sync with current develop
This commit is contained in:
Steve Plimpton
@ -1,4 +1,3 @@
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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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@ -18,6 +17,7 @@
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#include "comm.h"
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#include "error.h"
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#include "memory.h"
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#include "read_data.h"
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#include "tokenizer.h"
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#include <cstring>
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@ -25,7 +25,7 @@
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using namespace LAMMPS_NS;
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using namespace FixConst;
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enum{MOLECULE,CHARGE,RMASS,IVEC,DVEC,IARRAY,DARRAY};
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enum { MOLECULE, CHARGE, RMASS, IVEC, DVEC, IARRAY, DARRAY };
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/* ---------------------------------------------------------------------- */
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@ -33,13 +33,13 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg),
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nvalue(0), styles(nullptr), index(nullptr), astyle(nullptr)
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{
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if (narg < 4) error->all(FLERR,"Illegal fix property/atom command");
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if (narg < 4) error->all(FLERR, "Illegal fix property/atom command");
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restart_peratom = 1;
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wd_section = 1;
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int iarg = 3;
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nvalue = narg-iarg;
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nvalue = narg - iarg;
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styles = new int[nvalue];
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cols = new int[nvalue];
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index = new int[nvalue];
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@ -52,34 +52,30 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
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values_peratom = 0;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"mol") == 0) {
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if (strcmp(arg[iarg], "mol") == 0) {
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if (atom->molecule_flag)
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error->all(FLERR,"Fix property/atom mol when atom_style "
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"already has molecule attribute");
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if (molecule_flag)
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error->all(FLERR,"Fix property/atom cannot specify mol twice");
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error->all(FLERR, "Fix property/atom mol when atom_style already has molecule attribute");
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if (molecule_flag) error->all(FLERR, "Fix property/atom cannot specify mol twice");
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styles[nvalue] = MOLECULE;
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cols[nvalue] = 0;
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atom->molecule_flag = molecule_flag = 1;
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values_peratom++;
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nvalue++;
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iarg++;
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} else if (strcmp(arg[iarg],"q") == 0) {
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} else if (strcmp(arg[iarg], "q") == 0) {
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if (atom->q_flag)
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error->all(FLERR,"Fix property/atom q when atom_style already has charge attribute");
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if (q_flag)
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error->all(FLERR,"Fix property/atom cannot specify q twice");
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error->all(FLERR, "Fix property/atom q when atom_style already has charge attribute");
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if (q_flag) error->all(FLERR, "Fix property/atom cannot specify q twice");
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styles[nvalue] = CHARGE;
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cols[nvalue] = 0;
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atom->q_flag = q_flag = 1;
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values_peratom++;
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nvalue++;
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iarg++;
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} else if (strcmp(arg[iarg],"rmass") == 0) {
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} else if (strcmp(arg[iarg], "rmass") == 0) {
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if (atom->rmass_flag)
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error->all(FLERR,"Fix property/atom rmass when atom_style already has rmass attribute");
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if (rmass_flag)
