Created in.grid.local, fixed some problems in src
This commit is contained in:
Aidan Thompson
73
examples/snap/in.grid.local
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73
examples/snap/in.grid.local
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# Demonstrate bispectrum computes with local grid
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# Initialize simulation
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variable nsteps index 0
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variable nrep index 1
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variable a index 3.316
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variable ngrid index 2
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable ny equal ${nrep}
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variable nz equal ${nrep}
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boundary p p p
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lattice custom $a &
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a1 1 0 0 &
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a2 0 1 0 &
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a3 0 0 1 &
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basis 0 0 0 &
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basis 0.5 0.5 0.5 &
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# origin 0.25 0.25 0.25
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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create_box 1 box
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create_atoms 1 box
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mass 1 180.88
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# choose potential
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include Ta06A.snap
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# define grid compute and atom compute
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group snapgroup type 1
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variable twojmax equal 2
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variable rcutfac equal 4.67637
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable wj equal 1
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variable radelem equal 0.5
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variable bzero equal 0
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variable quad equal 0
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variable switch equal 1
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compute b all sna/atom &
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${rcutfac} ${rfac0} ${twojmax} ${radelem} &
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${wj} rmin0 ${rmin0} bzeroflag ${bzero} &
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quadraticflag ${quad} switchflag ${switch}
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compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} &
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${rcutfac} ${rfac0} ${twojmax} ${radelem} &
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${wj} rmin0 ${rmin0} bzeroflag ${bzero} &
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quadraticflag ${quad} switchflag ${switch}
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# define output
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# mygrid is ngrid by (3+nbis) = 8x8
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thermo_style custom step temp ke pe vol
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thermo_modify norm yes
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dump mydump_b all custom 1000 dump_b id c_b[*]
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dump mydump_bgridlocal all local 1000 dump_bgridlocal index c_mygridlocal[*]
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# run
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run 0
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308
src/ML-SNAP/compute_sna_grid_local.cpp
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308
src/ML-SNAP/compute_sna_grid_local.cpp
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@ -0,0 +1,308 @@
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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 "compute_grid_local.h"
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#include "compute_sna_grid_local.h"
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#include "sna.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 "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "force.h"
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#include "pair.h"
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#include "domain.h"
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#include "comm.h"
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#include "memory.h"
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#include "error.h"
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#include "tokenizer.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) :
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ComputeGridLocal(lmp, narg, arg), cutsq(nullptr),
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radelem(nullptr), wjelem(nullptr)
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{
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double rfac0, rmin0;
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int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
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// skip over arguments used by base class
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// so that argument positions are identical to
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// regular per-atom compute
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arg += nargbase;
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narg -= nargbase;
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int ntypes = atom->ntypes;
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int nargmin = 6+2*ntypes;
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if (narg < nargmin) error->all(FLERR,"Illegal compute sna/grid/local command");
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// default values
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rmin0 = 0.0;
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switchflag = 1;
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bzeroflag = 1;
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quadraticflag = 0;
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chemflag = 0;
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bnormflag = 0;
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wselfallflag = 0;
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nelements = 1;
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// process required arguments
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memory->create(radelem,ntypes+1,"sna/grid/local:radelem"); // offset by 1 to match up with types
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memory->create(wjelem,ntypes+1,"sna/grid/local:wjelem");
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rcutfac = atof(arg[3]);
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rfac0 = atof(arg[4]);
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twojmax = atoi(arg[5]);
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for(int i = 0; i < ntypes; i++)
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radelem[i+1] = atof(arg[6+i]);
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for(int i = 0; i < ntypes; i++)
