < nlocal; i++)
|
||||||
|
for (int m = 0; m < nvalues; m++)
|
||||||
|
array[i][m] = 0.0;
|
||||||
|
*/
|
||||||
|
|
||||||
|
// nvalid = next step on which end_of_step does something
|
||||||
|
// add nvalid to all computes that store invocation times
|
||||||
|
// since don't know a priori which are invoked by this fix
|
||||||
|
// once in end_of_step() can set timestep for ones actually invoked
|
||||||
|
|
||||||
|
irepeat = 0;
|
||||||
|
nvalid_last = -1;
|
||||||
|
nvalid = nextvalid();
|
||||||
|
modify->addstep_compute_all(nvalid);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
FixAveGrid::~FixAveGrid()
|
||||||
|
{
|
||||||
|
delete [] which;
|
||||||
|
delete [] argindex;
|
||||||
|
for (int m = 0; m < nvalues; m++) delete [] ids[m];
|
||||||
|
delete [] ids;
|
||||||
|
delete [] value2index;
|
||||||
|
delete [] value2grid;
|
||||||
|
delete [] value2data;
|
||||||
|
|
||||||
|
delete grid2d;
|
||||||
|
delete grid3d;
|
||||||
|
memory->destroy2d_offset(vec2d,nylo_out,nxlo_out);
|
||||||
|
memory->destroy2d_offset(array2d,nylo_out,nxlo_out);
|
||||||
|
memory->destroy3d_offset(vec3d,nzlo_out,nylo_out,nxlo_out);
|
||||||
|
memory->destroy4d_offset_last(array3d,nzlo_out,nylo_out,nxlo_out);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
int FixAveGrid::setmask()
|
||||||
|
{
|
||||||
|
int mask = 0;
|
||||||
|
mask |= END_OF_STEP;
|
||||||
|
return mask;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixAveGrid::init()
|
||||||
|
{
|
||||||
|
// set indices and check validity of all computes,fixes,variables
|
||||||
|
|
||||||
|
for (int m = 0; m < nvalues; m++) {
|
||||||
|
if (which[m] == ArgInfo::COMPUTE) {
|
||||||
|
int icompute = modify->find_compute(ids[m]);
|
||||||
|
if (icompute < 0)
|
||||||
|
error->all(FLERR,"Compute ID for fix ave/atom does not exist");
|
||||||
|
value2index[m] = icompute;
|
||||||
|
|
||||||
|
} else if (which[m] == ArgInfo::FIX) {
|
||||||
|
int ifix = modify->find_fix(ids[m]);
|
||||||
|
if (ifix < 0)
|
||||||
|
error->all(FLERR,"Fix ID for fix ave/atom does not exist");
|
||||||
|
value2index[m] = ifix;
|
||||||
|
|
||||||
|
} else if (which[m] == ArgInfo::VARIABLE) {
|
||||||
|
int ivariable = input->variable->find(ids[m]);
|
||||||
|
if (ivariable < 0)
|
||||||
|
error->all(FLERR,"Variable name for fix ave/atom does not exist");
|
||||||
|
value2index[m] = ivariable;
|
||||||
|
|
||||||
|
} else value2index[m] = -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// check that grid sizes for all fields match grid size for this fix
|
||||||
|
|
||||||
|
if (modegrid) {
|
||||||
|
Compute *icompute;
|
||||||
|
Fix *ifix;
|
||||||
|
Grid2d *grid2d;
|
||||||
|
Grid3d *grid3d;
|
||||||
|
|
||||||
|
int nxtmp,nytmp,nztmp;
|
||||||
|
|
||||||
|
for (int m = 0; m < nvalues; m++) {
|
||||||
|
if (dimension == 2) {
|
||||||
|
if (which[m] == ArgInfo::COMPUTE) {
|
||||||
|
icompute = modify->compute[value2index[m]];
|
||||||
|
grid2d = (Grid2d *) icompute->get_grid_by_index(value2grid[m]);
|
||||||
|
} else {
|
||||||
|
ifix = modify->fix[value2index[m]];
|
||||||
|
grid2d = (Grid2d *) ifix->get_grid_by_index(value2grid[m]);
|
||||||
|
}
|
||||||
|
grid2d->get_size(nxtmp,nytmp);
|
||||||
|
if (nxtmp != nx || nytmp != ny)
|
||||||
|
error->all(FLERR,"Fix ave/grid value grid sizes do not match");
|
||||||
|
|
||||||
|
} else {
|
||||||
|
if (which[m] == ArgInfo::COMPUTE) {
|
||||||
|
icompute = modify->compute[value2index[m]];
|
||||||
|
