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lammps/src/compute_chunk_atom.cpp
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compute_chunk_atom.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
// NOTE: allow for bin center to be variables for sphere/cylinder
#include <mpi.h>
#include <string.h>
#include <stdlib.h>
#include "compute_chunk_atom.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "region.h"
#include "lattice.h"
#include "modify.h"
#include "fix_store.h"
#include "comm.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include <map>
using namespace LAMMPS_NS;
using namespace MathConst;
enum{BIN1D,BIN2D,BIN3D,BINSPHERE,BINCYLINDER,
TYPE,MOLECULE,COMPUTE,FIX,VARIABLE};
enum{LOWER,CENTER,UPPER,COORD};
enum{BOX,LATTICE,REDUCED};
enum{NODISCARD,MIXED,YESDISCARD};
enum{ONCE,NFREQ,EVERY}; // used in several files
enum{LIMITMAX,LIMITEXACT};
#define IDMAX 1024*1024
#define INVOKED_PERATOM 8
// allocate space for static class variable
ComputeChunkAtom *ComputeChunkAtom::cptr;
/* ---------------------------------------------------------------------- */
ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute chunk/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
create_attribute = 1;
// chunk style and its args
int iarg;
binflag = 0;
ncoord = 0;
cfvid = NULL;
if (strcmp(arg[3],"bin/1d") == 0) {
binflag = 1;
which = BIN1D;
ncoord = 1;
iarg = 4;
readdim(narg,arg,iarg,0);
iarg += 3;
} else if (strcmp(arg[3],"bin/2d") == 0) {
binflag = 1;
which = BIN2D;
ncoord = 2;
iarg = 4;
readdim(narg,arg,iarg,0);
readdim(narg,arg,iarg+3,1);
iarg += 6;
} else if (strcmp(arg[3],"bin/3d") == 0) {
binflag = 1;
which = BIN3D;
ncoord = 3;
iarg = 4;
readdim(narg,arg,iarg,0);
readdim(narg,arg,iarg+3,1);
readdim(narg,arg,iarg+6,2);
iarg += 9;
} else if (strcmp(arg[3],"bin/sphere") == 0) {
binflag = 1;
which = BINSPHERE;
ncoord = 1;
iarg = 4;
if (iarg+6 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
sorigin_user[0] = force->numeric(FLERR,arg[iarg]);
sorigin_user[1] = force->numeric(FLERR,arg[iarg+1]);
sorigin_user[2] = force->numeric(FLERR,arg[iarg+2]);
sradmin_user = force->numeric(FLERR,arg[iarg+3]);
sradmax_user = force->numeric(FLERR,arg[iarg+4]);
nsbin = force->inumeric(FLERR,arg[iarg+5]);
iarg += 6;
} else if (strcmp(arg[3],"bin/cylinder") == 0) {
binflag = 1;
which = BINCYLINDER;
ncoord = 2;
iarg = 4;
readdim(narg,arg,iarg,0);
iarg += 3;
if (dim[0] == 0) {
cdim1 = 1;
cdim2 = 2;
} else if (dim[0] == 1) {
cdim1 = 0;
cdim2 = 2;
} else {
cdim1 = 0;
cdim2 = 1;
}
if (iarg+5 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
corigin_user[dim[0]] = 0.0;
corigin_user[cdim1] = force->numeric(FLERR,arg[iarg]);
corigin_user[cdim2] = force->numeric(FLERR,arg[iarg+1]);
cradmin_user = force->numeric(FLERR,arg[iarg+2]);
cradmax_user = force->numeric(FLERR,arg[iarg+3]);
ncbin = force->inumeric(FLERR,arg[iarg+4]);
iarg += 5;
} else if (strcmp(arg[3],"type") == 0) {
which = TYPE;
iarg = 4;
} else if (strcmp(arg[3],"molecule") == 0) {
which = MOLECULE;
iarg = 4;
} else if (strstr(arg[3],"c_") == arg[3] ||
strstr(arg[3],"f_") == arg[3] ||
strstr(arg[3],"v_") == arg[3]) {
if (arg[3][0] == 'c') which = COMPUTE;
else if (arg[3][0] == 'f') which = FIX;
else if (arg[3][0] == 'v') which = VARIABLE;
iarg = 4;
int n = strlen(arg[3]);
char *suffix = new char[n];
strcpy(suffix,&arg[3][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal fix ave/atom command");
argindex = atoi(ptr+1);
*ptr = '\0';
} else argindex = 0;
n = strlen(suffix) + 1;
cfvid = new char[n];
strcpy(cfvid,suffix);
delete [] suffix;
} else error->all(FLERR,"Illegal compute chunk/atom command");
// optional args
regionflag = 0;
idregion = NULL;
nchunksetflag = 0;
nchunkflag = EVERY;
limit = 0;
limitstyle = LIMITMAX;
limitfirst = 0;
idsflag = EVERY;
compress = 0;
int discardsetflag = 0;
discard = MIXED;
minflag[0] = LOWER;
minflag[1] = LOWER;
minflag[2] = LOWER;
maxflag[0] = UPPER;
maxflag[1] = UPPER;
maxflag[2] = UPPER;
scaleflag = LATTICE;
pbcflag = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
int iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all(FLERR,"Region ID for compute chunk/atom does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
regionflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"nchunk") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
if (strcmp(arg[iarg+1],"once") == 0) nchunkflag = ONCE;
else if (strcmp(arg[iarg+1],"every") == 0) nchunkflag = EVERY;
else error->all(FLERR,"Illegal compute chunk/atom command");
nchunksetflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"limit") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
limit = force->inumeric(FLERR,arg[iarg+1]);
if (limit < 0) error->all(FLERR,"Illegal compute chunk/atom command");
if (limit && !compress) limitfirst = 1;
iarg += 2;
if (limit) {
if (iarg+1 > narg)
error->all(FLERR,"Illegal compute chunk/atom command");
if (strcmp(arg[iarg+1],"max") == 0) limitstyle = LIMITMAX;
else if (strcmp(arg[iarg+1],"exact") == 0) limitstyle = LIMITEXACT;
else error->all(FLERR,"Illegal compute chunk/atom command");
iarg++;
}
} else if (strcmp(arg[iarg],"ids") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
if (strcmp(arg[iarg+1],"once") == 0) idsflag = ONCE;
else if (strcmp(arg[iarg+1],"nfreq") == 0) idsflag = NFREQ;
else if (strcmp(arg[iarg+1],"every") == 0) idsflag = EVERY;
else error->all(FLERR,"Illegal compute chunk/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"compress") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
else if (strcmp(arg[iarg+1],"no") == 0) compress = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) compress = 1;
else error->all(FLERR,"Illegal compute chunk/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"discard") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
if (strcmp(arg[iarg+1],"mixed") == 0) discard = MIXED;
else if (strcmp(arg[iarg+1],"no") == 0) discard = NODISCARD;
else if (strcmp(arg[iarg+1],"yes") == 0) discard = YESDISCARD;
else error->all(FLERR,"Illegal compute chunk/atom command");
discardsetflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"bound") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
int idim;
if (strcmp(arg[iarg+1],"x") == 0) idim = 0;
else if (strcmp(arg[iarg+1],"y") == 0) idim = 1;
else if (strcmp(arg[iarg+1],"z") == 0) idim = 2;
else error->all(FLERR,"Illegal compute chunk/atom command");
if (strcmp(arg[iarg+2],"lower") == 0) minflag[idim] = LOWER;
else minflag[idim] = COORD;
if (minflag[idim] == COORD)
minvalue[idim] = force->numeric(FLERR,arg[iarg+2]);
if (strcmp(arg[iarg+3],"upper") == 0) maxflag[idim] = UPPER;
else maxflag[idim] = COORD;
if (maxflag[idim] == COORD)
maxvalue[idim] = force->numeric(FLERR,arg[iarg+3]);
