2 new computes: chunk/spread/atom and reduce/chunk
This commit is contained in:
Steven J. Plimpton
512
src/compute_reduce_chunk.cpp
Normal file
512
src/compute_reduce_chunk.cpp
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@ -0,0 +1,512 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include <mpi.h>
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#include <string.h>
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#include "compute_reduce_chunk.h"
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "fix.h"
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#include "compute.h"
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#include "compute_chunk_atom.h"
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#include "input.h"
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#include "variable.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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enum{SUM,MINN,MAXX};
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enum{COMPUTE,FIX,VARIABLE};
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#define INVOKED_PERATOM 8
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#define BIG 1.0e20
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/* ---------------------------------------------------------------------- */
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ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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vlocal(NULL), vglobal(NULL), alocal(NULL), aglobal(NULL), varatom(NULL),
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which(NULL), argindex(NULL), value2index(NULL), idchunk(NULL), ids(NULL)
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{
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if (narg < 6) error->all(FLERR,"Illegal compute reduce/chunk command");
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// ID of compute chunk/atom
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int n = strlen(arg[3]) + 1;
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idchunk = new char[n];
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strcpy(idchunk,arg[3]);
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init_chunk();
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// mode
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if (strcmp(arg[4],"sum") == 0) mode = SUM;
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else if (strcmp(arg[4],"min") == 0) mode = MINN;
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else if (strcmp(arg[4],"max") == 0) mode = MAXX;
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else error->all(FLERR,"Illegal compute reduce/chunk command");
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int iarg = 5;
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// expand args if any have wildcard character "*"
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int expand = 0;
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char **earg;
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int nargnew = input->expand_args(narg-iarg,&arg[iarg],1,earg);
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if (earg != &arg[iarg]) expand = 1;
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arg = earg;
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// parse values until one isn't recognized
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which = new int[nargnew];
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argindex = new int[nargnew];
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ids = new char*[nargnew];
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value2index = new int[nargnew];
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nvalues = 0;
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iarg = 0;
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while (iarg < nargnew) {
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ids[nvalues] = NULL;
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if (strncmp(arg[iarg],"c_",2) == 0 ||
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strncmp(arg[iarg],"f_",2) == 0 ||
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strncmp(arg[iarg],"v_",2) == 0) {
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if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
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else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
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else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
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int n = strlen(arg[iarg]);
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char *suffix = new char[n];
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strcpy(suffix,&arg[iarg][2]);
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char *ptr = strchr(suffix,'[');
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if (ptr) {
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if (suffix[strlen(suffix)-1] != ']')
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error->all(FLERR,"Illegal compute reduce/chunk command");
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argindex[nvalues] = atoi(ptr+1);
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*ptr = '\0';
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} else argindex[nvalues] = 0;
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n = strlen(suffix) + 1;
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ids[nvalues] = new char[n];
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strcpy(ids[nvalues],suffix);
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nvalues++;
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delete [] suffix;
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} else error->all(FLERR,"Illegal compute reduce/chunk command");
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iarg++;
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}
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// if wildcard expansion occurred, free earg memory from expand_args()
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if (expand) {
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for (int i = 0; i < nargnew; i++) delete [] earg[i];
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memory->sfree(earg);
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}
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// error check
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == COMPUTE) {
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int icompute = modify->find_compute(ids[i]);
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if (icompute < 0)
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error->all(FLERR,"Compute ID for compute reduce/chunk does not exist");
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if (!modify->compute[icompute]->peratom_flag)
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error->all(FLERR,"Compute reduce/chunk compute does not "
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"calculate per-atom values");
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if (argindex[i] == 0 &&
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modify->compute[icompute]->size_peratom_cols != 0)
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error->all(FLERR,"Compute reduce/chunk compute does not "
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"calculate a per-atom vector");
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if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
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error->all(FLERR,"Compute reduce/chunk compute does not "
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"calculate a per-atom array");
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if (argindex[i] &&
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argindex[i] > modify->compute[icompute]->size_peratom_cols)
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error->all(FLERR,
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"Compute reduce/chunk compute array is accessed out-of-range");
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} else if (which[i] == FIX) {
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int ifix = modify->find_fix(ids[i]);
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if (ifix < 0)
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error->all(FLERR,"Fix ID for compute reduce/chunk does not exist");
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if (!modify->fix[ifix]->peratom_flag)
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error->all(FLERR,"Compute reduce/chunk fix does not "
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"calculate per-atom values");
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if (argindex[i] == 0 &&
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modify->fix[ifix]->size_peratom_cols != 0)
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error->all(FLERR,"Compute reduce/chunk fix does not "
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"calculate a per-atom vector");
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if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
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error->all(FLERR,"Compute reduce/chunk fix does not "
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"calculate a per-atom array");
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if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
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error->all(FLERR,"Compute reduce/chunk fix array is "
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"accessed out-of-range");
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} else if (which[i] == VARIABLE) {
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int ivariable = input->variable->find(ids[i]);
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if (ivariable < 0)
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error->all(FLERR,"Variable name for compute reduce/chunk does not exist");
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if (input->variable->atomstyle(ivariable) == 0)
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error->all(FLERR,"Compute reduce/chunk variable is "
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"not atom-style variable");
