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convert fix ave/atom and fix ave/chunk

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This commit is contained in:
Axel Kohlmeyer
2022-10-15 09:34:47 -04:00
parent b3557b81c1
commit 8ebad9ecd8
5 changed files with 307 additions and 352 deletions
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333
src/fix_ave_chunk.cpp
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@ -33,29 +33,24 @@
using namespace LAMMPS_NS;
using namespace FixConst;
enum{SCALAR,VECTOR};
enum{SAMPLE,ALL};
enum{NOSCALE,ATOM};
enum{ONE,RUNNING,WINDOW};
enum { SCALAR, VECTOR };
enum { SAMPLE, ALL };
enum { NOSCALE, ATOM };
enum { ONE, RUNNING, WINDOW };
/* ---------------------------------------------------------------------- */
FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
nvalues(0), nrepeat(0),
which(nullptr), argindex(nullptr), value2index(nullptr), ids(nullptr),
fp(nullptr), idchunk(nullptr), varatom(nullptr),
count_one(nullptr), count_many(nullptr), count_sum(nullptr),
values_one(nullptr), values_many(nullptr), values_sum(nullptr),
count_total(nullptr), count_list(nullptr),
values_total(nullptr), values_list(nullptr)
Fix(lmp, narg, arg), nvalues(0), nrepeat(0), fp(nullptr), idchunk(nullptr), varatom(nullptr),
count_one(nullptr), count_many(nullptr), count_sum(nullptr), values_one(nullptr),
values_many(nullptr), values_sum(nullptr), count_total(nullptr), count_list(nullptr),
values_total(nullptr), values_list(nullptr)
{
if (narg < 7) error->all(FLERR,"Illegal fix ave/chunk command");
if (narg < 7) utils::missing_cmd_args(FLERR, "fix ave/chunk", error);
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
nrepeat = utils::inumeric(FLERR,arg[4],false,lmp);
nfreq = utils::inumeric(FLERR,arg[5],false,lmp);
nevery = utils::inumeric(FLERR, arg[3], false, lmp);
nrepeat = utils::inumeric(FLERR, arg[4], false, lmp);
nfreq = utils::inumeric(FLERR, arg[5], false, lmp);
idchunk = utils::strdup(arg[6]);
@ -63,82 +58,81 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
no_change_box = 1;
time_depend = 1;
char * group = arg[1];
char *group = arg[1];
// expand args if any have wildcard character "*"
int expand = 0;
char **earg;
int nargnew = utils::expand_args(FLERR,narg-7,&arg[7],1,earg,lmp);
int nargnew = utils::expand_args(FLERR, narg - 7, &arg[7], 1, earg, lmp);
if (earg != &arg[7]) expand = 1;
arg = earg;
// parse values until one isn't recognized
which = new int[nargnew];
argindex = new int[nargnew];
ids = new char*[nargnew];
value2index = new int[nargnew];
densityflag = 0;
int iarg = 0;
values.clear();
while (iarg < nargnew) {
ids[nvalues] = nullptr;
value_t val;
val.id = "";
val.val.c = nullptr;
if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = ArgInfo::V;
argindex[nvalues++] = 0;
val.which = ArgInfo::V;
val.which = 0;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = ArgInfo::V;
argindex[nvalues++] = 1;
val.which = ArgInfo::V;
val.which = 1;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = ArgInfo::V;
argindex[nvalues++] = 2;
val.which = ArgInfo::V;
val.which = 2;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = ArgInfo::F;
argindex[nvalues++] = 0;
val.which = ArgInfo::F;
val.which = 0;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = ArgInfo::F;
argindex[nvalues++] = 1;
val.which = ArgInfo::F;
val.which = 1;
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = ArgInfo::F;
argindex[nvalues++] = 2;
val.which = ArgInfo::F;
val.which = 2;
} else if (strcmp(arg[iarg],"mass") == 0) {
which[nvalues] = ArgInfo::MASS;
argindex[nvalues++] = 0;
val.which = ArgInfo::MASS;
val.which = 0;
} else if (strcmp(arg[iarg],"density/number") == 0) {
densityflag = 1;
which[nvalues] = ArgInfo::DENSITY_NUMBER;
argindex[nvalues++] = 0;
val.which = ArgInfo::DENSITY_NUMBER;
val.which = 0;
} else if (strcmp(arg[iarg],"density/mass") == 0) {
densityflag = 1;
