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Introduce ComputeChunk class with shared functionality of all /chunk computes

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This commit is contained in:
Axel Kohlmeyer
2023-03-18 05:55:03 -04:00
parent fce1f8e0af
commit 1ccb0f8d8d
29 changed files with 958 additions and 2050 deletions
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390
src/compute_temp_chunk.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -27,42 +26,40 @@
using namespace LAMMPS_NS;
enum{TEMP,KECOM,INTERNAL};
enum { TEMP, KECOM, INTERNAL };
/* ---------------------------------------------------------------------- */
ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
which(nullptr), idchunk(nullptr), id_bias(nullptr), sum(nullptr), sumall(nullptr), count(nullptr),
countall(nullptr), massproc(nullptr), masstotal(nullptr), vcm(nullptr), vcmall(nullptr)
ComputeChunk(lmp, narg, arg), which(nullptr), id_bias(nullptr), sum(nullptr), sumall(nullptr),
count(nullptr), countall(nullptr), massproc(nullptr), masstotal(nullptr), vcm(nullptr),
vcmall(nullptr)
{
if (narg < 4) error->all(FLERR,"Illegal compute temp/chunk command");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
// ID of compute chunk/atom
idchunk = utils::strdup(arg[3]);
biasflag = 0;
ComputeTempChunk::init();
// optional per-chunk values
nvalues = narg-4;
nvalues = narg - 4;
which = new int[nvalues];
nvalues = 0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"temp") == 0) which[nvalues] = TEMP;
else if (strcmp(arg[iarg],"kecom") == 0) which[nvalues] = KECOM;
else if (strcmp(arg[iarg],"internal") == 0) which[nvalues] = INTERNAL;
else break;
if (strcmp(arg[iarg], "temp") == 0)
which[nvalues] = TEMP;
else if (strcmp(arg[iarg], "kecom") == 0)
which[nvalues] = KECOM;
else if (strcmp(arg[iarg], "internal") == 0)
which[nvalues] = INTERNAL;
else
break;
iarg++;
nvalues++;
}
@ -76,56 +73,49 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
cdof = 0.0;
while (iarg < narg) {
if (strcmp(arg[iarg],"com") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/chunk command");
comflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
if (strcmp(arg[iarg], "com") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute temp/chunk command");
comflag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"bias") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/chunk command");
} else if (strcmp(arg[iarg], "bias") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute temp/chunk command");
biasflag = 1;
id_bias = utils::strdup(arg[iarg+1]);
id_bias = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else if (strcmp(arg[iarg],"adof") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/chunk command");
adof = utils::numeric(FLERR,arg[iarg+1],false,lmp);
} else if (strcmp(arg[iarg], "adof") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute temp/chunk command");
adof = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"cdof") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/chunk command");
cdof = utils::numeric(FLERR,arg[iarg+1],false,lmp);
} else if (strcmp(arg[iarg], "cdof") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute temp/chunk command");
cdof = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else error->all(FLERR,"Illegal compute temp/chunk command");
} else
error->all(FLERR, "Illegal compute temp/chunk command");
}
// error check on bias compute
if (biasflag) {
int i = modify->find_compute(id_bias);
if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
if (tbias->tempflag == 0)
error->all(FLERR,"Bias compute does not calculate temperature");
if (tbias->tempbias == 0)
error->all(FLERR,"Bias compute does not calculate a velocity bias");
tbias = modify->get_compute_by_id(id_bias);
if (!tbias) error->all(FLERR, "Could not find compute {} for temperature bias", id_bias);
if (tbias->tempflag == 0) error->all(FLERR, "Bias compute does not calculate temperature");
