574 lines
18 KiB
C++
574 lines
18 KiB
C++
//
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// Created by charlie sievers on 6/21/18.
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//
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#include <mpi.h>
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#include <cstdlib>
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#include "dynamical_matrix.h"
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#include "atom.h"
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#include "modify.h"
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#include "domain.h"
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#include "comm.h"
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#include "group.h"
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#include "force.h"
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#include "math_extra.h"
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#include "memory.h"
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#include "bond.h"
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#include "angle.h"
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#include "dihedral.h"
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#include "improper.h"
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#include "kspace.h"
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#include "update.h"
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#include "neighbor.h"
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#include "pair.h"
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#include "timer.h"
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#include "finish.h"
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#include <algorithm>
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using namespace LAMMPS_NS;
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enum{REGULAR,ESKM};
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/* ---------------------------------------------------------------------- */
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DynamicalMatrix::DynamicalMatrix(LAMMPS *lmp) : Pointers(lmp), fp(NULL)
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{
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external_force_clear = 1;
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}
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/* ---------------------------------------------------------------------- */
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DynamicalMatrix::~DynamicalMatrix()
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{
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if (fp && me == 0) fclose(fp);
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memory->destroy(groupmap);
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fp = NULL;
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}
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/* ----------------------------------------------------------------------
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setup without output or one-time post-init setup
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flag = 0 = just force calculation
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flag = 1 = reneighbor and force calculation
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------------------------------------------------------------------------- */
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void DynamicalMatrix::setup()
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{
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// setup domain, communication and neighboring
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// acquire ghosts
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// build neighbor lists
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if (triclinic) domain->x2lamda(atom->nlocal);
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domain->pbc();
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domain->reset_box();
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comm->setup();
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if (neighbor->style) neighbor->setup_bins();
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comm->exchange();
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comm->borders();
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if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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domain->image_check();
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domain->box_too_small_check();
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neighbor->build(1);
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neighbor->ncalls = 0;
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neighbor->every = 2; // build every this many steps
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neighbor->delay = 1;
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neighbor->ago = 0;
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neighbor->ndanger = 0;
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// compute all forces
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external_force_clear = 0;
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eflag=0;
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vflag=0;
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update_force();
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//if all then skip communication groupmap population
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if (gcount == atom->natoms)
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for (bigint i=0; i<atom->natoms; i++)
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groupmap[i] = i;
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else
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create_groupmap();
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}
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/* ---------------------------------------------------------------------- */
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void DynamicalMatrix::command(int narg, char **arg)
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{
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MPI_Comm_rank(world,&me);
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if (domain->box_exist == 0)
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error->all(FLERR,"Dynamical_matrix command before simulation box is defined");
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if (narg < 2) error->all(FLERR,"Illegal dynamical_matrix command");
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lmp->init();
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// orthogonal vs triclinic simulation box
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triclinic = domain->triclinic;
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if (force->pair && force->pair->compute_flag) pair_compute_flag = 1;
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else pair_compute_flag = 0;
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if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1;
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else kspace_compute_flag = 0;
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// group and style
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igroup = group->find(arg[0]);
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if (igroup == -1) error->all(FLERR,"Could not find dynamical matrix group ID");
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groupbit = group->bitmask[igroup];
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gcount = group->count(igroup);
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dynlen = (gcount)*3;
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memory->create(groupmap,atom->natoms,"total_group_map:totalgm");
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update->setupflag = 1;
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int style = -1;
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if (strcmp(arg[1],"regular") == 0) style = REGULAR;
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else if (strcmp(arg[1],"eskm") == 0) style = ESKM;
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else error->all(FLERR,"Illegal Dynamical Matrix command");
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del = force->numeric(FLERR, arg[2]);
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// set option defaults
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binaryflag = 0;
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scaleflag = 0;
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compressed = 0;
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file_flag = 0;
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file_opened = 0;
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conversion = 1;
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// read options from end of input line
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if (style == REGULAR) options(narg-3,&arg[3]); //COME BACK
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else if (style == ESKM) options(narg-3,&arg[3]); //COME BACK
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else if (comm->me == 0 && screen) fprintf(screen,"Illegal Dynamical Matrix command\n");
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if (atom->map_style == 0)
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error->all(FLERR,"Dynamical_matrix command requires an atom map, see atom_modify");
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// move atoms by 3-vector or specified variable(s)
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if (style == REGULAR) {
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setup();
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timer->init();
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timer->barrier_start();
