import contributed code for computes coord/atom and orientorder/atom
This commit is contained in:
Axel Kohlmeyer
@ -15,6 +15,7 @@
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#include <string.h>
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#include <stdlib.h>
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#include "compute_coord_atom.h"
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#include "compute_orientorder_atom.h"
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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@ -29,37 +30,72 @@
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using namespace LAMMPS_NS;
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#define INVOKED_PERATOM 8
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/* ---------------------------------------------------------------------- */
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ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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typelo(NULL), typehi(NULL), cvec(NULL), carray(NULL)
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cstyle(NULL), id_orientorder(NULL), typelo(NULL), typehi(NULL), cvec(NULL), carray(NULL)
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{
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if (narg < 4) error->all(FLERR,"Illegal compute coord/atom command");
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if (narg < 5) error->all(FLERR,"Illegal compute coord/atom command");
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double cutoff = force->numeric(FLERR,arg[3]);
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cutsq = cutoff*cutoff;
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int n = strlen(arg[3]) + 1;
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cstyle = new char[n];
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strcpy(cstyle,arg[3]);
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ncol = narg-4 + 1;
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int ntypes = atom->ntypes;
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typelo = new int[ncol];
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typehi = new int[ncol];
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if (strcmp(cstyle,"cutoff") == 0) {
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double cutoff = force->numeric(FLERR,arg[4]);
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cutsq = cutoff*cutoff;
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ncol = narg-5 + 1;
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int ntypes = atom->ntypes;
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typelo = new int[ncol];
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typehi = new int[ncol];
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if (narg == 5) {
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ncol = 1;
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typelo[0] = 1;
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typehi[0] = ntypes;
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} else {
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ncol = 0;
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int iarg = 5;
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while (iarg < narg) {
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force->bounds(FLERR,arg[iarg],ntypes,typelo[ncol],typehi[ncol]);
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if (typelo[ncol] > typehi[ncol])
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error->all(FLERR,"Illegal compute coord/atom command");
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ncol++;
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iarg++;
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}
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if (narg == 4) {
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ncol = 1;
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typelo[0] = 1;
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typehi[0] = ntypes;
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} else {
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ncol = 0;
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int iarg = 4;
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while (iarg < narg) {
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force->bounds(FLERR,arg[iarg],ntypes,typelo[ncol],typehi[ncol]);
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if (typelo[ncol] > typehi[ncol])
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error->all(FLERR,"Illegal compute coord/atom command");
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ncol++;
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iarg++;
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}
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}
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} else if (strcmp(cstyle,"orientorder") == 0) {
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if (narg != 6) error->all(FLERR,"Illegal compute coord/atom command");
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n = strlen(arg[4]) + 1;
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id_orientorder = new char[n];
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strcpy(id_orientorder,arg[4]);
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int iorientorder = modify->find_compute(id_orientorder);
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if (iorientorder < 0)
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error->all(FLERR,"Could not find compute coord/atom compute ID");
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if (strcmp(modify->compute[iorientorder]->style,"orientorder/atom") != 0)
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error->all(FLERR,"Compute coord/atom compute ID does not compute orientorder/atom");
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threshold = force->numeric(FLERR,arg[5]);
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if (threshold <= -1.0 || threshold >= 1.0)
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error->all(FLERR,"Compute coord/atom threshold value must lie between -1 and 1");
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ncol = 1;
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typelo = new int[ncol];
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typehi = new int[ncol];
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typelo[0] = 1;
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typehi[0] = atom->ntypes;
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} else error->all(FLERR,"Invalid cstyle in compute coord/atom");
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peratom_flag = 1;
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if (ncol == 1) size_peratom_cols = 0;
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@ -82,6 +118,17 @@ ComputeCoordAtom::~ComputeCoordAtom()
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void ComputeCoordAtom::init()
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{
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if (strcmp(cstyle,"orientorder") == 0) {
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int iorientorder = modify->find_compute(id_orientorder);
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c_orientorder = (ComputeOrientOrderAtom*)(modify->compute[iorientorder]);
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cutsq = c_orientorder->cutsq;
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l = c_orientorder->qlcomp;
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// communicate real and imaginary 2*l+1 components of the normalized vector
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comm_forward = 2*(2*l+1);
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if (c_orientorder->iqlcomp < 0)
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error->all(FLERR,"Compute coord/atom requires components option in compute orientorder/atom be defined");