if (tbias->tempbias == 0) error->all(FLERR, "Bias compute does not calculate a velocity bias");
}
// this compute only calculates a bias, if comflag is set
// won't be two biases since comflag and biasflag cannot both be set
if (comflag && biasflag)
error->all(FLERR,"Cannot use both com and bias with compute temp/chunk");
error->all(FLERR, "Cannot use both com and bias with compute temp/chunk");
if (comflag) tempbias = 1;
// vector data
vector = new double[size_vector];
// chunk-based data
nchunk = 1;
maxchunk = 0;
if (nvalues) {
if (nvalues) {
array_flag = 1;
size_array_cols = nvalues;
size_array_rows = 0;
@ -133,7 +123,7 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
extarray = 0;
}
allocate();
ComputeTempChunk::allocate();
comstep = -1;
}
@ -141,10 +131,9 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
ComputeTempChunk::~ComputeTempChunk()
{
delete [] idchunk;
delete [] which;
delete [] id_bias;
delete [] vector;
delete[] which;
delete[] id_bias;
delete[] vector;
memory->destroy(sum);
memory->destroy(sumall);
memory->destroy(count);
@ -160,19 +149,11 @@ ComputeTempChunk::~ComputeTempChunk()
void ComputeTempChunk::init()
{
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for "
"compute temp/chunk");
cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Compute temp/chunk does not use chunk/atom compute");
ComputeChunk::init();
if (biasflag) {
int i = modify->find_compute(id_bias);
if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
tbias = modify->get_compute_by_id(id_bias);
if (!tbias) error->all(FLERR, "Could not find compute ID {} for temperature bias", id_bias);
}
}
@ -180,7 +161,7 @@ void ComputeTempChunk::init()
double ComputeTempChunk::compute_scalar()
{
int i,index;
int i, index;
invoked_scalar = update->ntimestep;
@ -224,47 +205,45 @@ double ComputeTempChunk::compute_scalar()
if (rmass) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
rmass[i];
t += (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]) * rmass[i];
mycount++;
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
t += (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]) * mass[type[i]];
mycount++;
}
}
}
} else {
double vx,vy,vz;
double vx, vy, vz;
if (rmass) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
vx = v[i][0] - vcmall[index][0];
vy = v[i][1] - vcmall[index][1];
vz = v[i][2] - vcmall[index][2];
t += (vx*vx + vy*vy + vz*vz) * rmass[i];
t += (vx * vx + vy * vy + vz * vz) * rmass[i];
mycount++;
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
vx = v[i][0] - vcmall[index][0];
vy = v[i][1] - vcmall[index][1];
vz = v[i][2] - vcmall[index][2];
t += (vx*vx + vy*vy + vz*vz) * mass[type[i]];
t += (vx * vx + vy * vy + vz * vz) * mass[type[i]];
mycount++;
}
}
}
}
@ -274,16 +253,15 @@ double ComputeTempChunk::compute_scalar()
// final temperature
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&t, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
double rcount = mycount;
double allcount;
MPI_Allreduce(&rcount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&rcount, &allcount, 1, MPI_DOUBLE, MPI_SUM, world);
double dof = nchunk*cdof + adof*allcount;
double dof = nchunk * cdof + adof * allcount;
double tfactor = 0.0;
if (dof > 0.0) tfactor = force->mvv2e / (dof * force->boltz);
if (dof < 0.0 && allcount > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
if (dof < 0.0 && allcount > 0.0) error->all(FLERR, "Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
}
@ -292,22 +270,11 @@ double ComputeTempChunk::compute_scalar()
void ComputeTempChunk::compute_vector()
{
int i,index;
int i, index;
invoked_vector = update->ntimestep;
// calculate chunk assignments,
// since only atoms in chunks contribute to global temperature
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk = cchunk->setup_chunks();
cchunk->compute_ichunk();
ComputeChunk::compute_vector();
int *ichunk = cchunk->ichunk;
if (nchunk > maxchunk) allocate();
// remove velocity bias
if (biasflag) {
@ -329,40 +296,44 @@ void ComputeTempChunk::compute_vector()