which[nvalues] = ArgInfo::DENSITY_MASS;
argindex[nvalues++] = 0;
val.which = ArgInfo::DENSITY_MASS;
val.which = 0;
} else if (strcmp(arg[iarg],"temp") == 0) {
which[nvalues] = ArgInfo::TEMPERATURE;
argindex[nvalues++] = 0;
val.which = ArgInfo::TEMPERATURE;
val.which = 0;
} else {
ArgInfo argi(arg[iarg]);
if (argi.get_type() == ArgInfo::NONE) break;
if ((argi.get_type() == ArgInfo::UNKNOWN) || (argi.get_dim() > 1))
error->all(FLERR,"Invalid fix ave/chunk command");
error->all(FLERR,"Unknown fix ave/chunk data value: {}", arg[iarg]);
which[nvalues] = argi.get_type();
argindex[nvalues] = argi.get_index1();
ids[nvalues] = argi.copy_name();
nvalues++;
val.which = argi.get_type();
val.argindex = argi.get_index1();
val.id = argi.get_name();
}
values.push_back(val);
iarg++;
}
if (nvalues == 0) error->all(FLERR,"No values in fix ave/chunk command");
nvalues = values.size();
if (nvalues == 0) error->all(FLERR, "No values in fix ave/chunk command");
// optional args
@ -159,7 +153,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
while (iarg < nargnew) {
if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk norm", error);
if (strcmp(arg[iarg+1],"all") == 0) {
normflag = ALL;
scaleflag = ATOM;
@ -169,127 +163,124 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg+1],"none") == 0) {
normflag = SAMPLE;
scaleflag = NOSCALE;
} else error->all(FLERR,"Illegal fix ave/chunk command");
} else error->all(FLERR,"Unknown fix ave/chunk norm mode: {}", arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk ave", error);
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all(FLERR,"Illegal fix ave/chunk command");
else error->all(FLERR,"Unknown fix ave/chunk ave mode: {}", arg[iarg+1]);
if (ave == WINDOW) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk ave window", error);
nwindow = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/chunk command");
if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/chunk number of windows: {}", nwindow);
}
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"bias") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/chunk command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk bias", error);
biasflag = 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 fix ave/chunk command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk adof", error);
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 fix ave/chunk command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk cdof", error);
cdof = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk file", error);
if (comm->me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == nullptr)
error->one(FLERR,"Cannot open fix ave/chunk file {}: {}",
arg[iarg+1], utils::getsyserror());
error->one(FLERR, "Cannot open fix ave/chunk file {}: {}",
arg[iarg+1], utils::getsyserror());
}
iarg += 2;
} else if (strcmp(arg[iarg],"overwrite") == 0) {
overwrite = 1;
iarg += 1;
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk format", error);
delete[] format_user;
format_user = utils::strdup(arg[iarg+1]);
format = format_user;
iarg += 2;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk title1", error);
delete[] title1;
title1 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk title2", error);
delete[] title2;
title2 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/chunk title3", error);
delete[] title3;
title3 = utils::strdup(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix ave/chunk command");
} else error->all(FLERR,"Unknown fix ave/chunk keyword: {}", arg[iarg]);
}
// setup and error check
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all(FLERR,"Illegal fix ave/chunk command");
if (nevery <= 0) error->all(FLERR,"Illegal fix ave/chunk nevery value: {}", nevery);
if (nrepeat <= 0) error->all(FLERR,"Illegal fix ave/chunk nrepeat value: {}", nrepeat);
if (nfreq <= 0) error->all(FLERR,"Illegal fix ave/chunk nfreq value: {}", nfreq);