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error->all(FLERR,"Fix property/atom cannot specify rmass twice");
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error->all(FLERR, "Fix property/atom rmass when atom_style already has rmass attribute");
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if (rmass_flag) error->all(FLERR, "Fix property/atom cannot specify rmass twice");
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styles[nvalue] = RMASS;
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cols[nvalue] = 0;
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atom->rmass_flag = rmass_flag = 1;
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@ -87,45 +83,49 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
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nvalue++;
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iarg++;
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// custom atom vector
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// custom atom vector
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} else if (utils::strmatch(arg[iarg],"^i_")) {
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} else if (utils::strmatch(arg[iarg], "^i_")) {
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styles[nvalue] = IVEC;
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int flag,ncols;
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index[nvalue] = atom->find_custom(&arg[iarg][2],flag,ncols);
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if (index[nvalue] >= 0)
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error->all(FLERR,"Fix property/atom vector name already exists");
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index[nvalue] = atom->add_custom(&arg[iarg][2],0,0);
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int flag, ncols;
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index[nvalue] = atom->find_custom(&arg[iarg][2], flag, ncols);
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if (index[nvalue] >= 0) error->all(FLERR, "Fix property/atom vector name already exists");
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if (ReadData::is_data_section(id))
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error->all(FLERR, "Fix property/atom fix ID must not be a data file section name");
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index[nvalue] = atom->add_custom(&arg[iarg][2], 0, 0);
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cols[nvalue] = 0;
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values_peratom++;
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nvalue++;
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iarg++;
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} else if (utils::strmatch(arg[iarg],"^d_")) {
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} else if (utils::strmatch(arg[iarg], "^d_")) {
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styles[nvalue] = DVEC;
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int flag,ncols;
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index[nvalue] = atom->find_custom(&arg[iarg][2],flag,ncols);
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if (index[nvalue] >= 0)
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error->all(FLERR,"Fix property/atom vector name already exists");
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index[nvalue] = atom->add_custom(&arg[iarg][2],1,0);
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int flag, ncols;
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index[nvalue] = atom->find_custom(&arg[iarg][2], flag, ncols);
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if (index[nvalue] >= 0) error->all(FLERR, "Fix property/atom vector name already exists");
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if (ReadData::is_data_section(id))
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error->all(FLERR, "Fix property/atom fix ID must not be a data file section name");
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index[nvalue] = atom->add_custom(&arg[iarg][2], 1, 0);
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cols[nvalue] = 0;
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values_peratom++;
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nvalue++;
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iarg++;
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// custom atom array
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// custom atom array
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} else if (utils::strmatch(arg[iarg],"^[id]2_")) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix property/atom command");
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} else if (utils::strmatch(arg[iarg], "^[id]2_")) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal fix property/atom command");
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int which,flag,ncols;
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which = atom->find_custom(&arg[iarg][3],flag,ncols);
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int which, flag, ncols;
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which = atom->find_custom(&arg[iarg][3], flag, ncols);
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if (which >= 0)
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error->all(FLERR,"Fix property/atom array name {} already exists", &arg[iarg][3]);
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error->all(FLERR, "Fix property/atom array name {} already exists", &arg[iarg][3]);