else error->all(FLERR,"Illegal compute chunk/atom command");
iarg += 4;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = BOX;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = LATTICE;
else if (strcmp(arg[iarg+1],"reduced") == 0) scaleflag = REDUCED;
else error->all(FLERR,"Illegal compute chunk/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"pbc") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
if (strcmp(arg[iarg+1],"no") == 0) pbcflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) pbcflag = 1;
else error->all(FLERR,"Illegal compute chunk/atom command");
iarg += 2;
} else error->all(FLERR,"Illegal compute chunk/atom command");
}
// set nchunkflag and discard to default values if not explicitly set
// for binning style, also check in init() if simulation box is static,
// which sets nchunkflag = ONCE
if (!nchunksetflag) {
if (binflag) {
if (scaleflag == REDUCED) nchunkflag = ONCE;
else nchunkflag = EVERY;
}
if (which == TYPE) nchunkflag = ONCE;
if (which == MOLECULE) {
if (regionflag) nchunkflag = EVERY;
else nchunkflag = ONCE;
}
if (compress) nchunkflag = EVERY;
}
if (!discardsetflag) {
if (binflag) discard = MIXED;
else discard = YESDISCARD;
}
// error checks
if (which == MOLECULE && !atom->molecule_flag)
error->all(FLERR,"Compute chunk/atom molecule for non-molecular system");
if (!binflag && discard == MIXED)
error->all(FLERR,"Compute chunk/atom without bins "
"cannot use discard mixed");
if (which == BIN1D && delta[0] <= 0.0)
error->all(FLERR,"Illegal compute chunk/atom command");
if (which == BIN2D && (delta[0] <= 0.0 || delta[1] <= 0.0))
error->all(FLERR,"Illegal compute chunk/atom command");
if (which == BIN3D &&
(delta[0] <= 0.0 || delta[1] <= 0.0 || delta[2] <= 0.0))
error->all(FLERR,"Illegal compute chunk/atom command");
if (which == BINSPHERE) {
if (domain->dimension == 2 && sorigin_user[2] != 0.0)
error->all(FLERR,"Compute chunk/atom sphere z origin must be 0.0 for 2d");
if (sradmin_user < 0.0 || sradmin_user >= sradmax_user || nsbin < 1)
error->all(FLERR,"Illegal compute chunk/atom command");
}
if (which == BINCYLINDER) {
if (delta[0] <= 0.0)
error->all(FLERR,"Illegal compute chunk/atom command");
if (domain->dimension == 2 && dim[0] != 2)
error->all(FLERR,"Compute chunk/atom cylinder axis must be z for 2d");
if (cradmin_user < 0.0 || cradmin_user >= cradmax_user || ncbin < 1)
error->all(FLERR,"Illegal compute chunk/atom command");
}
if (which == COMPUTE) {
int icompute = modify->find_compute(cfvid);
if (icompute < 0)
error->all(FLERR,"Compute ID for compute chunk /atom does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all(FLERR,
"Compute chunk/atom compute does not calculate "
"per-atom values");
if (argindex == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all(FLERR,"Compute chunk/atom compute does not "
"calculate a per-atom vector");
if (argindex && modify->compute[icompute]->size_peratom_cols == 0)
error->all(FLERR,"Compute chunk/atom compute does not "
"calculate a per-atom array");
if (argindex &&
argindex > modify->compute[icompute]->size_peratom_cols)
error->all(FLERR,"Compute chunk/atom compute array is "
"accessed out-of-range");
}
if (which == FIX) {
int ifix = modify->find_fix(cfvid);
if (ifix < 0)
error->all(FLERR,"Fix ID for compute chunk/atom does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all(FLERR,"Compute chunk/atom fix does not calculate "
"per-atom values");
if (argindex == 0 && modify->fix[ifix]->size_peratom_cols != 0)
error->all(FLERR,
"Compute chunk/atom fix does not calculate a per-atom vector");
if (argindex && modify->fix[ifix]->size_peratom_cols == 0)
error->all(FLERR,
"Compute chunk/atom fix does not calculate a per-atom array");
if (argindex && argindex > modify->fix[ifix]->size_peratom_cols)
error->all(FLERR,"Compute chunk/atom fix array is accessed out-of-range");
}
if (which == VARIABLE) {
int ivariable = input->variable->find(cfvid);
if (ivariable < 0)
error->all(FLERR,"Variable name for compute chunk/atom does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Compute chunk/atom variable is not "
"atom-style variable");
}
// setup scaling
if (binflag) {
if (domain->triclinic == 1 && scaleflag != REDUCED)
error->all(FLERR,"Compute chunk/atom for triclinic boxes "
"requires units reduced");
}
if (scaleflag == LATTICE) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
} else xscale = yscale = zscale = 1.0;
// apply scaling factors and cylinder dims orthogonal to axis
if (binflag) {
double scale;
if (which == BIN1D || which == BIN2D || which == BIN3D ||
which == BINCYLINDER) {
if (which == BIN1D || which == BINCYLINDER) ndim = 1;
if (which == BIN2D) ndim = 2;
if (which == BIN3D) ndim = 3;
for (int idim = 0; idim < ndim; idim++) {
if (dim[idim] == 0) scale = xscale;
else if (dim[idim] == 1) scale = yscale;
else if (dim[idim] == 2) scale = zscale;
delta[idim] *= scale;
invdelta[idim] = 1.0/delta[idim];
if (originflag[idim] == COORD) origin[idim] *= scale;
if (minflag[idim] == COORD) minvalue[idim] *= scale;
if (maxflag[idim] == COORD) maxvalue[idim] *= scale;
}
} else if (which == BINSPHERE) {
sorigin_user[0] *= xscale;
sorigin_user[1] *= yscale;
sorigin_user[2] *= zscale;
sradmin_user *= xscale; // radii are scaled by xscale
sradmax_user *= xscale;
} else if (which == BINCYLINDER) {
if (dim[0] == 0) {
corigin_user[cdim1] *= yscale;
corigin_user[cdim2] *= zscale;
cradmin_user *= yscale; // radii are scaled by first non-axis dim
cradmax_user *= yscale;
} else if (dim[0] == 1) {
corigin_user[cdim1] *= xscale;
corigin_user[cdim2] *= zscale;
cradmin_user *= xscale;
cradmax_user *= xscale;
} else {
corigin_user[cdim1] *= xscale;
corigin_user[cdim2] *= yscale;
cradmin_user *= xscale;
cradmax_user *= xscale;
}
}
}
// initialize chunk vector and per-chunk info
nmax = 0;
chunk = NULL;
nmaxint = -1;
ichunk = NULL;
exclude = NULL;
nchunk = 0;
chunk_volume_scalar = 1.0;
chunk_volume_vec = NULL;
coord = NULL;
chunkID = NULL;
// computeflag = 1 if this compute might invoke another compute
// during assign_chunk_ids()
if (which == COMPUTE || which == FIX || which == VARIABLE) computeflag = 1;
else computeflag = 0;
// other initializations
invoked_setup = -1;
invoked_ichunk = -1;
id_fix = NULL;
fixstore = NULL;
if (compress) hash = new std::map<tagint,int>();
else hash = NULL;
maxvar = 0;
varatom = NULL;
lockcount = 0;
lockfix = NULL;
if (which == MOLECULE) molcheck = 1;
else molcheck = 0;
}
/* ---------------------------------------------------------------------- */
ComputeChunkAtom::~ComputeChunkAtom()
{
// check nfix in case all fixes have already been deleted
if (modify->nfix) modify->delete_fix(id_fix);
delete [] id_fix;
memory->destroy(chunk);
memory->destroy(ichunk);
memory->destroy(exclude);
memory->destroy(chunk_volume_vec);