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wjelem[i+1] = atof(arg[6+ntypes+i]);
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// construct cutsq
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double cut;
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cutmax = 0.0;
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memory->create(cutsq,ntypes+1,ntypes+1,"sna/grid/local:cutsq");
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for(int i = 1; i <= ntypes; i++) {
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cut = 2.0*radelem[i]*rcutfac;
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if (cut > cutmax) cutmax = cut;
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cutsq[i][i] = cut*cut;
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for(int j = i+1; j <= ntypes; j++) {
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cut = (radelem[i]+radelem[j])*rcutfac;
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cutsq[i][j] = cutsq[j][i] = cut*cut;
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}
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}
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// process optional args
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int iarg = nargmin;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"rmin0") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute sna/grid/local command");
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rmin0 = atof(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"switchflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute sna/grid/local command");
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switchflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"bzeroflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute sna/grid/local command");
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bzeroflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"quadraticflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute sna/grid/local command");
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quadraticflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"chem") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute sna/grid/local command");
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chemflag = 1;
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memory->create(map,ntypes+1,"compute_sna_grid_local:map");
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nelements = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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for (int i = 0; i < ntypes; i++) {
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int jelem = utils::inumeric(FLERR,arg[iarg+2+i],false,lmp);
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if (jelem < 0 || jelem >= nelements)
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error->all(FLERR,"Illegal compute sna/grid/local command");
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map[i+1] = jelem;
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}
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iarg += 2+ntypes;
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} else if (strcmp(arg[iarg],"bnormflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute sna/grid/local command");
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bnormflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"wselfallflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute sna/grid/local command");
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wselfallflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else error->all(FLERR,"Illegal compute sna/grid/local command");
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}
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snaptr = new SNA(lmp, rfac0, twojmax,
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rmin0, switchflag, bzeroflag,
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chemflag, bnormflag, wselfallflag, nelements);
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ncoeff = snaptr->ncoeff;
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nvalues = ncoeff;
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if (quadraticflag) nvalues += (ncoeff*(ncoeff+1))/2;
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size_local_cols = size_local_cols_base + nvalues;
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}
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/* ---------------------------------------------------------------------- */
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ComputeSNAGridLocal::~ComputeSNAGridLocal()
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{
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memory->destroy(radelem);
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memory->destroy(wjelem);
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memory->destroy(cutsq);
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delete snaptr;
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if (chemflag) memory->destroy(map);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAGridLocal::init()
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{
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if (force->pair == nullptr)
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error->all(FLERR,"Compute sna/grid/local requires a pair style be defined");
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if (cutmax > force->pair->cutforce)
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error->all(FLERR,"Compute sna/grid/local cutoff is longer than pairwise cutoff");
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// need an occasional full neighbor list
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int irequest = neighbor->request(this,instance_me);
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neighbor->requests[irequest]->pair = 0;
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neighbor->requests[irequest]->compute = 1;
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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neighbor->requests[irequest]->occasional = 1;
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int count = 0;
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for (int i = 0; i < modify->ncompute; i++)
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if (strcmp(modify->compute[i]->style,"sna/grid/local") == 0) count++;
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if (count > 1 && comm->me == 0)
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error->warning(FLERR,"More than one compute sna/grid/local");
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snaptr->init();
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAGridLocal::init_list(int /*id*/, NeighList *ptr)
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{
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list = ptr;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAGridLocal::compute_local()
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{
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invoked_array = update->ntimestep;
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// compute sna for each gridpoint
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double** const x = atom->x;
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const int* const mask = atom->mask;
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int * const type = atom->type;
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const int ntotal = atom->nlocal + atom->nghost;