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if (ReadData::is_data_section(id))
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error->all(FLERR, "Fix property/atom fix ID must not be a data file section name");
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ncols = utils::inumeric(FLERR,arg[iarg+1],true,lmp);
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ncols = utils::inumeric(FLERR, arg[iarg + 1], true, lmp);
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if (ncols < 1)
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error->all(FLERR,"Invalid array columns number {} in fix property/atom", ncols);
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error->all(FLERR, "Invalid array columns number {} in fix property/atom", ncols);
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if (arg[iarg][0] == 'i') {
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which = 0;
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@ -134,28 +134,28 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
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which = 1;
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styles[nvalue] = DARRAY;
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}
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index[nvalue] = atom->add_custom(&arg[iarg][3],which,ncols);
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index[nvalue] = atom->add_custom(&arg[iarg][3], which, ncols);
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cols[nvalue] = ncols;
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values_peratom += ncols;
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nvalue++;
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iarg += 2;
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// no match
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// no match
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} else break;
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} else
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break;
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}
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// optional args
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border = 0;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"ghost") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix property/atom command");
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if (strcmp(arg[iarg+1],"no") == 0) border = 0;
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else if (strcmp(arg[iarg+1],"yes") == 0) border = 1;
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else error->all(FLERR,"Illegal fix property/atom command");
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if (strcmp(arg[iarg], "ghost") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal fix property/atom command");
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border = utils::logical(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else error->all(FLERR,"Illegal fix property/atom command");
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} else
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error->all(FLERR, "Illegal fix property/atom command");
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}
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if (border) comm_border = values_peratom;
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@ -165,11 +165,9 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
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if (border == 0) {
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int flag = 0;
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for (int i = 0; i < nvalue; i++)
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if (styles[i] == MOLECULE || styles[i] == CHARGE || styles[i] == RMASS)
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flag = 1;
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if (styles[i] == MOLECULE || styles[i] == CHARGE || styles[i] == RMASS) flag = 1;
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if (flag && comm->me == 0)
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error->warning(FLERR,"Fix property/atom mol or charge or rmass "
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"w/out ghost communication");
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error->warning(FLERR, "Fix property/atom mol or charge or rmass w/out ghost communication");
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}
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// store current atom style
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@ -180,7 +178,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
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// register with Atom class
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nmax_old = 0;
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if (!lmp->kokkos) grow_arrays(atom->nmax);
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if (!lmp->kokkos) FixPropertyAtom::grow_arrays(atom->nmax);
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atom->add_callback(Atom::GROW);
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atom->add_callback(Atom::RESTART);
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if (border) atom->add_callback(Atom::BORDER);
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@ -192,9 +190,9 @@ FixPropertyAtom::~FixPropertyAtom()
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{
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// unregister callbacks to this fix from Atom class
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atom->delete_callback(id,Atom::GROW);
