910 lines
26 KiB
C++
910 lines
26 KiB
C++
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
http://lammps.sandia.gov, Sandia National Laboratories
|
|
Steve Plimpton, sjplimp@sandia.gov
|
|
|
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
certain rights in this software. This software is distributed under
|
|
the GNU General Public License.
|
|
|
|
See the README file in the top-level LAMMPS directory.
|
|
------------------------------------------------------------------------- */
|
|
|
|
/* ----------------------------------------------------------------------
|
|
Contributing author: Aidan Thompson (SNL)
|
|
Axel Kohlmeyer (Temple U)
|
|
------------------------------------------------------------------------- */
|
|
|
|
#include "compute_orientorder_atom.h"
|
|
#include <cstring>
|
|
#include <cstdlib>
|
|
#include <cmath>
|
|
#include "atom.h"
|
|
#include "update.h"
|
|
#include "modify.h"
|
|
#include "neighbor.h"
|
|
#include "neigh_list.h"
|
|
#include "neigh_request.h"
|
|
#include "force.h"
|
|
#include "pair.h"
|
|
#include "comm.h"
|
|
#include "memory.h"
|
|
#include "error.h"
|
|
#include "math_const.h"
|
|
|
|
using namespace LAMMPS_NS;
|
|
using namespace MathConst;
|
|
using namespace std;
|
|
|
|
#ifdef DBL_EPSILON
|
|
#define MY_EPSILON (10.0*DBL_EPSILON)
|
|
#else
|
|
#define MY_EPSILON (10.0*2.220446049250313e-16)
|
|
#endif
|
|
|
|
#define QEPSILON 1.0e-6
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg) :
|
|
Compute(lmp, narg, arg),
|
|
qlist(NULL), distsq(NULL), nearest(NULL), rlist(NULL),
|
|
qnarray(NULL), qnm_r(NULL), qnm_i(NULL), cglist(NULL)
|
|
{
|
|
if (narg < 3 ) error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
|
|
// set default values for optional args
|
|
|
|
nnn = 12;
|
|
cutsq = 0.0;
|
|
wlflag = 0;
|
|
wlhatflag = 0;
|
|
qlcompflag = 0;
|
|
chunksize = 16384;
|
|
|
|
// specify which orders to request
|
|
|
|
nqlist = 5;
|
|
memory->create(qlist,nqlist,"orientorder/atom:qlist");
|
|
qlist[0] = 4;
|
|
qlist[1] = 6;
|
|
qlist[2] = 8;
|
|
qlist[3] = 10;
|
|
qlist[4] = 12;
|
|
qmax = 12;
|
|
|
|
// process optional args
|
|
|
|
int iarg = 3;
|
|
while (iarg < narg) {
|
|
if (strcmp(arg[iarg],"nnn") == 0) {
|
|
if (iarg+2 > narg)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
if (strcmp(arg[iarg+1],"NULL") == 0) {
|
|
nnn = 0;
|
|
} else {
|
|
nnn = force->numeric(FLERR,arg[iarg+1]);
|
|
if (nnn <= 0)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
}
|
|
iarg += 2;
|
|
} else if (strcmp(arg[iarg],"degrees") == 0) {
|
|
if (iarg+2 > narg)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
nqlist = force->numeric(FLERR,arg[iarg+1]);
|
|
if (nqlist <= 0)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
memory->destroy(qlist);
|
|
memory->create(qlist,nqlist,"orientorder/atom:qlist");
|
|
iarg += 2;
|
|
if (iarg+nqlist > narg)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
qmax = 0;
|
|
for (int il = 0; il < nqlist; il++) {
|
|
qlist[il] = force->numeric(FLERR,arg[iarg+il]);
|
|
if (qlist[il] < 0)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
if (qlist[il] > qmax) qmax = qlist[il];
|
|
}
|
|