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}
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}
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// this compute produces either a vector or array
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if (nvalues == 1) {
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vector_flag = 1;
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size_vector_variable = 1;
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extvector = 0;
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} else {
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array_flag = 1;
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size_array_rows_variable = 1;
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size_array_cols = nvalues;
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extarray = 0;
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}
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// setup
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if (mode == SUM) initvalue = 0.0;
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else if (mode == MINN) initvalue = BIG;
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else if (mode == MAXX) initvalue = -BIG;
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maxchunk = 0;
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vlocal = vglobal = NULL;
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alocal = aglobal = NULL;
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maxatom = 0;
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varatom = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputeReduceChunk::~ComputeReduceChunk()
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{
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delete [] idchunk;
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delete [] which;
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delete [] argindex;
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for (int m = 0; m < nvalues; m++) delete [] ids[m];
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delete [] ids;
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delete [] value2index;
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memory->destroy(vlocal);
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memory->destroy(vglobal);
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memory->destroy(alocal);
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memory->destroy(aglobal);
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memory->destroy(varatom);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeReduceChunk::init()
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{
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init_chunk();
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// set indices of all computes,fixes,variables
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for (int m = 0; m < nvalues; m++) {
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if (which[m] == COMPUTE) {
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int icompute = modify->find_compute(ids[m]);
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if (icompute < 0)
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error->all(FLERR,"Compute ID for compute reduce/chunk does not exist");
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value2index[m] = icompute;
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} else if (which[m] == FIX) {
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int ifix = modify->find_fix(ids[m]);
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if (ifix < 0)
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error->all(FLERR,"Fix ID for compute reduce/chunk does not exist");
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value2index[m] = ifix;
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} else if (which[m] == VARIABLE) {
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int ivariable = input->variable->find(ids[m]);
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if (ivariable < 0)
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error->all(FLERR,"Variable name for compute reduce/chunk does not exist");
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value2index[m] = ivariable;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeReduceChunk::init_chunk()
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{
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int icompute = modify->find_compute(idchunk);
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if (icompute < 0)
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error->all(FLERR,"Chunk/atom compute does not exist for "
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"compute reduce/chunk");
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cchunk = (ComputeChunkAtom *) modify->compute[icompute];
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if (strcmp(cchunk->style,"chunk/atom") != 0)
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error->all(FLERR,"Compute reduce/chunk does not use chunk/atom compute");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeReduceChunk::compute_vector()
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{
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invoked_vector = update->ntimestep;
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// compute chunk/atom assigns atoms to chunk IDs
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// extract ichunk index vector from compute
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// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
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nchunk = cchunk->setup_chunks();
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cchunk->compute_ichunk();
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ichunk = cchunk->ichunk;
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if (!nchunk) return;
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size_vector = nchunk;
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if (nchunk > maxchunk) {
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memory->destroy(vlocal);
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memory->destroy(vglobal);
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maxchunk = nchunk;
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memory->create(vlocal,maxchunk,"reduce/chunk:vlocal");
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memory->create(vglobal,maxchunk,"reduce/chunk:vglobal");
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vector = vglobal;
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}
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// perform local reduction of single peratom value
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compute_one(0,vlocal,1);
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// reduce the per-chunk values across all procs
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if (mode == SUM)
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MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_SUM,world);
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else if (mode == MINN)
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MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_MIN,world);
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else if (mode == MAXX)
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MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_MAX,world);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeReduceChunk::compute_array()
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{
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invoked_array = update->ntimestep;
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// compute chunk/atom assigns atoms to chunk IDs
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// extract ichunk index vector from compute
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// ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
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nchunk = cchunk->setup_chunks();
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cchunk->compute_ichunk();
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ichunk = cchunk->ichunk;
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if (!nchunk) return;
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size_array_rows = nchunk;
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if (nchunk > maxchunk) {
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memory->destroy(alocal);
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memory->destroy(aglobal);
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maxchunk = nchunk;
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memory->create(alocal,maxchunk,nvalues,"reduce/chunk:alocal");
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memory->create(aglobal,maxchunk,nvalues,"reduce/chunk:aglobal");
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array = aglobal;
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}
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// perform local reduction of all peratom values
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for (int m = 0; m < nvalues; m++) compute_one(m,&alocal[0][m],nvalues);
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// reduce the per-chunk values across all procs
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if (mode == SUM)
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MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues,
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MPI_DOUBLE,MPI_SUM,world);
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else if (mode == MINN)
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MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues,
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MPI_DOUBLE,MPI_MIN,world);
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else if (mode == MAXX)
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MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues,
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MPI_DOUBLE,MPI_MAX,world);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride)
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{
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// initialize per-chunk values in accumulation vector
