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Added average keyword

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14278 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
2015-12-02 05:06:52 +00:00
parent 3ca986fc6a
commit 00738a8baa
3 changed files with 77 additions and 22 deletions
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64
src/compute_msd.cpp
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@ -38,6 +38,7 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) :
// optional args
comflag = 0;
avflag = 0;
int iarg = 3;
while (iarg < narg) {
@ -47,10 +48,16 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
else error->all(FLERR,"Illegal compute msd command");
iarg += 2;
} else if (strcmp(arg[iarg],"average") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute msd command");
if (strcmp(arg[iarg+1],"no") == 0) avflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) avflag = 1;
else error->all(FLERR,"Illegal compute msd command");
iarg += 2;
} else error->all(FLERR,"Illegal compute msd command");
}
// create a new fix STORE style
// create a new fix STORE style for reference positions
// id = compute-ID + COMPUTE_STORE, fix group = compute group
int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
@ -97,6 +104,11 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) :
xoriginal[i][2] -= cm[2];
}
}
// initialize counter for average positions if requested
if (avflag) naverage = 1;
}
// displacement vector
@ -120,7 +132,7 @@ ComputeMSD::~ComputeMSD()
void ComputeMSD::init()
{
// set fix which stores original atom coords
// set fix which stores reference atom coords
int ifix = modify->find_fix(id_fix);
if (ifix < 0) error->all(FLERR,"Could not find compute msd fix ID");
@ -144,8 +156,8 @@ void ComputeMSD::compute_vector()
if (comflag) group->xcm(igroup,masstotal,cm);
else cm[0] = cm[1] = cm[2] = 0.0;
// dx,dy,dz = displacement of atom from original position
// original unwrapped position is stored by fix
// dx,dy,dz = displacement of atom from reference position
// reference unwrapped position is stored by fix
// relative to center of mass if comflag is set
// for triclinic, need to unwrap current atom coord via h matrix
@ -167,35 +179,63 @@ void ComputeMSD::compute_vector()
double msd[4];
msd[0] = msd[1] = msd[2] = msd[3] = 0.0;
double xtmp, ytmp, ztmp;
if (domain->triclinic == 0) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0];
dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1];
dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2];
xtmp = x[i][0] + xbox*xprd - cm[0];
ytmp = x[i][1] + ybox*yprd - cm[1];
ztmp = x[i][2] + zbox*zprd - cm[2];
dx = xtmp - xoriginal[i][0];
dy = ytmp - xoriginal[i][1];
dz = ztmp - xoriginal[i][2];
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;
msd[3] += dx*dx + dy*dy + dz*dz;
}
// use running average position for reference if requested
if (avflag) {
double navfac = 1.0/(naverage+1);
xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac;
xoriginal[i][1] = (xoriginal[i][1]*naverage + ytmp)*navfac;
xoriginal[i][2] = (xoriginal[i][2]*naverage + ztmp)*navfac;
naverage++;
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox -
cm[0] - xoriginal[i][0];
dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1];
dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2];
xtmp = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - cm[0];
ytmp = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1];
ztmp = x[i][2] + h[2]*zbox - cm[2];
dx = xtmp - xoriginal[i][0];
dy = ytmp - xoriginal[i][1];
dz = ztmp - xoriginal[i][2];
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;
msd[3] += dx*dx + dy*dy + dz*dz;
// use running average position for reference if requested
if (avflag) {
double navfac = 1.0/(naverage+1);
xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac;
xoriginal[i][1] = (xoriginal[i][0]*naverage + xtmp)*navfac;
xoriginal[i][2] = (xoriginal[i][0]*naverage + xtmp)*navfac;
naverage++;
}
}
}