iarg += nqlist;
|
|
} else if (strcmp(arg[iarg],"wl") == 0) {
|
|
if (iarg+2 > narg)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
if (strcmp(arg[iarg+1],"yes") == 0) wlflag = 1;
|
|
else if (strcmp(arg[iarg+1],"no") == 0) wlflag = 0;
|
|
else error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
iarg += 2;
|
|
} else if (strcmp(arg[iarg],"wl/hat") == 0) {
|
|
if (iarg+2 > narg)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
if (strcmp(arg[iarg+1],"yes") == 0) wlhatflag = 1;
|
|
else if (strcmp(arg[iarg+1],"no") == 0) wlhatflag = 0;
|
|
else error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
iarg += 2;
|
|
} else if (strcmp(arg[iarg],"components") == 0) {
|
|
qlcompflag = 1;
|
|
if (iarg+2 > narg)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
qlcomp = force->numeric(FLERR,arg[iarg+1]);
|
|
iqlcomp = -1;
|
|
for (int il = 0; il < nqlist; il++)
|
|
if (qlcomp == qlist[il]) {
|
|
iqlcomp = il;
|
|
break;
|
|
}
|
|
if (iqlcomp == -1)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
iarg += 2;
|
|
} else if (strcmp(arg[iarg],"cutoff") == 0) {
|
|
if (iarg+2 > narg)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
double cutoff = force->numeric(FLERR,arg[iarg+1]);
|
|
if (cutoff <= 0.0)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
cutsq = cutoff*cutoff;
|
|
iarg += 2;
|
|
} else if (strcmp(arg[iarg],"chunksize") == 0) {
|
|
if (iarg+2 > narg)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
chunksize = force->numeric(FLERR,arg[iarg+1]);
|
|
if (chunksize <= 0)
|
|
error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
iarg += 2;
|
|
} else error->all(FLERR,"Illegal compute orientorder/atom command");
|
|
}
|
|
|
|
ncol = nqlist;
|
|
if (wlflag) ncol += nqlist;
|
|
if (wlhatflag) ncol += nqlist;
|
|
if (qlcompflag) ncol += 2*(2*qlcomp+1);
|
|
|
|
peratom_flag = 1;
|
|
size_peratom_cols = ncol;
|
|
|
|
nmax = 0;
|
|
maxneigh = 0;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
ComputeOrientOrderAtom::~ComputeOrientOrderAtom()
|
|
{
|
|
if (copymode) return;
|
|
|
|
memory->destroy(qnarray);
|
|
memory->destroy(distsq);
|
|
memory->destroy(rlist);
|
|
memory->destroy(nearest);
|
|
memory->destroy(qlist);
|
|
memory->destroy(qnm_r);
|
|
memory->destroy(qnm_i);
|
|
memory->destroy(cglist);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeOrientOrderAtom::init()
|
|
{
|
|
if (force->pair == NULL)
|
|
error->all(FLERR,"Compute orientorder/atom requires a "
|
|
"pair style be defined");
|
|
if (cutsq == 0.0) cutsq = force->pair->cutforce * force->pair->cutforce;
|
|
else if (sqrt(cutsq) > force->pair->cutforce)
|
|
error->all(FLERR,"Compute orientorder/atom cutoff is "
|
|
"longer than pairwise cutoff");
|
|
|
|
memory->create(qnm_r,nqlist,2*qmax+1,"orientorder/atom:qnm_r");
|
|
memory->create(qnm_i,nqlist,2*qmax+1,"orientorder/atom:qnm_i");
|
|
|
|
// need an occasional full neighbor list
|
|
|
|
int irequest = neighbor->request(this,instance_me);
|
|
neighbor->requests[irequest]->pair = 0;
|
|
neighbor->requests[irequest]->compute = 1;
|
|
neighbor->requests[irequest]->half = 0;
|
|
neighbor->requests[irequest]->full = 1;
|
|
