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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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31
doc/compute_msd.txt
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@ -15,14 +15,15 @@ compute ID group-ID msd keyword values ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
msd = style name of this compute command :l
zero or more keyword/value pairs may be appended :l
keyword = {com} :l
{com} value = {yes} or {no} :pre
keyword = {com} or {average} :l
{com} value = {yes} or {no}
{average} value = {yes} or {no} :pre
:ule
[Examples:]
compute 1 all msd
compute 1 upper msd com yes :pre
compute 1 upper msd com yes average yes :pre
[Description:]
@ -41,13 +42,19 @@ averaged over atoms in the group.
The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.
The displacement of an atom is from its original position at the time
the compute command was issued. The value of the displacement will be
The displacement of an atom is from its reference position. This is
normally the original position at the time
the compute command was issued, unless the {average} keyword is set to {yes}.
The value of the displacement will be
0.0 for atoms not in the specified compute group.
If the {com} option is set to {yes} then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before xhe
displacment of each atom is calcluated.
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calculated.
If the {average} option is set to {yes} then the reference position of
an atom is a running average of the atom position over all the calls
to the msd calculation since the compute was invoked.
IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
using the image flags associated with each atom. See the "dump
@ -62,7 +69,13 @@ to be continuous when running from a "restart file"_read_restart.html,
then you should use the same ID for this compute, as in the original
run. This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with time=0 atom coordinates from the restart file.
correctly with atom reference positions from the restart file.
When {average} is set to yes, then the atom reference positions
are restored correctly, but not the number of samples used
obtain them. As a result, the reference positions from the restart
file are combined with subsequent positions as if they were from a
single sample, instead of many, which will change the values of msd
somewhat.
[Output info:]
@ -86,4 +99,4 @@ msd/chunk"_compute_msd_chunk.html
[Default:]
The option default is com = no.
The option default are com = no, average = no.

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++;
}
}
}

4
src/compute_msd.h
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@ -33,7 +33,9 @@ class ComputeMSD : public Compute {
void set_arrays(int);
protected:
int comflag;
int comflag; // comflag = 1 if reference moves with center of mass
int avflag; // avflag = 1 if using average position as reference
int naverage; // number of samples for average position
bigint nmsd;
double masstotal;
char *id_fix;