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compute_slice.cpp
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Thu, Nov 7, 06:02

compute_slice.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 "stdlib.h"
#include "string.h"
#include "compute_slice.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{COMPUTE,FIX};
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
/* ---------------------------------------------------------------------- */
ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 7) error->all(FLERR,"Illegal compute slice command");
MPI_Comm_rank(world,&me);
nstart = atoi(arg[3]);
nstop = atoi(arg[4]);
nskip = atoi(arg[5]);
if (nstart < 1 || nstop < nstart || nskip < 1)
error->all(FLERR,"Illegal compute slice command");
// parse remaining values until one isn't recognized
which = new int[narg-6];
argindex = new int[narg-6];
ids = new char*[narg-6];
value2index = new int[narg-6];
nvalues = 0;
for (int iarg = 6; iarg < narg; iarg++) {
if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
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 slice 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(FLERR,"Illegal compute slice command");
}
// 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(FLERR,"Compute ID for compute slice does not exist");
if (modify->compute[icompute]->vector_flag) {
if (argindex[i])
error->all(FLERR,"Compute slice compute does not calculate a global array");
if (nstop > modify->compute[icompute]->size_vector)
error->all(FLERR,"Compute slice compute vector is accessed out-of-range");
} else if (modify->compute[icompute]->array_flag) {
if (argindex[i] == 0)
error->all(FLERR,"Compute slice compute does not calculate a global vector");
if (argindex[i] > modify->compute[icompute]->size_array_cols)
error->all(FLERR,"Compute slice compute array is accessed out-of-range");
if (nstop > modify->compute[icompute]->size_array_rows)
error->all(FLERR,"Compute slice compute array is accessed out-of-range");
} else error->all(FLERR,"Compute slice compute does not calculate "
"global vector or array");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for compute slice does not exist");
if (modify->fix[ifix]->vector_flag) {
if (argindex[i])
error->all(FLERR,"Compute slice fix does not calculate a global array");
if (nstop > modify->fix[ifix]->size_vector)
error->all(FLERR,"Compute slice fix vector is accessed out-of-range");
} else if (modify->fix[ifix]->array_flag) {
if (argindex[i] == 0)
error->all(FLERR,"Compute slice fix does not calculate a global vector");
if (argindex[i] > modify->fix[ifix]->size_array_cols)
error->all(FLERR,"Compute slice fix array is accessed out-of-range");
if (nstop > modify->fix[ifix]->size_array_rows)
error->all(FLERR,"Compute slice fix array is accessed out-of-range");
} else error->all(FLERR,"Compute slice fix does not calculate "
"global vector or array");
}
}
// this compute produces either a vector or array
// for vector, set intensive/extensive to mirror input values
// for array, set intensive if all input values are intensive, else extensive
vector = NULL;
array = NULL;
extlist = NULL;
if (nvalues == 1) {
vector_flag = 1;
size_vector = (nstop-nstart) / nskip;
memory->create(vector,size_vector,"slice:vector");
if (which[0] == COMPUTE) {
int icompute = modify->find_compute(ids[0]);
if (argindex[0] == 0) {
extvector = modify->compute[icompute]->extvector;
if (modify->compute[icompute]->extvector == -1) {
extlist = new int[size_vector];
int j = 0;
for (int i = nstart; i < nstop; i += nskip)
extlist[j++] = modify->compute[icompute]->extlist[i-1];
}
} else extvector = modify->compute[icompute]->extarray;
} else if (which[0] == FIX) {
int ifix = modify->find_fix(ids[0]);
if (argindex[0] == 0) {
extvector = modify->fix[ifix]->extvector;
if (modify->fix[ifix]->extvector == -1) {
extlist = new int[size_vector];
int j = 0;
for (int i = nstart; i < nstop; i += nskip)
extlist[j++] = modify->fix[ifix]->extlist[i-1];
}
} else extvector = modify->fix[ifix]->extarray;
}
} else {
array_flag = 1;
size_array_rows = (nstop-nstart) / nskip;
size_array_cols = nvalues;
memory->create(array,size_array_rows,size_array_cols,"slice:array");
extarray = 0;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (argindex[i] == 0) {
if (modify->compute[icompute]->extvector == 1) extarray = 1;
if (modify->compute[icompute]->extvector == -1) {
for (int j = 0; j < modify->compute[icompute]->size_vector; j++)
if (modify->compute[icompute]->extlist[j]) extarray = 1;
}
} else {
if (modify->compute[icompute]->extarray) extarray = 1;
}
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (argindex[i] == 0) {
if (modify->fix[ifix]->extvector == 1) extarray = 1;
if (modify->fix[ifix]->extvector == -1) {
for (int j = 0; j < modify->fix[ifix]->size_vector; j++)
if (modify->fix[ifix]->extlist[j]) extarray = 1;
}
} else {
if (modify->fix[ifix]->extarray) extarray = 1;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
ComputeSlice::~ComputeSlice()
{
delete [] which;
delete [] argindex;
for (int m = 0; m < nvalues; m++) delete [] ids[m];
delete [] ids;
delete [] value2index;
memory->destroy(vector);
memory->destroy(array);
}
/* ---------------------------------------------------------------------- */
void ComputeSlice::init()
{
// set indices and check validity of all computes,fixes
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 slice 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 slice does not exist");
value2index[m] = ifix;
}
}
}
/* ---------------------------------------------------------------------- */
void ComputeSlice::compute_vector()
{
invoked_vector = update->ntimestep;
extract_one(0,vector,1);
}
/* ---------------------------------------------------------------------- */
void ComputeSlice::compute_array()
{
invoked_array = update->ntimestep;
for (int m = 0; m < nvalues; m++)
extract_one(0,&array[m][0],nvalues);
}
/* ----------------------------------------------------------------------
calculate sliced value for one input M and return it in vec
vec may be array so that returned values are with stride
------------------------------------------------------------------------- */
void ComputeSlice::extract_one(int m, double *vec, int stride)
{
int i,j;
// invoke the appropriate compute if needed
if (which[m] == COMPUTE) {
Compute *compute = modify->compute[value2index[m]];
if (argindex[m] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = cvector[i-1];
j += stride;
}
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[m]-1;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = carray[i-1][icol];
j += stride;
}
}
// access fix fields, check if fix frequency is a match
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[value2index[m]]->global_freq)
error->all(FLERR,"Fix used in compute slice not computed at compatible time");
Fix *fix = modify->fix[value2index[m]];
if (argindex[m] == 0) {
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = fix->compute_vector(i-1);
j += stride;
}
} else {
int icol = argindex[m]-1;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = fix->compute_array(i-1,icol);
j += stride;
}
}
}
}

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