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lammps/src/compute_reduce.cpp
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compute_reduce.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.
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include "compute_reduce.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "force.h"
#include "comm.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{SUM,SUMSQ,MINN,MAXX,AVE,AVESQ}; // also in ReduceRegion
enum{X,V,F,COMPUTE,FIX,VARIABLE};
enum{PERATOM,LOCAL};
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
#define INVOKED_PERATOM 8
#define INVOKED_LOCAL 16
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
nvalues(0), which(NULL), argindex(NULL), flavor(NULL), value2index(NULL), ids(NULL),
onevec(NULL), replace(NULL), indices(NULL), owner(NULL), idregion(NULL), varatom(NULL)
{
int iarg = 0;
if (strcmp(style,"reduce") == 0) {
if (narg < 5) error->all(FLERR,"Illegal compute reduce command");
idregion = NULL;
iarg = 3;
} else if (strcmp(style,"reduce/region") == 0) {
if (narg < 6) error->all(FLERR,"Illegal compute reduce/region command");
iregion = domain->find_region(arg[3]);
if (iregion == -1)
error->all(FLERR,"Region ID for compute reduce/region does not exist");
int n = strlen(arg[3]) + 1;
idregion = new char[n];
strcpy(idregion,arg[3]);
iarg = 4;
}
if (strcmp(arg[iarg],"sum") == 0) mode = SUM;
else if (strcmp(arg[iarg],"sumsq") == 0) mode = SUMSQ;
else if (strcmp(arg[iarg],"min") == 0) mode = MINN;
else if (strcmp(arg[iarg],"max") == 0) mode = MAXX;
else if (strcmp(arg[iarg],"ave") == 0) mode = AVE;
else if (strcmp(arg[iarg],"avesq") == 0) mode = AVESQ;
else error->all(FLERR,"Illegal compute reduce command");
iarg++;
MPI_Comm_rank(world,&me);
// expand args if any have wildcard character "*"
int expand = 0;
char **earg;
int nargnew = input->expand_args(narg-iarg,&arg[iarg],1,earg);
if (earg != &arg[iarg]) expand = 1;
arg = earg;
// parse values until one isn't recognized
which = new int[nargnew];
argindex = new int[nargnew];
flavor = new int[nargnew];
ids = new char*[nargnew];
value2index = new int[nargnew];
nvalues = 0;
iarg = 0;
while (iarg < nargnew) {
ids[nvalues] = NULL;
if (strcmp(arg[iarg],"x") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"y") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"z") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 2;
} else if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal compute reduce command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
nvalues++;
delete [] suffix;
} else break;
iarg++;
}
// optional args
replace = new int[nvalues];
for (int i = 0; i < nvalues; i++) replace[i] = -1;
while (iarg < nargnew) {
if (strcmp(arg[iarg],"replace") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal compute reduce command");
if (mode != MINN && mode != MAXX)
error->all(FLERR,"Compute reduce replace requires min or max mode");
int col1 = atoi(arg[iarg+1]) - 1;
int col2 = atoi(arg[iarg+2]) - 1;
if (col1 < 0 || col1 >= nvalues || col2 < 0 || col2 >= nvalues)
error->all(FLERR,"Illegal compute reduce command");
if (col1 == col2) error->all(FLERR,"Illegal compute reduce command");
if (replace[col1] >= 0 || replace[col2] >= 0)
error->all(FLERR,"Invalid replace values in compute reduce");
replace[col1] = col2;
iarg += 3;
} else error->all(FLERR,"Illegal compute reduce command");
}
// delete replace if not set
int flag = 0;
for (int i = 0; i < nvalues; i++)
if (replace[i] >= 0) flag = 1;
if (!flag) {
delete [] replace;
replace = NULL;
}
// if wildcard expansion occurred, free earg memory from expand_args()
if (expand) {
for (int i = 0; i < nargnew; i++) delete [] earg[i];
memory->sfree(earg);
}
// setup and error check
for (int i = 0; i < nvalues; i++) {
if (which[i] == X || which[i] == V || which[i] == F)
flavor[i] = PERATOM;
else if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all(FLERR,"Compute ID for compute reduce does not exist");
if (modify->compute[icompute]->peratom_flag) {
flavor[i] = PERATOM;
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all(FLERR,
"Compute reduce compute array is accessed out-of-range");
} else if (modify->compute[icompute]->local_flag) {
flavor[i] = LOCAL;
if (argindex[i] == 0 &&
modify->compute[icompute]->size_local_cols != 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a local vector");
if (argindex[i] && modify->compute[icompute]->size_local_cols == 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_local_cols)
error->all(FLERR,
"Compute reduce compute array is accessed out-of-range");
} else error->all(FLERR,
"Compute reduce compute calculates global values");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for compute reduce does not exist");
if (modify->fix[ifix]->peratom_flag) {
flavor[i] = PERATOM;
if (argindex[i] == 0 &&
modify->fix[ifix]->size_peratom_cols != 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all(FLERR,"Compute reduce fix array is accessed out-of-range");
} else if (modify->fix[ifix]->local_flag) {
flavor[i] = LOCAL;
if (argindex[i] == 0 &&