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atom->delete_callback(id,Atom::RESTART);
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if (border) atom->delete_callback(id,Atom::BORDER);
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atom->delete_callback(id, Atom::GROW);
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atom->delete_callback(id, Atom::RESTART);
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if (border) atom->delete_callback(id, Atom::BORDER);
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// deallocate per-atom vectors in Atom class
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// set ptrs to a null pointer, so they no longer exist for Atom class
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@ -213,20 +211,20 @@ FixPropertyAtom::~FixPropertyAtom()
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memory->destroy(atom->rmass);
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atom->rmass = nullptr;
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} else if (styles[nv] == IVEC) {
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atom->remove_custom(index[nv],0,cols[nv]);
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atom->remove_custom(index[nv], 0, cols[nv]);
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} else if (styles[nv] == DVEC) {
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atom->remove_custom(index[nv],1,cols[nv]);
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atom->remove_custom(index[nv], 1, cols[nv]);
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} else if (styles[nv] == IARRAY) {
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atom->remove_custom(index[nv],0,cols[nv]);
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atom->remove_custom(index[nv], 0, cols[nv]);
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} else if (styles[nv] == DARRAY) {
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atom->remove_custom(index[nv],1,cols[nv]);
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atom->remove_custom(index[nv], 1, cols[nv]);
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}
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}
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delete [] styles;
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delete [] cols;
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delete [] index;
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delete [] astyle;
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delete[] styles;
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delete[] cols;
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delete[] index;
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delete[] astyle;
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}
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/* ---------------------------------------------------------------------- */
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@ -244,8 +242,8 @@ void FixPropertyAtom::init()
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// error if atom style has changed since fix was defined
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// don't allow this because user could change to style that defines molecule,q
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if (strcmp(astyle,atom->atom_style) != 0)
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error->all(FLERR,"Atom style was redefined after using fix property/atom");
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if (strcmp(astyle, atom->atom_style) != 0)
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error->all(FLERR, "Atom style was redefined after using fix property/atom");
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}
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/* ----------------------------------------------------------------------
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@ -255,7 +253,7 @@ void FixPropertyAtom::init()
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void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint id_offset)
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{
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int j,k,m,ncol;
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int j, k, m, ncol;
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tagint itag;
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char *next;
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@ -273,18 +271,18 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint
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tagint map_tag_max = atom->map_tag_max;
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for (int i = 0; i < n; i++) {
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next = strchr(buf,'\n');
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next = strchr(buf, '\n');
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*next = '\0';
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try {
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ValueTokenizer values(buf);
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if ((int)values.count() != values_peratom+1)
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error->all(FLERR,"Incorrect format in {} section of data file: {}"
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" expected {} and got {}",keyword,buf,values_peratom+1,values.count());
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if ((int) values.count() != values_peratom + 1)