neighbor->requests[irequest]->occasional = 1;
|
|
|
|
int count = 0;
|
|
for (int i = 0; i < modify->ncompute; i++)
|
|
if (strcmp(modify->compute[i]->style,"orientorder/atom") == 0) count++;
|
|
if (count > 1 && comm->me == 0)
|
|
error->warning(FLERR,"More than one compute orientorder/atom");
|
|
|
|
if (wlflag || wlhatflag) init_clebsch_gordan();
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeOrientOrderAtom::init_list(int /*id*/, NeighList *ptr)
|
|
{
|
|
list = ptr;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeOrientOrderAtom::compute_peratom()
|
|
{
|
|
int i,j,ii,jj,inum,jnum;
|
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
|
int *ilist,*jlist,*numneigh,**firstneigh;
|
|
|
|
invoked_peratom = update->ntimestep;
|
|
|
|
// grow order parameter array if necessary
|
|
|
|
if (atom->nmax > nmax) {
|
|
memory->destroy(qnarray);
|
|
nmax = atom->nmax;
|
|
memory->create(qnarray,nmax,ncol,"orientorder/atom:qnarray");
|
|
array_atom = qnarray;
|
|
}
|
|
|
|
// invoke full neighbor list (will copy or build if necessary)
|
|
|
|
neighbor->build_one(list);
|
|
|
|
inum = list->inum;
|
|
ilist = list->ilist;
|
|
numneigh = list->numneigh;
|
|
firstneigh = list->firstneigh;
|
|
|
|
// compute order parameter for each atom in group
|
|
// use full neighbor list to count atoms less than cutoff
|
|
|
|
double **x = atom->x;
|
|
int *mask = atom->mask;
|
|
|
|
for (ii = 0; ii < inum; ii++) {
|
|
i = ilist[ii];
|
|
double* qn = qnarray[i];
|
|
if (mask[i] & groupbit) {
|
|
xtmp = x[i][0];
|
|
ytmp = x[i][1];
|
|
ztmp = x[i][2];
|
|
jlist = firstneigh[i];
|
|
jnum = numneigh[i];
|
|
|
|
// insure distsq and nearest arrays are long enough
|
|
|
|
if (jnum > maxneigh) {
|
|
memory->destroy(distsq);
|
|
memory->destroy(rlist);
|
|
memory->destroy(nearest);
|
|
maxneigh = jnum;
|
|
memory->create(distsq,maxneigh,"orientorder/atom:distsq");
|
|
memory->create(rlist,maxneigh,3,"orientorder/atom:rlist");
|
|
memory->create(nearest,maxneigh,"orientorder/atom:nearest");
|
|
}
|
|
|
|
// loop over list of all neighbors within force cutoff
|
|
// distsq[] = distance sq to each
|
|
// rlist[] = distance vector to each
|
|
// nearest[] = atom indices of neighbors
|
|
|
|
int ncount = 0;
|
|
for (jj = 0; jj < jnum; jj++) {
|
|
j = jlist[jj];
|
|
j &= NEIGHMASK;
|
|
|
|
delx = xtmp - x[j][0];
|
|
dely = ytmp - x[j][1];
|
|
delz = ztmp - x[j][2];
|
|
rsq = delx*delx + dely*dely + delz*delz;
|
|
if (rsq < cutsq) {
|
|
distsq[ncount] = rsq;
|
|
rlist[ncount][0] = delx;
|
|
rlist[ncount][1] = dely;
|
|
rlist[ncount][2] = delz;
|
|
nearest[ncount++] = j;
|
|
}
|
|
}
|
|
|
|
// if not nnn neighbors, order parameter = 0;
|
|
|
|
if ((ncount == 0) || (ncount < nnn)) {
|
|
for (int jj = 0; jj < ncol; jj++)
|
|
qn[jj] = 0.0;
|
|
continue;
|
|
}
|
|
|
|
// if nnn > 0, use only nearest nnn neighbors
|
|
|
|
if (nnn > 0) {
|
|
select3(nnn,ncount,distsq,nearest,rlist);
|
|
ncount = nnn;
|
|
}
|
|
|
|
calc_boop(rlist, ncount, qn, qlist, nqlist);
|
|
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
memory usage of local atom-based array
|
|
------------------------------------------------------------------------- */
