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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5741 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-03-07 21:25:10 +00:00
parent 10e24b27e1
commit 6edb314c91
1 changed files with 106 additions and 106 deletions
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212
src/fix_store_state.cpp
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@ -355,19 +355,19 @@ void FixStoreState::init()
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all("Compute ID for fix ave/atom does not exist");
error->all("Compute ID for fix store/state does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all("Fix ID for fix ave/atom does not exist");
error->all("Fix ID for fix store/state does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all("Variable name for fix ave/atom does not exist");
error->all("Variable name for fix store/state does not exist");
value2index[m] = ivariable;
}
}
@ -407,8 +407,8 @@ void FixStoreState::end_of_step()
// fill vector or array with per-atom values
if (values) buf = &values[0][0];
else buf = NULL;
if (values) vbuf = &values[0][0];
else vbuf = NULL;
for (int m = 0; m < nvalues; m++) {
if (which[m] == KEYWORD && kflag) (this->*pack_choice[m])(m);
@ -487,7 +487,7 @@ void FixStoreState::grow_arrays(int nmax)
{
values = memory->grow_2d_double_array(values,nmax,nvalues,
"fix_store:values");
if (nvalues == 0) {
if (nvalues == 1) {
if (nmax) vector_atom = &values[0][0];
else vector_atom = NULL;
} else array_atom = values;
@ -583,8 +583,8 @@ void FixStoreState::pack_id(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = tag[i];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = tag[i];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -598,8 +598,8 @@ void FixStoreState::pack_molecule(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = molecule[i];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = molecule[i];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -613,8 +613,8 @@ void FixStoreState::pack_type(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = type[i];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = type[i];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -631,14 +631,14 @@ void FixStoreState::pack_mass(int n)
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = rmass[i];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = rmass[i];
else vbuf[n] = 0.0;
n += nvalues;
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = mass[type[i]];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = mass[type[i]];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -653,8 +653,8 @@ void FixStoreState::pack_x(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = x[i][0];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = x[i][0];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -668,8 +668,8 @@ void FixStoreState::pack_y(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = x[i][1];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = x[i][1];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -683,8 +683,8 @@ void FixStoreState::pack_z(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = x[i][2];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = x[i][2];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -701,8 +701,8 @@ void FixStoreState::pack_xs(int n)
double invxprd = 1.0/domain->xprd;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = (x[i][0] - boxxlo) * invxprd;
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = (x[i][0] - boxxlo) * invxprd;
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -719,8 +719,8 @@ void FixStoreState::pack_ys(int n)
double invyprd = 1.0/domain->yprd;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = (x[i][1] - boxylo) * invyprd;
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = (x[i][1] - boxylo) * invyprd;
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -737,8 +737,8 @@ void FixStoreState::pack_zs(int n)
double invzprd = 1.0/domain->zprd;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = (x[i][2] - boxzlo) * invzprd;
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = (x[i][2] - boxzlo) * invzprd;
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -756,9 +756,9 @@ void FixStoreState::pack_xs_triclinic(int n)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = h_inv[0]*(x[i][0]-boxlo[0]) +
vbuf[n] = h_inv[0]*(x[i][0]-boxlo[0]) +
h_inv[5]*(x[i][1]-boxlo[1]) + h_inv[4]*(x[i][2]-boxlo[2]);
else buf[n] = 0.0;
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -776,8 +776,8 @@ void FixStoreState::pack_ys_triclinic(int n)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = h_inv[1]*(x[i][1]-boxlo[1]) + h_inv[3]*(x[i][2]-boxlo[2]);
else buf[n] = 0.0;
vbuf[n] = h_inv[1]*(x[i][1]-boxlo[1]) + h_inv[3]*(x[i][2]-boxlo[2]);
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -795,8 +795,8 @@ void FixStoreState::pack_zs_triclinic(int n)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = h_inv[2]*(x[i][2]-boxlo[2]);
else buf[n] = 0.0;
vbuf[n] = h_inv[2]*(x[i][2]-boxlo[2]);
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -814,9 +814,9 @@ void FixStoreState::pack_xu(int n)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
buf[n] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
if (comflag) buf[n] -= cm[0];
} else buf[n] = 0.0;
vbuf[n] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
if (comflag) vbuf[n] -= cm[0];
} else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -834,9 +834,9 @@ void FixStoreState::pack_yu(int n)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
buf[n] = x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
if (comflag) buf[n] -= cm[1];
} else buf[n] = 0.0;
vbuf[n] = x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
if (comflag) vbuf[n] -= cm[1];
} else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -854,9 +854,9 @@ void FixStoreState::pack_zu(int n)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
buf[n] = x[i][2] + ((image[i] >> 20) - 512) * zprd;
if (comflag) buf[n] -= cm[2];
} else buf[n] = 0.0;
vbuf[n] = x[i][2] + ((image[i] >> 20) - 512) * zprd;
if (comflag) vbuf[n] -= cm[2];
} else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -878,9 +878,9 @@ void FixStoreState::pack_xu_triclinic(int n)
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
buf[n] = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox;
if (comflag) buf[n] -= cm[0];
} else buf[n] = 0.0;
vbuf[n] = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox;
if (comflag) vbuf[n] -= cm[0];
} else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -901,9 +901,9 @@ void FixStoreState::pack_yu_triclinic(int n)
if (mask[i] & groupbit) {
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
buf[n] = x[i][1] + h[1]*ybox + h[3]*zbox;
if (comflag) buf[n] -= cm[1];