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error->all(FLERR, "Incorrect format in {} section of data file: {} expected {} and got {}",
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keyword, buf, values_peratom + 1, values.count());
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itag = values.next_tagint() + id_offset;
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if (itag <= 0 || itag > map_tag_max)
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error->all(FLERR,"Invalid atom ID {} in {} section of data file",itag, keyword);
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error->all(FLERR, "Invalid atom ID {} in {} section of data file", itag, keyword);
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// assign words in line to per-atom vectors
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@ -306,13 +304,14 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint
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atom->iarray[index[j]][m][k] = values.next_int();
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} else if (styles[j] == DARRAY) {
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ncol = cols[j];
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for (k = 0; k < ncol; k++)
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for (k = 0; k < ncol; k++)
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atom->darray[index[j]][m][k] = values.next_double();
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}
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}
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}
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} catch (TokenizerException &e) {
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error->all(FLERR,"Invalid format in {} section of data file '{}': {}",keyword, buf,e.what());
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error->all(FLERR, "Invalid format in {} section of data file '{}': {}", keyword, buf,
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e.what());
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}
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buf = next + 1;
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}
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@ -352,7 +351,7 @@ void FixPropertyAtom::write_data_section_size(int /*mth*/, int &nx, int &ny)
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void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf)
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{
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int i,k,ncol;
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int i, k, ncol;
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// 1st column = atom tag
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// rest of columns = per-atom values
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@ -388,15 +387,13 @@ void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf)
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int **iarray = atom->iarray[index[nv]];
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ncol = cols[nv];
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for (i = 0; i < nlocal; i++)
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for (k = 0; k < ncol; k++)
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buf[i][icol+k] = ubuf(iarray[i][k]).d;
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for (k = 0; k < ncol; k++) buf[i][icol + k] = ubuf(iarray[i][k]).d;
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icol += ncol;
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} else if (styles[nv] == DARRAY) {
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double **darray = atom->darray[index[nv]];
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ncol = cols[nv];
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for (i = 0; i < nlocal; i++)
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for (k = 0; k < ncol; k++)
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buf[i][icol+k] = darray[i][k];
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for (k = 0; k < ncol; k++) buf[i][icol + k] = darray[i][k];
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icol += ncol;
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}
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}
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@ -411,21 +408,30 @@ void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf)
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void FixPropertyAtom::write_data_section_keyword(int /*mth*/, FILE *fp)
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{
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if (nvalue == 1 && styles[0] == MOLECULE) fprintf(fp,"\nMolecules\n\n");
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else if (nvalue == 1 && styles[0] == CHARGE) fprintf(fp,"\nCharges\n\n");
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if (nvalue == 1 && styles[0] == MOLECULE)
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fprintf(fp, "\nMolecules\n\n");
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else if (nvalue == 1 && styles[0] == CHARGE)
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fprintf(fp, "\nCharges\n\n");
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else {
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fprintf(fp,"\n%s #",id);
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fprintf(fp, "\n%s #", id);
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// write column hint as comment
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for (int i = 0; i < nvalue; ++i) {
