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changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution

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This commit is contained in:
Steve Plimpton
2017-03-21 08:56:37 -06:00
parent 145e682ad3
commit dcede304df
112 changed files with 912 additions and 534 deletions
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97
src/fix_ave_chunk.cpp
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@ -31,6 +31,7 @@ using namespace LAMMPS_NS;
using namespace FixConst;
enum{V,F,DENSITY_NUMBER,DENSITY_MASS,MASS,TEMPERATURE,COMPUTE,FIX,VARIABLE};
enum{SCALAR,VECTOR};
enum{SAMPLE,ALL};
enum{NOSCALE,ATOM};
enum{ONE,RUNNING,WINDOW};
@ -79,6 +80,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
argindex = new int[nargnew];
ids = new char*[nargnew];
value2index = new int[nargnew];
densityflag = 0;
int iarg = 0;
while (iarg < nargnew) {
@ -106,9 +108,11 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"density/number") == 0) {
densityflag = 1;
which[nvalues] = DENSITY_NUMBER;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"density/mass") == 0) {
densityflag = 1;
which[nvalues] = DENSITY_MASS;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"mass") == 0) {
@ -604,6 +608,12 @@ void FixAveChunk::end_of_step()
count_many[m] = count_sum[m] = 0.0;
for (i = 0; i < nvalues; i++) values_many[m][i] = 0.0;
}
// if any DENSITY requested, invoke setup_chunks() on each sampling step
// nchunk will not change but bin volumes might, e.g. for NPT simulation
} else if (densityflag) {
cchunk->setup_chunks();
}
// zero out arrays for one sample
@ -782,11 +792,16 @@ void FixAveChunk::end_of_step()
// if normflag = SAMPLE, one = value/count, accumulate one to many
// count is MPI summed here, value is MPI summed below across samples
// exception is TEMPERATURE: normalize by DOF
// exception is DENSITYs: no normalize by atom count
// exception is scaleflag = NOSCALE : no normalize by atom count
// exception is DENSITY_NUMBER:
// normalize by bin volume, not by atom count
// exception is DENSITY_MASS:
// scale by mv2d, normalize by bin volume, not by atom count
// exception is scaleflag = NOSCALE (norm = NONE):
// no normalize by atom count
// check last so other options can take precedence
double mvv2e = force->mvv2e;
double mv2d = force->mv2d;
double boltz = force->boltz;
if (normflag == ALL) {
@ -797,17 +812,34 @@ void FixAveChunk::end_of_step()
}
} else if (normflag == SAMPLE) {
MPI_Allreduce(count_one,count_many,nchunk,MPI_DOUBLE,MPI_SUM,world);
if (cchunk->chunk_volume_vec) {
volflag = VECTOR;
chunk_volume_vec = cchunk->chunk_volume_vec;
} else {
volflag = SCALAR;
chunk_volume_scalar = cchunk->chunk_volume_scalar;
}
for (m = 0; m < nchunk; m++) {
if (count_many[m] > 0.0)
for (j = 0; j < nvalues; j++) {
if (which[j] == TEMPERATURE)
if (which[j] == TEMPERATURE) {
values_many[m][j] += mvv2e*values_one[m][j] /
((cdof + adof*count_many[m]) * boltz);
else if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS ||
scaleflag == NOSCALE)
} else if (which[j] == DENSITY_NUMBER) {
if (volflag == SCALAR) values_one[m][j] /= chunk_volume_scalar;
else values_one[m][j] /= chunk_volume_vec[m];
values_many[m][j] += values_one[m][j];
else
} else if (which[j] == DENSITY_MASS) {
if (volflag == SCALAR) values_one[m][j] /= chunk_volume_scalar;
else values_one[m][j] /= chunk_volume_vec[m];
values_many[m][j] += mv2d*values_one[m][j];
} else if (scaleflag == NOSCALE) {
values_many[m][j] += values_one[m][j];
} else {
values_many[m][j] += values_one[m][j]/count_many[m];
}
}
count_sum[m] += count_many[m];
}
@ -835,28 +867,48 @@ void FixAveChunk::end_of_step()
// time average across samples
// if normflag = ALL, final is total value / total count
// exception is TEMPERATURE: normalize by DOF for total count
// exception is DENSITYs: normalize by repeat, not total count
// exception is scaleflag == NOSCALE: normalize by repeat, not total count
// exception is DENSITY_NUMBER:
// normalize by final bin_volume and repeat, not by total count
// exception is DENSITY_MASS:
// scale by mv2d, normalize by bin volume and repeat, not by total count
// exception is scaleflag == NOSCALE:
// normalize by repeat, not by total count
// check last so other options can take precedence
// if normflag = SAMPLE, final is sum of ave / repeat
double repeat = nrepeat;
double mv2d = force->mv2d;
if (normflag == ALL) {
MPI_Allreduce(count_many,count_sum,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nchunk*nvalues,
MPI_DOUBLE,MPI_SUM,world);
if (cchunk->chunk_volume_vec) {
volflag = VECTOR;
chunk_volume_vec = cchunk->chunk_volume_vec;
} else {
volflag = SCALAR;
chunk_volume_scalar = cchunk->chunk_volume_scalar;
}
for (m = 0; m < nchunk; m++) {
if (count_sum[m] > 0.0)
for (j = 0; j < nvalues; j++) {
if (which[j] == TEMPERATURE)
if (which[j] == TEMPERATURE) {
values_sum[m][j] *= mvv2e / ((cdof + adof*count_sum[m]) * boltz);
else if (which[j] == DENSITY_MASS)
values_sum[m][j] *= mv2d/repeat;
else if (which[j] == DENSITY_NUMBER || scaleflag == NOSCALE)
} else if (which[j] == DENSITY_NUMBER) {
if (volflag == SCALAR) values_sum[m][j] /= chunk_volume_scalar;
else values_sum[m][j] /= chunk_volume_vec[m];
values_sum[m][j] /= repeat;
else values_sum[m][j] /= count_sum[m];
} else if (which[j] == DENSITY_MASS) {
if (volflag == SCALAR) values_sum[m][j] /= chunk_volume_scalar;
else values_sum[m][j] /= chunk_volume_vec[m];
values_sum[m][j] *= mv2d/repeat;
} else if (scaleflag == NOSCALE) {
values_sum[m][j] /= repeat;
} else {
values_sum[m][j] /= count_sum[m];
}
}
count_sum[m] /= repeat;
}
@ -869,23 +921,6 @@ void FixAveChunk::end_of_step()
}
}
// DENSITYs are additionally normalized by chunk volume
// use scalar or vector values for volume(s)
// if chunks are not spatial bins, chunk_volume_scalar = 1.0
for (j = 0; j < nvalues; j++)
if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS) {
if (cchunk->chunk_volume_vec) {
double *chunk_volume_vec = cchunk->chunk_volume_vec;
for (m = 0; m < nchunk; m++)
values_sum[m][j] /= chunk_volume_vec[m];
} else {
double chunk_volume_scalar = cchunk->chunk_volume_scalar;
for (m = 0; m < nchunk; m++)
values_sum[m][j] /= chunk_volume_scalar;
}
}
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, comine with nwindow most recent Nfreq timestep values