memory->destroy(coord);
memory->destroy(chunkID);
delete [] idregion;
delete [] cfvid;
delete hash;
memory->destroy(varatom);
}
/* ---------------------------------------------------------------------- */
void ComputeChunkAtom::init()
{
// set and check validity of region
if (regionflag) {
int iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for compute chunk/atom does not exist");
region = domain->regions[iregion];
}
// set compute,fix,variable
if (which == COMPUTE) {
int icompute = modify->find_compute(cfvid);
if (icompute < 0)
error->all(FLERR,"Compute ID for compute chunk/atom does not exist");
cchunk = modify->compute[icompute];
} else if (which == FIX) {
int ifix = modify->find_fix(cfvid);
if (ifix < 0)
error->all(FLERR,"Fix ID for compute chunk/atom does not exist");
fchunk = modify->fix[ifix];
} else if (which == VARIABLE) {
int ivariable = input->variable->find(cfvid);
if (ivariable < 0)
error->all(FLERR,"Variable name for compute chunk/atom does not exist");
vchunk = ivariable;
}
// for style MOLECULE, check that no mol IDs exceed MAXSMALLINT
// don't worry about group or optional region
if (which == MOLECULE) {
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
tagint maxone = -1;
for (int i = 0; i < nlocal; i++)
if (molecule[i] > maxone) maxone = molecule[i];
tagint maxall;
MPI_Allreduce(&maxone,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (maxall > MAXSMALLINT)
error->all(FLERR,"Molecule IDs too large for compute chunk/atom");
}
// for binning, if nchunkflag not already set, set it to ONCE or EVERY
// depends on whether simulation box size is static or dynamic
// reset invoked_setup if this is not first run and box just became static
if (binflag && !nchunksetflag && !compress && scaleflag != REDUCED) {
if (domain->box_change_size == 0) {
if (nchunkflag == EVERY && invoked_setup >= 0) invoked_setup = -1;
nchunkflag = ONCE;
} else nchunkflag = EVERY;
}
// require nchunkflag = ONCE if idsflag = ONCE
// b/c nchunk cannot change if chunk IDs are frozen
// can't check until now since nchunkflag may have been adjusted in init()
if (idsflag == ONCE && nchunkflag != ONCE)
error->all(FLERR,"Compute chunk/atom ids once but nchunk is not once");
// create/destroy fix STORE for persistent chunk IDs as needed
// need to do this if idsflag = ONCE or locks will be used by other commands
// need to wait until init() so that fix ave/chunk command(s) are in place
// they increment lockcount if they lock this compute
// fixstore ID = compute-ID + COMPUTE_STORE, fix group = compute group
// fixstore initializes all values to 0.0
if ((idsflag == ONCE || lockcount) && !fixstore) {
int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
id_fix = new char[n];
strcpy(id_fix,id);
strcat(id_fix,"_COMPUTE_STORE");
char **newarg = new char*[6];
newarg[0] = id_fix;
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "peratom";
newarg[4] = (char *) "1";
newarg[5] = (char *) "1";
modify->add_fix(6,newarg);
fixstore = (FixStore *) modify->fix[modify->nfix-1];
delete [] newarg;
}
if ((idsflag != ONCE && !lockcount) && fixstore) {
modify->delete_fix(id_fix);
fixstore = NULL;
}
}
/* ----------------------------------------------------------------------
invoke setup_chunks and/or compute_ichunk if only done ONCE
so that nchunks or chunk IDs are assigned when this compute was specified
as opposed to first times compute_peratom() or compute_ichunk() is called
------------------------------------------------------------------------- */
void ComputeChunkAtom::setup()
{
if (nchunkflag == ONCE) setup_chunks();
if (idsflag == ONCE) compute_ichunk();
}
/* ----------------------------------------------------------------------
only called by classes that use per-atom computes in standard way
dump, variable, thermo output, other computes, etc
not called by fix ave/chunk or compute chunk commands
they invoke setup_chunks() and compute_ichunk() directly
------------------------------------------------------------------------- */
void ComputeChunkAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow floating point chunk vector if necessary
if (atom->nlocal > nmax) {
memory->destroy(chunk);
nmax = atom->nmax;
memory->create(chunk,nmax,"chunk/atom:chunk");
vector_atom = chunk;
}
setup_chunks();
compute_ichunk();
// copy integer indices into floating-point chunk vector
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) chunk[i] = ichunk[i];
}
/* ----------------------------------------------------------------------
set lock, so that nchunk will not change from startstep to stopstep
called by fix ave/chunk for duration of its Nfreq epoch
OK if called by multiple fix ave/chunk commands
error if all callers do not have same duration
last caller holds the lock, so it can also unlock
lockstop can be positive for final step of finite-size time window
or can be -1 for infinite-size time window
------------------------------------------------------------------------- */
void ComputeChunkAtom::lock(Fix *fixptr, bigint startstep, bigint stopstep)
{
if (lockfix == NULL) {
lockfix = fixptr;
lockstart = startstep;
lockstop = stopstep;
return;
}
if (startstep != lockstart || stopstep != lockstop)
error->all(FLERR,"Two fix ave commands using "
"same compute chunk/atom command in incompatible ways");
// set lock to last calling Fix, since it will be last to unlock()
lockfix = fixptr;
}
/* ----------------------------------------------------------------------
unset lock
can only be done by fix ave/chunk command that holds the lock
------------------------------------------------------------------------- */
void ComputeChunkAtom::unlock(Fix *fixptr)
{
if (fixptr != lockfix) return;
lockfix = NULL;
}
/* ----------------------------------------------------------------------
assign chunk IDs from 1 to Nchunk to every atom, or 0 if not in chunk
------------------------------------------------------------------------- */
void ComputeChunkAtom::compute_ichunk()
{
int i;
// skip if already done on this step
if (invoked_ichunk == update->ntimestep) return;
// if old IDs persist via storage in fixstore, then just retrieve them
// yes if idsflag = ONCE, and already done once
// or if idsflag = NFREQ and lock is in place and are on later timestep
// else proceed to recalculate per-atom chunk assignments
int restore = 0;
if (idsflag == ONCE && invoked_ichunk >= 0) restore = 1;
if (idsflag == NFREQ && lockfix && update->ntimestep > lockstart) restore = 1;
if (restore) {
invoked_ichunk = update->ntimestep;
double *vstore = fixstore->vstore;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) ichunk[i] = static_cast<int> (vstore[i]);
return;
}
invoked_ichunk = update->ntimestep;
// assign chunk IDs to atoms
// will exclude atoms not in group or in optional region
