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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3581 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-12-18 21:02:30 +00:00
parent e02002f46c
commit bc155995d7
7 changed files with 364 additions and 164 deletions
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104
src/compute_angle_local.cpp
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@ -25,8 +25,6 @@
using namespace LAMMPS_NS;
enum{THETA,ENERGY};
#define DELTA 10000
/* ---------------------------------------------------------------------- */
@ -44,28 +42,19 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
if (nvalues == 1) size_local_cols = 0;
else size_local_cols = nvalues;
which = new int[nvalues];
pack_choice = new FnPtrPack[nvalues];
tflag = eflag = 0;
tflag = eflag = -1;
nvalues = 0;
int i;
for (int iarg = 3; iarg < narg; iarg++) {
i = iarg-3;
if (strcmp(arg[iarg],"theta") == 0) {
tflag = 1;
which[i] = THETA;
pack_choice[i] = &ComputeAngleLocal::pack_theta;
} else if (strcmp(arg[iarg],"energy") == 0) {
eflag = 1;
which[i] = ENERGY;
pack_choice[i] = &ComputeAngleLocal::pack_energy;
} else error->all("Invalid keyword in compute angle/local command");
if (strcmp(arg[iarg],"theta") == 0) tflag = nvalues++;
else if (strcmp(arg[iarg],"eng") == 0) eflag = nvalues++;
else error->all("Invalid keyword in compute angle/local command");
}
nmax = 0;
theta = energy = NULL;
vector = NULL;
array = NULL;
}
@ -73,10 +62,7 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
ComputeAngleLocal::~ComputeAngleLocal()
{
delete [] which;
delete [] pack_choice;
memory->sfree(theta);
memory->sfree(energy);
memory->sfree(vector);
memory->destroy_2d_double_array(array);
}
@ -106,14 +92,6 @@ void ComputeAngleLocal::compute_local()
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
ncount = compute_angles(1);
// fill array with theta/energy values
if (nvalues > 1) {
if (array) buf = array[0];
for (int n = 0; n < nvalues; n++)
(this->*pack_choice[n])(n);
}
}
/* ----------------------------------------------------------------------
@ -129,9 +107,10 @@ void ComputeAngleLocal::compute_local()
int ComputeAngleLocal::compute_angles(int flag)
{
int i,atom1,atom2,atom3;
int i,m,n,atom1,atom2,atom3;
double delx1,dely1,delz1,delx2,dely2,delz2;
double rsq1,rsq2,r1,r2,c;
double *tbuf,*ebuf;
double **x = atom->x;
int *num_angle = atom->num_angle;
@ -143,10 +122,20 @@ int ComputeAngleLocal::compute_angles(int flag)
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (flag) {
if (nvalues == 1) {
if (tflag >= 0) tbuf = vector;
if (eflag >= 0) ebuf = vector;
} else {
if (tflag >= 0) tbuf = &array[0][tflag];
if (eflag >= 0) ebuf = &array[0][eflag];
}
}
Angle *angle = force->angle;
double PI = 4.0*atan(1.0);
int m = 0;
m = n = 0;
for (atom2 = 0; atom2 < nlocal; atom2++) {
if (!(mask[atom2] & groupbit)) continue;
for (i = 0; i < num_angle[atom2]; i++) {
@ -158,7 +147,7 @@ int ComputeAngleLocal::compute_angles(int flag)
if (angle_type[atom2][i] == 0) continue;
if (flag) {
if (tflag) {
if (tflag >= 0) {
delx1 = x[atom1][0] - x[atom2][0];
dely1 = x[atom1][1] - x[atom2][1];
delz1 = x[atom1][2] - x[atom2][2];
@ -181,14 +170,15 @@ int ComputeAngleLocal::compute_angles(int flag)
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
theta[m] = 180.0*acos(c)/PI;
tbuf[n] = 180.0*acos(c)/PI;
}
if (eflag) {
if (eflag >= 0) {
if (angle_type[atom2][i] > 0)
energy[m] = angle->single(angle_type[atom2][i],atom1,atom2,atom3);
else energy[m] = 0.0;
ebuf[n] = angle->single(angle_type[atom2][i],atom1,atom2,atom3);
else ebuf[n] = 0.0;
}
n += nvalues;
}
m++;
@ -200,46 +190,17 @@ int ComputeAngleLocal::compute_angles(int flag)
/* ---------------------------------------------------------------------- */
void ComputeAngleLocal::pack_theta(int n)
{
for (int m = 0; m < ncount; m++) {
buf[n] = theta[m];
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeAngleLocal::pack_energy(int n)
{
for (int m = 0; m < ncount; m++) {
buf[n] = energy[m];
n += nvalues;
}
}
/* ---------------------------------------------------------------------- */
void ComputeAngleLocal::reallocate(int n)
{
// grow vector or array and indices array
while (nmax < n) nmax += DELTA;
if (tflag) {
memory->sfree(theta);
theta = (double *) memory->smalloc(nmax*sizeof(double),
"bond/local:theta");
}
if (eflag) {
memory->sfree(energy);
energy = (double *) memory->smalloc(nmax*sizeof(double),
"bond/local:energy");
}
if (nvalues == 1) {
if (tflag) vector_local = theta;
if (eflag) vector_local = energy;
memory->sfree(vector);
vector = (double *) memory->smalloc(nmax*sizeof(double),
"bond/local:vector");
vector_local = vector;
} else {
memory->destroy_2d_double_array(array);
array = memory->create_2d_double_array(nmax,nvalues,
@ -254,9 +215,6 @@ void ComputeAngleLocal::reallocate(int n)
double ComputeAngleLocal::memory_usage()
{
double bytes = 0.0;
if (tflag) bytes += nmax * sizeof(double);
if (eflag) bytes += nmax * sizeof(double);
if (nvalues > 1) bytes += nmax*nvalues * sizeof(double);
double bytes = nmax*nvalues * sizeof(double);
return bytes;
}