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aa9b805cc9c77cb774c6d5b329a48d87d8357e8e
lammps/src/compute_orientorder_atom.cpp
Aidan Thompson aa9b805cc9 started on W_l
2019-08-23 18:11:52 -06:00

570 lines
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/* ----------------------------------------------------------------------
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
/* ---------------------------------------------------------------------- */
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)
{
if (narg < 3 ) error->all(FLERR,"Illegal compute orientorder/atom command");
// set default values for optional args
nnn = 12;
cutsq = 0.0;
qlcompflag = 0;
// 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],"components") == 0) {
qlcompflag = 1;
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute orientorder/atom command");
qlcomp = force->numeric(FLERR,arg[iarg+1]);
if (qlcomp <= 0)
error->all(FLERR,"Illegal compute orientorder/atom command");
iqlcomp = -1;
for (int il = 0; il < nqlist; il++)
if (qlcomp == qlist[il]) {
iqlcomp = il;
break;
}
if (iqlcomp < 0)
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 error->all(FLERR,"Illegal compute orientorder/atom command");
}
if (qlcompflag) ncol = nqlist + 2*(2*qlcomp+1);
else ncol = nqlist;
peratom_flag = 1;
size_peratom_cols = ncol;
nmax = 0;
maxneigh = 0;
}
/* ---------------------------------------------------------------------- */
ComputeOrientOrderAtom::~ComputeOrientOrderAtom()
{
memory->destroy(qnarray);
memory->destroy(distsq);
memory->destroy(rlist);
memory->destroy(nearest);
memory->destroy(qlist);
memory->destroy(qnm_r);
memory->destroy(qnm_i);
}
/* ---------------------------------------------------------------------- */
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,qmax,2*qmax+1,"orientorder/atom:qnm_r");
memory->create(qnm_i,qmax,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");
}
/* ---------------------------------------------------------------------- */
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 il = 0; il < nqlist; il++)
qn[il] = 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];
qn[il] = 0.0;
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;
}
}
}
// calculate Q_l
double fac = sqrt(MY_4PI) / ncount;
double normfac = 0.0;
int jcount = 0;
for (int il = 0; il < nqlist; il++) {
int l = qlist[il];
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[jcount++] = fac * sqrt(qm_sum / (2*l+1));
if (qlcompflag && iqlcomp == il) normfac = 1.0/sqrt(qm_sum);
}
// TODO:
// 1. Need to allocate extra memory in qn[] for this option
// 2. Need to add keyword option
// 3. Need to caclulate Clebsch-Gordan/Wigner 3j coefficients
// 4. Compate to bcc values in /Users/athomps/netapp/codes/MatMiner/matminer/matminer/featurizers/boop
// // calculate W_l
// if (wlflag) {
// 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; m2++)) {
// int m = m1 + m2 - l;
// qm1qm2_r = qnm_r[il][m1]*qnm_r[il][m2] - qnm_i[il][m1]*qnm_i[il][m2];
// 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])*cg;
// }
// }
// qn[jcount++] = wlsum;
// }
// }
// output of the complex vector
if (qlcompflag) {
for(int m = 0; m < 2*qlcomp+1; m++) {
qn[jcount++] = qnm_r[iqlcomp][m] * normfac;
qn[jcount++] = qnm_i[iqlcomp][m] * normfac;
}
}
}
/* ----------------------------------------------------------------------
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;
}
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