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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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88
src/fix_spring.cpp
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@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -71,10 +71,10 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
group2 = new char[n];
strcpy(group2,arg[4]);
igroup2 = group->find(arg[4]);
if (igroup2 == -1)
error->all(FLERR,"Fix spring couple group ID does not exist");
if (igroup2 == igroup)
error->all(FLERR,"Two groups cannot be the same in fix spring couple");
if (igroup2 == -1)
error->all(FLERR,"Fix spring couple group ID does not exist");
if (igroup2 == igroup)
error->all(FLERR,"Two groups cannot be the same in fix spring couple");
group2bit = group->bitmask[igroup2];
k_spring = atof(arg[5]);
@ -120,14 +120,14 @@ void FixSpring::init()
if (group2) {
igroup2 = group->find(group2);
if (igroup2 == -1)
error->all(FLERR,"Fix spring couple group ID does not exist");
if (igroup2 == -1)
error->all(FLERR,"Fix spring couple group ID does not exist");
group2bit = group->bitmask[igroup2];
}
masstotal = group->mass(igroup);
if (styleflag == COUPLE) masstotal2 = group->mass(igroup2);
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
@ -168,9 +168,9 @@ void FixSpring::spring_tether()
group->xcm(igroup,masstotal,xcm);
// fx,fy,fz = components of k * (r-r0) / masstotal
double dx,dy,dz,fx,fy,fz,r,dr;
dx = xcm[0] - xc;
dy = xcm[1] - yc;
dz = xcm[2] - zc;
@ -188,7 +188,7 @@ void FixSpring::spring_tether()
ftotal[1] = -fy;
ftotal[2] = -fz;
ftotal[3] = sqrt(fx*fx + fy*fy + fz*fz);
if (dr < 0.0) ftotal[3] = -ftotal[3];
if (dr < 0.0) ftotal[3] = -ftotal[3];
espring = 0.5*k_spring * dr*dr;
fx /= masstotal;
@ -203,24 +203,24 @@ void FixSpring::spring_tether()
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
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;
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;
massone = mass[type[i]];
f[i][0] -= fx*massone;
f[i][1] -= fy*massone;
f[i][2] -= fz*massone;
}
}
}
@ -232,22 +232,22 @@ void FixSpring::spring_couple()
double xcm[3],xcm2[3];
group->xcm(igroup,masstotal,xcm);
group->xcm(igroup2,masstotal2,xcm2);
// 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,fx2,fy2,fz2,r,dr;
dx = xcm2[0] - xcm[0] - xc;
dy = xcm2[1] - xcm[1] - yc;
dz = xcm2[2] - xcm[2] - zc;
dz = xcm2[2] - xcm[2] - zc;
if (!xflag) dx = 0.0;
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;
@ -255,7 +255,7 @@ void FixSpring::spring_couple()
ftotal[1] = fy;
ftotal[2] = fz;
ftotal[3] = sqrt(fx*fx + fy*fy + fz*fz);
if (dr < 0.0) ftotal[3] = -ftotal[3];
if (dr < 0.0) ftotal[3] = -ftotal[3];
espring = 0.5*k_spring * dr*dr;
fx2 = fx/masstotal2;
@ -278,33 +278,33 @@ void FixSpring::spring_couple()
double massone;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
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;
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;
massone = rmass[i];
f[i][0] -= fx2*massone;
f[i][1] -= fy2*massone;
f[i][2] -= fz2*massone;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
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;
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;
massone = mass[type[i]];
f[i][0] -= fx2*massone;
f[i][1] -= fy2*massone;
f[i][2] -= fz2*massone;
}
}
}