int *mask = atom->mask;
int nlocal = atom->nlocal;
double massone,t[6];
double massone, t[6];
for (i = 0; i < 6; i++) t[i] = 0.0;
if (!comflag) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
t[0] += massone * v[i][0]*v[i][0];
t[1] += massone * v[i][1]*v[i][1];
t[2] += massone * v[i][2]*v[i][2];
t[3] += massone * v[i][0]*v[i][1];
t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2];
if (rmass)
massone = rmass[i];
else
massone = mass[type[i]];
t[0] += massone * v[i][0] * v[i][0];
t[1] += massone * v[i][1] * v[i][1];
t[2] += massone * v[i][2] * v[i][2];
t[3] += massone * v[i][0] * v[i][1];
t[4] += massone * v[i][0] * v[i][2];
t[5] += massone * v[i][1] * v[i][2];
}
} else {
double vx,vy,vz;
double vx, vy, vz;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
if (rmass)
massone = rmass[i];
else
massone = mass[type[i]];
vx = v[i][0] - vcmall[index][0];
vy = v[i][1] - vcmall[index][1];
vz = v[i][2] - vcmall[index][2];
t[0] += massone * vx*vx;
t[1] += massone * vy*vy;
t[2] += massone * vz*vz;
t[3] += massone * vx*vy;
t[4] += massone * vx*vz;
t[5] += massone * vy*vz;
t[0] += massone * vx * vx;
t[1] += massone * vy * vy;
t[2] += massone * vz * vz;
t[3] += massone * vx * vy;
t[4] += massone * vx * vz;
t[5] += massone * vy * vz;
}
}
@ -372,7 +343,7 @@ void ComputeTempChunk::compute_vector()
// final KE
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(t, vector, 6, MPI_DOUBLE, MPI_SUM, world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
@ -380,17 +351,7 @@ void ComputeTempChunk::compute_vector()
void ComputeTempChunk::compute_array()
{
invoked_array = update->ntimestep;
// compute chunk/atom assigns atoms to chunk IDs
// extract ichunk index vector from compute
// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
nchunk = cchunk->setup_chunks();
cchunk->compute_ichunk();
if (nchunk > maxchunk) allocate();
size_array_rows = nchunk;
ComputeChunk::compute_array();
// remove velocity bias
@ -409,9 +370,12 @@ void ComputeTempChunk::compute_array()
// compute each value
for (int i = 0; i < nvalues; i++) {
if (which[i] == TEMP) temperature(i);
else if (which[i] == KECOM) kecom(i);
else if (which[i] == INTERNAL) internal(i);
if (which[i] == TEMP)
temperature(i);
else if (which[i] == KECOM)
kecom(i);
else if (which[i] == INTERNAL)
internal(i);
}
// restore velocity bias
@ -425,7 +389,7 @@ void ComputeTempChunk::compute_array()
void ComputeTempChunk::vcm_compute()
{
int i,index;
int i, index;
double massone;
// avoid re-computing VCM more than once per step
@ -448,18 +412,20 @@ void ComputeTempChunk::vcm_compute()
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
if (rmass)
massone = rmass[i];
else
massone = mass[type[i]];
vcm[index][0] += v[i][0] * massone;
vcm[index][1] += v[i][1] * massone;
vcm[index][2] += v[i][2] * massone;
massproc[index] += massone;
}
MPI_Allreduce(&vcm[0][0],&vcmall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&vcm[0][0], &vcmall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
for (i = 0; i < nchunk; i++) {
if (masstotal[i] > 0.0) {
@ -478,7 +444,7 @@ void ComputeTempChunk::vcm_compute()
void ComputeTempChunk::temperature(int icol)
{
int i,index;
int i, index;
int *ichunk = cchunk->ichunk;
// zero local per-chunk values
@ -501,65 +467,65 @@ void ComputeTempChunk::temperature(int icol)
if (rmass) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
sum[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
rmass[i];
sum[index] += (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]) * rmass[i];
count[index]++;
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
sum[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
sum[index] += (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]) * mass[type[i]];
count[index]++;
}
}
}
} else {
double vx,vy,vz;
double vx, vy, vz;
if (rmass) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
vx = v[i][0] - vcmall[index][0];
vy = v[i][1] - vcmall[index][1];
vz = v[i][2] - vcmall[index][2];
