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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11027 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-11-20 17:21:27 +00:00
parent 5ec8a7c930
commit ec6c602730
17 changed files with 1273 additions and 1221 deletions
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177
src/atom_vec_line.cpp
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@ -480,13 +480,13 @@ int AtomVecLine::pack_border(int n, int *list, double *buf,
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
if (line[j] < 0) buf[m++] = 0;
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d;
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = 1;
buf[m++] = ubuf(1).d;
buf[m++] = bonus[line[j]].length;
buf[m++] = bonus[line[j]].theta;
}
@ -506,13 +506,13 @@ int AtomVecLine::pack_border(int n, int *list, double *buf,
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
if (line[j] < 0) buf[m++] = 0;
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d;
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = 1;
buf[m++] = ubuf(1).d;
buf[m++] = bonus[line[j]].length;
buf[m++] = bonus[line[j]].theta;
}
@ -541,13 +541,13 @@ int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
if (line[j] < 0) buf[m++] = 0;
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d;
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = 1;
buf[m++] = ubuf(1).d;
buf[m++] = bonus[line[j]].length;
buf[m++] = bonus[line[j]].theta;
}
@ -574,13 +574,13 @@ int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
if (line[j] < 0) buf[m++] = 0;
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d;
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = 1;
buf[m++] = ubuf(1).d;
buf[m++] = bonus[line[j]].length;
buf[m++] = bonus[line[j]].theta;
}
@ -600,13 +600,13 @@ int AtomVecLine::pack_border_vel(int n, int *list, double *buf,
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
if (line[j] < 0) buf[m++] = 0;
buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = ubuf(molecule[j]).d;
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = 1;
buf[m++] = ubuf(1).d;
buf[m++] = bonus[line[j]].length;
buf[m++] = bonus[line[j]].theta;
}
@ -643,9 +643,9 @@ int AtomVecLine::pack_border_hybrid(int n, int *list, double *buf)
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = molecule[j];
if (line[j] < 0) buf[m++] = 0;
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = 1;
buf[m++] = ubuf(1).d;
buf[m++] = bonus[line[j]].length;
buf[m++] = bonus[line[j]].theta;
}
@ -666,11 +666,11 @@ void AtomVecLine::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
molecule[i] = static_cast<int> (buf[m++]);
line[i] = static_cast<int> (buf[m++]);
tag[i] = (int) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
@ -702,11 +702,11 @@ void AtomVecLine::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
molecule[i] = static_cast<int> (buf[m++]);
line[i] = static_cast<int> (buf[m++]);
tag[i] = (int) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
@ -740,8 +740,8 @@ int AtomVecLine::unpack_border_hybrid(int n, int first, double *buf)
m = 0;
last = first + n;
for (i = first; i < last; i++) {
molecule[i] = static_cast<int> (buf[m++]);
line[i] = static_cast<int> (buf[m++]);
molecule[i] = (int) ubuf(buf[m++]).i;
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
@ -770,20 +770,20 @@ int AtomVecLine::pack_exchange(int i, double *buf)
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
*((tagint *) &buf[m++]) = image[i];
buf[m++] = ubuf(tag[i]).d;
buf[m++] = ubuf(type[i]).d;
buf[m++] = ubuf(mask[i]).d;
buf[m++] = ubuf(image[i]).d;
buf[m++] = molecule[i];
buf[m++] = ubuf(molecule[i]).d;
buf[m++] = rmass[i];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
if (line[i] < 0) buf[m++] = 0;
if (line[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = 1;
buf[m++] = ubuf(1).d;
int j = line[i];
buf[m++] = bonus[j].length;
buf[m++] = bonus[j].theta;
@ -811,18 +811,18 @@ int AtomVecLine::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = *((tagint *) &buf[m++]);
tag[nlocal] = (int) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (tagint) ubuf(buf[m++]).i;
molecule[nlocal] = static_cast<int> (buf[m++]);
molecule[nlocal] = (int) ubuf(buf[m++]).i;
rmass[nlocal] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
line[nlocal] = static_cast<int> (buf[m++]);