// already invoked if this is same timestep as last setup_chunks()
if (update->ntimestep > invoked_setup) assign_chunk_ids();
// compress chunk IDs via hash of the original uncompressed IDs
// also apply discard rule except for binning styles which already did
int nlocal = atom->nlocal;
if (compress) {
if (binflag) {
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
if (hash->find(ichunk[i]) == hash->end()) exclude[i] = 1;
else ichunk[i] = hash->find(ichunk[i])->second;
}
} else if (discard == NODISCARD) {
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
if (hash->find(ichunk[i]) == hash->end()) ichunk[i] = nchunk;
else ichunk[i] = hash->find(ichunk[i])->second;
}
} else {
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
if (hash->find(ichunk[i]) == hash->end()) exclude[i] = 1;
else ichunk[i] = hash->find(ichunk[i])->second;
}
}
// else if no compression apply discard rule by itself
} else {
if (discard == NODISCARD) {
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
if (ichunk[i] < 1 || ichunk[i] > nchunk) ichunk[i] = nchunk;;
}
} else {
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
if (ichunk[i] < 1 || ichunk[i] > nchunk) exclude[i] = 1;
}
}
}
// set ichunk = 0 for excluded atoms
// this should set any ichunk values which have not yet been set
for (i = 0; i < nlocal; i++)
if (exclude[i]) ichunk[i] = 0;
// if newly calculated IDs need to persist, store them in fixstore
// yes if idsflag = ONCE or idsflag = NFREQ and lock is in place
if (idsflag == ONCE || (idsflag == NFREQ && lockfix)) {
double *vstore = fixstore->vstore;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) vstore[i] = ichunk[i];
}
// one-time check if which = MOLECULE and
// any chunks do not contain all atoms in the molecule
if (molcheck) {
check_molecules();
molcheck = 0;
}
}
/* ----------------------------------------------------------------------
setup chunks
return nchunk = # of chunks
all atoms will be assigned a chunk ID from 1 to Nchunk, or 0
also setup any internal state needed to quickly assign atoms to chunks
called from compute_peratom() and also directly from
fix ave/chunk and compute chunk commands
------------------------------------------------------------------------- */
int ComputeChunkAtom::setup_chunks()
{
if (invoked_setup == update->ntimestep) return nchunk;
// check if setup needs to be done
// no if lock is in place
// no if nchunkflag = ONCE, and already done once
// otherwise yes
// even if no, check if need to re-compute bin volumes
// so that fix ave/chunk can do proper density normalization
int flag = 0;
if (lockfix) flag = 1;
if (nchunkflag == ONCE && invoked_setup >= 0) flag = 1;
if (flag) {
if (binflag && scaleflag == REDUCED && domain->box_change_size)
bin_volumes();
return nchunk;
}
invoked_setup = update->ntimestep;
// assign chunk IDs to atoms
// will exclude atoms not in group or in optional region
// for binning styles, need to setup bins and their volume first
// else chunk_volume_scalar = entire box volume
// IDs are needed to scan for max ID and for compress()
if (binflag) {
if (which == BIN1D || which == BIN2D || which == BIN3D)
nchunk = setup_xyz_bins();
else if (which == BINSPHERE) nchunk = setup_sphere_bins();
else if (which == BINCYLINDER) nchunk = setup_cylinder_bins();
bin_volumes();
} else {
chunk_volume_scalar = domain->xprd * domain->yprd;
if (domain->dimension == 3) chunk_volume_scalar *= domain->zprd;
}
assign_chunk_ids();
// set nchunk for chunk styles other than binning
// for styles other than TYPE, scan for max ID
if (which == TYPE) nchunk = atom->ntypes;
else if (!binflag) {
int nlocal = atom->nlocal;
int hi = -1;
for (int i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
if (ichunk[i] > hi) hi = ichunk[i];
}
MPI_Allreduce(&hi,&nchunk,1,MPI_INT,MPI_MAX,world);
if (nchunk <= 0) nchunk = 1;
}
// apply limit setting as well as compression of chunks with no atoms
// if limit is set, there are 3 cases:
// no compression, limit specified before compression, or vice versa
if (limit && !binflag) {
if (!compress) {
if (limitstyle == LIMITMAX) nchunk = MIN(nchunk,limit);
else if (limitstyle == LIMITEXACT) nchunk = limit;
} else if (limitfirst) {
nchunk = MIN(nchunk,limit);
}
}
if (compress) compress_chunk_ids();
if (limit && !binflag && compress) {
if (limitstyle == LIMITMAX) nchunk = MIN(nchunk,limit);
else if (limitstyle == LIMITEXACT) nchunk = limit;
}
return nchunk;
}
/* ----------------------------------------------------------------------
assign chunk IDs for all atoms, via ichunk vector
except excluded atoms, their chunk IDs are set to 0 later
also set exclude vector to 0/1 for all atoms
excluded atoms are those not in group or in optional region
called from compute_ichunk() and setup_chunks()
------------------------------------------------------------------------- */
void ComputeChunkAtom::assign_chunk_ids()
{
int i;
// grow integer chunk index vector if necessary
if (atom->nlocal > nmaxint) {
memory->destroy(ichunk);
memory->destroy(exclude);
nmaxint = atom->nmax;
memory->create(ichunk,nmaxint,"chunk/atom:ichunk");
memory->create(exclude,nmaxint,"chunk/atom:exclude");
}
// update region if necessary
if (regionflag) region->prematch();
// exclude = 1 if atom is not assigned to a chunk
// exclude atoms not in group or not in optional region
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (regionflag) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit &&
region->match(x[i][0],x[i][1],x[i][2])) exclude[i] = 0;
else exclude[i] = 1;
}
} else {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) exclude[i] = 0;
else exclude[i] = 1;
}
}
// set ichunk to style value for included atoms
// binning styles apply discard rule, others do not yet
if (binflag) {
if (which == BIN1D) atom2bin1d();
else if (which == BIN2D) atom2bin2d();
else if (which == BIN3D) atom2bin3d();
else if (which == BINSPHERE) atom2binsphere();
else if (which == BINCYLINDER) atom2bincylinder();
} else if (which == TYPE) {
int *type = atom->type;
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
ichunk[i] = type[i];
}
} else if (which == MOLECULE) {
tagint *molecule = atom->molecule;
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
ichunk[i] = static_cast<int> (molecule[i]);
}
} else if (which == COMPUTE) {
if (!(cchunk->invoked_flag & INVOKED_PERATOM)) {
cchunk->compute_peratom();
cchunk->invoked_flag |= INVOKED_PERATOM;
}
if (argindex == 0) {
double *vec = cchunk->vector_atom;
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
ichunk[i] = static_cast<int> (vec[i]);
}
} else {
double **array = cchunk->array_atom;
int argm1 = argindex - 1;
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
ichunk[i] = static_cast<int> (array[i][argm1]);
}