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}
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if (force->pair == NULL)
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error->all(FLERR,"Compute coord/atom requires a pair style be defined");
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if (sqrt(cutsq) > force->pair->cutforce)
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@ -122,6 +169,9 @@ void ComputeCoordAtom::compute_peratom()
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invoked_peratom = update->ntimestep;
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// printf("Number of degrees %i components degree %i",nqlist,l);
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// printf("Particle \t %i \t Norm \t %g \n",0,norm[0][0]);
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// grow coordination array if necessary
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if (atom->nmax > nmax) {
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@ -138,6 +188,19 @@ void ComputeCoordAtom::compute_peratom()
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}
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}
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if (strcmp(cstyle,"orientorder") == 0) {
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if (!(c_orientorder->invoked_flag & INVOKED_PERATOM)) {
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c_orientorder->compute_peratom();
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c_orientorder->invoked_flag |= INVOKED_PERATOM;
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}
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nqlist = c_orientorder->nqlist;
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int ltmp = l;
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// l = c_orientorder->qlcomp;
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if (ltmp != l) error->all(FLERR,"Debug error, ltmp != l\n");
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normv = c_orientorder->array_atom;
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comm->forward_comm_compute(this);
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}
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// invoke full neighbor list (will copy or build if necessary)
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neighbor->build_one(list);
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@ -154,65 +217,131 @@ void ComputeCoordAtom::compute_peratom()
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int *type = atom->type;
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int *mask = atom->mask;
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if (ncol == 1) {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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if (strcmp(cstyle,"cutoff") == 0) {
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n = 0;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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if (ncol == 1) {
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jtype = type[j];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0]) n++;
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}
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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cvec[i] = n;
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} else cvec[i] = 0.0;
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}
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n = 0;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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} else {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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count = carray[i];
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for (m = 0; m < ncol; m++) count[m] = 0.0;
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jtype = type[j];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0])
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n++;
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}
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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cvec[i] = n;
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} else cvec[i] = 0.0;
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}
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} else {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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count = carray[i];
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for (m = 0; m < ncol; m++) count[m] = 0.0;
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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jtype = type[j];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq) {
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for (m = 0; m < ncol; m++)
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if (jtype >= typelo[m] && jtype <= typehi[m])
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count[m] += 1.0;
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jtype = type[j];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq) {
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for (m = 0; m < ncol; m++)
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if (jtype >= typelo[m] && jtype <= typehi[m])
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count[m] += 1.0;
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}
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}
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}
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}
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}
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} else if (strcmp(cstyle,"orientorder") == 0) {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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n = 0;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq) {
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double dot_product = 0.0;
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for (int m=0; m < 2*(2*l+1); m++) {
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dot_product += normv[i][nqlist+m]*normv[j][nqlist+m];
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}
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if (dot_product > threshold) n++;
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}
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}
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cvec[i] = n;
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} else cvec[i] = 0.0;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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{
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int i,m=0,j;
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for (i = 0; i < n; ++i) {
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for (j = nqlist; j < nqlist + 2*(2*l+1); ++j) {
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buf[m++] = normv[list[i]][j];
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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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void ComputeCoordAtom::unpack_forward_comm(int n, int first, double *buf)
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{
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int i,last,m=0,j;
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last = first + n;
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for (i = first; i < last; ++i) {
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for (j = nqlist; j < nqlist + 2*(2*l+1); ++j) {
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normv[i][j] = buf[m++];
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}
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}
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}
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/* ----------------------------------------------------------------------
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