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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2902 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2009-06-26 18:23:16 +00:00
parent 3df8b6e355
commit 2d5a69385a
32 changed files with 2015 additions and 781 deletions
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394
src/fix_npt_sphere.cpp
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@ -35,41 +35,61 @@ enum{NOBIAS,BIAS};
FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) :
FixNPT(lmp, narg, arg)
{
// error checks
if (!atom->omega_flag || !atom->torque_flag)
error->all("Fix npt/sphere requires atom attributes omega, torque");
dttype = new double[atom->ntypes+1];
}
/* ---------------------------------------------------------------------- */
FixNPTSphere::~FixNPTSphere()
{
delete [] dttype;
if (!atom->radius_flag && !atom->avec->shape_type)
error->all("Fix npt/sphere requires atom attribute radius or shape");
}
/* ---------------------------------------------------------------------- */
void FixNPTSphere::init()
{
int i,itype;
// check that all particles are finite-size and spherical
// no point particles allowed
if (atom->radius_flag) {
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (radius[i] == 0.0)
error->one("Fix nvt/sphere requires extended particles");
}
} else {
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
itype = type[i];
if (shape[itype][0] == 0.0)
error->one("Fix nvt/sphere requires extended particles");
if (shape[itype][0] != shape[itype][1] ||
shape[itype][0] != shape[itype][2])
error->one("Fix nvt/sphere requires spherical particle shapes");
}
}
FixNPT::init();
if (!atom->shape)
error->all("Fix npt/sphere requires atom attribute shape");
double **shape = atom->shape;
for (int i = 1; i <= atom->ntypes; i++)
if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])
error->all("Fix npt/sphere requires spherical particle shapes");
}
/* ----------------------------------------------------------------------
1st half of Verlet update
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void FixNPTSphere::initial_integrate(int vflag)
{
int i;
int i,itype;
double dtfm,dtirotate;
double delta = update->ntimestep - update->beginstep;
@ -102,37 +122,63 @@ void FixNPTSphere::initial_integrate(int vflag)
}
factor_rotate = exp(-dthalf*eta_dot);
// v update only for atoms in group
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
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;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
if (rmass) {
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / rmass[i];
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
temperature->restore_bias(i,v[i]);
}
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
temperature->restore_bias(i,v[i]);
} else {
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
temperature->restore_bias(i,v[i]);
}
}
}
}
@ -151,24 +197,57 @@ void FixNPTSphere::initial_integrate(int vflag)
}
}
// recompute timesteps since dt may have changed or come via rRESPA
// set timestep here since dt may have changed or come via rRESPA
double dtfrotate = dtf / INERTIA;
int ntypes = atom->ntypes;
double **shape = atom->shape;
for (int i = 1; i <= ntypes; i++)
dttype[i] = dtfrotate / (shape[i][0]*shape[i][0]*mass[i]);
// update angular momentum by 1/2 step
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
// update omega for all particles
// d_omega/dt = torque / inertia
// 4 cases depending on radius vs shape and rmass vs mass
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtirotate = dttype[type[i]];
omega[i][0] = omega[i][0]*factor_rotate + dtirotate*torque[i][0];
omega[i][1] = omega[i][1]*factor_rotate + dtirotate*torque[i][1];
omega[i][2] = omega[i][2]*factor_rotate + dtirotate*torque[i][2];
if (radius) {
if (rmass) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] = omega[i][0]*factor_rotate + dtirotate*torque[i][0];
omega[i][1] = omega[i][1]*factor_rotate + dtirotate*torque[i][1];
omega[i][2] = omega[i][2]*factor_rotate + dtirotate*torque[i][2];
}
}
} else {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtirotate = dtfrotate / (radius[i]*radius[i]*mass[type[i]]);
omega[i][0] = omega[i][0]*factor_rotate + dtirotate*torque[i][0];
omega[i][1] = omega[i][1]*factor_rotate + dtirotate*torque[i][1];
omega[i][2] = omega[i][2]*factor_rotate + dtirotate*torque[i][2];
}
}
}
} else {
if (rmass) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[i]);
omega[i][0] = omega[i][0]*factor_rotate + dtirotate*torque[i][0];
omega[i][1] = omega[i][1]*factor_rotate + dtirotate*torque[i][1];
omega[i][2] = omega[i][2]*factor_rotate + dtirotate*torque[i][2];
}
}
} else {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtirotate = dtfrotate /
(shape[itype][0]*shape[itype][0]*mass[itype]);
omega[i][0] = omega[i][0]*factor_rotate + dtirotate*torque[i][0];
omega[i][1] = omega[i][1]*factor_rotate + dtirotate*torque[i][1];
omega[i][2] = omega[i][2]*factor_rotate + dtirotate*torque[i][2];
}
}
}
}
@ -179,68 +258,199 @@ void FixNPTSphere::initial_integrate(int vflag)
if (kspace_flag) force->kspace->setup();
}
/* ----------------------------------------------------------------------
2nd half of Verlet update
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void FixNPTSphere::final_integrate()
{
int i,itype;
double dtfm,dtirotate;
// v update only for atoms in group
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
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;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// recompute timesteps since dt may have changed or come via rRESPA
// set timestep here since dt may have changed or come via rRESPA
double dtfrotate = dtf / INERTIA;
int ntypes = atom->ntypes;
double **shape = atom->shape;
for (int i = 1; i <= ntypes; i++)
dttype[i] = dtfrotate / (shape[i][0]*shape[i][0]*mass[i]);
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / mass[itype];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
dtirotate = dttype[itype];
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor_rotate;
// update v,omega for all particles
// d_omega/dt = torque / inertia
// 8 cases depending on radius vs shape, rmass vs mass, bias vs nobias
if (radius) {
if (rmass) {
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
factor_rotate;
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / rmass[i];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
temperature->restore_bias(i,v[i]);
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
factor_rotate;
}
}
}
} else {
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / mass[itype];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
dtirotate = dtfrotate / (radius[i]*radius[i]*mass[itype]);
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
factor_rotate;
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[itype];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
temperature->restore_bias(i,v[i]);
dtirotate = dtfrotate / (radius[i]*radius[i]*mass[itype]);
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
factor_rotate;
}
}
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[itype];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
temperature->restore_bias(i,v[i]);
} else {
if (rmass) {
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / rmass[i];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[i]);
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
factor_rotate;
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
temperature->remove_bias(i,v[i]);
dtfm = dtf / rmass[i];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
temperature->restore_bias(i,v[i]);
dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[i]);
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
factor_rotate;
}
}
}
dtirotate = dttype[itype];
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) * factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) * factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) * factor_rotate;
} else {
if (which == NOBIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
dtfm = dtf / mass[itype];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
dtirotate = dtfrotate /
(shape[itype][0]*shape[itype][0]*mass[itype]);
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
factor_rotate;
}
}
} else if (which == BIAS) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
itype = type[i];
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[itype];
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
temperature->restore_bias(i,v[i]);
dtirotate = dtfrotate /
(shape[itype][0]*shape[itype][0]*mass[itype]);
omega[i][0] = (omega[i][0] + dtirotate*torque[i][0]) *
factor_rotate;
omega[i][1] = (omega[i][1] + dtirotate*torque[i][1]) *
factor_rotate;
omega[i][2] = (omega[i][2] + dtirotate*torque[i][2]) *
factor_rotate;
}
}
}
}
}