|
|
|
|
double ComputeOrientOrderAtom::memory_usage()
|
|
{
|
|
double bytes = ncol*nmax * sizeof(double);
|
|
bytes += (qmax*(2*qmax+1)+maxneigh*4) * sizeof(double);
|
|
bytes += (nqlist+maxneigh) * sizeof(int);
|
|
return bytes;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
select3 routine from Numerical Recipes (slightly modified)
|
|
find k smallest values in array of length n
|
|
sort auxiliary arrays at same time
|
|
------------------------------------------------------------------------- */
|
|
|
|
// Use no-op do while to create single statement
|
|
|
|
#define SWAP(a,b) do { \
|
|
tmp = a; a = b; b = tmp; \
|
|
} while(0)
|
|
|
|
#define ISWAP(a,b) do { \
|
|
itmp = a; a = b; b = itmp; \
|
|
} while(0)
|
|
|
|
#define SWAP3(a,b) do { \
|
|
tmp = a[0]; a[0] = b[0]; b[0] = tmp; \
|
|
tmp = a[1]; a[1] = b[1]; b[1] = tmp; \
|
|
tmp = a[2]; a[2] = b[2]; b[2] = tmp; \
|
|
} while(0)
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeOrientOrderAtom::select3(int k, int n, double *arr, int *iarr, double **arr3)
|
|
{
|
|
int i,ir,j,l,mid,ia,itmp;
|
|
double a,tmp,a3[3];
|
|
|
|
arr--;
|
|
iarr--;
|
|
arr3--;
|
|
l = 1;
|
|
ir = n;
|
|
for (;;) {
|
|
if (ir <= l+1) {
|
|
if (ir == l+1 && arr[ir] < arr[l]) {
|
|
SWAP(arr[l],arr[ir]);
|
|
ISWAP(iarr[l],iarr[ir]);
|
|
SWAP3(arr3[l],arr3[ir]);
|
|
}
|
|
return;
|
|
} else {
|
|
mid=(l+ir) >> 1;
|
|
SWAP(arr[mid],arr[l+1]);
|
|
ISWAP(iarr[mid],iarr[l+1]);
|
|
SWAP3(arr3[mid],arr3[l+1]);
|
|
if (arr[l] > arr[ir]) {
|
|
SWAP(arr[l],arr[ir]);
|
|
ISWAP(iarr[l],iarr[ir]);
|
|
SWAP3(arr3[l],arr3[ir]);
|
|
}
|
|
if (arr[l+1] > arr[ir]) {
|
|
SWAP(arr[l+1],arr[ir]);
|
|
ISWAP(iarr[l+1],iarr[ir]);
|
|
SWAP3(arr3[l+1],arr3[ir]);
|
|
}
|
|
if (arr[l] > arr[l+1]) {
|
|
SWAP(arr[l],arr[l+1]);
|
|
ISWAP(iarr[l],iarr[l+1]);
|
|
SWAP3(arr3[l],arr3[l+1]);
|
|
}
|
|
i = l+1;
|
|
j = ir;
|
|
a = arr[l+1];
|
|
ia = iarr[l+1];
|
|
a3[0] = arr3[l+1][0];
|
|
a3[1] = arr3[l+1][1];
|
|
a3[2] = arr3[l+1][2];
|
|
for (;;) {
|
|
do i++; while (arr[i] < a);
|
|
do j--; while (arr[j] > a);
|
|
if (j < i) break;
|
|
SWAP(arr[i],arr[j]);
|
|
ISWAP(iarr[i],iarr[j]);
|
|
SWAP3(arr3[i],arr3[j]);
|
|
}
|
|
arr[l+1] = arr[j];
|
|
arr[j] = a;
|
|
iarr[l+1] = iarr[j];
|
|
iarr[j] = ia;
|
|
arr3[l+1][0] = arr3[j][0];
|
|
arr3[l+1][1] = arr3[j][1];
|
|
arr3[l+1][2] = arr3[j][2];
|
|
arr3[j][0] = a3[0];
|
|
arr3[j][1] = a3[1];
|
|
arr3[j][2] = a3[2];
|
|
if (j >= k) ir = j-1;
|
|
if (j <= k) l = i;
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
calculate the bond orientational order parameters
|
|
------------------------------------------------------------------------- */
|
|
|
|
void ComputeOrientOrderAtom::calc_boop(double **rlist,
|
|
int ncount, double qn[],
|
|
int qlist[], int nqlist) {
|
|
|
|
for (int il = 0; il < nqlist; il++) {
|
|
int l = qlist[il];
|
|
for(int m = 0; m < 2*l+1; m++) {
|
|
qnm_r[il][m] = 0.0;
|
|
qnm_i[il][m] = 0.0;
|
|
}
|
|
}
|
|
|
|
for(int ineigh = 0; ineigh < ncount; ineigh++) {
|
|
const double * const r = rlist[ineigh];
|
|
double rmag = dist(r);
|
|
if(rmag <= MY_EPSILON) {
|
|
return;
|
|
}
|
|
|
|
