git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1547 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
357
src/compute_reduce.cpp
Normal file
357
src/compute_reduce.cpp
Normal file
@ -0,0 +1,357 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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 "modify.h"
|
||||
#include "fix.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "input.h"
|
||||
#include "variable.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define INVOKED_SCALAR 1
|
||||
#define INVOKED_VECTOR 2
|
||||
#define INVOKED_PERATOM 4
|
||||
|
||||
enum{SUM,MINN,MAXX};
|
||||
enum{X,V,F,COMPUTE,FIX,VARIABLE};
|
||||
|
||||
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
|
||||
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
|
||||
#define BIG 1.0e20
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg)
|
||||
{
|
||||
if (narg < 5) error->all("Illegal compute reduce command");
|
||||
|
||||
if (strcmp(arg[3],"sum") == 0) mode = SUM;
|
||||
else if (strcmp(arg[3],"min") == 0) mode = MINN;
|
||||
else if (strcmp(arg[3],"max") == 0) mode = MAXX;
|
||||
else error->all("Illegal compute reduce command");
|
||||
|
||||
// parse remaining values
|
||||
|
||||
which = new int[narg-4];
|
||||
argindex = new int[narg-4];
|
||||
ids = new char*[narg-4];
|
||||
value2index = new int[narg-4];
|
||||
nvalues = 0;
|
||||
|
||||
int iarg = 4;
|
||||
while (iarg < narg) {
|
||||
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("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 error->all("Illegal compute reduce command");
|
||||
|
||||
iarg++;
|
||||
}
|
||||
|
||||
// setup and error check
|
||||
|
||||
for (int i = 0; i < nvalues; i++) {
|
||||
if (which[i] == COMPUTE) {
|
||||
int icompute = modify->find_compute(ids[i]);
|
||||
if (icompute < 0)
|
||||
error->all("Compute ID for compute reduce does not exist");
|
||||
if (modify->compute[icompute]->peratom_flag == 0)
|
||||
error->all("Compute reduce compute does not calculate per-atom values");
|
||||
if (argindex[i] == 0 && modify->compute[icompute]->size_peratom != 0)
|
||||
error->all("Compute reduce compute does not calculate a per-atom scalar");
|
||||
if (argindex[i] && modify->compute[icompute]->size_peratom == 0)
|
||||
error->all("Compute reduce compute does not calculate a per-atom vector");
|
||||
} else if (which[i] == FIX) {
|
||||
int ifix = modify->find_fix(ids[i]);
|
||||
if (ifix < 0)
|
||||
error->all("Fix ID for compute reduce does not exist");
|
||||
if (modify->fix[ifix]->peratom_flag == 0)
|
||||
error->all("Compute reduce fix does not calculate per-atom values");
|
||||
if (argindex[i] == 0 && modify->fix[ifix]->size_peratom != 0)
|
||||
error->all("Compute reduce fix does not calculate a per-atom scalar");
|
||||
if (argindex[i] && modify->fix[ifix]->size_peratom == 0)
|
||||
error->all("Compute reduce fix does not calculate a per-atom vector");
|
||||
} else if (which[i] == VARIABLE) {
|
||||
int ivariable = input->variable->find(ids[i]);
|
||||
if (ivariable < 0)
|
||||
error->all("Variable name for compute reduce does not exist");
|
||||
if (input->variable->atomstyle(ivariable) == 0)
|
||||
error->all("Compute reduce variable is not atom-style variable");
|
||||
}
|
||||
}
|
||||
|
||||
// this compute produces either a scalar or vector
|
||||
|
||||
if (nvalues == 1) {
|
||||
scalar_flag = 1;
|
||||
extscalar = 1;
|
||||
vector = NULL;
|
||||
onevec = NULL;
|
||||
} else {
|
||||
vector_flag = 1;
|
||||
size_vector = nvalues;
|
||||
extvector = 1;
|
||||
vector = new double[size_vector];
|
||||
onevec = new double[size_vector];
|
||||
}
|
||||
|
||||
maxatom = 0;
|
||||
varatom = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeReduce::~ComputeReduce()
|
||||
{
|
||||
delete [] which;
|
||||
delete [] argindex;
|
||||
for (int m = 0; m < nvalues; m++) delete [] ids[m];
|
||||
delete [] ids;
|
||||
delete [] value2index;
|
||||
|
||||
delete [] vector;
|
||||
delete [] onevec;
|
||||
|
||||
memory->sfree(varatom);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeReduce::init()
|
||||
{
|
||||
// set indices and check validity 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("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("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("Variable name for compute reduce does not exist");