}
} else if (which == FIX) {
if (update->ntimestep % fchunk->peratom_freq)
error->all(FLERR,"Fix used in compute chunk/atom not "
"computed at compatible time");
if (argindex == 0) {
double *vec = fchunk->vector_atom;
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
ichunk[i] = static_cast<int> (vec[i]);
}
} else {
double **array = fchunk->array_atom;
int argm1 = argindex - 1;
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
ichunk[i] = static_cast<int> (array[i][argm1]);
}
}
} else if (which == VARIABLE) {
if (nlocal > maxvar) {
maxvar = atom->nmax;
memory->destroy(varatom);
memory->create(varatom,maxvar,"chunk/atom:varatom");
}
input->variable->compute_atom(vchunk,igroup,varatom,1,0);
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
ichunk[i] = static_cast<int> (varatom[i]);
}
}
}
/* ----------------------------------------------------------------------
compress chunk IDs currently assigned to atoms across all processors
by removing those with no atoms assigned
current assignment excludes atoms not in group or in optional region
current Nchunk = max ID
operation:
use hash to store list of populated IDs that I own
add new IDs to populated lists communicated from all other procs
final hash has global list of populated ideas
reset Nchunk = length of global list
called by setup_chunks() when setting Nchunk
remapping of chunk IDs to smaller Nchunk occurs later in compute_ichunk()
------------------------------------------------------------------------- */
void ComputeChunkAtom::compress_chunk_ids()
{
hash->clear();
// put my IDs into hash
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
if (hash->find(ichunk[i]) == hash->end()) (*hash)[ichunk[i]] = 0;
}
// n = # of my populated IDs
// nall = n summed across all procs
int n = hash->size();
bigint nbone = n;
bigint nball;
MPI_Allreduce(&nbone,&nball,1,MPI_LMP_BIGINT,MPI_SUM,world);
// create my list of populated IDs
int *list = NULL;
memory->create(list,n,"chunk/atom:list");
n = 0;
std::map<tagint,int>::iterator pos;
for (pos = hash->begin(); pos != hash->end(); ++pos)
list[n++] = pos->first;
// if nall < 1M, just allgather all ID lists on every proc
// else perform ring comm
// add IDs from all procs to my hash
if (nball <= IDMAX) {
// setup for allgatherv
int nprocs = comm->nprocs;
int nall = nball;
int *recvcounts,*displs,*listall;
memory->create(recvcounts,nprocs,"chunk/atom:recvcounts");
memory->create(displs,nprocs,"chunk/atom:displs");
memory->create(listall,nall,"chunk/atom:listall");
MPI_Allgather(&n,1,MPI_INT,recvcounts,1,MPI_INT,world);
displs[0] = 0;
for (int iproc = 1; iproc < nprocs; iproc++)
displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
// allgatherv acquires list of populated IDs from all procs
MPI_Allgatherv(list,n,MPI_INT,listall,recvcounts,displs,MPI_INT,world);
// add all unique IDs in listall to my hash
for (int i = 0; i < nall; i++)
if (hash->find(listall[i]) == hash->end()) (*hash)[listall[i]] = 0;
// clean up
memory->destroy(recvcounts);
memory->destroy(displs);
memory->destroy(listall);
} else {
cptr = this;
comm->ring(n,sizeof(int),list,1,idring,NULL,0);
}
memory->destroy(list);
// nchunk = length of hash containing populated IDs from all procs
nchunk = hash->size();
// reset hash value of each original chunk ID to ordered index
// ordered index = new compressed chunk ID (1 to Nchunk)
// leverages fact that map stores keys in ascending order
// also allocate and set chunkID = list of original chunk IDs
// used by fix ave/chunk and compute property/chunk
memory->destroy(chunkID);
memory->create(chunkID,nchunk,"chunk/atom:chunkID");
n = 0;
for (pos = hash->begin(); pos != hash->end(); ++pos) {
chunkID[n] = pos->first;
(*hash)[pos->first] = ++n;
}
}
/* ----------------------------------------------------------------------
callback from comm->ring()
cbuf = list of N chunk IDs from another proc
loop over the list, add each to my hash
hash ends up storing all unique IDs across all procs
------------------------------------------------------------------------- */
void ComputeChunkAtom::idring(int n, char *cbuf)
{
tagint *list = (tagint *) cbuf;
std::map<tagint,int> *hash = cptr->hash;
for (int i = 0; i < n; i++) (*hash)[list[i]] = 0;
}
/* ----------------------------------------------------------------------
one-time check for which = MOLECULE to check
if each chunk contains all atoms in the molecule
issue warning if not
note that this check is without regard to discard rule
if discard == NODISCARD, there is no easy way to check that all
atoms in an out-of-bounds molecule were added to a chunk,
some could have been excluded by group or region, others not
------------------------------------------------------------------------- */
void ComputeChunkAtom::check_molecules()
{
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int flag = 0;
if (!compress) {
for (int i = 0; i < nlocal; i++) {
if (molecule[i] > 0 && molecule[i] <= nchunk &&
ichunk[i] == 0) flag = 1;
}
} else {
int molid;
for (int i = 0; i < nlocal; i++) {
molid = static_cast<int> (molecule[i]);
if (hash->find(molid) != hash->end() && ichunk[i] == 0) flag = 1;
}
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning(FLERR,
"One or more chunks do not contain all atoms in molecule");
}
/* ----------------------------------------------------------------------
setup xyz spatial bins and their extent and coordinates
return nbins = # of bins, will become # of chunks
called from setup_chunks()
------------------------------------------------------------------------- */
int ComputeChunkAtom::setup_xyz_bins()
{
int i,j,k,m,n,idim;
double lo,hi,coord1,coord2;
// lo = bin boundary immediately below boxlo or minvalue
// hi = bin boundary immediately above boxhi or maxvalue
// allocate and initialize arrays based on new bin count
double binlo[3],binhi[3];
if (scaleflag == REDUCED) {
binlo[0] = domain->boxlo_lamda[0];
binlo[1] = domain->boxlo_lamda[1];
binlo[2] = domain->boxlo_lamda[2];
binhi[0] = domain->boxhi_lamda[0];
binhi[1] = domain->boxhi_lamda[1];
binhi[2] = domain->boxhi_lamda[2];
} else {
binlo[0] = domain->boxlo[0];
binlo[1] = domain->boxlo[1];
binlo[2] = domain->boxlo[2];
binhi[0] = domain->boxhi[0];
binhi[1] = domain->boxhi[1];
binhi[2] = domain->boxhi[2];
}
if (minflag[0] == COORD) binlo[0] = minvalue[0];
if (minflag[1] == COORD) binlo[1] = minvalue[1];
if (minflag[2] == COORD) binlo[2] = minvalue[2];
if (maxflag[0] == COORD) binhi[0] = maxvalue[0];
if (maxflag[1] == COORD) binhi[1] = maxvalue[1];
if (maxflag[2] == COORD) binhi[2] = maxvalue[2];
int nbins = 1;
for (m = 0; m < ndim; m++) {
idim = dim[m];
if (originflag[m] == LOWER) origin[m] = binlo[idim];
else if (originflag[m] == UPPER) origin[m] = binhi[idim];
else if (originflag[m] == CENTER)