if (nfreq % nevery || nrepeat*nevery > nfreq)
error->all(FLERR,"Illegal fix ave/chunk command");
error->all(FLERR,"Inconsistent fix ave/chunk nevery/nrepeat/nfreq values");
if (ave != RUNNING && overwrite)
error->all(FLERR,"Illegal fix ave/chunk command");
error->all(FLERR,"Fix ave/chunk overwrite keyword requires ave running setting");
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);
if (tbias->tempflag == 0)
error->all(FLERR,"Bias compute does not calculate temperature");
error->all(FLERR,"Bias compute {} does not calculate temperature", id_bias);
if (tbias->tempbias == 0)
error->all(FLERR,"Bias compute does not calculate a velocity bias");
error->all(FLERR,"Bias compute {} does not calculate a velocity bias", id_bias);
}
for (int i = 0; i < nvalues; i++) {
if (which[i] == ArgInfo::COMPUTE) {
auto icompute = modify->get_compute_by_id(ids[i]);
if (!icompute)
error->all(FLERR,"Compute ID {} for fix ave/chunk does not exist",ids[i]);
if (icompute->peratom_flag == 0)
error->all(FLERR,"Fix ave/chunk compute {} does not calculate per-atom values",ids[i]);
if (argindex[i] == 0 && (icompute->size_peratom_cols != 0))
error->all(FLERR,"Fix ave/chunk compute {} does not calculate a per-atom vector",ids[i]);
if (argindex[i] && (icompute->size_peratom_cols == 0))
error->all(FLERR,"Fix ave/chunk compute {} does not calculate a per-atom array",ids[i]);
if (argindex[i] && (argindex[i] > icompute->size_peratom_cols))
error->all(FLERR,"Fix ave/chunk compute {} vector is accessed out-of-range",ids[i]);
for (auto &val : values) {
} else if (which[i] == ArgInfo::FIX) {
auto ifix = modify->get_fix_by_id(ids[i]);
if (!ifix)
error->all(FLERR, "Fix ID {} for fix ave/chunk does not exist",ids[i]);
if (ifix->peratom_flag == 0)
error->all(FLERR, "Fix ave/chunk fix {} does not calculate per-atom values",ids[i]);
if (argindex[i] == 0 && (ifix->size_peratom_cols != 0))
error->all(FLERR, "Fix ave/chunk fix {} does not calculate a per-atom vector",ids[i]);
if (argindex[i] && (ifix->size_peratom_cols == 0))
error->all(FLERR, "Fix ave/chunk fix {} does not calculate a per-atom array",ids[i]);
if (argindex[i] && argindex[i] > ifix->size_peratom_cols)
error->all(FLERR,"Fix ave/chunk fix {} vector is accessed out-of-range",ids[i]);
} else if (which[i] == ArgInfo::VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all(FLERR,"Variable name {} for fix ave/chunk does not exist",ids[i]);
if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Fix ave/chunk variable {} is not atom-style variable",ids[i]);
if (val.which == ArgInfo::COMPUTE) {
val.val.c = modify->get_compute_by_id(val.id);
if (!val.val.c)
error->all(FLERR,"Compute ID {} for fix ave/chunk does not exist",val.id);
if (val.val.c->peratom_flag == 0)
error->all(FLERR,"Fix ave/chunk compute {} does not calculate per-atom values",val.id);
if (val.argindex == 0 && (val.val.c->size_peratom_cols != 0))
error->all(FLERR,"Fix ave/chunk compute {} does not calculate a per-atom vector",val.id);
if (val.argindex && (val.val.c->size_peratom_cols == 0))
error->all(FLERR,"Fix ave/chunk compute {} does not calculate a per-atom array",val.id);
if (val.argindex && (val.argindex > val.val.c->size_peratom_cols))
error->all(FLERR,"Fix ave/chunk compute {} vector is accessed out-of-range",val.id);
} else if (val.which == ArgInfo::FIX) {
val.val.f = modify->get_fix_by_id(val.id);
if (!val.val.f)
error->all(FLERR, "Fix ID {} for fix ave/chunk does not exist",val.id);
if (val.val.f->peratom_flag == 0)
error->all(FLERR, "Fix ave/chunk fix {} does not calculate per-atom values",val.id);
if (val.argindex == 0 && (val.val.f->size_peratom_cols != 0))
error->all(FLERR, "Fix ave/chunk fix {} does not calculate a per-atom vector",val.id);
if (val.argindex && (val.val.f->size_peratom_cols == 0))
error->all(FLERR, "Fix ave/chunk fix {} does not calculate a per-atom array",val.id);
