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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@642 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-06-22 16:59:17 +00:00
parent 988a4479e8
commit cea0208207
42 changed files with 245 additions and 194 deletions
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133
src/set.cpp
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@ -26,6 +26,7 @@
#include "force.h"
#include "pair.h"
#include "random_park.h"
#include "math_extra.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -94,7 +95,7 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->molecule == NULL)
if (!atom->molecule_flag)
error->all("Cannot set this attribute for this atom style");
set(MOLECULE);
iarg += 2;
@ -131,7 +132,7 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"charge") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (atom->q == NULL)
if (!atom->q_flag)
error->all("Cannot set this attribute for this atom style");
set(CHARGE);
iarg += 2;
@ -140,31 +141,32 @@ void Set::command(int narg, char **arg)
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (atom->mu == NULL || atom->dipole == NULL)
if (!atom->mu_flag || atom->dipole == NULL)
error->all("Cannot set this attribute for this atom style");
set(DIPOLE);
iarg += 4;
} else if (strcmp(arg[iarg],"dipole/random") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->mu == NULL || atom->shape == NULL)
if (!atom->mu_flag || atom->shape == NULL)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0) error->all("Invalid random number seed in set command");
setrandom(DIPOLE_RANDOM);
iarg += 2;
} else if (strcmp(arg[iarg],"quat") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
if (iarg+5 > narg) error->all("Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (atom->quat == NULL)
wvalue = atof(arg[iarg+4]);
if (!atom->quat_flag)
error->all("Cannot set this attribute for this atom style");
set(QUAT);
iarg += 4;
iarg += 5;
} else if (strcmp(arg[iarg],"quat/random") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->quat == NULL)
if (!atom->quat_flag)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0) error->all("Invalid random number seed in set command");
setrandom(QUAT_RANDOM);
@ -305,11 +307,15 @@ void Set::set(int keyword)
}
} else if (keyword == QUAT) {
// need to set orientation correctly and normalize quat
double PI = 4.0*atan(1.0);
double theta2 = 0.5 * PI * wvalue/180.0;
double sintheta2 = sin(theta2);
double **quat = atom->quat;
quat[i][0] = xvalue;
quat[i][1] = yvalue;
quat[i][2] = zvalue;
quat[i][0] = cos(theta2);
quat[i][1] = xvalue * sintheta2;
quat[i][2] = yvalue * sintheta2;
quat[i][3] = zvalue * sintheta2;
MathExtra::normalize4(quat[i]);
}
count++;
}
@ -345,55 +351,90 @@ void Set::setrandom(int keyword)
count++;
}
// set dipole moments to random orientations
// set dipole moments to random orientations in 3d or 2d
// dipole length is determined by dipole type array
} else if (keyword == DIPOLE) {
} else if (keyword == DIPOLE_RANDOM) {
int *type = atom->type;
double *dipole = atom->dipole;
double **mu = atom->mu;
int nlocal = atom->nlocal;
double msq,scale;
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (dipole[type[i]] > 0.0) {
random->reset(seed,x[i]);
mu[i][0] = random->uniform() - 0.5;
mu[i][1] = random->uniform() - 0.5;
mu[i][2] = random->uniform() - 0.5;
msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2];
scale = dipole[type[i]]/sqrt(msq);
mu[i][0] *= scale;
mu[i][1] *= scale;
mu[i][2] *= scale;
count++;
if (domain->dimension == 3) {
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (dipole[type[i]] > 0.0) {
random->reset(seed,x[i]);
mu[i][0] = random->uniform() - 0.5;
mu[i][1] = random->uniform() - 0.5;
mu[i][2] = random->uniform() - 0.5;
msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2];
scale = dipole[type[i]]/sqrt(msq);
mu[i][0] *= scale;
mu[i][1] *= scale;
mu[i][2] *= scale;
count++;
}
}
}
// set quaternions to random orientations
} else {
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (dipole[type[i]] > 0.0) {
random->reset(seed,x[i]);
mu[i][0] = random->uniform() - 0.5;
mu[i][1] = random->uniform() - 0.5;
mu[i][2] = 0.0;
msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1];
scale = dipole[type[i]]/sqrt(msq);
mu[i][0] *= scale;
mu[i][1] *= scale;
count++;
}
}
}
} else if (keyword == QUAT) {
// set quaternions to random orientations in 3d or 2d
// no need to normalize quats since creations algorithms already do
} else if (keyword == QUAT_RANDOM) {
double **quat = atom->quat;
int nlocal = atom->nlocal;
double s,t1,t2,theta1,theta2;
double PI = 4.0*atan(1.0);
if (domain->dimension == 3) {
double s,t1,t2,theta1,theta2;
double PI = 4.0*atan(1.0);
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
s = random->uniform();
t1 = sqrt(1.0-s);
t2 = sqrt(s);
theta1 = 2.0*PI*random->uniform();
theta2 = 2.0*PI*random->uniform();
quat[i][0] = cos(theta2)*t2;
quat[i][1] = sin(theta1)*t1;
quat[i][2] = cos(theta1)*t1;
quat[i][3] = sin(theta2)*t2;
count++;
}
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
s = random->uniform();
t1 = sqrt(1.0-s);
t2 = sqrt(s);
theta1 = 2.0*PI*random->uniform();
theta2 = 2.0*PI*random->uniform();
quat[i][0] = cos(theta2)*t2;
quat[i][1] = sin(theta1)*t1;
quat[i][2] = cos(theta1)*t1;
quat[i][3] = sin(theta2)*t2;
count++;
}
} else {
double theta2;
double PI = 4.0*atan(1.0);
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
theta2 = PI*random->uniform();
quat[i][0] = cos(theta2);
quat[i][1] = 0.0;
quat[i][2] = 0.0;
quat[i][3] = sin(theta2);
count++;
}
}
}
delete random;