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// insure rij, inside, and typej are of size jnum
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snaptr->grow_rij(ntotal);
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for (int iz = nzlo; iz <= nzhi; iz++)
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for (int iy = nylo; iy <= nyhi; iy++)
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for (int ix = nxlo; ix <= nxhi; ix++) {
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double xgrid[3];
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grid2x(ix, iy, iz, xgrid);
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const double xtmp = xgrid[0];
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const double ytmp = xgrid[1];
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const double ztmp = xgrid[2];
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// currently, all grid points are type 1
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const int itype = 1;
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int ielem = 0;
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if (chemflag)
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ielem = map[itype];
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const double radi = radelem[itype];
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// rij[][3] = displacements between atom I and those neighbors
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// inside = indices of neighbors of I within cutoff
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// typej = types of neighbors of I within cutoff
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int ninside = 0;
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for (int j = 0; j < ntotal; j++) {
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// check that j is in compute group
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if (!(mask[j] & groupbit)) continue;
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const double delx = xtmp - x[j][0];
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const double dely = ytmp - x[j][1];
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const double delz = ztmp - x[j][2];
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const double rsq = delx*delx + dely*dely + delz*delz;
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int jtype = type[j];
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int jelem = 0;
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if (chemflag)
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jelem = map[jtype];
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if (rsq < cutsq[jtype][jtype] && rsq > 1e-20) {
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snaptr->rij[ninside][0] = delx;
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snaptr->rij[ninside][1] = dely;
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snaptr->rij[ninside][2] = delz;
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snaptr->inside[ninside] = j;
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snaptr->wj[ninside] = wjelem[jtype];
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snaptr->rcutij[ninside] = 2.0*radelem[jtype]*rcutfac;
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snaptr->element[ninside] = jelem; // element index for multi-element snap
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ninside++;
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}
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}
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snaptr->compute_ui(ninside, ielem);
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snaptr->compute_zi();
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snaptr->compute_bi(ielem);
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// linear contributions
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for (int icoeff = 0; icoeff < ncoeff; icoeff++)
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gridlocal[size_local_cols_base+icoeff][iz][iy][ix] = snaptr->blist[icoeff];
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// quadratic contributions
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if (quadraticflag) {
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int ncount = ncoeff;
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for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
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double bveci = snaptr->blist[icoeff];
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gridlocal[size_local_cols_base+ncount++][iz][iy][ix] = 0.5*bveci*bveci;
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for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
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gridlocal[size_local_cols_base+ncount++][iz][iy][ix] = bveci*snaptr->blist[jcoeff];
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}
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}
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}
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// copy 4d array to 2d array
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copy_gridlocal_to_local_array();
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}
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/* ----------------------------------------------------------------------
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memory usage
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------------------------------------------------------------------------- */
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double ComputeSNAGridLocal::memory_usage()
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{
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double nbytes = snaptr->memory_usage(); // SNA object
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int n = atom->ntypes+1;
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nbytes += (double)n*sizeof(int); // map
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return nbytes;
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||||||
|
}
|
||||||
|
|
||||||
75
src/ML-SNAP/compute_sna_grid_local.h
Normal file
75
src/ML-SNAP/compute_sna_grid_local.h
Normal file
@ -0,0 +1,75 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef COMPUTE_CLASS
|
||||||
|
|
||||||
|
ComputeStyle(sna/grid/local,ComputeSNAGridLocal)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_COMPUTE_SNA_GRID_LOCAL_H
|
||||||
|
#define LMP_COMPUTE_SNA_GRID_LOCAL_H
|
||||||
|
|
||||||
|
#include "compute_grid_local.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class ComputeSNAGridLocal : public ComputeGridLocal {
|
||||||
|
public:
|
||||||
|
ComputeSNAGridLocal(class LAMMPS *, int, char **);
|
||||||
|
~ComputeSNAGridLocal();
|
||||||
|
void init();
|
||||||
|
void init_list(int, class NeighList *);
|
||||||
|
void compute_local();
|
||||||
|
double memory_usage();
|
||||||
|
|
||||||
|
private:
|
||||||
|
int ncoeff;
|
||||||
|
double **cutsq;
|
||||||
|
class NeighList *list;
|
||||||
|
double rcutfac;
|
||||||
|
double *radelem;
|
||||||
|
double *wjelem;
|
||||||
|
int *map; // map types to [0,nelements)
|
||||||
|
int nelements, chemflag;
|
||||||
|
class SNA *snaptr;
|
||||||
|
double cutmax;
|
||||||
|
int quadraticflag;
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script syntax and compare to the
|
||||||
|
documentation for the command. You can use -echo screen as a
|
||||||
|
command-line option when running LAMMPS to see the offending line.
