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import contributed code for computes coord/atom and orientorder/atom

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This commit is contained in:
Axel Kohlmeyer
2017-01-10 12:29:22 -05:00
parent c31f1e9f22
commit 95706ac846
6 changed files with 299 additions and 83 deletions
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32
src/compute_orientorder_atom.cpp
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@ -54,6 +54,7 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
nnn = 12;
cutsq = 0.0;
qlcompflag = 0;
// specify which orders to request
@ -96,6 +97,20 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
if (qlist[iw] > qmax) qmax = qlist[iw];
}
iarg += nqlist;
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 iw = 0; iw < nqlist; iw++)
if (qlcomp == qlist[iw]) {
iqlcomp = iw;
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]);
@ -105,7 +120,9 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
} else error->all(FLERR,"Illegal compute orientorder/atom command");
}
ncol = nqlist;
if (qlcompflag) ncol = nqlist + 2*(2*qlcomp+1);
else ncol = nqlist;
peratom_flag = 1;
size_peratom_cols = ncol;
@ -434,6 +451,7 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist,
}
double fac = sqrt(MY_4PI) / ncount;
double normfac = 0.0;
for (int iw = 0; iw < nqlist; iw++) {
int n = qlist[iw];
double qm_sum = 0.0;
@ -443,6 +461,18 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist,
// qnm_r[iw][m]*qnm_r[iw][m] + qnm_i[iw][m]*qnm_i[iw][m]);
}
qn[iw] = fac * sqrt(qm_sum / (2*n+1));
if (qlcompflag && iqlcomp == iw) normfac = 1.0/sqrt(qm_sum);
}
// output of the complex vector
if (qlcompflag) {
int j = nqlist;
for(int m = 0; m < 2*qlcomp+1; m++) {
qn[j++] = qnm_r[iqlcomp][m] * normfac;
qn[j++] = qnm_i[iqlcomp][m] * normfac;
}
}
}