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if (styles[i] == MOLECULE) fputs(" mol",fp);
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else if (styles[i] == CHARGE) fputs(" q",fp);
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else if (styles[i] == RMASS) fputs(" rmass",fp);
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else if (styles[i] == IVEC) fprintf(fp," i_%s", atom->ivname[index[i]]);
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else if (styles[i] == DVEC) fprintf(fp, " d_%s", atom->dvname[index[i]]);
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else if (styles[i] == IARRAY) fprintf(fp, " i_%s", atom->ianame[index[i]]);
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else if (styles[i] == DARRAY) fprintf(fp, " d_%s", atom->daname[index[i]]);
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if (styles[i] == MOLECULE)
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fputs(" mol", fp);
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else if (styles[i] == CHARGE)
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fputs(" q", fp);
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else if (styles[i] == RMASS)
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fputs(" rmass", fp);
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else if (styles[i] == IVEC)
|
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fprintf(fp, " i_%s", atom->ivname[index[i]]);
|
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else if (styles[i] == DVEC)
|
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fprintf(fp, " d_%s", atom->dvname[index[i]]);
|
||||
else if (styles[i] == IARRAY)
|
||||
fprintf(fp, " i_%s", atom->ianame[index[i]]);
|
||||
else if (styles[i] == DARRAY)
|
||||
fprintf(fp, " d_%s", atom->daname[index[i]]);
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||||
}
|
||||
fputs("\n\n",fp);
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fputs("\n\n", fp);
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||||
}
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||||
}
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||||
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||||
@ -436,38 +442,36 @@ void FixPropertyAtom::write_data_section_keyword(int /*mth*/, FILE *fp)
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only called by proc 0
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------------------------------------------------------------------------- */
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|
||||
void FixPropertyAtom::write_data_section(int /*mth*/, FILE *fp,
|
||||
int n, double **buf, int /*index*/)
|
||||
void FixPropertyAtom::write_data_section(int /*mth*/, FILE *fp, int n, double **buf, int /*index*/)
|
||||
{
|
||||
int k,icol,ncol,nv;
|
||||
int k, icol, ncol, nv;
|
||||
std::string line;
|
||||
|
||||
for (int i = 0; i < n; i++) {
|
||||
fprintf(fp,TAGINT_FORMAT,(tagint) ubuf(buf[i][0]).i);
|
||||
line = fmt::format("{}", (tagint) ubuf(buf[i][0]).i);
|
||||
icol = 1;
|
||||
for (nv = 0; nv < nvalue; nv++) {
|
||||
if (styles[nv] == MOLECULE)
|
||||
fprintf(fp," " TAGINT_FORMAT,(tagint) ubuf(buf[i][icol++]).i);
|
||||
line += fmt::format(" {}", (tagint) ubuf(buf[i][icol++]).i);
|
||||
else if (styles[nv] == CHARGE)
|
||||
fprintf(fp," %g",buf[i][icol++]);
|
||||
line += fmt::format(" {}", buf[i][icol++]);
|
||||
else if (styles[nv] == RMASS)
|
||||
fprintf(fp," %g",buf[i][icol++]);
|
||||
line += fmt::format(" {}", buf[i][icol++]);
|
||||
else if (styles[nv] == IVEC)
|
||||
fprintf(fp," %d",(int) ubuf(buf[i][icol++]).i);
|
||||
line += fmt::format(" {}", (int) ubuf(buf[i][icol++]).i);
|
||||
else if (styles[nv] == DVEC)
|
||||
fprintf(fp," %g",buf[i][icol++]);
|
||||
line += fmt::format(" {}", buf[i][icol++]);
|
||||
else if (styles[nv] == IARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
fprintf(fp," %d",(int) ubuf(buf[i][icol+k]).i);
|
||||
for (k = 0; k < ncol; k++) line += fmt::format(" {}", (int) ubuf(buf[i][icol + k]).i);
|
||||
icol += ncol;
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
fprintf(fp," %g",buf[i][icol+k]);
|
||||
for (k = 0; k < ncol; k++) line += fmt::format(" {}", buf[i][icol + k]);
|
||||
icol += ncol;
|
||||
}
|
||||
}
|
||||
fprintf(fp,"\n");
|
||||
fmt::print(fp, line + "\n");
|
||||
}
|
||||
}
|
||||
|
||||
@ -479,13 +483,20 @@ double FixPropertyAtom::memory_usage()
|
||||
{
|
||||
double bytes = 0.0;
|
||||
for (int m = 0; m < nvalue; m++) {
|
||||
if (styles[m] == MOLECULE) bytes = atom->nmax * sizeof(tagint);
|
||||
else if (styles[m] == CHARGE) bytes = atom->nmax * sizeof(double);
|
||||
else if (styles[m] == RMASS) bytes = atom->nmax * sizeof(double);
|
||||
else if (styles[m] == IVEC) bytes = atom->nmax * sizeof(int);
|
||||
else if (styles[m] == DVEC) bytes = atom->nmax * sizeof(double);
|
||||
else if (styles[m] == IARRAY) bytes = atom->nmax * cols[m] * sizeof(int);
|
||||
else if (styles[m] == DARRAY) bytes = atom->nmax * cols[m] * sizeof(double);
|
||||
if (styles[m] == MOLECULE)
|
||||
bytes = atom->nmax * sizeof(tagint);
|
||||
else if (styles[m] == CHARGE)
|
||||
bytes = atom->nmax * sizeof(double);
|
||||
else if (styles[m] == RMASS)
|
||||
bytes = atom->nmax * sizeof(double);
|
||||
else if (styles[m] == IVEC)
|
||||
bytes = atom->nmax * sizeof(int);
|
||||
else if (styles[m] == DVEC)
|
||||
bytes = atom->nmax * sizeof(double);
|
||||
else if (styles[m] == IARRAY)
|
||||
bytes = (size_t) atom->nmax * cols[m] * sizeof(int);
|
||||
else if (styles[m] == DARRAY)
|
||||
bytes = (size_t) atom->nmax * cols[m] * sizeof(double);
|
||||
}
|
||||
return bytes;
|
||||
}
|
||||
@ -501,33 +512,33 @@ void FixPropertyAtom::grow_arrays(int nmax)