origin[m] = 0.5 * (binlo[idim] + binhi[idim]);
if (origin[m] < binlo[idim]) {
n = static_cast<int> ((binlo[idim] - origin[m]) * invdelta[m]);
lo = origin[m] + n*delta[m];
} else {
n = static_cast<int> ((origin[m] - binlo[idim]) * invdelta[m]);
lo = origin[m] - n*delta[m];
if (lo > binlo[idim]) lo -= delta[m];
}
if (origin[m] < binhi[idim]) {
n = static_cast<int> ((binhi[idim] - origin[m]) * invdelta[m]);
hi = origin[m] + n*delta[m];
if (hi < binhi[idim]) hi += delta[m];
} else {
n = static_cast<int> ((origin[m] - binhi[idim]) * invdelta[m]);
hi = origin[m] - n*delta[m];
}
if (lo > hi) error->all(FLERR,"Invalid bin bounds in compute chunk/atom");
offset[m] = lo;
nlayers[m] = static_cast<int> ((hi-lo) * invdelta[m] + 0.5);
nbins *= nlayers[m];
}
// allocate and set bin coordinates
memory->destroy(coord);
memory->create(coord,nbins,ndim,"chunk/atom:coord");
if (ndim == 1) {
for (i = 0; i < nlayers[0]; i++)
coord[i][0] = offset[0] + (i+0.5)*delta[0];
} else if (ndim == 2) {
m = 0;
for (i = 0; i < nlayers[0]; i++) {
coord1 = offset[0] + (i+0.5)*delta[0];
for (j = 0; j < nlayers[1]; j++) {
coord[m][0] = coord1;
coord[m][1] = offset[1] + (j+0.5)*delta[1];
m++;
}
}
} else if (ndim == 3) {
m = 0;
for (i = 0; i < nlayers[0]; i++) {
coord1 = offset[0] + (i+0.5)*delta[0];
for (j = 0; j < nlayers[1]; j++) {
coord2 = offset[1] + (j+0.5)*delta[1];
for (k = 0; k < nlayers[2]; k++) {
coord[m][0] = coord1;
coord[m][1] = coord2;
coord[m][2] = offset[2] + (k+0.5)*delta[2];
m++;
}
}
}
}
return nbins;
}
/* ----------------------------------------------------------------------
setup spherical spatial bins and their single coordinate
return nsphere = # of bins, will become # of chunks
called from setup_chunks()
------------------------------------------------------------------------- */
int ComputeChunkAtom::setup_sphere_bins()
{
// convert sorigin_user to sorigin
// sorigin,srad are always in box units, for orthogonal or triclinic domains
// lamda2x works for either orthogonal or triclinic
if (scaleflag == REDUCED) {
domain->lamda2x(sorigin_user,sorigin);
sradmin = sradmin_user * (domain->boxhi[0]-domain->boxlo[0]);
sradmax = sradmax_user * (domain->boxhi[0]-domain->boxlo[0]);
} else {
sorigin[0] = sorigin_user[0];
sorigin[1] = sorigin_user[1];
sorigin[2] = sorigin_user[2];
sradmin = sradmin_user;
sradmax = sradmax_user;
}
// if pbcflag set, sradmax must be < 1/2 box in any periodic dim
// treat orthongonal and triclinic the same
// check every time bins are created
if (pbcflag) {
double *prd_half = domain->prd_half;
int *periodicity = domain->periodicity;
int flag = 0;
if (periodicity[0] && sradmax > prd_half[0]) flag = 1;
if (periodicity[1] && sradmax > prd_half[1]) flag = 1;
if (domain->dimension == 3 &&
periodicity[2] && sradmax > prd_half[2]) flag = 1;
if (flag)
error->all(FLERR,"Compute chunk/atom bin/sphere radius "
"is too large for periodic box");
}
sinvrad = nsbin / (sradmax-sradmin);
// allocate and set bin coordinates
// coord = midpt of radii for a spherical shell
memory->destroy(coord);
memory->create(coord,nsbin,1,"chunk/atom:coord");
double rlo,rhi;
for (int i = 0; i < nsbin; i++) {
rlo = sradmin + i * (sradmax-sradmin) / nsbin;
rhi = sradmin + (i+1) * (sradmax-sradmin) / nsbin;
if (i == nsbin-1) rhi = sradmax;
coord[i][0] = 0.5 * (rlo+rhi);
}
return nsbin;
}
/* ----------------------------------------------------------------------
setup cylindrical spatial bins and their single coordinate
return nsphere = # of bins, will become # of chunks
called from setup_chunks()
------------------------------------------------------------------------- */
int ComputeChunkAtom::setup_cylinder_bins()
{
// setup bins along cylinder axis
// ncplane = # of axis bins
ncplane = setup_xyz_bins();
// convert corigin_user to corigin
// corigin is always in box units, for orthogonal or triclinic domains
// lamda2x works for either orthogonal or triclinic
if (scaleflag == REDUCED) {
domain->lamda2x(corigin_user,corigin);
cradmin = cradmin_user * (domain->boxhi[cdim1]-domain->boxlo[cdim1]);
cradmax = cradmax_user * (domain->boxhi[cdim1]-domain->boxlo[cdim1]);
} else {
corigin[cdim1] = corigin_user[cdim1];
corigin[cdim2] = corigin_user[cdim2];
cradmin = cradmin_user;
cradmax = cradmax_user;
}
// if pbcflag set, sradmax must be < 1/2 box in any periodic non-axis dim
// treat orthongonal and triclinic the same
// check every time bins are created
if (pbcflag) {
double *prd_half = domain->prd_half;
int *periodicity = domain->periodicity;
int flag = 0;
if (periodicity[cdim1] && sradmax > prd_half[cdim1]) flag = 1;
if (periodicity[cdim2] && sradmax > prd_half[cdim2]) flag = 1;
if (flag)
error->all(FLERR,"Compute chunk/atom bin/cylinder radius "
"is too large for periodic box");
}
cinvrad = ncbin / (cradmax-cradmin);
// allocate and set radial bin coordinates
// radial coord = midpt of radii for a cylindrical shell
// axiscoord = saved bin coords along cylndrical axis
// radcoord = saved bin coords in radial direction
double **axiscoord = coord;
memory->create(coord,ncbin,1,"chunk/atom:coord");
double **radcoord = coord;
double rlo,rhi;
for (int i = 0; i < ncbin; i++) {
rlo = cradmin + i * (cradmax-cradmin) / ncbin;
rhi = cradmin + (i+1) * (cradmax-cradmin) / ncbin;
if (i == ncbin-1) rhi = cradmax;
coord[i][0] = 0.5 * (rlo+rhi);
}
// create array of combined coords for all bins
memory->create(coord,ncbin*ncplane,2,"chunk/atom:coord");
int m = 0;
for (int i = 0; i < ncbin; i++)
for (int j = 0; j < ncplane; j++) {
coord[m][0] = radcoord[i][0];
coord[m][1] = axiscoord[j][0];
m++;
}
memory->destroy(axiscoord);
memory->destroy(radcoord);
return ncbin*ncplane;
}
/* ----------------------------------------------------------------------
calculate chunk volumes = bin volumes
scalar if all bins have same volume
vector if per-bin volumes are different
------------------------------------------------------------------------- */
void ComputeChunkAtom::bin_volumes()
{
if (which == BIN1D || which == BIN2D || which == BIN3D) {
if (domain->dimension == 3)
chunk_volume_scalar = domain->xprd * domain->yprd * domain->zprd;
else chunk_volume_scalar = domain->xprd * domain->yprd;
double *prd;
if (scaleflag == REDUCED) prd = domain->prd_lamda;
else prd = domain->prd;
for (int m = 0; m < ndim; m++)
chunk_volume_scalar *= delta[m]/prd[dim[m]];
} else if (which == BINSPHERE) {
memory->destroy(chunk_volume_vec);
memory->create(chunk_volume_vec,nchunk,"chunk/atom:chunk_volume_vec");
double rlo,rhi,vollo,volhi;
for (int i = 0; i < nchunk; i++) {
rlo = sradmin + i * (sradmax-sradmin) / nsbin;
rhi = sradmin + (i+1) * (sradmax-sradmin) / nsbin;
if (i == nchunk-1) rhi = sradmax;
vollo = 4.0/3.0 * MY_PI * rlo*rlo*rlo;
volhi = 4.0/3.0 * MY_PI * rhi*rhi*rhi;