sum[index] += (vx*vx + vy*vy + vz*vz) * rmass[i];
sum[index] += (vx * vx + vy * vy + vz * vz) * rmass[i];
count[index]++;
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
vx = v[i][0] - vcmall[index][0];
vy = v[i][1] - vcmall[index][1];
vz = v[i][2] - vcmall[index][2];
sum[index] += (vx*vx + vy*vy + vz*vz) * mass[type[i]];
sum[index] += (vx * vx + vy * vy + vz * vz) * mass[type[i]];
count[index]++;
}
}
}
}
// sum across procs
MPI_Allreduce(sum,sumall,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(count,countall,nchunk,MPI_INT,MPI_SUM,world);
MPI_Allreduce(sum, sumall, nchunk, MPI_DOUBLE, MPI_SUM, world);
MPI_Allreduce(count, countall, nchunk, MPI_INT, MPI_SUM, world);
// normalize temperatures by per-chunk DOF
double dof,tfactor;
double dof, tfactor;
double mvv2e = force->mvv2e;
double boltz = force->boltz;
for (i = 0; i < nchunk; i++) {
dof = cdof + adof*countall[i];
if (dof > 0.0) tfactor = mvv2e / (dof * boltz);
else tfactor = 0.0;
dof = cdof + adof * countall[i];
if (dof > 0.0)
tfactor = mvv2e / (dof * boltz);
else
tfactor = 0.0;
array[i][icol] = tfactor * sumall[i];
}
}
@ -585,37 +551,35 @@ void ComputeTempChunk::kecom(int icol)
int *type = atom->type;
int nlocal = atom->nlocal;
double vx,vy,vz;
double vx, vy, vz;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
vx = vcmall[index][0];
vy = vcmall[index][1];
vz = vcmall[index][2];
sum[index] += (vx*vx + vy*vy + vz*vz) * rmass[i];
sum[index] += (vx * vx + vy * vy + vz * vz) * rmass[i];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
vx = vcmall[index][0];
vy = vcmall[index][1];
vz = vcmall[index][2];
sum[index] += (vx*vx + vy*vy + vz*vz) * mass[type[i]];
sum[index] += (vx * vx + vy * vy + vz * vz) * mass[type[i]];
}
}
// sum across procs
MPI_Allreduce(sum,sumall,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(sum, sumall, nchunk, MPI_DOUBLE, MPI_SUM, world);
double mvv2e = force->mvv2e;
for (int i = 0; i < nchunk; i++)
array[i][icol] = 0.5 * mvv2e * sumall[i];
for (int i = 0; i < nchunk; i++) array[i][icol] = 0.5 * mvv2e * sumall[i];
}
/* ----------------------------------------------------------------------
@ -641,36 +605,35 @@ void ComputeTempChunk::internal(int icol)
int *type = atom->type;
int nlocal = atom->nlocal;
double vx,vy,vz;
double vx, vy, vz;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
vx = v[i][0] - vcmall[index][0];
vy = v[i][1] - vcmall[index][1];
vz = v[i][2] - vcmall[index][2];
sum[index] += (vx*vx + vy*vy + vz*vz) * rmass[i];
sum[index] += (vx * vx + vy * vy + vz * vz) * rmass[i];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
vx = v[i][0] - vcmall[index][0];
vy = v[i][1] - vcmall[index][1];
vz = v[i][2] - vcmall[index][2];
sum[index] += (vx*vx + vy*vy + vz*vz) * mass[type[i]];
sum[index] += (vx * vx + vy * vy + vz * vz) * mass[type[i]];
}
}
// sum across procs
MPI_Allreduce(sum,sumall,nchunk,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(sum, sumall, nchunk, MPI_DOUBLE, MPI_SUM, world);
double mvv2e = force->mvv2e;
for (int i = 0; i < nchunk; i++)
array[i][icol] = 0.5 * mvv2e * sumall[i];
for (int i = 0; i < nchunk; i++) array[i][icol] = 0.5 * mvv2e * sumall[i];
}
/* ----------------------------------------------------------------------
@ -683,7 +646,7 @@ void ComputeTempChunk::internal(int icol)
void ComputeTempChunk::remove_bias(int i, double *v)
{
int index = cchunk->ichunk[i]-1;
int index = cchunk->ichunk[i] - 1;
if (index < 0) return;
v[0] -= vcmall[index][0];
v[1] -= vcmall[index][1];
@ -705,7 +668,7 @@ void ComputeTempChunk::remove_bias_all()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
v[i][0] -= vcmall[index][0];
v[i][1] -= vcmall[index][1];
@ -720,7 +683,7 @@ void ComputeTempChunk::remove_bias_all()
void ComputeTempChunk::restore_bias(int i, double *v)
{
int index = cchunk->ichunk[i]-1;
int index = cchunk->ichunk[i] - 1;
if (index < 0) return;
v[0] += vcmall[index][0];
v[1] += vcmall[index][1];