double costheta = r[2] / rmag;
|
|
double expphi_r = r[0];
|
|
double expphi_i = r[1];
|
|
double rxymag = sqrt(expphi_r*expphi_r+expphi_i*expphi_i);
|
|
if(rxymag <= MY_EPSILON) {
|
|
expphi_r = 1.0;
|
|
expphi_i = 0.0;
|
|
} else {
|
|
double rxymaginv = 1.0/rxymag;
|
|
expphi_r *= rxymaginv;
|
|
expphi_i *= rxymaginv;
|
|
}
|
|
|
|
for (int il = 0; il < nqlist; il++) {
|
|
int l = qlist[il];
|
|
|
|
qnm_r[il][l] += polar_prefactor(l, 0, costheta);
|
|
double expphim_r = expphi_r;
|
|
double expphim_i = expphi_i;
|
|
for(int m = 1; m <= +l; m++) {
|
|
double prefactor = polar_prefactor(l, m, costheta);
|
|
double c_r = prefactor * expphim_r;
|
|
double c_i = prefactor * expphim_i;
|
|
qnm_r[il][m+l] += c_r;
|
|
qnm_i[il][m+l] += c_i;
|
|
if(m & 1) {
|
|
qnm_r[il][-m+l] -= c_r;
|
|
qnm_i[il][-m+l] += c_i;
|
|
} else {
|
|
qnm_r[il][-m+l] += c_r;
|
|
qnm_i[il][-m+l] -= c_i;
|
|
}
|
|
double tmp_r = expphim_r*expphi_r - expphim_i*expphi_i;
|
|
double tmp_i = expphim_r*expphi_i + expphim_i*expphi_r;
|
|
expphim_r = tmp_r;
|
|
expphim_i = tmp_i;
|
|
}
|
|
|
|
}
|
|
}
|
|
|
|
// convert sums to averages
|
|
|
|
double facn = 1.0 / ncount;
|
|
for (int il = 0; il < nqlist; il++) {
|
|
int l = qlist[il];
|
|
for(int m = 0; m < 2*l+1; m++) {
|
|
qnm_r[il][m] *= facn;
|
|
qnm_i[il][m] *= facn;
|
|
}
|
|
}
|
|
|
|
// calculate Q_l
|
|
// NOTE: optional W_l_hat and components of Q_qlcomp use these stored Q_l values
|
|
|
|
int jj = 0;
|
|
for (int il = 0; il < nqlist; il++) {
|
|
int l = qlist[il];
|
|
double qnormfac = sqrt(MY_4PI/(2*l+1));
|
|
double qm_sum = 0.0;
|
|
for(int m = 0; m < 2*l+1; m++)
|
|
qm_sum += qnm_r[il][m]*qnm_r[il][m] + qnm_i[il][m]*qnm_i[il][m];
|
|
qn[jj++] = qnormfac * sqrt(qm_sum);
|
|
}
|
|
|
|
// TODO:
|
|
// 1. [done]Need to allocate extra memory in qnarray[] for this option
|
|
// 2. [done]Need to add keyword option
|
|
// 3. [done]Need to calculate Clebsch-Gordan/Wigner 3j coefficients
|
|
// (Can try getting them from boop.py first)
|
|
// 5. [done]Compare to bcc values in /Users/athomps/netapp/codes/MatMiner/matminer/matminer/featurizers/boop.py
|
|
// 6. [done]I get the right answer for W_l, but need to make sure that factor of 1/sqrt(l+1) is right for cglist
|
|
// 7. Add documentation
|
|
// 8. [done] run valgrind
|
|
// 9. [done] Add Wlhat
|
|
// 10. Update memory_usage()
|
|
// 11. Add exact FCC values for W_4, W_4_hat
|
|
|
|
// calculate W_l
|
|
|
|
if (wlflag) {
|
|
int idxcg_count = 0;
|
|
for (int il = 0; il < nqlist; il++) {
|
|
int l = qlist[il];
|
|
double wlsum = 0.0;
|
|
for(int m1 = 0; m1 < 2*l+1; m1++) {
|
|
for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) {
|
|
int m = m1 + m2 - l;
|
|
double qm1qm2_r = qnm_r[il][m1]*qnm_r[il][m2] - qnm_i[il][m1]*qnm_i[il][m2];
|
|
double qm1qm2_i = qnm_r[il][m1]*qnm_i[il][m2] + qnm_i[il][m1]*qnm_r[il][m2];
|
|
wlsum += (qm1qm2_r*qnm_r[il][m] + qm1qm2_i*qnm_i[il][m])*cglist[idxcg_count];
|
|
idxcg_count++;
|
|
}
|
|
}
|
|
qn[jj++] = wlsum/sqrt(2*l+1);
|
|
}
|
|
}
|
|
|
|
// calculate W_l_hat
|
|
|
|
if (wlhatflag) {
|
|
int idxcg_count = 0;
|
|
for (int il = 0; il < nqlist; il++) {
|
|
int l = qlist[il];
|
|