grid3d = (Grid3d *) icompute->get_grid_by_index(value2grid[m]);
|
||||||
|
} else {
|
||||||
|
ifix = modify->fix[value2index[m]];
|
||||||
|
grid3d = (Grid3d *) ifix->get_grid_by_index(value2grid[m]);
|
||||||
|
}
|
||||||
|
grid3d->get_size(nxtmp,nytmp,nztmp);
|
||||||
|
if (nxtmp != nx || nytmp != ny || nztmp != nz)
|
||||||
|
error->all(FLERR,"Fix ave/grid value grid sizes do not match");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
|
||||||
|
|
||||||
|
if (nvalid < update->ntimestep) {
|
||||||
|
irepeat = 0;
|
||||||
|
nvalid = nextvalid();
|
||||||
|
modify->addstep_compute_all(nvalid);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
only does something if nvalid = current timestep
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixAveGrid::setup(int /*vflag*/)
|
||||||
|
{
|
||||||
|
end_of_step();
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixAveGrid::end_of_step()
|
||||||
|
{
|
||||||
|
int i,j,m,n;
|
||||||
|
|
||||||
|
// skip if not step which requires doing something
|
||||||
|
|
||||||
|
bigint ntimestep = update->ntimestep;
|
||||||
|
if (ntimestep != nvalid) return;
|
||||||
|
nvalid_last = nvalid;
|
||||||
|
|
||||||
|
// zero if first step
|
||||||
|
|
||||||
|
/*
|
||||||
|
if (irepeat == 0)
|
||||||
|
for (i = 0; i < nlocal; i++)
|
||||||
|
for (m = 0; m < nvalues; m++)
|
||||||
|
array[i][m] = 0.0;
|
||||||
|
*/
|
||||||
|
|
||||||
|
// ATOM mode
|
||||||
|
// accumulate per-atom attributes,computes,fixes,variables to local grid
|
||||||
|
// compute/fix/variable may invoke computes so wrap with clear/add
|
||||||
|
|
||||||
|
/*
|
||||||
|
if (modeatom) {
|
||||||
|
modify->clearstep_compute();
|
||||||
|
|
||||||
|
int *mask = atom->mask;
|
||||||
|
|
||||||
|
for (m = 0; m < nvalues; m++) {
|
||||||
|
n = value2index[m];
|
||||||
|
j = argindex[m];
|
||||||
|
|
||||||
|
if (which[m] == ArgInfo::X) {
|
||||||
|
double **x = atom->x;
|
||||||
|
for (i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit) array[i][m] += x[i][j];
|
||||||
|
|
||||||
|
} else if (which[m] == ArgInfo::V) {
|
||||||
|
double **v = atom->v;
|
||||||
|
for (i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit) array[i][m] += v[i][j];
|
||||||
|
|
||||||
|
} else if (which[m] == ArgInfo::F) {
|
||||||
|
double **f = atom->f;
|
||||||
|
for (i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit) array[i][m] += f[i][j];
|
||||||
|
|
||||||
|
// invoke compute if not previously invoked
|
||||||
|
|
||||||
|
} else if (which[m] == ArgInfo::COMPUTE) {
|
||||||
|
Compute *compute = modify->compute[n];
|
||||||
|
if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
|
||||||
|
compute->compute_peratom();
|
||||||
|
compute->invoked_flag |= Compute::INVOKED_PERATOM;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (j == 0) {
|
||||||
|
double *compute_vector = compute->vector_atom;
|
||||||
|
for (i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit) array[i][m] += compute_vector[i];
|
||||||
|
} else {
|
||||||
|
int jm1 = j - 1;
|
||||||
|
double **compute_array = compute->array_atom;
|
||||||
|
for (i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit) array[i][m] += compute_array[i][jm1];
|
||||||
|
}
|
||||||
|
|
||||||
|
// access fix fields, guaranteed to be ready
|
||||||
|
|
||||||
|
} else if (which[m] == ArgInfo::FIX) {
|
||||||
|
if (j == 0) {
|
||||||
|
double *fix_vector = modify->fix[n]->vector_atom;
|
||||||
|
for (i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit) array[i][m] += fix_vector[i];