@ -743,7 +706,7 @@ void ComputeTempChunk::restore_bias_all()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
index = ichunk[i] - 1;
if (index < 0) continue;
v[i][0] += vcmall[index][0];
v[i][1] += vcmall[index][1];
@ -751,89 +714,34 @@ void ComputeTempChunk::restore_bias_all()
}
}
/* ----------------------------------------------------------------------
lock methods: called by fix ave/time
these methods ensure vector/array size is locked for Nfreq epoch
by passing lock info along to compute chunk/atom
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
increment lock counter
------------------------------------------------------------------------- */
void ComputeTempChunk::lock_enable()
{
cchunk->lockcount++;
}
/* ----------------------------------------------------------------------
decrement lock counter in compute chunk/atom, it if still exists
------------------------------------------------------------------------- */
void ComputeTempChunk::lock_disable()
{
int icompute = modify->find_compute(idchunk);
if (icompute >= 0) {
cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
cchunk->lockcount--;
}
}
/* ----------------------------------------------------------------------
calculate and return # of chunks = length of vector/array
------------------------------------------------------------------------- */
int ComputeTempChunk::lock_length()
{
nchunk = cchunk->setup_chunks();
return nchunk;
}
/* ----------------------------------------------------------------------
set the lock from startstep to stopstep
------------------------------------------------------------------------- */
void ComputeTempChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
cchunk->lock(fixptr,startstep,stopstep);
}
/* ----------------------------------------------------------------------
unset the lock
------------------------------------------------------------------------- */
void ComputeTempChunk::unlock(Fix *fixptr)
{
cchunk->unlock(fixptr);
}
/* ----------------------------------------------------------------------
free and reallocate per-chunk arrays
------------------------------------------------------------------------- */
void ComputeTempChunk::allocate()
{
ComputeChunk::allocate();
memory->destroy(sum);
memory->destroy(sumall);
memory->destroy(count);
memory->destroy(countall);
memory->destroy(array);
maxchunk = nchunk;
memory->create(sum,maxchunk,"temp/chunk:sum");
memory->create(sumall,maxchunk,"temp/chunk:sumall");
memory->create(count,maxchunk,"temp/chunk:count");
memory->create(countall,maxchunk,"temp/chunk:countall");
memory->create(array,maxchunk,nvalues,"temp/chunk:array");
memory->create(sum, maxchunk, "temp/chunk:sum");
memory->create(sumall, maxchunk, "temp/chunk:sumall");
memory->create(count, maxchunk, "temp/chunk:count");
memory->create(countall, maxchunk, "temp/chunk:countall");
memory->create(array, maxchunk, nvalues, "temp/chunk:array");
if (comflag || nvalues) {
memory->destroy(massproc);
memory->destroy(masstotal);
memory->destroy(vcm);
memory->destroy(vcmall);
memory->create(massproc,maxchunk,"vcm/chunk:massproc");
memory->create(masstotal,maxchunk,"vcm/chunk:masstotal");
memory->create(vcm,maxchunk,3,"vcm/chunk:vcm");
memory->create(vcmall,maxchunk,3,"vcm/chunk:vcmall");
memory->create(massproc, maxchunk, "vcm/chunk:massproc");
memory->create(masstotal, maxchunk, "vcm/chunk:masstotal");
memory->create(vcm, maxchunk, 3, "vcm/chunk:vcm");
memory->create(vcmall, maxchunk, 3, "vcm/chunk:vcmall");
}
}
@ -843,12 +751,12 @@ void ComputeTempChunk::allocate()
double ComputeTempChunk::memory_usage()
{
double bytes = (bigint) maxchunk * 2 * sizeof(double);
double bytes = (double) maxchunk * 2 * sizeof(double) + ComputeChunk::memory_usage();
bytes += (double) maxchunk * 2 * sizeof(int);
bytes += (double) maxchunk * nvalues * sizeof(double);
if (comflag || nvalues) {
bytes += (double) maxchunk * 2 * sizeof(double);
bytes += (double) maxchunk * 2*3 * sizeof(double);
bytes += (double) maxchunk * 2 * 3 * sizeof(double);
}
return bytes;
}