modify->fix[ifix]->size_local_cols != 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a local vector");
if (argindex[i] && modify->fix[ifix]->size_local_cols == 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_local_cols)
error->all(FLERR,"Compute reduce fix array is accessed out-of-range");
} else error->all(FLERR,"Compute reduce fix calculates global values");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all(FLERR,"Variable name for compute reduce does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Compute reduce variable is not atom-style variable");
flavor[i] = PERATOM;
}
}
// this compute produces either a scalar or vector
if (nvalues == 1) {
scalar_flag = 1;
if (mode == SUM || mode == SUMSQ) extscalar = 1;
else extscalar = 0;
vector = onevec = NULL;
indices = owner = NULL;
} else {
vector_flag = 1;
size_vector = nvalues;
if (mode == SUM || mode == SUMSQ) extvector = 1;
else extvector = 0;
vector = new double[size_vector];
onevec = new double[size_vector];
indices = new int[size_vector];
owner = new int[size_vector];
}
maxatom = 0;
varatom = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeReduce::~ComputeReduce()
{
delete [] which;
delete [] argindex;
delete [] flavor;
for (int m = 0; m < nvalues; m++) delete [] ids[m];
delete [] ids;
delete [] value2index;
delete [] replace;
delete [] idregion;
delete [] vector;
delete [] onevec;
delete [] indices;
delete [] owner;
memory->destroy(varatom);
}
/* ---------------------------------------------------------------------- */
void ComputeReduce::init()
{
// set indices of all computes,fixes,variables
for (int m = 0; m < nvalues; m++) {
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all(FLERR,"Compute ID for compute reduce does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all(FLERR,"Fix ID for compute reduce does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all(FLERR,"Variable name for compute reduce does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
}
// set index and check validity of region
if (idregion) {
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for compute reduce/region does not exist");
}
}
/* ---------------------------------------------------------------------- */
double ComputeReduce::compute_scalar()
{
invoked_scalar = update->ntimestep;
double one = compute_one(0,-1);
if (mode == SUM || mode == SUMSQ) {
MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
} else if (mode == MINN) {
MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_MIN,world);
} else if (mode == MAXX) {
MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_MAX,world);
} else if (mode == AVE || mode == AVESQ) {
MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
bigint n = count(0);
if (n) scalar /= n;
}
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeReduce::compute_vector()
{
invoked_vector = update->ntimestep;
for (int m = 0; m < nvalues; m++)
if (!replace || replace[m] < 0) {
onevec[m] = compute_one(m,-1);
indices[m] = index;
}
if (mode == SUM || mode == SUMSQ) {
for (int m = 0; m < nvalues; m++)
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_SUM,world);
} else if (mode == MINN) {
if (!replace) {
for (int m = 0; m < nvalues; m++)
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MIN,world);
} else {
for (int m = 0; m < nvalues; m++)
if (replace[m] < 0) {
pairme.value = onevec[m];
pairme.proc = me;
MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MINLOC,world);
vector[m] = pairall.value;
owner[m] = pairall.proc;
}
for (int m = 0; m < nvalues; m++)
if (replace[m] >= 0) {
if (me == owner[replace[m]])
vector[m] = compute_one(m,indices[replace[m]]);
MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
}
}
} else if (mode == MAXX) {
if (!replace) {
for (int m = 0; m < nvalues; m++)
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MAX,world);
} else {
for (int m = 0; m < nvalues; m++)
if (replace[m] < 0) {
pairme.value = onevec[m];
pairme.proc = me;
MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MAXLOC,world);
vector[m] = pairall.value;
owner[m] = pairall.proc;
}
for (int m = 0; m < nvalues; m++)
if (replace[m] >= 0) {
if (me == owner[replace[m]])
vector[m] = compute_one(m,indices[replace[m]]);
MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
}
}
} else if (mode == AVE || mode == AVESQ) {
for (int m = 0; m < nvalues; m++) {
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_SUM,world);
bigint n = count(m);
if (n) vector[m] /= n;
}
}
}
/* ----------------------------------------------------------------------
calculate reduced value for one input M and return it
if flag = -1:
sum/min/max/ave all values in vector
for per-atom quantities, limit to atoms in group
if mode = MIN or MAX, also set index to which vector value wins
if flag >= 0: simply return vector[flag]
------------------------------------------------------------------------- */
double ComputeReduce::compute_one(int m, int flag)
{
int i;
// invoke the appropriate attribute,compute,fix,variable
// for flag = -1, compute scalar quantity by scanning over atom properties
