git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3562 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
671
src/compute_property_local.cpp
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671
src/compute_property_local.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "compute_property_local.h"
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#include "atom.h"
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#include "update.h"
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#include "force.h"
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#include "domain.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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// customize by adding keyword
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// same list as in dump_custom.cpp
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enum{ID,MOL,TYPE,MASS,
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X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,IX,IY,IZ,
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VX,VY,VZ,FX,FY,FZ,
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Q,MUX,MUY,MUZ,RADIUS,OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
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QUATW,QUATI,QUATJ,QUATK,TQX,TQY,TQZ};
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enum{NONE,BOND,ANGLE,DIHEDRAL,IMPROPER};
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#define DELTA 10000
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/* ---------------------------------------------------------------------- */
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ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg < 4) error->all("Illegal compute property/atom command");
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local_flag = 1;
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nvalues = narg - 3;
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if (nvalues == 1) size_local_cols = 0;
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else size_local_cols = nvalues;
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pack_choice = new FnPtrPack[nvalues];
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kindflag = NONE;
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int i;
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for (int iarg = 3; iarg < narg; iarg++) {
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i = iarg-3;
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if (strcmp(arg[iarg],"batom1") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_batom1;
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if (kindflag != NONE && kindflag != BOND)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = BOND;
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} else if (strcmp(arg[iarg],"batom2") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_batom2;
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if (kindflag != NONE && kindflag != BOND)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = BOND;
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} else if (strcmp(arg[iarg],"btype") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_btype;
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if (kindflag != NONE && kindflag != BOND)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = BOND;
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} else if (strcmp(arg[iarg],"aatom1") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_aatom1;
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if (kindflag != NONE && kindflag != ANGLE)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = ANGLE;
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} else if (strcmp(arg[iarg],"aatom2") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_aatom2;
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if (kindflag != NONE && kindflag != ANGLE)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = ANGLE;
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} else if (strcmp(arg[iarg],"aatom3") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_aatom3;
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if (kindflag != NONE && kindflag != ANGLE)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = ANGLE;
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} else if (strcmp(arg[iarg],"atype") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_atype;
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if (kindflag != NONE && kindflag != ANGLE)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = ANGLE;
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} else if (strcmp(arg[iarg],"datom1") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_datom1;
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if (kindflag != NONE && kindflag != DIHEDRAL)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = DIHEDRAL;
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} else if (strcmp(arg[iarg],"datom2") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_datom2;
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if (kindflag != NONE && kindflag != DIHEDRAL)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = DIHEDRAL;
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} else if (strcmp(arg[iarg],"datom3") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_datom3;
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if (kindflag != NONE && kindflag != DIHEDRAL)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = DIHEDRAL;
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} else if (strcmp(arg[iarg],"datom4") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_datom3;
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if (kindflag != NONE && kindflag != DIHEDRAL)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = DIHEDRAL;
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} else if (strcmp(arg[iarg],"dtype") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_dtype;
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if (kindflag != NONE && kindflag != DIHEDRAL)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = DIHEDRAL;
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} else if (strcmp(arg[iarg],"iatom1") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_iatom1;
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if (kindflag != NONE && kindflag != IMPROPER)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = IMPROPER;
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} else if (strcmp(arg[iarg],"iatom2") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_iatom2;
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if (kindflag != NONE && kindflag != IMPROPER)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = IMPROPER;
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} else if (strcmp(arg[iarg],"iatom3") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_iatom3;
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if (kindflag != NONE && kindflag != IMPROPER)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = IMPROPER;
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} else if (strcmp(arg[iarg],"iatom4") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_iatom3;
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if (kindflag != NONE && kindflag != IMPROPER)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = IMPROPER;
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} else if (strcmp(arg[iarg],"itype") == 0) {
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pack_choice[i] = &ComputePropertyLocal::pack_itype;
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if (kindflag != NONE && kindflag != IMPROPER)
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error->all("Compute property/local cannot use these inputs together");
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kindflag = IMPROPER;
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} else error->all("Invalid keyword in compute property/local command");
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}
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nmax = 0;
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vector = NULL;
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array = NULL;
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indices = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputePropertyLocal::~ComputePropertyLocal()
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{
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delete [] pack_choice;
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memory->sfree(vector);
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memory->destroy_2d_double_array(array);
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memory->destroy_2d_int_array(indices);
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyLocal::init()
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{
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// do initial memory allocation so that memory_usage() is correct
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if (kindflag == BOND) ncount = count_bonds(0);
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else if (kindflag == ANGLE) ncount = count_angles(0);
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else if (kindflag == DIHEDRAL) ncount = count_dihedrals(0);
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else if (kindflag == IMPROPER) ncount = count_impropers(0);
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if (ncount > nmax) reallocate(ncount);
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}
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/* ---------------------------------------------------------------------- */
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void ComputePropertyLocal::compute_local()
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{
