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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5947 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-04-15 22:25:19 +00:00
parent 74c219743e
commit 8ff0659bae
62 changed files with 1016 additions and 822 deletions
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78
src/set.cpp
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@ -18,6 +18,7 @@
#include "set.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "domain.h"
#include "region.h"
#include "group.h"
@ -142,7 +143,7 @@ void Set::command(int narg, char **arg)
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->shape_flag)
if (!atom->ellipsoid_flag)
error->all("Cannot set this attribute for this atom style");
if (xvalue < 0.0 || yvalue < 0.0 || zvalue < 0.0)
error->all("Invalid shape in set command");
@ -177,14 +178,14 @@ void Set::command(int narg, char **arg)
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
wvalue = atof(arg[iarg+4]);
if (!atom->quat_flag)
if (!atom->ellipsoid_flag)
error->all("Cannot set this attribute for this atom style");
set(QUAT);
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_flag)
if (!atom->ellipsoid_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);
@ -358,6 +359,9 @@ void Set::selection(int n)
void Set::set(int keyword)
{
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
selection(atom->nlocal);
int nlocal = atom->nlocal;
@ -376,25 +380,22 @@ void Set::set(int keyword)
// set shape
else if (keyword == SHAPE) {
double **shape = atom->shape;
shape[i][0] = 0.5 * xvalue;
shape[i][1] = 0.5 * yvalue;
shape[i][2] = 0.5 * zvalue;
else if (keyword == SHAPE)
avec_ellipsoid->set_bonus(i,0.5*xvalue,0.5*yvalue,0.5*zvalue);
// set rmass via density
// if radius > 0.0, assume sphere
// if shape > 0.0, assume ellipsoid
// else set rmass to density directly
} else if (keyword == DENSITY) {
else if (keyword == DENSITY) {
if (atom->radius_flag && atom->radius[i] > 0.0)
atom->rmass[i] = 4.0*PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] * dvalue;
else if (atom->shape_flag && atom->shape[i][0] > 0.0)
atom->rmass[i] = 4.0*PI/3.0 *
atom->shape[i][0]*atom->shape[i][1]*atom->shape[i][2] * dvalue;
else atom->rmass[i] = dvalue;
else if (atom->ellipsoid_flag && atom->ellipsoid[i] >= 0) {
double *shape = avec_ellipsoid->bonus[atom->ellipsoid[i]].shape;
atom->rmass[i] = 4.0*PI/3.0 * shape[0]*shape[1]*shape[2] * dvalue;
} else atom->rmass[i] = dvalue;
// reset any or all of 3 image flags
@ -419,17 +420,18 @@ void Set::set(int keyword)
mu[i][2]*mu[i][2]);
// set quaternion orientation
} else if (keyword == QUAT) {
double PI = 4.0*atan(1.0);
if (atom->ellipsoid[i] < 0)
error->one("Cannot set quaternion for atom that is not an ellipsoid");
double *quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
double theta2 = 0.5 * PI * wvalue/180.0;
double sintheta2 = sin(theta2);
double **quat = atom->quat;
quat[i][0] = cos(theta2);
quat[i][1] = xvalue * sintheta2;
quat[i][2] = yvalue * sintheta2;
quat[i][3] = zvalue * sintheta2;
MathExtra::normalize4(quat[i]);
quat[0] = cos(theta2);
quat[1] = xvalue * sintheta2;
quat[2] = yvalue * sintheta2;
quat[3] = zvalue * sintheta2;
MathExtra::normalize4(quat);
}
count++;
}
@ -509,38 +511,48 @@ void Set::setrandom(int keyword)
// no need to normalize quats since creations algorithms already do
} else if (keyword == QUAT_RANDOM) {
double **quat = atom->quat;
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
int *ellipsoid = atom->ellipsoid;
int nlocal = atom->nlocal;
double *quat;
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]) {
if (ellipsoid[i] < 0)
error->one("Cannot set quaternion for atom "
"that is not an ellipsoid");
quat = bonus[ellipsoid[i]].quat;
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;
quat[0] = cos(theta2)*t2;
quat[1] = sin(theta1)*t1;
quat[2] = cos(theta1)*t1;
quat[3] = sin(theta2)*t2;
count++;
}
} else {
double theta2;
double PI = 4.0*atan(1.0);
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (ellipsoid[i] < 0)
error->one("Cannot set quaternion for atom "
"that is not an ellipsoid");
quat = bonus[ellipsoid[i]].quat;
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);
quat[0] = cos(theta2);
quat[1] = 0.0;
quat[2] = 0.0;
quat[3] = sin(theta2);
count++;
}
}