|
||||||
|
} else {
|
||||||
|
int jm1 = j - 1;
|
||||||
|
double **fix_array = modify->fix[n]->array_atom;
|
||||||
|
for (i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit) array[i][m] += fix_array[i][jm1];
|
||||||
|
}
|
||||||
|
|
||||||
|
// evaluate atom-style variable
|
||||||
|
// final argument = 1 sums result to array
|
||||||
|
|
||||||
|
} else if (which[m] == ArgInfo::VARIABLE) {
|
||||||
|
if (array) input->variable->compute_atom(n,igroup,&array[0][m],nvalues,1);
|
||||||
|
else input->variable->compute_atom(n,igroup,nullptr,nvalues,1);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
*/
|
||||||
|
|
||||||
|
// GRID mode
|
||||||
|
// accumulate results of computes & fixes to local grid
|
||||||
|
|
||||||
|
if (modegrid) {
|
||||||
|
}
|
||||||
|
|
||||||
|
// done if irepeat < nrepeat
|
||||||
|
// else reset irepeat and nvalid
|
||||||
|
|
||||||
|
irepeat++;
|
||||||
|
if (irepeat < nrepeat) {
|
||||||
|
nvalid += nevery;
|
||||||
|
modify->addstep_compute(nvalid);
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
irepeat = 0;
|
||||||
|
nvalid = ntimestep+peratom_freq - ((bigint)nrepeat-1)*nevery;
|
||||||
|
modify->addstep_compute(nvalid);
|
||||||
|
|
||||||
|
// if (array == nullptr) return;
|
||||||
|
|
||||||
|
|
||||||
|
//NOTE: need to do comm for atom mode ?
|
||||||
|
|
||||||
|
|
||||||
|
// average the final result for the Nfreq timestep
|
||||||
|
|
||||||
|
/*
|
||||||
|
double repeat = nrepeat;
|
||||||
|
for (i = 0; i < nlocal; i++)
|
||||||
|
for (m = 0; m < nvalues; m++)
|
||||||
|
array[i][m] /= repeat;
|
||||||
|
*/
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
return index of grid associated with name
|
||||||
|
this class can store M named grids, indexed 0 to M-1
|
||||||
|
also set dim for 2d vs 3d grid
|
||||||
|
return -1 if grid name not found
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
int FixAveGrid::get_grid_by_name(char *name, int &dim)
|
||||||
|
{
|
||||||
|
if (strcmp(name,"grid") == 0) {
|
||||||
|
dim = dimension;
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
return ptr to Grid data struct for grid with index
|
||||||
|
this class can store M named grids, indexed 0 to M-1
|
||||||
|
return nullptr if index is invalid
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void *FixAveGrid::get_grid_by_index(int index)
|
||||||
|
{
|
||||||
|
if (index == 0) {
|
||||||
|
if (dimension == 2) return grid2d;
|
||||||
|
else return grid3d;
|
||||||
|
}
|
||||||
|
return nullptr;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
return index of data associated with name in grid with index igrid
|
||||||
|
this class can store M named grids, indexed 0 to M-1
|
||||||
|
each grid can store G named data sets, indexed 0 to G-1
|
||||||
|
a data set name can be associated with multiple grids
|
||||||
|
set ncol for data set, 0 = vector, 1-N for array with N columns
|
||||||
|
vector = single value per grid pt, array = N values per grid pt
|
||||||
|
return -1 if data name not found
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
int FixAveGrid::get_griddata_by_name(int igrid, char *name, int &ncol)
|
||||||
|
{
|
||||||
|
if (igrid == 0 && strcmp(name,"data") == 0) {
|
||||||
|
if (nvalues == 1) ncol = 0;
|
||||||
|
else ncol = nvalues;
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
return ptr to multidim data array associated with index
|
||||||
|
this class can store G named data sets, indexed 0 to M-1