chunk_volume_vec[i] = volhi - vollo;
}
} else if (which == BINCYLINDER) {
memory->destroy(chunk_volume_vec);
memory->create(chunk_volume_vec,nchunk,"chunk/atom:chunk_volume_vec");
// slabthick = delta of bins along cylinder axis
double *prd;
if (scaleflag == REDUCED) prd = domain->prd_lamda;
else prd = domain->prd;
double slabthick = domain->prd[dim[0]] * delta[0]/prd[dim[0]];
// area lo/hi of concentric circles in radial direction
int iradbin;
double rlo,rhi,arealo,areahi;
for (int i = 0; i < nchunk; i++) {
iradbin = i / ncplane;
rlo = cradmin + iradbin * (cradmax-cradmin) / ncbin;
rhi = cradmin + (iradbin+1) * (cradmax-cradmin) / ncbin;
if (iradbin == ncbin-1) rhi = cradmax;
arealo = MY_PI * rlo*rlo;
areahi = MY_PI * rhi*rhi;
chunk_volume_vec[i] = (areahi-arealo) * slabthick;
}
}
}
/* ----------------------------------------------------------------------
assign each atom to a 1d spatial bin (layer)
------------------------------------------------------------------------- */
void ComputeChunkAtom::atom2bin1d()
{
int i,ibin;
double *boxlo,*boxhi,*prd;
double xremap;
double **x = atom->x;
int nlocal = atom->nlocal;
int idim = dim[0];
int nlayer1m1 = nlayers[0] - 1;
int periodicity = domain->periodicity[idim];
if (periodicity) {
if (scaleflag == REDUCED) {
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
prd = domain->prd_lamda;
} else {
boxlo = domain->boxlo;
boxhi = domain->boxhi;
prd = domain->prd;
}
}
// remap each atom's relevant coord back into box via PBC if necessary
// if scaleflag = REDUCED, box coords -> lamda coords
// apply discard rule
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
xremap = x[i][idim];
if (periodicity) {
if (xremap < boxlo[idim]) xremap += prd[idim];
if (xremap >= boxhi[idim]) xremap -= prd[idim];
}
ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
if (xremap < offset[0]) ibin--;
if (discard == MIXED) {
if (!minflag[idim]) ibin = MAX(ibin,0);
else if (ibin < 0) {
exclude[i] = 1;
continue;
}
if (!maxflag[idim]) ibin = MIN(ibin,nlayer1m1);
else if (ibin > nlayer1m1) {
exclude[i] = 1;
continue;
}
} else if (discard == NODISCARD) {
ibin = MAX(ibin,0);
ibin = MIN(ibin,nlayer1m1);
} else if (ibin < 0 || ibin > nlayer1m1) {
exclude[i] = 1;
continue;
}
ichunk[i] = ibin+1;
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
}
/* ----------------------------------------------------------------------
assign each atom to a 2d spatial bin (pencil)
------------------------------------------------------------------------- */
void ComputeChunkAtom::atom2bin2d()
{
int i,ibin,i1bin,i2bin;
double *boxlo,*boxhi,*prd;
double xremap,yremap;
double **x = atom->x;
int nlocal = atom->nlocal;
int idim = dim[0];
int jdim = dim[1];
int nlayer1m1 = nlayers[0] - 1;
int nlayer2m1 = nlayers[1] - 1;
int *periodicity = domain->periodicity;
if (periodicity[idim] || periodicity[jdim]) {
if (scaleflag == REDUCED) {
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
prd = domain->prd_lamda;
} else {
boxlo = domain->boxlo;
boxhi = domain->boxhi;
prd = domain->prd;
}
}
// remap each atom's relevant coord back into box via PBC if necessary
// if scaleflag = REDUCED, box coords -> lamda coords
// apply discard rule
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
xremap = x[i][idim];
if (periodicity[idim]) {
if (xremap < boxlo[idim]) xremap += prd[idim];
if (xremap >= boxhi[idim]) xremap -= prd[idim];
}
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
if (xremap < offset[0]) i1bin--;
if (discard == MIXED) {
if (!minflag[idim]) i1bin = MAX(i1bin,0);
else if (i1bin < 0) {
exclude[i] = 1;
continue;
}
if (!maxflag[idim]) i1bin = MIN(i1bin,nlayer1m1);
else if (i1bin > nlayer1m1) {
exclude[i] = 1;
continue;
}
} else if (discard == NODISCARD) {
i1bin = MAX(i1bin,0);
i1bin = MIN(i1bin,nlayer1m1);
} else if (i1bin < 0 || i1bin > nlayer1m1) {
exclude[i] = 1;
continue;
}
yremap = x[i][jdim];
if (periodicity[jdim]) {
if (yremap < boxlo[jdim]) yremap += prd[jdim];
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
}
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
if (yremap < offset[1]) i2bin--;
if (discard == MIXED) {
if (!minflag[jdim]) i2bin = MAX(i2bin,0);
else if (i2bin < 0) {
exclude[i] = 1;
continue;
}
if (!maxflag[jdim]) i2bin = MIN(i2bin,nlayer2m1);
else if (i2bin > nlayer2m1) {
exclude[i] = 1;
continue;
}
} else if (discard == NODISCARD) {
i2bin = MAX(i2bin,0);
i2bin = MIN(i2bin,nlayer2m1);
} else if (i2bin < 0 || i2bin > nlayer2m1) {
exclude[i] = 1;
continue;
}
ibin = i1bin*nlayers[1] + i2bin;
ichunk[i] = ibin+1;
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
}
/* ----------------------------------------------------------------------
assign each atom to a 3d spatial bin (brick)
------------------------------------------------------------------------- */
void ComputeChunkAtom::atom2bin3d()
{
int i,ibin,i1bin,i2bin,i3bin;
double *boxlo,*boxhi,*prd;
double xremap,yremap,zremap;
double **x = atom->x;
int nlocal = atom->nlocal;
int idim = dim[0];
int jdim = dim[1];
int kdim = dim[2];
int nlayer1m1 = nlayers[0] - 1;
int nlayer2m1 = nlayers[1] - 1;
int nlayer3m1 = nlayers[2] - 1;
int *periodicity = domain->periodicity;
if (periodicity[idim] || periodicity[jdim] || periodicity[kdim]) {
if (scaleflag == REDUCED) {
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
prd = domain->prd_lamda;
} else {
boxlo = domain->boxlo;
boxhi = domain->boxhi;
prd = domain->prd;
}
}
// remap each atom's relevant coord back into box via PBC if necessary
// if scaleflag = REDUCED, box coords -> lamda coords
// apply discard rule
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
xremap = x[i][idim];
if (periodicity[idim]) {
if (xremap < boxlo[idim]) xremap += prd[idim];
if (xremap >= boxhi[idim]) xremap -= prd[idim];
}
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
if (xremap < offset[0]) i1bin--;
if (discard == MIXED) {
if (!minflag[idim]) i1bin = MAX(i1bin,0);
else if (i1bin < 0) {
exclude[i] = 1;
continue;
}
if (!maxflag[idim]) i1bin = MIN(i1bin,nlayer1m1);
else if (i1bin > nlayer1m1) {
exclude[i] = 1;
continue;
}
} else if (discard == NODISCARD) {
i1bin = MAX(i1bin,0);
i1bin = MIN(i1bin,nlayer1m1);
} else if (i1bin < 0 || i1bin > nlayer1m1) {
exclude[i] = 1;
continue;
}
yremap = x[i][jdim];
if (periodicity[jdim]) {
if (yremap < boxlo[jdim]) yremap += prd[jdim];
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
}
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
if (yremap < offset[1]) i2bin--;
if (discard == MIXED) {
if (!minflag[jdim]) i2bin = MAX(i2bin,0);
else if (i2bin < 0) {
exclude[i] = 1;
continue;
}
if (!maxflag[jdim]) i2bin = MIN(i2bin,nlayer2m1);
else if (i2bin > nlayer2m1) {
exclude[i] = 1;
continue;
}
} else if (discard == NODISCARD) {
i2bin = MAX(i2bin,0);
