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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2515 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-01-22 18:05:16 +00:00
parent d12d662c1c
commit a9ca91a02e
2 changed files with 87 additions and 46 deletions
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131
src/fix_spring.cpp
View File

@ -28,6 +28,11 @@
using namespace LAMMPS_NS;
#define SMALL 1.0e-10
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
enum{TETHER,COUPLE};
/* ---------------------------------------------------------------------- */
@ -39,7 +44,7 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
vector_flag = 1;
size_vector = 3;
size_vector = 4;
scalar_vector_freq = 1;
extscalar = 1;
extvector = 1;
@ -80,8 +85,7 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
} else error->all("Illegal fix spring command");
force_flag = 0;
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
ftotal[0] = ftotal[1] = ftotal[2] = ftotal[3] = 0.0;
}
/* ---------------------------------------------------------------------- */
@ -142,7 +146,7 @@ void FixSpring::spring_tether()
double xcm[3];
group->xcm(igroup,masstotal,xcm);
// fx,fy,fz = components of k * (r-r0)
// fx,fy,fz = components of k * (r-r0) / masstotal
double dx,dy,dz,fx,fy,fz,r,dr;
@ -153,35 +157,51 @@ void FixSpring::spring_tether()
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
r = sqrt(dx*dx + dy*dy + dz*dz);
r = MAX(r,SMALL);
dr = r - r0;
fx = k_spring*dx*dr/r;
fy = k_spring*dy*dr/r;
fz = k_spring*dz*dr/r;
ftotal[0] = -fx;
ftotal[1] = -fy;
ftotal[2] = -fz;
ftotal[3] = sqrt(fx*fx + fy*fy + fz*fz);
if (dr < 0.0) ftotal[3] = -ftotal[3];
espring = 0.5*k_spring * dr*dr;
fx /= masstotal;
fy /= masstotal;
fz /= masstotal;
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
double **f = atom->f;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double massfrac;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massfrac = mass[type[i]]/masstotal;
f[i][0] -= fx*massfrac;
f[i][1] -= fy*massfrac;
f[i][2] -= fz*massfrac;
}
double massone;
ftotal[0] = -fx;
ftotal[1] = -fy;
ftotal[2] = -fz;
force_flag = 0;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = rmass[i];
f[i][0] -= fx*massone;
f[i][1] -= fy*massone;
f[i][2] -= fz*massone;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = mass[type[i]];
f[i][0] -= fx*massone;
f[i][1] -= fy*massone;
f[i][2] -= fz*massone;
}
}
}
/* ---------------------------------------------------------------------- */
@ -192,9 +212,10 @@ void FixSpring::spring_couple()
group->xcm(igroup,masstotal,xcm);
group->xcm(igroup2,masstotal2,xcm2);
// fx,fy,fz = components of k * (r-r0)
// fx,fy,fz = components of k * (r-r0) / masstotal
// fx2,fy2,fz2 = components of k * (r-r0) / masstotal2
double dx,dy,dz,fx,fy,fz,r,dr;
double dx,dy,dz,fx,fy,fz,fx2,fy2,fz2,r,dr;
dx = xcm2[0] - xcm[0] - xc;
dy = xcm2[1] - xcm[1] - yc;
@ -203,13 +224,26 @@ void FixSpring::spring_couple()
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
r = sqrt(dx*dx + dy*dy + dz*dz);
r = MAX(r,SMALL);
dr = r - r0;
fx = k_spring*dx*dr/r;
fy = k_spring*dy*dr/r;
fz = k_spring*dz*dr/r;
ftotal[0] = fx;
ftotal[1] = fy;
ftotal[2] = fz;
ftotal[3] = sqrt(fx*fx + fy*fy + fz*fz);
if (dr < 0.0) ftotal[3] = -ftotal[3];
espring = 0.5*k_spring * dr*dr;
fx2 = fx/masstotal2;
fy2 = fy/masstotal2;
fz2 = fz/masstotal2;
fx /= masstotal;
fy /= masstotal;
fz /= masstotal;
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
@ -217,28 +251,42 @@ void FixSpring::spring_couple()
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double massfrac;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
massfrac = mass[type[i]]/masstotal;
f[i][0] += fx*massfrac;
f[i][1] += fy*massfrac;
f[i][2] += fz*massfrac;
double massone;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
massone = rmass[i];
f[i][0] += fx*massone;
f[i][1] += fy*massone;
f[i][2] += fz*massone;
}
if (mask[i] & group2bit) {
massone = rmass[i];
f[i][0] -= fx2*massone;
f[i][1] -= fy2*massone;
f[i][2] -= fz2*massone;
}
}
if (mask[i] & group2bit) {
massfrac = mass[type[i]]/masstotal2;
f[i][0] -= fx*massfrac;
f[i][1] -= fy*massfrac;
f[i][2] -= fz*massfrac;
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
massone = mass[type[i]];
f[i][0] += fx*massone;
f[i][1] += fy*massone;
f[i][2] += fz*massone;
}
if (mask[i] & group2bit) {
massone = mass[type[i]];
f[i][0] -= fx2*massone;
f[i][1] -= fy2*massone;
f[i][2] -= fz2*massone;
}
}
}
ftotal[0] = fx;
ftotal[1] = fy;
ftotal[2] = fz;
force_flag = 1;
}
/* ---------------------------------------------------------------------- */
@ -270,12 +318,5 @@ double FixSpring::compute_scalar()
double FixSpring::compute_vector(int n)
{
// only sum across procs one time
// spring_couple should not do thie
if (force_flag == 0) {
MPI_Allreduce(ftotal,ftotal_all,3,MPI_DOUBLE,MPI_SUM,world);
force_flag = 1;
}
return ftotal_all[n];
return ftotal[n];
}

2
src/fix_spring.h
View File

@ -39,7 +39,7 @@ class FixSpring : public Fix {
int igroup2,group2bit;
double masstotal,masstotal2;
int nlevels_respa;
double espring,ftotal[3],ftotal_all[3];
double espring,ftotal[4];
int force_flag;
void spring_tether();