|
||||||
|
return nullptr if index is invalid
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void *FixAveGrid::get_griddata_by_index(int index)
|
||||||
|
{
|
||||||
|
if (index == 0) {
|
||||||
|
if (dimension == 2) {
|
||||||
|
if (nvalues == 1) return vec2d;
|
||||||
|
else return array2d;
|
||||||
|
} else {
|
||||||
|
if (nvalues == 1) return vec3d;
|
||||||
|
else return array3d;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return nullptr;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
memory usage of local atom-based array
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double FixAveGrid::memory_usage()
|
||||||
|
{
|
||||||
|
double bytes = (double) ngridout * nvalues * sizeof(double);
|
||||||
|
return bytes;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
calculate nvalid = next step on which end_of_step does something
|
||||||
|
can be this timestep if multiple of nfreq and nrepeat = 1
|
||||||
|
else backup from next multiple of nfreq
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
bigint FixAveGrid::nextvalid()
|
||||||
|
{
|
||||||
|
bigint nvalid = (update->ntimestep/peratom_freq)*peratom_freq + peratom_freq;
|
||||||
|
if (nvalid-peratom_freq == update->ntimestep && nrepeat == 1)
|
||||||
|
nvalid = update->ntimestep;
|
||||||
|
else
|
||||||
|
nvalid -= ((bigint)nrepeat-1)*nevery;
|
||||||
|
if (nvalid < update->ntimestep) nvalid += peratom_freq;
|
||||||
|
return nvalid;
|
||||||
|
}
|
||||||
70
src/fix_ave_grid.h
Normal file
70
src/fix_ave_grid.h
Normal file
@ -0,0 +1,70 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://www.lammps.org/, 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
|
||||||
|
// clang-format off
|
||||||
|
FixStyle(ave/grid,FixAveGrid);
|
||||||
|
// clang-format on
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_FIX_AVE_GRID_H
|
||||||
|
#define LMP_FIX_AVE_GRID_H
|
||||||
|
|
||||||
|
#include "fix.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class FixAveGrid : public Fix {
|
||||||
|
public:
|
||||||
|
FixAveGrid(class LAMMPS *, int, char **);
|
||||||
|
~FixAveGrid() override;
|
||||||
|
int setmask() override;
|
||||||
|
void init() override;
|
||||||
|
void setup(int) override;
|
||||||
|
void end_of_step() override;
|
||||||
|
int get_grid_by_name(char *, int &) override;
|
||||||
|
void *get_grid_by_index(int) override;
|
||||||
|
int get_griddata_by_name(int, char *, int &) override;
|
||||||
|
void *get_griddata_by_index(int) override;
|
||||||
|
double memory_usage() override;
|
||||||
|
|
||||||
|
private:
|
||||||
|
int nx,ny,nz;
|
||||||
|
int nvalues;
|
||||||
|
int nrepeat, irepeat;
|
||||||
|
bigint nvalid, nvalid_last;
|
||||||
|
int modeatom,modegrid;
|
||||||
|
int normflag,scaleflag,ave,nwindow;
|
||||||
|
int dimension;
|
||||||
|
|
||||||
|
int *which, *argindex;
|
||||||
|
char **ids;
|
||||||
|
int *value2index, *value2grid, *value2data;
|
||||||
|
|
||||||
|
class Grid2d *grid2d;
|
||||||
|
class Grid3d *grid3d;
|
||||||
|
|
||||||
|
int nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in;
|
||||||
|
int nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out;
|
||||||
|
int ngridout;
|
||||||
|
|
||||||
|
double **vec2d,***vec3d;
|
||||||
|
double ***array2d,****array3d;
|
||||||
|
|
||||||
|
bigint nextvalid();
|
||||||
|
};
|
||||||
|
|
||||||
|
} // namespace LAMMPS_NS
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
Reference in New Issue
Block a user