i2bin = MIN(i2bin,nlayer2m1);
} else if (i2bin < 0 || i2bin > nlayer2m1) {
exclude[i] = 1;
continue;
}
zremap = x[i][kdim];
if (periodicity[kdim]) {
if (zremap < boxlo[kdim]) zremap += prd[kdim];
if (zremap >= boxhi[kdim]) zremap -= prd[kdim];
}
i3bin = static_cast<int> ((zremap - offset[2]) * invdelta[2]);
if (zremap < offset[2]) i3bin--;
if (discard == MIXED) {
if (!minflag[kdim]) i3bin = MAX(i3bin,0);
else if (i3bin < 0) {
exclude[i] = 1;
continue;
}
if (!maxflag[kdim]) i3bin = MIN(i3bin,nlayer3m1);
else if (i3bin > nlayer3m1) {
exclude[i] = 1;
continue;
}
} else if (discard == NODISCARD) {
i3bin = MAX(i3bin,0);
i3bin = MIN(i3bin,nlayer3m1);
} else if (i3bin < 0 || i3bin > nlayer3m1) {
exclude[i] = 1;
continue;
}
ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
ichunk[i] = ibin+1;
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
}
/* ----------------------------------------------------------------------
assign each atom to a spherical bin
------------------------------------------------------------------------- */
void ComputeChunkAtom::atom2binsphere()
{
int i,ibin;
double dx,dy,dz,r;
double xremap,yremap,zremap;
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
double *prd = domain->prd;
double *prd_half = domain->prd_half;
int *periodicity = domain->periodicity;
// remap each atom's relevant coords back into box via PBC if necessary
// apply discard rule based on rmin and rmax
double **x = atom->x;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
xremap = x[i][0];
if (periodicity[0]) {
if (xremap < boxlo[0]) xremap += prd[0];
if (xremap >= boxhi[0]) xremap -= prd[0];
}
yremap = x[i][1];
if (periodicity[1]) {
if (xremap < boxlo[1]) yremap += prd[1];
if (xremap >= boxhi[1]) yremap -= prd[1];
}
zremap = x[i][2];
if (periodicity[2]) {
if (xremap < boxlo[2]) zremap += prd[2];
if (xremap >= boxhi[2]) zremap -= prd[2];
}
dx = xremap - sorigin[0];
dy = yremap - sorigin[1];
dz = zremap - sorigin[2];
// if requested, apply PBC to distance from sphere center
// treat orthogonal and triclinic the same
// with dx,dy,dz = lengths independent of each other
// so do not use domain->minimum_image() which couples for triclinic
if (pbcflag) {
if (periodicity[0]) {
if (fabs(dx) > prd_half[0]) {
if (dx < 0.0) dx += prd[0];
else dx -= prd[0];
}
}
if (periodicity[1]) {
if (fabs(dy) > prd_half[1]) {
if (dy < 0.0) dy += prd[1];
else dy -= prd[1];
}
}
if (periodicity[2]) {
if (fabs(dz) > prd_half[2]) {
if (dz < 0.0) dz += prd[2];
else dz -= prd[2];
}
}
}
r = sqrt(dx*dx + dy*dy + dz*dz);
ibin = static_cast<int> ((r - sradmin) * sinvrad);
if (r < sradmin) ibin--;
if (discard == MIXED || discard == NODISCARD) {
ibin = MAX(ibin,0);
ibin = MIN(ibin,nchunk-1);
} else if (ibin < 0 || ibin >= nchunk) {
exclude[i] = 1;
continue;
}
ichunk[i] = ibin+1;
}
}
/* ----------------------------------------------------------------------
assign each atom to a cylindrical bin
------------------------------------------------------------------------- */
void ComputeChunkAtom::atom2bincylinder()
{
int i,rbin,kbin;
double d1,d2,r;
double remap1,remap2;
// first use atom2bin1d() to bin all atoms along cylinder axis
atom2bin1d();
// now bin in radial direction
// kbin = bin along cylinder axis
// rbin = bin in radial direction
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
double *prd = domain->prd;
double *prd_half = domain->prd_half;
int *periodicity = domain->periodicity;
// remap each atom's relevant coords back into box via PBC if necessary
// apply discard rule based on rmin and rmax
double **x = atom->x;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
kbin = ichunk[i] - 1;
remap1 = x[i][cdim1];
if (periodicity[cdim1]) {
if (remap1 < boxlo[cdim1]) remap1 += prd[cdim1];
if (remap1 >= boxhi[cdim1]) remap1 -= prd[cdim1];
}
remap2 = x[i][cdim2];
if (periodicity[cdim2]) {
if (remap2 < boxlo[cdim2]) remap2 += prd[cdim2];
if (remap2 >= boxhi[cdim2]) remap2 -= prd[cdim2];
}
d1 = remap1 - corigin[cdim1];
d2 = remap2 - corigin[cdim2];
// if requested, apply PBC to distance from cylinder axis
// treat orthogonal and triclinic the same
// with d1,d2 = lengths independent of each other
if (pbcflag) {
if (periodicity[cdim1]) {
if (fabs(d1) > prd_half[cdim1]) {
if (d1 < 0.0) d1 += prd[cdim1];
else d1 -= prd[cdim1];
}
}
if (periodicity[cdim2]) {
if (fabs(d2) > prd_half[cdim2]) {
if (d2 < 0.0) d2 += prd[cdim2];
else d2 -= prd[cdim2];
}
}
}
r = sqrt(d1*d1 + d2*d2);
rbin = static_cast<int> ((r - cradmin) * cinvrad);
if (r < cradmin) rbin--;
if (discard == MIXED || discard == NODISCARD) {
rbin = MAX(rbin,0);
rbin = MIN(rbin,ncbin-1);
} else if (rbin < 0 || rbin >= ncbin) {
exclude[i] = 1;
continue;
}
// combine axis and radial bin indices to set ichunk
ichunk[i] = rbin*ncplane + kbin + 1;
}
}
/* ----------------------------------------------------------------------
process args for one dimension of binning info
set dim, originflag, origin, delta
------------------------------------------------------------------------- */
void ComputeChunkAtom::readdim(int narg, char **arg, int iarg, int idim)
{
if (narg < iarg+3) error->all(FLERR,"Illegal compute chunk/atom command");
if (strcmp(arg[iarg],"x") == 0) dim[idim] = 0;
else if (strcmp(arg[iarg],"y") == 0) dim[idim] = 1;
else if (strcmp(arg[iarg],"z") == 0) dim[idim] = 2;
else error->all(FLERR,"Illegal compute chunk/atom command");
if (dim[idim] == 2 && domain->dimension == 2)
error->all(FLERR,"Cannot use compute chunk/atom bin z for 2d model");
if (strcmp(arg[iarg+1],"lower") == 0) originflag[idim] = LOWER;
else if (strcmp(arg[iarg+1],"center") == 0) originflag[idim] = CENTER;
else if (strcmp(arg[iarg+1],"upper") == 0) originflag[idim] = UPPER;
else originflag[idim] = COORD;
if (originflag[idim] == COORD)
origin[idim] = force->numeric(FLERR,arg[iarg+1]);
delta[idim] = force->numeric(FLERR,arg[iarg+2]);
}
/* ----------------------------------------------------------------------
initialize one atom's storage values, called when atom is created
just set chunkID to 0 for new atom
------------------------------------------------------------------------- */
void ComputeChunkAtom::set_arrays(int i)
{
if (!fixstore) return;
double *vstore = fixstore->vstore;
vstore[i] = 0.0;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays and per-chunk arrays
note: nchunk is actually 0 until first call
------------------------------------------------------------------------- */
double ComputeChunkAtom::memory_usage()
{
double bytes = 2*MAX(nmaxint,0) * sizeof(int); // ichunk,exclude
bytes += nmax * sizeof(double); // chunk
bytes += ncoord*nchunk * sizeof(double); // coord
if (compress) bytes += nchunk * sizeof(int); // chunkID
return bytes;
}
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