double wlsum = 0.0;
|
|
for(int m1 = 0; m1 < 2*l+1; m1++) {
|
|
for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) {
|
|
int m = m1 + m2 - l;
|
|
double qm1qm2_r = qnm_r[il][m1]*qnm_r[il][m2] - qnm_i[il][m1]*qnm_i[il][m2];
|
|
double qm1qm2_i = qnm_r[il][m1]*qnm_i[il][m2] + qnm_i[il][m1]*qnm_r[il][m2];
|
|
wlsum += (qm1qm2_r*qnm_r[il][m] + qm1qm2_i*qnm_i[il][m])*cglist[idxcg_count];
|
|
idxcg_count++;
|
|
}
|
|
}
|
|
// Whats = [w/(q/np.sqrt(np.pi * 4 / (2 * l + 1)))**3 if abs(q) > 1.0e-6 else 0.0 for l,q,w in zip(range(1,max_l+1),Qs,Ws)]
|
|
if (qn[il] < QEPSILON)
|
|
qn[jj++] = 0.0;
|
|
else {
|
|
double qnormfac = sqrt(MY_4PI/(2*l+1));
|
|
double qnfac = qnormfac/qn[il];
|
|
qn[jj++] = wlsum/sqrt(2*l+1)*(qnfac*qnfac*qnfac);
|
|
}
|
|
}
|
|
}
|
|
|
|
// Calculate components of Q_l, for l=qlcomp
|
|
|
|
if (qlcompflag) {
|
|
int il = iqlcomp;
|
|
int l = qlcomp;
|
|
if (qn[il] < QEPSILON)
|
|
for(int m = 0; m < 2*l+1; m++) {
|
|
qn[jj++] = 0.0;
|
|
qn[jj++] = 0.0;
|
|
}
|
|
else {
|
|
double qnormfac = sqrt(MY_4PI/(2*l+1));
|
|
double qnfac = qnormfac/qn[il];
|
|
for(int m = 0; m < 2*l+1; m++) {
|
|
qn[jj++] = qnm_r[il][m] * qnfac;
|
|
qn[jj++] = qnm_i[il][m] * qnfac;
|
|
}
|
|
}
|
|
}
|
|
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
calculate scalar distance
|
|
------------------------------------------------------------------------- */
|
|
|
|
double ComputeOrientOrderAtom::dist(const double r[])
|
|
{
|
|
return sqrt(r[0]*r[0] + r[1]*r[1] + r[2]*r[2]);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
polar prefactor for spherical harmonic Y_l^m, where
|
|
Y_l^m (theta, phi) = prefactor(l, m, cos(theta)) * exp(i*m*phi)
|
|
------------------------------------------------------------------------- */
|
|
|
|
double ComputeOrientOrderAtom::polar_prefactor(int l, int m, double costheta)
|
|
{
|
|
const int mabs = abs(m);
|
|
|
|
double prefactor = 1.0;
|
|
for (int i=l-mabs+1; i < l+mabs+1; ++i)
|
|
prefactor *= static_cast<double>(i);
|
|
|
|
prefactor = sqrt(static_cast<double>(2*l+1)/(MY_4PI*prefactor))
|
|
* associated_legendre(l,mabs,costheta);
|
|
|
|
if ((m < 0) && (m % 2)) prefactor = -prefactor;
|
|
|
|
return prefactor;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
associated legendre polynomial
|
|
------------------------------------------------------------------------- */
|
|
|
|
double ComputeOrientOrderAtom::associated_legendre(int l, int m, double x)
|
|
{
|
|
if (l < m) return 0.0;
|
|
|
|
double p(1.0), pm1(0.0), pm2(0.0);
|
|
|
|
if (m != 0) {
|
|
const double sqx = sqrt(1.0-x*x);
|
|
for (int i=1; i < m+1; ++i)
|
|
p *= static_cast<double>(2*i-1) * sqx;
|
|
}
|
|
|
|
for (int i=m+1; i < l+1; ++i) {
|
|
pm2 = pm1;
|
|
pm1 = p;
|
|
p = (static_cast<double>(2*i-1)*x*pm1
|
|
- static_cast<double>(i+m-1)*pm2) / static_cast<double>(i-m);
|
|
}
|
|
|
|
return p;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
assign Clebsch-Gordan coefficients
|
|
using the quasi-binomial formula VMK 8.2.1(3)
|
|
specialized for case j1=j2=j=l
|
|
------------------------------------------------------------------------- */
|
|
|
|