|
||||||
|
|
||||||
|
E: Compute sna/grid/local requires a pair style be defined
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Compute sna/grid/local cutoff is longer than pairwise cutoff
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
W: More than one compute sna/grid/local
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
*/
|
||||||
253
src/compute_grid_local.cpp
Normal file
253
src/compute_grid_local.cpp
Normal file
@ -0,0 +1,253 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
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 "compute_grid_local.h"
|
||||||
|
#include <mpi.h>
|
||||||
|
#include <cstring>
|
||||||
|
#include "atom.h"
|
||||||
|
#include "update.h"
|
||||||
|
#include "modify.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "comm.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
ComputeGridLocal::ComputeGridLocal(LAMMPS *lmp, int narg, char **arg) :
|
||||||
|
Compute(lmp, narg, arg), gridlocal(nullptr), alocal(nullptr)
|
||||||
|
{
|
||||||
|
if (narg < 6) error->all(FLERR,"Illegal compute grid/local command");
|
||||||
|
|
||||||
|
local_flag = 1;
|
||||||
|
size_local_cols = 0;
|
||||||
|
size_local_rows = 0;
|
||||||
|
extarray = 0;
|
||||||
|
|
||||||
|
int iarg0 = 3;
|
||||||
|
int iarg = iarg0;
|
||||||
|
if (strcmp(arg[iarg],"grid") == 0) {
|
||||||
|
if (iarg+4 > narg) error->all(FLERR,"Illegal compute grid/local command");
|
||||||
|
nx = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
|
||||||
|
ny = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
|
||||||
|
nz = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
|
||||||
|
if (nx <= 0 || ny <= 0 || nz <= 0)
|
||||||
|
error->all(FLERR,"All grid/local dimensions must be positive");
|
||||||
|
iarg += 4;
|
||||||
|
} else error->all(FLERR,"Illegal compute grid/local command");
|
||||||
|
|
||||||
|
nargbase = iarg - iarg0;
|
||||||
|
|
||||||
|
size_local_cols_base = 6;
|
||||||
|
gridlocal_allocated = 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
ComputeGridLocal::~ComputeGridLocal()
|
||||||
|
{
|
||||||
|
if (gridlocal_allocated) {
|
||||||
|
gridlocal_allocated = 0;
|
||||||
|
memory->destroy4d_offset(gridlocal,nzlo,nylo,nxlo);
|
||||||
|
}
|
||||||
|
memory->destroy(alocal);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeGridLocal::init()
|
||||||
|
{
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeGridLocal::setup()
|
||||||
|
{
|
||||||
|
set_grid_global();
|
||||||
|
set_grid_local();
|
||||||
|
allocate();
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
convert global array indexes to box coords
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeGridLocal::grid2x(int ix, int iy, int iz, double *x)
|
||||||
|
{
|
||||||
|
x[0] = ix*delx;
|
||||||
|
x[1] = iy*dely;
|
||||||
|
x[2] = iz*delz;
|
||||||
|
|
||||||
|
if (triclinic) domain->lamda2x(x, x);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
free and reallocate arrays
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeGridLocal::allocate()
|
||||||
|
{
|
||||||
|
// allocate local array
|
||||||
|
|
||||||
|
if (gridlocal_allocated) {
|
||||||
|
gridlocal_allocated = 0;
|
||||||
|
// MEMORY LEAK!!
|
||||||
|
// can't seem to free this memory without seg-fault
|
||||||
|
// printf("Before allocate destroy4d, proc %d %p\n",comm->me,gridlocal);
|
||||||
|
// memory->destroy4d_offset(gridlocal,nzlo,nylo,nxlo);
|
||||||
|
// printf("After allocate destroy4d, proc %d %p\n",comm->me,gridlocal);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (nxlo <= nxhi && nylo <= nyhi && nzlo <= nzhi) {
|
||||||
|