if (val.argindex && val.argindex > val.val.f->size_peratom_cols)
error->all(FLERR,"Fix ave/chunk fix {} vector is accessed out-of-range",val.id);
} else if (val.which == ArgInfo::VARIABLE) {
val.val.v = input->variable->find(val.id.c_str());
if (val.val.v < 0)
error->all(FLERR,"Variable name {} for fix ave/chunk does not exist",val.id);
if (input->variable->atomstyle(val.val.v) == 0)
error->all(FLERR,"Fix ave/chunk variable {} is not atom-style variable",val.id);
}
}
@ -396,12 +387,6 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
FixAveChunk::~FixAveChunk()
{
delete[] which;
delete[] argindex;
for (int i = 0; i < nvalues; i++) delete[] ids[i];
delete[] ids;
delete[] value2index;
if (fp && comm->me == 0) fclose(fp);
memory->destroy(varatom);
@ -427,10 +412,6 @@ FixAveChunk::~FixAveChunk()
}
delete[] idchunk;
which = nullptr;
argindex = nullptr;
ids = nullptr;
value2index = nullptr;
fp = nullptr;
varatom = nullptr;
count_one = nullptr;
@ -463,42 +444,34 @@ void FixAveChunk::init()
// set indices and check validity of all computes,fixes,variables
// check that fix frequency is acceptable
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for fix ave/chunk");
cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
cchunk = dynamic_cast<ComputeChunkAtom *>(modify->get_compute_by_id(idchunk));
if (!cchunk)
error->all(FLERR,"Chunk/atom compute {} does not exist or is "
"incorrect style for fix ave/chunk",idchunk);
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);
}
for (int m = 0; m < nvalues; m++) {
if (which[m] == ArgInfo::COMPUTE) {
icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/chunk does not exist");
value2index[m] = icompute;
for (auto &val : values) {
if (val.which == ArgInfo::COMPUTE) {
val.val.c = modify->get_compute_by_id(val.id);
if (!val.val.c) error->all(FLERR,"Compute ID {} for fix ave/chunk does not exist", val.id);
} else if (which[m] == ArgInfo::FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/chunk does not exist");
value2index[m] = ifix;
} else if (val.which == ArgInfo::FIX) {
val.val.f = modify->get_fix_by_id(val.id);
if (!val.val.f) error->all(FLERR,"Fix ID {} for fix ave/chunk does not exist", val.id);
if (nevery % modify->fix[ifix]->peratom_freq)
error->all(FLERR,
"Fix for fix ave/chunk not computed at compatible time");
if (nevery % val.val.f->peratom_freq)
error->all(FLERR, "Fix {} for fix ave/chunk not computed at compatible time", val.id);
} else if (which[m] == ArgInfo::VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix ave/chunk does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
} else if (val.which == ArgInfo::VARIABLE) {
val.val.v = input->variable->find(val.id.c_str());
if (val.val.v < 0)
error->all(FLERR,"Variable name {} for fix ave/chunk does not exist", val.id);
}
}
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
@ -527,7 +500,7 @@ void FixAveChunk::setup(int /*vflag*/)
void FixAveChunk::end_of_step()
{
int i,j,m,n,index;
int i,j,m,index;
// skip if not step which requires doing something
@ -609,15 +582,15 @@ void FixAveChunk::end_of_step()
modify->clearstep_compute();
for (m = 0; m < nvalues; m++) {
n = value2index[m];
j = argindex[m];
m = 0;
for (auto &val : values) {
j = val.argindex;
// V,F adds velocities,forces to values
if (which[m] == ArgInfo::V || which[m] == ArgInfo::F) {
if (val.which == ArgInfo::V || val.which == ArgInfo::F) {
double **attribute;
if (which[m] == ArgInfo::V) attribute = atom->v;
if (val.which == ArgInfo::V) attribute = atom->v;
else attribute = atom->f;
for (i = 0; i < nlocal; i++)
@ -628,7 +601,7 @@ void FixAveChunk::end_of_step()
// DENSITY_NUMBER adds 1 to values
} else if (which[m] == ArgInfo::DENSITY_NUMBER) {
} else if (val.which == ArgInfo::DENSITY_NUMBER) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
@ -638,8 +611,7 @@ void FixAveChunk::end_of_step()
// DENSITY_MASS or MASS adds mass to values
