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replace string compare with enums, fix memory leak, formatting cleanup

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This commit is contained in:
Axel Kohlmeyer
2017-01-10 12:52:37 -05:00
parent 95706ac846
commit 92d15d4a89
4 changed files with 145 additions and 137 deletions
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150
src/compute_orientorder_atom.cpp
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@ -46,7 +46,8 @@ using namespace std;
ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
distsq(NULL), nearest(NULL), rlist(NULL), qlist(NULL), qnarray(NULL), qnm_r(NULL), qnm_i(NULL)
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");
@ -57,7 +58,7 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
qlcompflag = 0;
// specify which orders to request
nqlist = 5;
memory->create(qlist,nqlist,"orientorder/atom:qlist");
qlist[0] = 4;
@ -73,48 +74,55 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
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");
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");
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");
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 iw = 0; iw < nqlist; iw++) {
qlist[iw] = force->numeric(FLERR,arg[iarg+iw]);
if (qlist[iw] < 0)
error->all(FLERR,"Illegal compute orientorder/atom command");
if (qlist[iw] > qmax) qmax = qlist[iw];
qlist[iw] = force->numeric(FLERR,arg[iarg+iw]);
if (qlist[iw] < 0)
error->all(FLERR,"Illegal compute orientorder/atom command");
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");
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;
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");
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");
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");
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");
@ -141,7 +149,7 @@ ComputeOrientOrderAtom::~ComputeOrientOrderAtom()
memory->destroy(qlist);
memory->destroy(qnm_r);
memory->destroy(qnm_i);
}
/* ---------------------------------------------------------------------- */
@ -224,7 +232,7 @@ void ComputeOrientOrderAtom::compute_peratom()
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
// insure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
@ -253,9 +261,9 @@ void ComputeOrientOrderAtom::compute_peratom()
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;
rlist[ncount][0] = delx;
rlist[ncount][1] = dely;
rlist[ncount][2] = delz;
nearest[ncount++] = j;
}
}
@ -263,16 +271,16 @@ void ComputeOrientOrderAtom::compute_peratom()
// if not nnn neighbors, order parameter = 0;
if ((ncount == 0) || (ncount < nnn)) {
for (int iw = 0; iw < nqlist; iw++)
qn[iw] = 0.0;
for (int iw = 0; iw < nqlist; iw++)
qn[iw] = 0.0;
continue;
}
// if nnn > 0, use only nearest nnn neighbors
if (nnn > 0) {
select3(nnn,ncount,distsq,nearest,rlist);
ncount = nnn;
select3(nnn,ncount,distsq,nearest,rlist);
ncount = nnn;
}
calc_boop(rlist, ncount, qn, qlist, nqlist);
@ -287,8 +295,8 @@ void ComputeOrientOrderAtom::compute_peratom()
double ComputeOrientOrderAtom::memory_usage()
{
double bytes = ncol*nmax * sizeof(double);
bytes += (qmax*(2*qmax+1)+maxneigh*4) * sizeof(double);
bytes += (nqlist+maxneigh) * sizeof(int);
bytes += (qmax*(2*qmax+1)+maxneigh*4) * sizeof(double);
bytes += (nqlist+maxneigh) * sizeof(int);
return bytes;
}
@ -300,18 +308,18 @@ double ComputeOrientOrderAtom::memory_usage()
// Use no-op do while to create single statement
#define SWAP(a,b) do { \
tmp = a; a = b; b = tmp; \
#define SWAP(a,b) do { \
tmp = a; a = b; b = tmp; \
} while(0)
#define ISWAP(a,b) do { \
itmp = a; a = b; b = itmp; \
#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; \
#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)
/* ---------------------------------------------------------------------- */
@ -330,7 +338,7 @@ void ComputeOrientOrderAtom::select3(int k, int n, double *arr, int *iarr, doubl
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
SWAP(arr[l],arr[ir]);
ISWAP(iarr[l],iarr[ir]);
ISWAP(iarr[l],iarr[ir]);
SWAP3(arr3[l],arr3[ir]);
}
return;
@ -342,17 +350,17 @@ void ComputeOrientOrderAtom::select3(int k, int n, double *arr, int *iarr, doubl
if (arr[l] > arr[ir]) {
SWAP(arr[l],arr[ir]);
ISWAP(iarr[l],iarr[ir]);
SWAP3(arr3[l],arr3[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]);
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]);
SWAP3(arr3[l],arr3[l+1]);
}
i = l+1;
j = ir;
@ -367,7 +375,7 @@ void ComputeOrientOrderAtom::select3(int k, int n, double *arr, int *iarr, doubl
if (j < i) break;
SWAP(arr[i],arr[j]);
ISWAP(iarr[i],iarr[j]);
SWAP3(arr3[i],arr3[j]);
SWAP3(arr3[i],arr3[j]);
}
arr[l+1] = arr[j];
arr[j] = a;
@ -389,9 +397,9 @@ void ComputeOrientOrderAtom::select3(int k, int n, double *arr, int *iarr, doubl
calculate the bond orientational order parameters
------------------------------------------------------------------------- */
void ComputeOrientOrderAtom::calc_boop(double **rlist,
int ncount, double qn[],
int qlist[], int nqlist) {
void ComputeOrientOrderAtom::calc_boop(double **rlist,
int ncount, double qn[],
int qlist[], int nqlist) {
for (int iw = 0; iw < nqlist; iw++) {
int n = qlist[iw];
@ -429,22 +437,22 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist,
double expphim_r = expphi_r;
double expphim_i = expphi_i;
for(int m = 1; m <= +n; m++) {
double prefactor = polar_prefactor(n, m, costheta);
double c_r = prefactor * expphim_r;
double c_i = prefactor * expphim_i;
qnm_r[iw][m+n] += c_r;
qnm_i[iw][m+n] += c_i;
if(m & 1) {
qnm_r[iw][-m+n] -= c_r;
qnm_i[iw][-m+n] += c_i;
} else {
qnm_r[iw][-m+n] += c_r;
qnm_i[iw][-m+n] -= 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;
double prefactor = polar_prefactor(n, m, costheta);
double c_r = prefactor * expphim_r;
double c_i = prefactor * expphim_i;
qnm_r[iw][m+n] += c_r;
qnm_i[iw][m+n] += c_i;
if(m & 1) {
qnm_r[iw][-m+n] -= c_r;
qnm_i[iw][-m+n] += c_i;
} else {
qnm_r[iw][-m+n] += c_r;
qnm_i[iw][-m+n] -= 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;
}
}
@ -458,15 +466,15 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist,
for(int m = 0; m < 2*n+1; m++) {
qm_sum += qnm_r[iw][m]*qnm_r[iw][m] + qnm_i[iw][m]*qnm_i[iw][m];
// printf("Ylm^2 = %d %d %g\n",n,m,
// qnm_r[iw][m]*qnm_r[iw][m] + qnm_i[iw][m]*qnm_i[iw][m]);
// 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++) {
@ -485,7 +493,7 @@ double ComputeOrientOrderAtom::dist(const double r[]) {
}
/* ----------------------------------------------------------------------
polar prefactor for spherical harmonic Y_l^m, where
polar prefactor for spherical harmonic Y_l^m, where
Y_l^m (theta, phi) = prefactor(l, m, cos(theta)) * exp(i*m*phi)
------------------------------------------------------------------------- */