|
||||
{
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (styles[nv] == MOLECULE) {
|
||||
memory->grow(atom->molecule,nmax,"atom:molecule");
|
||||
size_t nbytes = (nmax-nmax_old) * sizeof(tagint);
|
||||
memset(&atom->molecule[nmax_old],0,nbytes);
|
||||
memory->grow(atom->molecule, nmax, "atom:molecule");
|
||||
size_t nbytes = (nmax - nmax_old) * sizeof(tagint);
|
||||
memset(&atom->molecule[nmax_old], 0, nbytes);
|
||||
} else if (styles[nv] == CHARGE) {
|
||||
memory->grow(atom->q,nmax,"atom:q");
|
||||
size_t nbytes = (nmax-nmax_old) * sizeof(double);
|
||||
memset(&atom->q[nmax_old],0,nbytes);
|
||||
memory->grow(atom->q, nmax, "atom:q");
|
||||
size_t nbytes = (nmax - nmax_old) * sizeof(double);
|
||||
memset(&atom->q[nmax_old], 0, nbytes);
|
||||
} else if (styles[nv] == RMASS) {
|
||||
memory->grow(atom->rmass,nmax,"atom:rmass");
|
||||
size_t nbytes = (nmax-nmax_old) * sizeof(double);
|
||||
memset(&atom->rmass[nmax_old],0,nbytes);
|
||||
memory->grow(atom->rmass, nmax, "atom:rmass");
|
||||
size_t nbytes = (nmax - nmax_old) * sizeof(double);
|
||||
memset(&atom->rmass[nmax_old], 0, nbytes);
|
||||
} else if (styles[nv] == IVEC) {
|
||||
memory->grow(atom->ivector[index[nv]],nmax,"atom:ivector");
|
||||
size_t nbytes = (nmax-nmax_old) * sizeof(int);
|
||||
memset(&atom->ivector[index[nv]][nmax_old],0,nbytes);
|
||||
memory->grow(atom->ivector[index[nv]], nmax, "atom:ivector");
|
||||
size_t nbytes = (nmax - nmax_old) * sizeof(int);
|
||||
memset(&atom->ivector[index[nv]][nmax_old], 0, nbytes);
|
||||
} else if (styles[nv] == DVEC) {
|
||||
memory->grow(atom->dvector[index[nv]],nmax,"atom:dvector");
|
||||
size_t nbytes = (nmax-nmax_old) * sizeof(double);
|
||||
memset(&atom->dvector[index[nv]][nmax_old],0,nbytes);
|
||||
memory->grow(atom->dvector[index[nv]], nmax, "atom:dvector");
|
||||
size_t nbytes = (nmax - nmax_old) * sizeof(double);
|
||||
memset(&atom->dvector[index[nv]][nmax_old], 0, nbytes);
|
||||
} else if (styles[nv] == IARRAY) {
|
||||
memory->grow(atom->iarray[index[nv]],nmax,cols[nv],"atom:iarray");
|
||||
size_t nbytes = (nmax-nmax_old) * cols[nv] * sizeof(int);
|
||||
if (nbytes) memset(&atom->iarray[index[nv]][nmax_old][0],0,nbytes);
|
||||
memory->grow(atom->iarray[index[nv]], nmax, cols[nv], "atom:iarray");
|
||||
size_t nbytes = (size_t) (nmax - nmax_old) * cols[nv] * sizeof(int);
|
||||
if (nbytes) memset(&atom->iarray[index[nv]][nmax_old][0], 0, nbytes);
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
memory->grow(atom->darray[index[nv]],nmax,cols[nv],"atom:darray");
|
||||
size_t nbytes = (nmax-nmax_old) * cols[nv] * sizeof(double);
|
||||
if (nbytes) memset(&atom->darray[index[nv]][nmax_old][0],0,nbytes);
|
||||
memory->grow(atom->darray[index[nv]], nmax, cols[nv], "atom:darray");
|
||||
size_t nbytes = (size_t) (nmax - nmax_old) * cols[nv] * sizeof(double);
|
||||
if (nbytes) memset(&atom->darray[index[nv]][nmax_old][0], 0, nbytes);
|
||||
}
|
||||
}
|
||||
|
||||
@ -540,7 +551,7 @@ void FixPropertyAtom::grow_arrays(int nmax)
|
||||
|
||||
void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/)
|
||||
{
|
||||
int k,ncol;
|
||||
int k, ncol;
|
||||
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (styles[nv] == MOLECULE)
|
||||
@ -559,7 +570,7 @@ void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/)
|
||||
atom->iarray[index[nv]][j][k] = atom->iarray[index[nv]][i][k];
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
for (k = 0; k < ncol; k++)
|
||||
atom->darray[index[nv]][j][k] = atom->darray[index[nv]][i][k];
|
||||
}
|
||||
}
|
||||
@ -571,7 +582,7 @@ void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/)
|
||||
|
||||
int FixPropertyAtom::pack_border(int n, int *list, double *buf)
|
||||
{
|
||||
int i,j,k,ncol;
|
||||
int i, j, k, ncol;
|
||||
|
||||
int m = 0;
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
@ -610,16 +621,14 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf)
|
||||
ncol = cols[nv];
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[m++] = ubuf(iarray[j][k]).d;
|
||||
for (k = 0; k < ncol; k++) buf[m++] = ubuf(iarray[j][k]).d;
|
||||
}
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
double **darray = atom->darray[index[nv]];
|
||||
ncol = cols[nv];
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[m++] = darray[j][k];
|
||||
for (k = 0; k < ncol; k++) buf[m++] = darray[j][k];
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -633,35 +642,30 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf)
|
||||
|
||||
int FixPropertyAtom::unpack_border(int n, int first, double *buf)
|
||||
{
|
||||
int i,k,last,ncol;
|
||||
int i, k, last, ncol;
|
||||
|
||||
int m = 0;
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (styles[nv] == MOLECULE) {
|
||||
tagint *molecule = atom->molecule;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
molecule[i] = (tagint) ubuf(buf[m++]).i;
|
||||
for (i = first; i < last; i++) molecule[i] = (tagint) ubuf(buf[m++]).i;
|
||||
} else if (styles[nv] == CHARGE) {
|
||||
double *q = atom->q;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
q[i] = buf[m++];
|
||||
for (i = first; i < last; i++) q[i] = buf[m++];
|
||||
} else if (styles[nv] == RMASS) {
|
||||
double *rmass = atom->rmass;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
rmass[i] = buf[m++];
|
||||
for (i = first; i < last; i++) rmass[i] = buf[m++];
|
||||
} else if (styles[nv] == IVEC) {
|
||||
int *ivector = atom->ivector[index[nv]];
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
ivector[i] = (int) ubuf(buf[m++]).i;
|
||||
for (i = first; i < last; i++) ivector[i] = (int) ubuf(buf[m++]).i;
|
||||
} else if (styles[nv] == DVEC) {
|
||||