|
||||
value2index[m] = ivariable;
|
||||
|
||||
} else value2index[m] = -1;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double ComputeReduce::compute_scalar()
|
||||
{
|
||||
invoked |= INVOKED_SCALAR;
|
||||
|
||||
double one = compute_one(0);
|
||||
if (mode == SUM)
|
||||
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);
|
||||
return scalar;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeReduce::compute_vector()
|
||||
{
|
||||
invoked |= INVOKED_VECTOR;
|
||||
|
||||
for (int m = 0; m < nvalues; m++) onevec[m] = compute_one(m);
|
||||
if (mode == SUM)
|
||||
MPI_Allreduce(onevec,vector,size_vector,MPI_DOUBLE,MPI_SUM,world);
|
||||
else if (mode == MINN)
|
||||
MPI_Allreduce(onevec,vector,size_vector,MPI_DOUBLE,MPI_MIN,world);
|
||||
else if (mode == MAXX)
|
||||
MPI_Allreduce(onevec,vector,size_vector,MPI_DOUBLE,MPI_MAX,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double ComputeReduce::compute_one(int m)
|
||||
{
|
||||
int i;
|
||||
|
||||
// invoke the appropriate attribute,compute,fix,variable
|
||||
// compute scalar quantity by summing over atom scalars
|
||||
// only include atoms in group
|
||||
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int n = value2index[m];
|
||||
int j = argindex[m];
|
||||
|
||||
double one;
|
||||
if (mode == SUM) one = 0.0;
|
||||
else if (mode == MINN) one = BIG;
|
||||
else if (mode == MAXX) one = -BIG;
|
||||
|
||||
if (which[m] == X) {
|
||||
double **x = atom->x;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) combine(one,x[i][j]);
|
||||
} else if (which[m] == V) {
|
||||
double **v = atom->v;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) combine(one,v[i][j]);
|
||||
} else if (which[m] == F) {
|
||||
double **f = atom->f;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) combine(one,f[i][j]);
|
||||
|
||||
// invoke compute if not previously invoked
|
||||
|
||||
} else if (which[m] == COMPUTE) {
|
||||
if (!(modify->compute[n]->invoked & INVOKED_PERATOM))
|
||||
modify->compute[n]->compute_peratom();
|
||||
|
||||
if (j == 0) {
|
||||
double *compute_scalar = modify->compute[n]->scalar_atom;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) combine(one,compute_scalar[i]);
|
||||
} else {
|
||||
double **compute_vector = modify->compute[n]->vector_atom;
|
||||
int jm1 = j - 1;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) combine(one,compute_vector[i][jm1]);
|
||||
}
|
||||
|
||||
// access fix fields, check if frequency is a match
|
||||
|
||||
} else if (which[m] == FIX) {
|
||||
if (update->ntimestep % modify->fix[n]->peratom_freq)
|
||||
error->all("Fix used in compute reduce not computed at compatible time");
|
||||
|
||||
if (j == 0) {
|
||||
double *fix_scalar = modify->fix[n]->scalar_atom;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) combine(one,fix_scalar[i]);
|
||||
} else {
|
||||
double **fix_vector = modify->fix[n]->vector_atom;
|
||||
int jm1 = j - 1;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) combine(one,fix_vector[i][jm1]);
|
||||
}
|
||||
|
||||
// evaluate atom-style variable
|
||||
|
||||
} else if (which[m] == VARIABLE) {
|
||||
if (nlocal > maxatom) {
|
||||
maxatom = atom->nmax;
|
||||
memory->sfree(varatom);
|
||||
varatom = (double *)
|
||||
memory->smalloc(maxatom*sizeof(double),"compute/reduce:varatom");
|
||||
}
|
||||
|
||||
input->variable->compute_atom(n,igroup,varatom,1,0);
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) combine(one,varatom[i]);
|
||||
}
|
||||
|
||||
return one;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
combine two values according to reduction mode
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeReduce::combine(double &one, double two)
|
||||
{
|
||||
if (mode == SUM) one += two;
|
||||
else if (mode == MINN) one = MIN(one,two);
|
||||
else if (mode == MAXX) one = MAX(one,two);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of varatom
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeReduce::memory_usage()
|
||||
{
|
||||
double bytes = maxatom * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
Reference in New Issue
Block a user