} else if ((which[m] == ArgInfo::DENSITY_MASS)
|| (which[m] == ArgInfo::MASS)) {
} else if ((val.which == ArgInfo::DENSITY_MASS) || (val.which == ArgInfo::MASS)) {
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
@ -661,7 +633,7 @@ void FixAveChunk::end_of_step()
// TEMPERATURE adds KE to values
// subtract and restore velocity bias if requested
} else if (which[m] == ArgInfo::TEMPERATURE) {
} else if (val.which == ArgInfo::TEMPERATURE) {
if (biasflag) {
if (tbias->invoked_scalar != ntimestep) tbias->compute_scalar();
@ -695,14 +667,13 @@ void FixAveChunk::end_of_step()
// COMPUTE adds its scalar or vector component to values
// invoke compute if not previously invoked
} else if (which[m] == ArgInfo::COMPUTE) {
Compute *compute = modify->compute[n];
if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= Compute::INVOKED_PERATOM;
} else if (val.which == ArgInfo::COMPUTE) {
if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) {
val.val.c->compute_peratom();
val.val.c->invoked_flag |= Compute::INVOKED_PERATOM;
}
double *vector = compute->vector_atom;
double **array = compute->array_atom;
double *vector = val.val.c->vector_atom;
double **array = val.val.c->array_atom;
int jm1 = j - 1;
for (i = 0; i < nlocal; i++)
@ -715,9 +686,9 @@ void FixAveChunk::end_of_step()
// FIX adds its scalar or vector component to values
// access fix fields, guaranteed to be ready
} else if (which[m] == ArgInfo::FIX) {
double *vector = modify->fix[n]->vector_atom;
double **array = modify->fix[n]->array_atom;
} else if (val.which == ArgInfo::FIX) {
double *vector = val.val.f->vector_atom;
double **array = val.val.f->array_atom;
int jm1 = j - 1;
for (i = 0; i < nlocal; i++)
@ -730,14 +701,14 @@ void FixAveChunk::end_of_step()
// VARIABLE adds its per-atom quantities to values
// evaluate atom-style variable
} else if (which[m] == ArgInfo::VARIABLE) {
} else if (val.which == ArgInfo::VARIABLE) {
if (atom->nmax > maxvar) {
maxvar = atom->nmax;
memory->destroy(varatom);
memory->create(varatom,maxvar,"ave/chunk:varatom");
}
input->variable->compute_atom(n,igroup,varatom,1,0);
input->variable->compute_atom(val.val.v,igroup,varatom,1,0);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
@ -745,6 +716,7 @@ void FixAveChunk::end_of_step()
values_one[index][m] += varatom[i];
}
}
++m;
}
// process the current sample
@ -784,14 +756,14 @@ void FixAveChunk::end_of_step()
for (m = 0; m < nchunk; m++) {
if (count_many[m] > 0.0)
for (j = 0; j < nvalues; j++) {
if (which[j] == ArgInfo::TEMPERATURE) {
if (values[j].which == ArgInfo::TEMPERATURE) {
values_many[m][j] += mvv2e*values_one[m][j] /
((cdof + adof*count_many[m]) * boltz);
} else if (which[j] == ArgInfo::DENSITY_NUMBER) {
} else if (values[j].which == ArgInfo::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 if (which[j] == ArgInfo::DENSITY_MASS) {
} else if (values[j].which == ArgInfo::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];
@ -854,13 +826,13 @@ void FixAveChunk::end_of_step()
for (m = 0; m < nchunk; m++) {
if (count_sum[m] > 0.0)
for (j = 0; j < nvalues; j++) {
if (which[j] == ArgInfo::TEMPERATURE) {
if (values[j].which == ArgInfo::TEMPERATURE) {
values_sum[m][j] *= mvv2e/((repeat*cdof + adof*count_sum[m])*boltz);
} else if (which[j] == ArgInfo::DENSITY_NUMBER) {
} else if (values[j].which == ArgInfo::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 if (which[j] == ArgInfo::DENSITY_MASS) {
} else if (values[j].which == ArgInfo::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;
@ -1045,8 +1017,7 @@ void FixAveChunk::allocate()
if (ave == WINDOW) {
memory->create(count_list,nwindow,nchunk,"ave/chunk:count_list");
memory->create(values_list,nwindow,nchunk,nvalues,
"ave/chunk:values_list");
memory->create(values_list,nwindow,nchunk,nvalues,"ave/chunk:values_list");
}
// reinitialize regrown count/values total since they accumulate