double *dvector = atom->dvector[index[nv]];
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
dvector[i] = buf[m++];
|
||||
for (i = first; i < last; i++) dvector[i] = buf[m++];
|
||||
} else if (styles[nv] == IARRAY) {
|
||||
int **iarray = atom->iarray[index[nv]];
|
||||
ncol = cols[nv];
|
||||
@ -674,8 +678,7 @@ int FixPropertyAtom::unpack_border(int n, int first, double *buf)
|
||||
ncol = cols[nv];
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
for (k = 0; k < ncol; k++)
|
||||
darray[i][k] = buf[m++];
|
||||
for (k = 0; k < ncol; k++) darray[i][k] = buf[m++];
|
||||
}
|
||||
}
|
||||
|
||||
@ -688,23 +691,26 @@ int FixPropertyAtom::unpack_border(int n, int first, double *buf)
|
||||
|
||||
int FixPropertyAtom::pack_exchange(int i, double *buf)
|
||||
{
|
||||
int k,ncol;
|
||||
int k, ncol;
|
||||
|
||||
int m = 0;
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (styles[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
|
||||
else if (styles[nv] == CHARGE) buf[m++] = atom->q[i];
|
||||
else if (styles[nv] == RMASS) buf[m++] = atom->rmass[i];
|
||||
else if (styles[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
|
||||
else if (styles[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i];
|
||||
if (styles[nv] == MOLECULE)
|
||||
buf[m++] = ubuf(atom->molecule[i]).d;
|
||||
else if (styles[nv] == CHARGE)
|
||||
buf[m++] = atom->q[i];
|
||||
else if (styles[nv] == RMASS)
|
||||
buf[m++] = atom->rmass[i];
|
||||
else if (styles[nv] == IVEC)
|
||||
buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
|
||||
else if (styles[nv] == DVEC)
|
||||
buf[m++] = atom->dvector[index[nv]][i];
|
||||
else if (styles[nv] == IARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[m++] = ubuf(atom->iarray[index[nv]][i][k]).d;
|
||||
for (k = 0; k < ncol; k++) buf[m++] = ubuf(atom->iarray[index[nv]][i][k]).d;
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[m++] = atom->darray[index[nv]][i][k];
|
||||
for (k = 0; k < ncol; k++) buf[m++] = atom->darray[index[nv]][i][k];
|
||||
}
|
||||
}
|
||||
|
||||
@ -717,7 +723,7 @@ int FixPropertyAtom::pack_exchange(int i, double *buf)
|
||||
|
||||
int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
|
||||
{
|
||||
int k,ncol;
|
||||
int k, ncol;
|
||||
|
||||
int m = 0;
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
@ -737,8 +743,7 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
|
||||
atom->iarray[index[nv]][nlocal][k] = (int) ubuf(buf[m++]).i;
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
atom->darray[index[nv]][nlocal][k] = buf[m++];
|
||||
for (k = 0; k < ncol; k++) atom->darray[index[nv]][nlocal][k] = buf[m++];
|
||||
}
|
||||
}
|
||||
|
||||
@ -751,31 +756,36 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
|
||||
|
||||
int FixPropertyAtom::pack_restart(int i, double *buf)
|
||||
{
|
||||
int k,ncol;
|
||||
int k, ncol;
|
||||
|
||||
// pack buf[0] this way because other fixes unpack it
|
||||
|
||||
buf[0] = values_peratom+1;
|
||||
buf[0] = values_peratom + 1;
|
||||
|
||||
int m = 1;
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (styles[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
|
||||
else if (styles[nv] == CHARGE) buf[m++] = atom->q[i];
|
||||
else if (styles[nv] == RMASS) buf[m++] = atom->rmass[i];
|
||||
else if (styles[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
|
||||
else if (styles[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i];
|
||||
if (styles[nv] == MOLECULE)
|
||||
buf[m++] = ubuf(atom->molecule[i]).d;
|
||||
else if (styles[nv] == CHARGE)
|
||||
buf[m++] = atom->q[i];
|
||||
else if (styles[nv] == RMASS)
|
||||
buf[m++] = atom->rmass[i];
|
||||
else if (styles[nv] == IVEC)
|
||||
buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
|
||||
else if (styles[nv] == DVEC)
|
||||
buf[m++] = atom->dvector[index[nv]][i];
|
||||
else if (styles[nv] == IARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[m++] = ubuf(atom->iarray[index[nv]][i][k]).d;
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[m++] = atom->darray[index[nv]][i][k];
|
||||
}
|
||||
}
|
||||
|
||||
return values_peratom+1;
|
||||
return values_peratom + 1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -784,14 +794,14 @@ int FixPropertyAtom::pack_restart(int i, double *buf)
|
||||
|
||||
void FixPropertyAtom::unpack_restart(int nlocal, int nth)
|
||||
{
|
||||
int k,ncol;
|
||||
int k, ncol;
|
||||
double **extra = atom->extra;
|
||||
|
||||
// skip to Nth set of extra values
|
||||
// unpack the Nth first values this way because other fixes pack them
|
||||
|
||||
int m = 0;
|
||||
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
|
||||
for (int i = 0; i < nth; i++) m += static_cast<int>(extra[nlocal][m]);
|
||||
m++;
|
||||
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
@ -811,8 +821,7 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
|
||||
atom->iarray[index[nv]][nlocal][k] = (int) ubuf(extra[nlocal][m++]).i;
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
atom->darray[index[nv]][nlocal][k] = extra[nlocal][m++];
|
||||
for (k = 0; k < ncol; k++) atom->darray[index[nv]][nlocal][k] = extra[nlocal][m++];
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -823,7 +832,7 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
|
||||
|
||||
int FixPropertyAtom::maxsize_restart()
|
||||
{
|
||||
return values_peratom+1;
|
||||
return values_peratom + 1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -832,5 +841,5 @@ int FixPropertyAtom::maxsize_restart()
|
||||
|
||||
int FixPropertyAtom::size_restart(int /*nlocal*/)
|
||||
{
|
||||
return values_peratom+1;
|
||||
return values_peratom + 1;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user