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invoked_local = update->ntimestep;
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// count local entries and generate list of indices
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if (kindflag == BOND) ncount = count_bonds(0);
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else if (kindflag == ANGLE) ncount = count_angles(0);
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else if (kindflag == DIHEDRAL) ncount = count_dihedrals(0);
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else if (kindflag == IMPROPER) ncount = count_impropers(0);
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if (ncount > nmax) reallocate(ncount);
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if (kindflag == BOND) ncount = count_bonds(1);
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else if (kindflag == ANGLE) ncount = count_angles(1);
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else if (kindflag == DIHEDRAL) ncount = count_dihedrals(1);
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else if (kindflag == IMPROPER) ncount = count_impropers(1);
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// fill vector or array with local values
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if (nvalues == 1) {
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buf = vector;
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(this->*pack_choice[0])(0);
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} else {
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buf = array[0];
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for (int n = 0; n < nvalues; n++)
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(this->*pack_choice[n])(n);
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}
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}
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/* ----------------------------------------------------------------------
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count bonds on this proc
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only count bond once if newton_bond is off
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all atoms in interaction must be in group
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all atoms in interaction must be known to proc
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if bond is deleted (type = 0), do not count
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if bond is turned off (type < 0), still count
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------------------------------------------------------------------------- */
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int ComputePropertyLocal::count_bonds(int flag)
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{
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int *num_bond = atom->num_bond;
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int **bond_atom = atom->bond_atom;
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int **bond_type = atom->bond_type;
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int *tag = atom->tag;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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int i,atom1,atom2;
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int m = 0;
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for (atom1 = 0; atom1 < nlocal; atom1++) {
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if (!(mask[atom1] & groupbit)) continue;
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for (i = 0; i < num_bond[atom1]; i++) {
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atom2 = atom->map(bond_atom[atom1][i]);
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if (atom2 < 0 || !(mask[atom2] & groupbit)) continue;
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if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
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if (bond_type[atom1][i] == 0) continue;
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if (flag) {
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indices[m][0] = atom1;
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indices[m][1] = i;
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}
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m++;
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}
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}
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return m;
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}
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/* ----------------------------------------------------------------------
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count angles on this proc
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only count if 2nd atom is the one storing the angle
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all atoms in interaction must be in group
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all atoms in interaction must be known to proc
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------------------------------------------------------------------------- */
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int ComputePropertyLocal::count_angles(int flag)
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{
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int *num_angle = atom->num_angle;
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int **angle_atom1 = atom->angle_atom1;
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int **angle_atom2 = atom->angle_atom2;
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int **angle_atom3 = atom->angle_atom3;
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int **angle_type = atom->angle_type;
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int *tag = atom->tag;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int i,atom1,atom2,atom3;
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int m = 0;
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for (atom2 = 0; atom2 < nlocal; atom2++) {
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if (!(mask[atom2] & groupbit)) continue;
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for (i = 0; i < num_angle[atom2]; i++) {
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if (tag[atom2] != angle_atom2[atom2][i]) continue;
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atom1 = atom->map(angle_atom1[atom2][i]);
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if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
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atom3 = atom->map(angle_atom3[atom2][i]);
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if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
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if (flag) {
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indices[m][0] = atom2;
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indices[m][1] = i;
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}
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m++;
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}
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}
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return m;
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}
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/* ----------------------------------------------------------------------
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count dihedrals on this proc
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only count if 2nd atom is the one storing the dihedral
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all atoms in interaction must be in group
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all atoms in interaction must be known to proc
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------------------------------------------------------------------------- */
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int ComputePropertyLocal::count_dihedrals(int flag)
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{
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int *num_dihedral = atom->num_dihedral;
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int **dihedral_atom1 = atom->dihedral_atom1;
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int **dihedral_atom2 = atom->dihedral_atom2;
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int **dihedral_atom3 = atom->dihedral_atom3;
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int **dihedral_atom4 = atom->dihedral_atom4;
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int **dihedral_type = atom->dihedral_type;
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int *tag = atom->tag;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int i,atom1,atom2,atom3,atom4;
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int m = 0;
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for (atom2 = 0; atom2 < nlocal; atom2++) {
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if (!(mask[atom2] & groupbit)) continue;
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for (i = 0; i < num_dihedral[atom2]; i++) {
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if (tag[atom2] != dihedral_atom2[atom2][i]) continue;
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atom1 = atom->map(dihedral_atom1[atom2][i]);
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if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
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atom3 = atom->map(dihedral_atom3[atom2][i]);
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if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
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atom4 = atom->map(dihedral_atom4[atom2][i]);
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if (atom4 < 0 || !(mask[atom4] & groupbit)) continue;