void ComputeOrientOrderAtom::init_clebsch_gordan()
|
|
{
|
|
double sum,dcg,sfaccg, sfac1, sfac2;
|
|
int m, aa2, bb2, cc2;
|
|
int ifac, idxcg_count;
|
|
|
|
idxcg_count = 0;
|
|
for (int il = 0; il < nqlist; il++) {
|
|
int l = qlist[il];
|
|
for(int m1 = 0; m1 < 2*l+1; m1++)
|
|
for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++)
|
|
idxcg_count++;
|
|
}
|
|
idxcg_max = idxcg_count;
|
|
memory->create(cglist, idxcg_max, "computeorientorderatom:cglist");
|
|
|
|
idxcg_count = 0;
|
|
for (int il = 0; il < nqlist; il++) {
|
|
int l = qlist[il];
|
|
for(int m1 = 0; m1 < 2*l+1; m1++) {
|
|
aa2 = m1 - l;
|
|
for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) {
|
|
bb2 = m2 - l;
|
|
m = aa2 + bb2 + l;
|
|
|
|
sum = 0.0;
|
|
for (int z = MAX(0, MAX(-aa2, bb2));
|
|
z <= MIN(l, MIN(l - aa2, l + bb2)); z++) {
|
|
ifac = z % 2 ? -1 : 1;
|
|
sum += ifac /
|
|
(factorial(z) *
|
|
factorial(l - z) *
|
|
factorial(l - aa2 - z) *
|
|
factorial(l + bb2 - z) *
|
|
factorial(aa2 + z) *
|
|
factorial(-bb2 + z));
|
|
}
|
|
|
|
cc2 = m - l;
|
|
sfaccg = sqrt(factorial(l + aa2) *
|
|
factorial(l - aa2) *
|
|
factorial(l + bb2) *
|
|
factorial(l - bb2) *
|
|
factorial(l + cc2) *
|
|
factorial(l - cc2) *
|
|
(2*l + 1));
|
|
|
|
sfac1 = factorial(3*l + 1);
|
|
sfac2 = factorial(l);
|
|
dcg = sqrt(sfac2*sfac2*sfac2 / sfac1);
|
|
|
|
cglist[idxcg_count] = sum * dcg * sfaccg;
|
|
idxcg_count++;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
factorial n, wrapper for precomputed table
|
|
------------------------------------------------------------------------- */
|
|
|
|
double ComputeOrientOrderAtom::factorial(int n)
|
|
{
|
|
if (n < 0 || n > nmaxfactorial) {
|
|
char str[128];
|
|
sprintf(str, "Invalid argument to factorial %d", n);
|
|
error->all(FLERR, str);
|
|
}
|
|
|
|
return nfac_table[n];
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
factorial n table, size SNA::nmaxfactorial+1
|
|
------------------------------------------------------------------------- */
|
|
|
|
const double ComputeOrientOrderAtom::nfac_table[] = {
|
|
1,
|
|
1,
|
|
2,
|
|
6,
|
|
24,
|
|
120,
|
|
720,
|
|
5040,
|
|
40320,
|
|
362880,
|
|
3628800,
|
|
39916800,
|
|
479001600,
|
|
6227020800,
|
|
87178291200,
|
|
1307674368000,
|
|
20922789888000,
|
|
355687428096000,
|
|
6.402373705728e+15,
|
|
1.21645100408832e+17,
|
|
2.43290200817664e+18,
|
|
5.10909421717094e+19,
|
|
1.12400072777761e+21,
|
|
2.5852016738885e+22,
|
|
6.20448401733239e+23,
|
|
1.5511210043331e+25,
|
|
4.03291461126606e+26,
|
|
1.08888694504184e+28,
|
|
3.04888344611714e+29,
|
|
8.8417619937397e+30,
|
|
2.65252859812191e+32,
|
|
8.22283865417792e+33,
|
|
2.63130836933694e+35,
|
|
8.68331761881189e+36,
|
|
2.95232799039604e+38,
|
|
1.03331479663861e+40,
|
|
3.71993326789901e+41,
|
|
1.37637530912263e+43,
|
|
5.23022617466601e+44,
|
|
2.03978820811974e+46,
|
|
8.15915283247898e+47,
|
|
3.34525266131638e+49,
|
|
1.40500611775288e+51,
|
|
6.04152630633738e+52,
|
|
2.65827157478845e+54,
|
|
1.1962222086548e+56,
|
|
5.50262215981209e+57,
|
|
2.58623241511168e+59,
|
|
1.24139155925361e+61,
|
|
6.08281864034268e+62,
|
|
3.04140932017134e+64,
|
|
1.55111875328738e+66,