line[nlocal] = (int) ubuf(buf[m++]).i;
if (line[nlocal] == 0) line[nlocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
@ -876,23 +876,23 @@ int AtomVecLine::pack_restart(int i, double *buf)
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
*((tagint *) &buf[m++]) = image[i];
buf[m++] = ubuf(tag[i]).d;
buf[m++] = ubuf(type[i]).d;
buf[m++] = ubuf(mask[i]).d;
buf[m++] = ubuf(image[i]).d;
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = molecule[i];
buf[m++] = ubuf(molecule[i]).d;
buf[m++] = rmass[i];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
if (line[i] < 0) buf[m++] = 0;
if (line[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = 1;
buf[m++] = ubuf(1).d;
int j = line[i];
buf[m++] = bonus[j].length;
buf[m++] = bonus[j].theta;
@ -923,21 +923,21 @@ int AtomVecLine::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = *((tagint *) &buf[m++]);
tag[nlocal] = (int) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (tagint) ubuf(buf[m++]).i;
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
molecule[nlocal] = static_cast<int> (buf[m++]);
molecule[nlocal] = (int) ubuf(buf[m++]).i;
rmass[nlocal] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
line[nlocal] = static_cast<int> (buf[m++]);
line[nlocal] = (int) ubuf(buf[m++]).i;
if (line[nlocal] == 0) line[nlocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
@ -1133,19 +1133,19 @@ void AtomVecLine::pack_data(double **buf)
{
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = tag[i];
buf[i][1] = molecule[i];
buf[i][2] = type[i];
if (line[i] < 0) buf[i][3] = 0;
else buf[i][3] = 1;
buf[i][0] = ubuf(tag[i]).d;
buf[i][1] = ubuf(molecule[i]).d;
buf[i][2] = ubuf(type[i]).d;
if (line[i] < 0) buf[i][3] = ubuf(0).d;
else buf[i][3] = ubuf(1).d;
if (line[i] < 0) buf[i][4] = rmass[i];
else buf[i][4] = rmass[i]/bonus[line[i]].length;
buf[i][5] = x[i][0];
buf[i][6] = x[i][1];
buf[i][7] = x[i][2];
buf[i][8] = (image[i] & IMGMASK) - IMGMAX;
buf[i][9] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
buf[i][10] = (image[i] >> IMG2BITS) - IMGMAX;
buf[i][8] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
buf[i][9] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][10] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
}
}
@ -1155,9 +1155,9 @@ void AtomVecLine::pack_data(double **buf)
int AtomVecLine::pack_data_hybrid(int i, double *buf)
{
buf[0] = molecule[i];
if (line[i] < 0) buf[1] = 0;
else buf[1] = 1;
buf[0] = ubuf(molecule[i]).d;
if (line[i] < 0) buf[1] = ubuf(0).d;
else buf[1] = ubuf(1).d;
if (line[i] < 0) buf[2] = rmass[i];
else buf[2] = rmass[i]/bonus[line[i]].length;
return 3;
@ -1171,9 +1171,11 @@ void AtomVecLine::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,"%d %d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(int) buf[i][0],(int) buf[i][1],(int) buf[i][2],(int) buf[i][3],
(int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,(int) ubuf(buf[i][3]).i,
buf[i][4],buf[i][5],buf[i][6],buf[i][7],
(int) buf[i][8],(int) buf[i][9],(int) buf[i][10]);
(int) ubuf(buf[i][8]).i,(int) ubuf(buf[i][9]).i,
(int) ubuf(buf[i][10]).i);
}
/* ----------------------------------------------------------------------
@ -1182,7 +1184,7 @@ void AtomVecLine::write_data(FILE *fp, int n, double **buf)
int AtomVecLine::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %d %d %-1.16e",(int) buf[0],(int) buf[1],buf[2]);
fprintf(fp," %d %d %-1.16e",(int) ubuf(buf[0]).i,(int) ubuf(buf[1]).i,buf[2]);
return 3;
}
@ -1194,7 +1196,7 @@ void AtomVecLine::pack_vel(double **buf)
{
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = tag[i];
buf[i][0] = ubuf(tag[i]).d;
buf[i][1] = v[i][0];
buf[i][2] = v[i][1];
buf[i][3] = v[i][2];
@ -1224,7 +1226,7 @@ void AtomVecLine::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
(int) buf[i][0],buf[i][1],buf[i][2],buf[i][3],
(int) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
}
@ -1257,7 +1259,8 @@ bigint AtomVecLine::memory_usage()
if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
if (atom->memcheck("omega")) bytes += memory->usage(omega,nmax,3);
if (atom->memcheck("torque")) bytes += memory->usage(torque,nmax*comm->nthreads,3);
if (atom->memcheck("torque"))
bytes += memory->usage(torque,nmax*comm->nthreads,3);
if (atom->memcheck("line")) bytes += memory->usage(line,nmax);
bytes += nmax_bonus*sizeof(Bonus);