// only include atoms in group for atom properties and per-atom quantities
index = -1;
int vidx = value2index[m];
int aidx = argindex[m];
int *mask = atom->mask;
int nlocal = atom->nlocal;
double one = 0.0;
if (mode == MINN) one = BIG;
if (mode == MAXX) one = -BIG;
if (which[m] == X) {
double **x = atom->x;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,x[i][aidx],i);
} else one = x[flag][aidx];
} else if (which[m] == V) {
double **v = atom->v;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,v[i][aidx],i);
} else one = v[flag][aidx];
} else if (which[m] == F) {
double **f = atom->f;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,f[i][aidx],i);
} else one = f[flag][aidx];
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[vidx];
if (flavor[m] == PERATOM) {
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (aidx == 0) {
double *comp_vec = compute->vector_atom;
int n = nlocal;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,comp_vec[i],i);
} else one = comp_vec[flag];
} else {
double **carray_atom = compute->array_atom;
int n = nlocal;
int aidxm1 = aidx - 1;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,carray_atom[i][aidxm1],i);
} else one = carray_atom[flag][aidxm1];
}
} else if (flavor[m] == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
compute->compute_local();
compute->invoked_flag |= INVOKED_LOCAL;
}
if (aidx == 0) {
double *comp_vec = compute->vector_local;
int n = compute->size_local_rows;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,comp_vec[i],i);
else one = comp_vec[flag];
} else {
double **carray_local = compute->array_local;
int n = compute->size_local_rows;
int aidxm1 = aidx - 1;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,carray_local[i][aidxm1],i);
else one = carray_local[flag][aidxm1];
}
}
// access fix fields, check if fix frequency is a match
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[vidx]->peratom_freq)
error->all(FLERR,"Fix used in compute reduce not "
"computed at compatible time");
Fix *fix = modify->fix[vidx];
if (flavor[m] == PERATOM) {
if (aidx == 0) {
double *fix_vector = fix->vector_atom;
int n = nlocal;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,fix_vector[i],i);
} else one = fix_vector[flag];
} else {
double **fix_array = fix->array_atom;
int aidxm1 = aidx - 1;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,fix_array[i][aidxm1],i);
} else one = fix_array[flag][aidxm1];
}
} else if (flavor[m] == LOCAL) {
if (aidx == 0) {
double *fix_vector = fix->vector_local;
int n = fix->size_local_rows;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,fix_vector[i],i);
else one = fix_vector[flag];
} else {
double **fix_array = fix->array_local;
int n = fix->size_local_rows;
int aidxm1 = aidx - 1;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,fix_array[i][aidxm1],i);
else one = fix_array[flag][aidxm1];
}
}
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
if (atom->nmax > maxatom) {
maxatom = atom->nmax;
memory->destroy(varatom);
memory->create(varatom,maxatom,"reduce:varatom");
}
input->variable->compute_atom(vidx,igroup,varatom,1,0);
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,varatom[i],i);
} else one = varatom[flag];
}
return one;
}
/* ---------------------------------------------------------------------- */
bigint ComputeReduce::count(int m)
{
int vidx = value2index[m];
if (which[m] == X || which[m] == V || which[m] == F)
return group->count(igroup);
else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[vidx];
if (flavor[m] == PERATOM) {
return group->count(igroup);
} else if (flavor[m] == LOCAL) {
bigint ncount = compute->size_local_rows;
bigint ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_LMP_BIGINT,MPI_SUM,world);
return ncountall;
}
} else if (which[m] == FIX) {
Fix *fix = modify->fix[vidx];
if (flavor[m] == PERATOM) {
return group->count(igroup);
} else if (flavor[m] == LOCAL) {
bigint ncount = fix->size_local_rows;
bigint ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_LMP_BIGINT,MPI_SUM,world);
return ncountall;
}
} else if (which[m] == VARIABLE)
return group->count(igroup);
bigint dummy = 0;
return dummy;
}
/* ----------------------------------------------------------------------
combine two values according to reduction mode
for MIN/MAX, also update index with winner
------------------------------------------------------------------------- */
void ComputeReduce::combine(double &one, double two, int i)
{
if (mode == SUM || mode == AVE) one += two;
else if (mode == SUMSQ || mode == AVESQ) one += two*two;
else if (mode == MINN) {
if (two < one) {
one = two;
index = i;
}
} else if (mode == MAXX) {
if (two > one) {
one = two;
index = i;
}
}
}
/* ----------------------------------------------------------------------
memory usage of varatom
------------------------------------------------------------------------- */
double ComputeReduce::memory_usage()
{
double bytes = maxatom * sizeof(double);
return bytes;
}
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