forked from lijiext/lammps
Added axes keyword
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15377 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
parent
5241c0326e
commit
e8c5280ad9
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@ -27,6 +27,7 @@
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#include "force.h"
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#include "pair.h"
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#include "comm.h"
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#include "math_extra.h"
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#include "memory.h"
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#include "error.h"
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@ -37,23 +38,42 @@ using namespace LAMMPS_NS;
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ComputeCentroAtom::ComputeCentroAtom(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(FLERR,"Illegal compute centro/atom command");
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if (narg < 4 || narg > 6) error->all(FLERR,"Illegal compute centro/atom command");
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if (strcmp(arg[3],"fcc") == 0) nnn = 12;
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else if (strcmp(arg[3],"bcc") == 0) nnn = 8;
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else nnn = force->inumeric(FLERR,arg[3]);
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// default values
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axes_flag = 0;
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// optional keywords
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int iarg = 4;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"axes") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal compute centro/atom command3");
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if (strcmp(arg[iarg+1],"yes") == 0) axes_flag = 1;
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else if (strcmp(arg[iarg+1],"no") == 0) axes_flag = 0;
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else error->all(FLERR,"Illegal compute centro/atom command2");
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iarg += 2;
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} else error->all(FLERR,"Illegal compute centro/atom command1");
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}
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if (nnn <= 0 || nnn % 2)
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error->all(FLERR,"Illegal neighbor value for compute centro/atom command");
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peratom_flag = 1;
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size_peratom_cols = 0;
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if (!axes_flag) size_peratom_cols = 0;
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else size_peratom_cols = 10;
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nmax = 0;
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centro = NULL;
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maxneigh = 0;
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distsq = NULL;
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nearest = NULL;
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array_atom = NULL;
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}
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/* ---------------------------------------------------------------------- */
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@ -63,6 +83,7 @@ ComputeCentroAtom::~ComputeCentroAtom()
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memory->destroy(centro);
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memory->destroy(distsq);
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memory->destroy(nearest);
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if (axes_flag) memory->destroy(array_atom);
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}
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/* ---------------------------------------------------------------------- */
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@ -106,12 +127,21 @@ void ComputeCentroAtom::compute_peratom()
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invoked_peratom = update->ntimestep;
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// grow centro array if necessary
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// grow array_atom array if axes_flag set
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if (atom->nmax > nmax) {
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memory->destroy(centro);
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nmax = atom->nmax;
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memory->create(centro,nmax,"centro/atom:centro");
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vector_atom = centro;
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if (!axes_flag) {
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memory->destroy(centro);
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nmax = atom->nmax;
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memory->create(centro,nmax,"centro/atom:centro");
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vector_atom = centro;
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} else {
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memory->destroy(centro);
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memory->destroy(array_atom);
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nmax = atom->nmax;
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memory->create(centro,nmax,"centro/atom:centro");
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memory->create(array_atom,nmax,size_peratom_cols,"centro/atom:array_atom");
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}
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}
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// invoke full neighbor list (will copy or build if necessary)
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@ -174,45 +204,122 @@ void ComputeCentroAtom::compute_peratom()
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}
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}
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// if not nnn neighbors, centro = 0.0
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// check whether to include local crystal symmetry axes
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if (!axes_flag) {
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// if not nnn neighbors, centro = 0.0
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if (n < nnn) {
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centro[i] = 0.0;
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continue;
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if (n < nnn) {
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centro[i] = 0.0;
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continue;
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}
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// store nnn nearest neighs in 1st nnn locations of distsq and nearest
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select2(nnn,n,distsq,nearest);
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// R = Ri + Rj for each of npairs i,j pairs among nnn neighbors
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// pairs = squared length of each R
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n = 0;
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for (j = 0; j < nnn; j++) {
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jj = nearest[j];
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for (k = j+1; k < nnn; k++) {
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kk = nearest[k];
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delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
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dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
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delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
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pairs[n++] = delx*delx + dely*dely + delz*delz;
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}
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}
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} else {
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// calculate local crystal symmetry axes
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// rsq1, rsq2 are two smallest values of R^2
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// R1, R2 are corresponding vectors Ri - Rj
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// R3 is normal to R1, R2
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double rsq1,rsq2;
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double* r1 = &array_atom[i][1];
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double* r2 = &array_atom[i][4];
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double* r3 = &array_atom[i][7];
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if (n < nnn) {
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centro[i] = 0.0;
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MathExtra::zero3(r1);
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MathExtra::zero3(r2);
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MathExtra::zero3(r3);
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continue;
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}
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// store nnn nearest neighs in 1st nnn locations of distsq and nearest
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select2(nnn,n,distsq,nearest);
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n = 0;
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rsq1 = rsq2 = cutsq;
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for (j = 0; j < nnn; j++) {
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jj = nearest[j];
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for (k = j+1; k < nnn; k++) {
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kk = nearest[k];