gridlocal_allocated = 1;
|
||||||
|
memory->create4d_offset(gridlocal,size_array_cols,nzlo,nzhi,nylo,nyhi,
|
||||||
|
nxlo,nxhi,"grid:gridlocal");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
set global grid
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeGridLocal::set_grid_global()
|
||||||
|
{
|
||||||
|
// calculate grid layout
|
||||||
|
|
||||||
|
triclinic = domain->triclinic;
|
||||||
|
|
||||||
|
if (triclinic == 0) {
|
||||||
|
prd = domain->prd;
|
||||||
|
boxlo = domain->boxlo;
|
||||||
|
sublo = domain->sublo;
|
||||||
|
subhi = domain->subhi;
|
||||||
|
} else {
|
||||||
|
prd = domain->prd_lamda;
|
||||||
|
boxlo = domain->boxlo_lamda;
|
||||||
|
sublo = domain->sublo_lamda;
|
||||||
|
subhi = domain->subhi_lamda;
|
||||||
|
}
|
||||||
|
|
||||||
|
double xprd = prd[0];
|
||||||
|
double yprd = prd[1];
|
||||||
|
double zprd = prd[2];
|
||||||
|
|
||||||
|
delxinv = nx/xprd;
|
||||||
|
delyinv = ny/yprd;
|
||||||
|
delzinv = nz/zprd;
|
||||||
|
|
||||||
|
delx = 1.0/delxinv;
|
||||||
|
dely = 1.0/delyinv;
|
||||||
|
delz = 1.0/delzinv;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
set local subset of grid that I own
|
||||||
|
n xyz lo/hi = 3d brick that I own (inclusive)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeGridLocal::set_grid_local()
|
||||||
|
{
|
||||||
|
// nx,ny,nz = extent of global grid
|
||||||
|
// indices into the global grid range from 0 to N-1 in each dim
|
||||||
|
// if grid point is inside my sub-domain I own it,
|
||||||
|
// this includes sub-domain lo boundary but excludes hi boundary
|
||||||
|
// ixyz lo/hi = inclusive lo/hi bounds of global grid sub-brick I own
|
||||||
|
// if proc owns no grid cells in a dim, then ilo > ihi
|
||||||
|
// if 2 procs share a boundary a grid point is exactly on,
|
||||||
|
// the 2 equality if tests insure a consistent decision
|
||||||
|
// as to which proc owns it
|
||||||
|
|
||||||
|
double xfraclo,xfrachi,yfraclo,yfrachi,zfraclo,zfrachi;
|
||||||
|
|
||||||
|
if (comm->layout != Comm::LAYOUT_TILED) {
|
||||||
|
xfraclo = comm->xsplit[comm->myloc[0]];
|
||||||
|
xfrachi = comm->xsplit[comm->myloc[0]+1];
|
||||||
|
yfraclo = comm->ysplit[comm->myloc[1]];
|
||||||
|
yfrachi = comm->ysplit[comm->myloc[1]+1];
|
||||||
|
zfraclo = comm->zsplit[comm->myloc[2]];
|
||||||
|
zfrachi = comm->zsplit[comm->myloc[2]+1];
|
||||||
|
} else {
|
||||||
|
xfraclo = comm->mysplit[0][0];
|
||||||
|
xfrachi = comm->mysplit[0][1];
|
||||||
|
yfraclo = comm->mysplit[1][0];
|
||||||
|
yfrachi = comm->mysplit[1][1];
|
||||||
|
zfraclo = comm->mysplit[2][0];
|
||||||
|
zfrachi = comm->mysplit[2][1];
|
||||||
|
}
|
||||||
|
|
||||||
|
nxlo = static_cast<int> (xfraclo * nx);
|
||||||
|
if (1.0*nxlo != xfraclo*nx) nxlo++;
|
||||||
|
nxhi = static_cast<int> (xfrachi * nx);
|
||||||
|
if (1.0*nxhi == xfrachi*nx) nxhi--;
|
||||||
|
|
||||||
|
nylo = static_cast<int> (yfraclo * ny);
|
||||||
|
if (1.0*nylo != yfraclo*ny) nylo++;
|
||||||
|
nyhi = static_cast<int> (yfrachi * ny);
|
||||||
|
if (1.0*nyhi == yfrachi*ny) nyhi--;
|
||||||
|
|
||||||
|
nzlo = static_cast<int> (zfraclo * nz);
|
||||||
|
if (1.0*nzlo != zfraclo*nz) nzlo++;
|
||||||
|
nzhi = static_cast<int> (zfrachi * nz);
|
||||||
|
if (1.0*nzhi == zfrachi*nz) nzhi--;
|
||||||
|
|
||||||
|
ngridlocal = (nxhi - nxlo + 1) * (nyhi - nylo + 1) * (nzhi - nzlo + 1);
|
||||||
|
size_local_rows = ngridlocal;
|
||||||
|
|
||||||
|
memory->destroy(alocal);
|
||||||
|
memory->create(alocal, size_local_rows, size_local_cols, "compute/grid/local:alocal");
|
||||||
|
array_local = alocal;
|
||||||
|
|
||||||
|
int igrid = 0;