} else buf[n] = 0.0;
vbuf[n] = x[i][1] + h[1]*ybox + h[3]*zbox;
if (comflag) vbuf[n] -= cm[1];
} else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -923,9 +923,9 @@ void FixStoreState::pack_zu_triclinic(int n)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
zbox = (image[i] >> 20) - 512;
buf[n] = x[i][2] + h[2]*zbox;
if (comflag) buf[n] -= cm[2];
} else buf[n] = 0.0;
vbuf[n] = x[i][2] + h[2]*zbox;
if (comflag) vbuf[n] -= cm[2];
} else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -939,8 +939,8 @@ void FixStoreState::pack_ix(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = (image[i] & 1023) - 512;
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = (image[i] & 1023) - 512;
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -954,8 +954,8 @@ void FixStoreState::pack_iy(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = (image[i] >> 10 & 1023) - 512;
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = (image[i] >> 10 & 1023) - 512;
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -969,8 +969,8 @@ void FixStoreState::pack_iz(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = (image[i] >> 20) - 512;
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = (image[i] >> 20) - 512;
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -984,8 +984,8 @@ void FixStoreState::pack_vx(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = v[i][0];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = v[i][0];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -999,8 +999,8 @@ void FixStoreState::pack_vy(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = v[i][1];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = v[i][1];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1014,8 +1014,8 @@ void FixStoreState::pack_vz(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = v[i][2];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = v[i][2];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1029,8 +1029,8 @@ void FixStoreState::pack_fx(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = f[i][0];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = f[i][0];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1044,8 +1044,8 @@ void FixStoreState::pack_fy(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = f[i][1];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = f[i][1];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1059,8 +1059,8 @@ void FixStoreState::pack_fz(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = f[i][2];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = f[i][2];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1074,8 +1074,8 @@ void FixStoreState::pack_q(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = q[i];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = q[i];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1089,8 +1089,8 @@ void FixStoreState::pack_mux(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = mu[i][0];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = mu[i][0];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1104,8 +1104,8 @@ void FixStoreState::pack_muy(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = mu[i][1];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = mu[i][1];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1119,8 +1119,8 @@ void FixStoreState::pack_muz(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = mu[i][2];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = mu[i][2];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1134,8 +1134,8 @@ void FixStoreState::pack_radius(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = radius[i];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = radius[i];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1149,8 +1149,8 @@ void FixStoreState::pack_omegax(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = omega[i][0];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = omega[i][0];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1164,8 +1164,8 @@ void FixStoreState::pack_omegay(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = omega[i][1];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = omega[i][1];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1179,8 +1179,8 @@ void FixStoreState::pack_omegaz(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = omega[i][2];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = omega[i][2];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1194,8 +1194,8 @@ void FixStoreState::pack_angmomx(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = angmom[i][0];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = angmom[i][0];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1209,8 +1209,8 @@ void FixStoreState::pack_angmomy(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = angmom[i][1];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = angmom[i][1];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1224,8 +1224,8 @@ void FixStoreState::pack_angmomz(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = angmom[i][2];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = angmom[i][2];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1239,8 +1239,8 @@ void FixStoreState::pack_quatw(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = quat[i][0];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = quat[i][0];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1254,8 +1254,8 @@ void FixStoreState::pack_quati(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = quat[i][1];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = quat[i][1];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1269,8 +1269,8 @@ void FixStoreState::pack_quatj(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = quat[i][2];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = quat[i][2];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1284,8 +1284,8 @@ void FixStoreState::pack_quatk(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = quat[i][3];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = quat[i][3];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1299,8 +1299,8 @@ void FixStoreState::pack_tqx(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = torque[i][0];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = torque[i][0];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1314,8 +1314,8 @@ void FixStoreState::pack_tqy(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = torque[i][1];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = torque[i][1];
else vbuf[n] = 0.0;
n += nvalues;
}
}
@ -1329,8 +1329,8 @@ void FixStoreState::pack_tqz(int n)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = torque[i][2];
else buf[n] = 0.0;
if (mask[i] & groupbit) vbuf[n] = torque[i][2];
else vbuf[n] = 0.0;
n += nvalues;
}
}