|
|
8.06581751709439e+67,
|
|
4.27488328406003e+69,
|
|
2.30843697339241e+71,
|
|
1.26964033536583e+73,
|
|
7.10998587804863e+74,
|
|
4.05269195048772e+76,
|
|
2.35056133128288e+78,
|
|
1.3868311854569e+80,
|
|
8.32098711274139e+81,
|
|
5.07580213877225e+83,
|
|
3.14699732603879e+85,
|
|
1.98260831540444e+87,
|
|
1.26886932185884e+89,
|
|
8.24765059208247e+90,
|
|
5.44344939077443e+92,
|
|
3.64711109181887e+94,
|
|
2.48003554243683e+96,
|
|
1.71122452428141e+98,
|
|
1.19785716699699e+100,
|
|
8.50478588567862e+101,
|
|
6.12344583768861e+103,
|
|
4.47011546151268e+105,
|
|
3.30788544151939e+107,
|
|
2.48091408113954e+109,
|
|
1.88549470166605e+111,
|
|
1.45183092028286e+113,
|
|
1.13242811782063e+115,
|
|
8.94618213078297e+116,
|
|
7.15694570462638e+118,
|
|
5.79712602074737e+120,
|
|
4.75364333701284e+122,
|
|
3.94552396972066e+124,
|
|
3.31424013456535e+126,
|
|
2.81710411438055e+128,
|
|
2.42270953836727e+130,
|
|
2.10775729837953e+132,
|
|
1.85482642257398e+134,
|
|
1.65079551609085e+136,
|
|
1.48571596448176e+138,
|
|
1.3520015276784e+140,
|
|
1.24384140546413e+142,
|
|
1.15677250708164e+144,
|
|
1.08736615665674e+146,
|
|
1.03299784882391e+148,
|
|
9.91677934870949e+149,
|
|
9.61927596824821e+151,
|
|
9.42689044888324e+153,
|
|
9.33262154439441e+155,
|
|
9.33262154439441e+157,
|
|
9.42594775983835e+159,
|
|
9.61446671503512e+161,
|
|
9.90290071648618e+163,
|
|
1.02990167451456e+166,
|
|
1.08139675824029e+168,
|
|
1.14628056373471e+170,
|
|
1.22652020319614e+172,
|
|
1.32464181945183e+174,
|
|
1.44385958320249e+176,
|
|
1.58824554152274e+178,
|
|
1.76295255109024e+180,
|
|
1.97450685722107e+182,
|
|
2.23119274865981e+184,
|
|
2.54355973347219e+186,
|
|
2.92509369349301e+188,
|
|
3.3931086844519e+190,
|
|
3.96993716080872e+192,
|
|
4.68452584975429e+194,
|
|
5.5745857612076e+196,
|
|
6.68950291344912e+198,
|
|
8.09429852527344e+200,
|
|
9.8750442008336e+202,
|
|
1.21463043670253e+205,
|
|
1.50614174151114e+207,
|
|
1.88267717688893e+209,
|
|
2.37217324288005e+211,
|
|
3.01266001845766e+213,
|
|
3.8562048236258e+215,
|
|
4.97450422247729e+217,
|
|
6.46685548922047e+219,
|
|
8.47158069087882e+221,
|
|
1.118248651196e+224,
|
|
1.48727070609069e+226,
|
|
1.99294274616152e+228,
|
|
2.69047270731805e+230,
|
|
3.65904288195255e+232,
|
|
5.01288874827499e+234,
|
|
6.91778647261949e+236,
|
|
9.61572319694109e+238,
|
|
1.34620124757175e+241,
|
|
1.89814375907617e+243,
|
|
2.69536413788816e+245,
|
|
3.85437071718007e+247,
|
|
5.5502938327393e+249,
|
|
8.04792605747199e+251,
|
|
1.17499720439091e+254,
|
|
1.72724589045464e+256,
|
|
2.55632391787286e+258,
|
|
3.80892263763057e+260,
|
|
5.71338395644585e+262,
|
|
8.62720977423323e+264,
|
|
1.31133588568345e+267,
|
|
2.00634390509568e+269,
|
|
3.08976961384735e+271,
|
|
4.78914290146339e+273,
|
|
7.47106292628289e+275,
|
|
1.17295687942641e+278,
|
|
1.85327186949373e+280,
|
|
2.94670227249504e+282,
|
|
4.71472363599206e+284,
|
|
7.59070505394721e+286,
|
|
1.22969421873945e+289,
|
|
2.0044015765453e+291,
|
|
3.28721858553429e+293,
|
|
5.42391066613159e+295,
|
|
9.00369170577843e+297,
|
|
1.503616514865e+300, // nmaxfactorial = 167
|
|
};
|
|
|