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if (flag) {
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indices[m][0] = atom2;
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indices[m][1] = i;
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}
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m++;
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}
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}
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return m;
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}
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/* ----------------------------------------------------------------------
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count impropers on this proc
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only count if 2nd atom is the one storing the improper
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all atoms in interaction must be in group
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all atoms in interaction must be known to proc
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------------------------------------------------------------------------- */
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int ComputePropertyLocal::count_impropers(int flag)
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{
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int *num_improper = atom->num_improper;
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int **improper_atom1 = atom->improper_atom1;
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int **improper_atom2 = atom->improper_atom2;
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int **improper_atom3 = atom->improper_atom3;
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int **improper_atom4 = atom->improper_atom4;
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int **improper_type = atom->improper_type;
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int *tag = atom->tag;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int i,atom1,atom2,atom3,atom4;
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int m = 0;
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for (atom2 = 0; atom2 < nlocal; atom2++) {
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if (!(mask[atom2] & groupbit)) continue;
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for (i = 0; i < num_improper[atom2]; i++) {
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if (tag[atom2] != improper_atom2[atom2][i]) continue;
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atom1 = atom->map(improper_atom1[atom2][i]);
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if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
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||||
atom3 = atom->map(improper_atom3[atom2][i]);
|
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if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
|
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atom4 = atom->map(improper_atom4[atom2][i]);
|
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if (atom4 < 0 || !(mask[atom4] & groupbit)) continue;
|
||||
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||||
if (flag) {
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||||
indices[m][0] = atom2;
|
||||
indices[m][1] = i;
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||||
}
|
||||
m++;
|
||||
}
|
||||
}
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||||
return m;
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||||
}
|
||||
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||||
/* ---------------------------------------------------------------------- */
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||||
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||||
void ComputePropertyLocal::reallocate(int n)
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||||
{
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||||
// grow vector or array and indices array
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||||
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||||
size_local_rows = n;
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||||
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||||
while (nmax < n) nmax += DELTA;
|
||||
if (nvalues == 1) {
|
||||
memory->sfree(vector);
|
||||
vector = (double *) memory->smalloc(nmax*sizeof(double),
|
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"property/local:vector");
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vector_local = vector;
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||||
} else {
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||||
memory->destroy_2d_double_array(array);
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array = memory->create_2d_double_array(nmax,nvalues,
|
||||
"property/local:array");
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||||
array_local = array;
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||||
}
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||||
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||||
memory->destroy_2d_int_array(indices);
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||||
indices = memory->create_2d_int_array(nmax,2,"property/local:indices");
|
||||
}
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||||
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||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local data
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||||
------------------------------------------------------------------------- */
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||||
|
||||
double ComputePropertyLocal::memory_usage()
|
||||
{
|
||||
double bytes = nmax*nvalues * sizeof(double);
|
||||
bytes += nmax*2 * sizeof(int);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
one method for every keyword compute property/local can output
|
||||
the atom property is packed into buf starting at n with stride nvalues
|
||||
customize a new keyword by adding a method
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_batom1(int n)
|
||||
{
|
||||
int i;
|
||||
int *tag = atom->tag;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
buf[n] = tag[i];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_batom2(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **bond_atom = atom->bond_atom;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = bond_atom[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_btype(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **bond_type = atom->bond_type;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = bond_type[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_aatom1(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **angle_atom1 = atom->angle_atom1;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = angle_atom1[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_aatom2(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **angle_atom2 = atom->angle_atom2;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = angle_atom2[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_aatom3(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **angle_atom3 = atom->angle_atom3;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = angle_atom3[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_atype(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **angle_type = atom->angle_type;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = angle_type[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_datom1(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **dihedral_atom1 = atom->dihedral_atom1;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = dihedral_atom1[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_datom2(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **dihedral_atom2 = atom->dihedral_atom2;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = dihedral_atom2[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_datom3(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **dihedral_atom3 = atom->dihedral_atom3;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = dihedral_atom3[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_datom4(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **dihedral_atom4 = atom->dihedral_atom4;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = dihedral_atom4[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_dtype(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **dihedral_type = atom->dihedral_type;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = dihedral_type[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_iatom1(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **improper_atom1 = atom->improper_atom1;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = improper_atom1[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_iatom2(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **improper_atom2 = atom->improper_atom2;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = improper_atom2[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_iatom3(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **improper_atom3 = atom->improper_atom3;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = improper_atom3[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_iatom4(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **improper_atom4 = atom->improper_atom4;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = improper_atom4[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputePropertyLocal::pack_itype(int n)
|
||||
{
|
||||
int i,j;
|
||||
int **improper_type = atom->improper_type;
|
||||
|
||||
for (int m = 0; m < ncount; m++) {
|
||||
i = indices[m][0];
|
||||
j = indices[m][1];
|
||||
buf[n] = improper_type[i][j];
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user