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delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
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dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
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delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
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double rsq = delx*delx + dely*dely + delz*delz;
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pairs[n++] = rsq;
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if (rsq < rsq2)
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if (rsq < rsq1) {
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rsq2 = rsq1;
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MathExtra::copy3(r1, r2);
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rsq1 = rsq;
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MathExtra::sub3(x[jj],x[kk],r1);
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} else {
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rsq2 = rsq;
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MathExtra::sub3(x[jj],x[kk],r2);
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}
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}
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}
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MathExtra::cross3(r1,r2,r3);
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MathExtra::norm3(r1);
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MathExtra::norm3(r2);
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MathExtra::norm3(r3);
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}
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// store nnn nearest neighs in 1st nnn locations of distsq and nearest
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select2(nnn,n,distsq,nearest);
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// R = Ri + Rj for each of npairs i,j pairs among nnn neighbors
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// pairs = squared length of each R
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n = 0;
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for (j = 0; j < nnn; j++) {
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jj = nearest[j];
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for (k = j+1; k < nnn; k++) {
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kk = nearest[k];
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delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
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dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
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delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
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pairs[n++] = delx*delx + dely*dely + delz*delz;
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}
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}
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// store nhalf smallest pair distances in 1st nhalf locations of pairs
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select(nhalf,npairs,pairs);
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// centrosymmetry = sum of nhalf smallest squared values
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value = 0.0;
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for (j = 0; j < nhalf; j++) value += pairs[j];
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centro[i] = value;
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} else centro[i] = 0.0;
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} else {
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centro[i] = 0.0;
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if (axes_flag) {
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MathExtra::zero3(&array_atom[i][1]);
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MathExtra::zero3(&array_atom[i][4]);
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MathExtra::zero3(&array_atom[i][7]);
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}
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}
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}
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delete [] pairs;
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if (axes_flag)
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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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array_atom[i][0] = centro[i];
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}
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}
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/* ----------------------------------------------------------------------
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@ -39,7 +39,8 @@ class ComputeCentroAtom : public Compute {
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int *nearest;
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class NeighList *list;
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double *centro;
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int axes_flag;
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void select(int, int, double *);
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void select2(int, int, double *, int *);
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};
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@ -27,12 +27,15 @@ namespace MathExtra {
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// 3 vector operations
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inline void copy3(const double *v, double *ans);
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inline void zero3(double *v);
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inline void norm3(double *v);
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inline void normalize3(const double *v, double *ans);
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inline void snormalize3(const double, const double *v, double *ans);
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inline void negate3(double *v);
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inline void scale3(double s, double *v);
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inline void add3(const double *v1, const double *v2, double *ans);
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inline void scaleadd3(double s, const double *v1, const double *v2, double *ans);
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inline void sub3(const double *v1, const double *v2, double *ans);
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inline double len3(const double *v);
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inline double lensq3(const double *v);
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@ -128,6 +131,28 @@ namespace MathExtra {
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double *inertia);
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}
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/* ----------------------------------------------------------------------
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copy a vector, return in ans
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------------------------------------------------------------------------- */
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inline void MathExtra::copy3(const double *v, double *ans)
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{
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ans[0] = v[0];
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ans[1] = v[1];
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ans[2] = v[2];
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}
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/* ----------------------------------------------------------------------
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set vector equal to zero
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------------------------------------------------------------------------- */
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inline void MathExtra::zero3(double *v)
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{
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v[0] = 0.0;
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v[1] = 0.0;
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v[2] = 0.0;
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}
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/* ----------------------------------------------------------------------
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normalize a vector in place
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------------------------------------------------------------------------- */
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@ -198,6 +223,17 @@ inline void MathExtra::add3(const double *v1, const double *v2, double *ans)
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ans[2] = v1[2] + v2[2];
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}
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/* ----------------------------------------------------------------------
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ans = s*v1 + v2
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------------------------------------------------------------------------- */
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inline void MathExtra::scaleadd3(double s, const double *v1, const double *v2, double *ans)
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{
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ans[0] = s*v1[0] + v2[0];
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ans[1] = s*v1[1] + v2[1];
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ans[2] = s*v1[2] + v2[2];
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}
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/* ----------------------------------------------------------------------
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ans = v1 - v2
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------------------------------------------------------------------------- */
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