|
||||||
|
for (int iz = nzlo; iz <= nzhi; iz++)
|
||||||
|
for (int iy = nylo; iy <= nyhi; iy++)
|
||||||
|
for (int ix = nxlo; ix <= nxhi; ix++) {
|
||||||
|
alocal[igrid][0] = ix;
|
||||||
|
alocal[igrid][1] = iy;
|
||||||
|
alocal[igrid][2] = iz;
|
||||||
|
double xgrid[3];
|
||||||
|
grid2x(ix, iy, iz, xgrid);
|
||||||
|
alocal[igrid][3] = xgrid[0];
|
||||||
|
alocal[igrid][4] = xgrid[1];
|
||||||
|
alocal[igrid][5] = xgrid[2];
|
||||||
|
igrid++;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
copy the 4d gridlocal array values to the 2d local array
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeGridLocal::copy_gridlocal_to_local_array()
|
||||||
|
{
|
||||||
|
int igrid = 0;
|
||||||
|
for (int iz = nzlo; iz <= nzhi; iz++)
|
||||||
|
for (int iy = nylo; iy <= nyhi; iy++)
|
||||||
|
for (int ix = nxlo; ix <= nxhi; ix++) {
|
||||||
|
for (int icol = size_local_cols_base; icol < size_local_cols; icol++)
|
||||||
|
alocal[igrid][icol] = gridlocal[icol][iz][iy][ix];
|
||||||
|
igrid++;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
memory usage of local data
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double ComputeGridLocal::memory_usage()
|
||||||
|
{
|
||||||
|
int nbytes = size_array_cols*ngridlocal*sizeof(double); // gridlocal
|
||||||
|
return nbytes;
|
||||||
|
}
|
||||||
69
src/compute_grid_local.h
Normal file
69
src/compute_grid_local.h
Normal file
@ -0,0 +1,69 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifndef LMP_COMPUTE_GRID_LOCAL_H
|
||||||
|
#define LMP_COMPUTE_GRID_LOCAL_H
|
||||||
|
|
||||||
|
#include "compute.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class ComputeGridLocal : public Compute {
|
||||||
|
public:
|
||||||
|
|
||||||
|
ComputeGridLocal(class LAMMPS *, int, char **);
|
||||||
|
virtual ~ComputeGridLocal();
|
||||||
|
void init();
|
||||||
|
void setup();
|
||||||
|
virtual void compute_local() = 0;
|
||||||
|
|
||||||
|
double memory_usage();
|
||||||
|
|
||||||
|
protected:
|
||||||
|
int nx, ny, nz; // global grid dimensions
|
||||||
|
int nxlo, nxhi, nylo, nyhi, nzlo, nzhi; // local grid bounds, inclusive
|
||||||
|
int ngridlocal; // number of local grid points
|
||||||
|
int nvalues; // number of values per grid point
|
||||||
|
double ****gridlocal; // local grid
|
||||||
|
double **alocal; // pointer to Compute::array_local
|
||||||
|
int triclinic; // triclinic flag
|
||||||
|
double *boxlo, *prd; // box info (units real/ortho or reduced/tri)
|
||||||
|
double *sublo, *subhi; // subdomain info (units real/ortho or reduced/tri)
|
||||||
|
double delxinv,delyinv,delzinv; // inverse grid spacing
|
||||||
|
double delx,dely,delz; // grid spacing
|
||||||
|
int nargbase; // number of base class args
|
||||||
|
double cutmax; // largest cutoff distance
|
||||||
|
int size_local_cols_base; // number of columns used for coords, etc.
|
||||||
|
int gridlocal_allocated; // shows if gridlocal allocated
|
||||||
|
|
||||||
|
void allocate();
|
||||||
|
void grid2x(int, int, int, double*); // convert global indices to coordinates
|
||||||
|
void set_grid_global(); // set global grid
|
||||||
|
void set_grid_local(); // set bounds for local grid
|
||||||
|
void copy_gridlocal_to_local_array();// copy 4d gridlocal array to 2d local array
|
||||||
|
private:
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script syntax and compare to the
|
||||||
|
documentation for the command. You can use -echo screen as a
|
||||||
|
command-line option when running LAMMPS to see the offending line.
|
||||||
|
|
||||||
|
*/
|
||||||
Reference in New Issue
Block a user