ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

64
src/ASPHERE/fix_nve_asphere.cpp
View File

@ -34,24 +34,10 @@ using namespace LAMMPS_NS;
FixNVEAsphere::FixNVEAsphere(LAMMPS *lmp, int narg, char **arg) :
FixNVE(lmp, narg, arg)
{
memory->create(inertia,atom->ntypes+1,3,"fix_nve_asphere:inertia");
// error checks
if (!atom->angmom_flag || !atom->quat_flag || !atom->torque_flag ||
!atom->avec->shape_type)
error->all("Fix nve/asphere requires atom attributes "
"angmom, quat, torque, shape");
if (atom->radius_flag || atom->rmass_flag)
error->all("Fix nve/asphere cannot be used with atom attributes "
"diameter or rmass");
}
/* ---------------------------------------------------------------------- */
FixNVEAsphere::~FixNVEAsphere()
{
memory->destroy(inertia);
if (!atom->ellipsoid_flag)
error->all("Fix nve/asphere requires atom style ellipsoid");
}
/* ---------------------------------------------------------------------- */
@ -62,17 +48,15 @@ void FixNVEAsphere::init()
// no point particles allowed, spherical is OK
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (shape[type[i]][0] == 0.0)
if (shape[i][0] == 0.0)
error->one("Fix nve/asphere requires extended particles");
FixNVE::init();
calculate_inertia();
}
/* ---------------------------------------------------------------------- */
@ -80,6 +64,7 @@ void FixNVEAsphere::init()
void FixNVEAsphere::initial_integrate(int vflag)
{
double dtfm;
double inertia[3];
double **x = atom->x;
double **v = atom->v;
@ -87,8 +72,8 @@ void FixNVEAsphere::initial_integrate(int vflag)
double **quat = atom->quat;
double **angmom = atom->angmom;
double **torque = atom->torque;
double *mass = atom->mass;
int *type = atom->type;
double **shape = atom->shape;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
@ -99,7 +84,7 @@ void FixNVEAsphere::initial_integrate(int vflag)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[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];
@ -115,7 +100,16 @@ void FixNVEAsphere::initial_integrate(int vflag)
angmom[i][1] += dtf * torque[i][1];
angmom[i][2] += dtf * torque[i][2];
richardson(quat[i],angmom[i],inertia[type[i]]);
// principal moments of inertia
inertia[0] = rmass[i] *
(shape[i][1]*shape[i][1]+shape[i][2]*shape[i][2]) / 5.0;
inertia[1] = rmass[i] *
(shape[i][0]*shape[i][0]+shape[i][2]*shape[i][2]) / 5.0;
inertia[2] = rmass[i] *
(shape[i][0]*shape[i][0]+shape[i][1]*shape[i][1]) / 5.0;
richardson(quat[i],angmom[i],inertia);
}
}
@ -129,15 +123,14 @@ void FixNVEAsphere::final_integrate()
double **f = atom->f;
double **angmom = atom->angmom;
double **torque = atom->torque;
double *mass = atom->mass;
int *type = atom->type;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[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];
@ -224,22 +217,3 @@ void FixNVEAsphere::omega_from_mq(double *q, double *m, double *moments,
wbody[2] /= moments[2];
MathExtra::times_column3(rot,wbody,w);
}
/* ----------------------------------------------------------------------
principal moments of inertia for ellipsoids
------------------------------------------------------------------------- */
void FixNVEAsphere::calculate_inertia()
{
double *mass = atom->mass;
double **shape = atom->shape;
for (int i = 1; i <= atom->ntypes; i++) {
inertia[i][0] = 0.2*mass[i] *
(shape[i][1]*shape[i][1]+shape[i][2]*shape[i][2]);
inertia[i][1] = 0.2*mass[i] *
(shape[i][0]*shape[i][0]+shape[i][2]*shape[i][2]);
inertia[i][2] = 0.2*mass[i] *
(shape[i][0]*shape[i][0]+shape[i][1]*shape[i][1]);
}
}