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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5932 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-04-13 21:40:14 +00:00
parent e45fbd89d1
commit 819524ebd6
71 changed files with 1167 additions and 2718 deletions
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232
src/fix_nve_sphere.cpp
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@ -53,10 +53,8 @@ FixNVESphere::FixNVESphere(LAMMPS *lmp, int narg, char **arg) :
// error checks
if (!atom->omega_flag || !atom->torque_flag)
error->all("Fix nve/sphere requires atom attributes omega, torque");
if (!atom->radius_flag && !atom->avec->shape_type)
error->all("Fix nve/sphere requires atom attribute diameter or shape");
if (!atom->sphere_flag)
error->all("Fix nve/sphere requires atom style sphere");
if (extra == DIPOLE && !atom->mu_flag)
error->all("Fix nve/sphere requires atom attribute mu");
}
@ -77,38 +75,17 @@ int FixNVESphere::setmask()
void FixNVESphere::init()
{
int i,itype;
// check that all particles are finite-size and spherical
// check that all particles are finite-size
// no point particles allowed
if (atom->radius_flag) {
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (radius[i] == 0.0)
error->one("Fix nve/sphere requires extended particles");
}
} else {
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
itype = type[i];
if (shape[itype][0] == 0.0)
error->one("Fix nve/sphere requires extended particles");
if (shape[itype][0] != shape[itype][1] ||
shape[itype][0] != shape[itype][2])
error->one("Fix nve/sphere requires spherical particle shapes");
}
}
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (radius[i] == 0.0)
error->one("Fix nve/sphere requires extended particles");
FixNVE::init();
}
@ -128,8 +105,6 @@ void FixNVESphere::initial_integrate(int vflag)
double **torque = atom->torque;
double *radius = atom->radius;
double *rmass = atom->rmass;
double *mass = atom->mass;
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -141,86 +116,21 @@ void FixNVESphere::initial_integrate(int vflag)
// update v,x,omega for all particles
// d_omega/dt = torque / inertia
// 4 cases depending on radius vs shape and rmass vs mass
if (radius) {
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / mass[itype];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
dtirotate = dtfrotate / (radius[i]*radius[i]*mass[itype]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
}
} else {
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / mass[itype];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
dtirotate = dtfrotate /
(shape[itype][0]*shape[itype][0]*mass[itype]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
@ -230,21 +140,18 @@ void FixNVESphere::initial_integrate(int vflag)
if (extra == DIPOLE) {
double **mu = atom->mu;
double *dipole = atom->dipole;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (dipole[type[i]] > 0.0) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (mu[i][3] > 0.0) {
g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
scale = dipole[type[i]]/sqrt(msq);
scale = mu[i][3]/sqrt(msq);
mu[i][0] = g[0]*scale;
mu[i][1] = g[1]*scale;
mu[i][2] = g[2]*scale;
}
}
}
}
}
@ -252,18 +159,14 @@ void FixNVESphere::initial_integrate(int vflag)
void FixNVESphere::final_integrate()
{
int itype;
double dtfm,dtirotate;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *mass = atom->mass;
double *rmass = atom->rmass;
double *radius = atom->radius;
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
@ -274,74 +177,17 @@ void FixNVESphere::final_integrate()
// update v,omega for all particles
// d_omega/dt = torque / inertia
// 4 cases depending on radius vs shape and rmass vs mass
if (radius) {
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / mass[itype];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
dtirotate = dtfrotate / (radius[i]*radius[i]*mass[itype]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
} else {
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[i]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / mass[itype];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
dtirotate = dtfrotate /
(shape[itype][0]*shape[itype][0]*mass[itype]);
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
}
}
}
}
}