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for (int i = 0; i < nchunk; i += nstride) vchunk[i] = initvalue;
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// loop over my atoms
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// use peratom input and chunk ID of each atom to update vector
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int index;
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if (which[m] == COMPUTE) {
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Compute *compute = modify->compute[value2index[m]];
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if (!(compute->invoked_flag & INVOKED_PERATOM)) {
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compute->compute_peratom();
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compute->invoked_flag |= INVOKED_PERATOM;
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}
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if (argindex[m] == 0) {
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double *vcompute = compute->vector_atom;
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for (int i = 0; i < nlocal; i++) {
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if (!(mask[i] & groupbit)) continue;
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index = ichunk[i]-1;
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if (index < 0) continue;
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combine(vchunk[index*nstride],vcompute[i]);
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}
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} else {
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double **acompute = compute->array_atom;
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int argindexm1 = argindex[m] - 1;
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for (int i = 0; i < nlocal; i++) {
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if (!(mask[i] & groupbit)) continue;
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index = ichunk[i]-1;
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if (index < 0) continue;
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combine(vchunk[index*nstride],acompute[i][argindexm1]);
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}
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}
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// access fix fields, check if fix frequency is a match
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} else if (which[m] == FIX) {
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Fix *fix = modify->fix[value2index[m]];
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if (update->ntimestep % fix->peratom_freq)
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error->all(FLERR,"Fix used in compute reduce/chunk not "
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"computed at compatible time");
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if (argindex[m] == 0) {
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double *vfix = fix->vector_atom;
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for (int i = 0; i < nlocal; i++) {
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if (!(mask[i] & groupbit)) continue;
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index = ichunk[i]-1;
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if (index < 0) continue;
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combine(vchunk[index*nstride],vfix[i]);
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}
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} else {
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double **afix = fix->array_atom;
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int argindexm1 = argindex[m] - 1;
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for (int i = 0; i < nlocal; i++) {
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if (!(mask[i] & groupbit)) continue;
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index = ichunk[i]-1;
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if (index < 0) continue;
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combine(vchunk[index*nstride],afix[i][argindexm1]);
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}
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}
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// evaluate atom-style variable
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} else if (which[m] == VARIABLE) {
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if (atom->nmax > maxatom) {
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memory->destroy(varatom);
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maxatom = atom->nmax;
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memory->create(varatom,maxatom,"reduce/chunk:varatom");
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}
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input->variable->compute_atom(value2index[m],igroup,varatom,1,0);
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for (int i = 0; i < nlocal; i++) {
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if (!(mask[i] & groupbit)) continue;
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index = ichunk[i]-1;
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if (index < 0) continue;
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combine(vchunk[index*nstride],varatom[i]);
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}
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}
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}
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/* ----------------------------------------------------------------------
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combine two values according to reduction mode
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------------------------------------------------------------------------- */
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void ComputeReduceChunk::combine(double &one, double two)
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{
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if (mode == SUM) one += two;
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else if (mode == MINN) {
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if (two < one) one = two;
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} else if (mode == MAXX) {
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if (two > one) one = two;
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}
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}
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/* ----------------------------------------------------------------------
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lock methods: called by fix ave/time
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these methods insure vector/array size is locked for Nfreq epoch
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by passing lock info along to compute chunk/atom
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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increment lock counter
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------------------------------------------------------------------------- */
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void ComputeReduceChunk::lock_enable()
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{
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cchunk->lockcount++;
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}
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/* ----------------------------------------------------------------------
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decrement lock counter in compute chunk/atom, if it still exists
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------------------------------------------------------------------------- */
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void ComputeReduceChunk::lock_disable()
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{
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int icompute = modify->find_compute(idchunk);
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if (icompute >= 0) {
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cchunk = (ComputeChunkAtom *) modify->compute[icompute];
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cchunk->lockcount--;
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}
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}
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/* ----------------------------------------------------------------------
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calculate and return # of chunks = length of vector/array
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||||
------------------------------------------------------------------------- */
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||||
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int ComputeReduceChunk::lock_length()
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{
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nchunk = cchunk->setup_chunks();
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return nchunk;
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}
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||||
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||||
/* ----------------------------------------------------------------------
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||||
set the lock from startstep to stopstep
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||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeReduceChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
|
||||
{
|
||||
cchunk->lock(fixptr,startstep,stopstep);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unset the lock
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeReduceChunk::unlock(Fix *fixptr)
|
||||
{
|
||||
cchunk->unlock(fixptr);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local data
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeReduceChunk::memory_usage()
|
||||
{
|
||||
double bytes = (bigint) maxatom * sizeof(double);
|
||||
if (nvalues == 1) bytes += (bigint) maxchunk * 2 * sizeof(double);
|
||||
else bytes += (bigint) maxchunk * nvalues * 2 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
Reference in New Issue
Block a user