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calculateMatrix();
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timer->barrier_stop();
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}
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if (style == ESKM) {
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setup();
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convert_units(update->unit_style);
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conversion = conv_energy/conv_distance/conv_mass;
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timer->init();
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timer->barrier_start();
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calculateMatrix();
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timer->barrier_stop();
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}
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Finish finish(lmp);
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finish.end(1);
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}
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/* ----------------------------------------------------------------------
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parse optional parameters
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------------------------------------------------------------------------- */
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void DynamicalMatrix::options(int narg, char **arg)
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{
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if (narg < 0) error->all(FLERR,"Illegal dynamical_matrix command");
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int iarg = 0;
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const char* filename = "dynmat.dyn";
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while (iarg < narg) {
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if (strcmp(arg[iarg],"binary") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal dynamical_matrix command");
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if (strcmp(arg[iarg+1],"gzip") == 0) {
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compressed = 1;
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}
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else if (strcmp(arg[iarg+1],"yes") == 0) {
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binaryflag = 1;
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}
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iarg += 2;
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}
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else if (strcmp(arg[iarg],"file") == 0) {
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if (iarg+2 > narg) error->all(FLERR, "Illegal dynamical_matrix command");
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filename = arg[iarg + 1];
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file_flag = 1;
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iarg += 2;
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} else error->all(FLERR,"Illegal dynamical_matrix command");
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}
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if (file_flag == 1) {
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openfile(filename);
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}
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}
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/* ----------------------------------------------------------------------
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generic opening of a file
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ASCII or binary or gzipped
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some derived classes override this function
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------------------------------------------------------------------------- */
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void DynamicalMatrix::openfile(const char* filename)
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{
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// if file already opened, return
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//if (me!=0) return;
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if (file_opened) return;
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if (compressed) {
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#ifdef LAMMPS_GZIP
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char gzip[128];
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sprintf(gzip,"gzip -6 > %s",filename);
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#ifdef _WIN32
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fp = _popen(gzip,"wb");
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#else
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fp = popen(gzip,"w");
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#endif
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#else
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error->one(FLERR,"Cannot open gzipped file");
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#endif
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} else if (binaryflag) {
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fp = fopen(filename,"wb");
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} else {
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fp = fopen(filename,"w");
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}
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if (fp == NULL) error->one(FLERR,"Cannot open dump file");
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file_opened = 1;
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}
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/* ----------------------------------------------------------------------
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create dynamical matrix
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------------------------------------------------------------------------- */
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void DynamicalMatrix::calculateMatrix()
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{
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int local_idx; // local index
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int local_jdx; // second local index
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int nlocal = atom->nlocal;
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bigint natoms = atom->natoms;
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int *type = atom->type;
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bigint *gm = groupmap;
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double imass; // dynamical matrix element
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double *m = atom->mass;
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double **f = atom->f;
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double **dynmat = new double*[3];
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for (int i=0; i<3; i++)
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dynmat[i] = new double[dynlen];
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double **fdynmat = new double*[3];
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for (int i=0; i<3; i++)
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fdynmat[i] = new double[dynlen];
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//initialize dynmat to all zeros
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dynmat_clear(dynmat);
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if (comm->me == 0 && screen) {
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fprintf(screen,"Calculating Dynamical Matrix ...\n");
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fprintf(screen," Total # of atoms = " BIGINT_FORMAT "\n", natoms);
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fprintf(screen," Atoms in group = " BIGINT_FORMAT "\n", gcount);
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fprintf(screen," Total dynamical matrix elements = " BIGINT_FORMAT "\n", (dynlen*dynlen) );
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}
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// emit dynlen rows of dimalpha*dynlen*dimbeta elements
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update->nsteps = 0;
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int prog = 0;
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for (bigint i=1; i<=natoms; i++){
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local_idx = atom->map(i);
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if (gm[i-1] < 0)
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continue;
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for (bigint alpha=0; alpha<3; alpha++){
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displace_atom(local_idx, alpha, 1);
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update_force();
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for (bigint j=1; j<=natoms; j++){
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local_jdx = atom->map(j);
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if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal
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&& gm[j-1] >= 0){
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for (int beta=0; beta<3; beta++){
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dynmat[alpha][gm[j-1]*3+beta] -= f[local_jdx][beta];
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}
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}
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}
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displace_atom(local_idx,alpha,-2);
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update_force();
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for (bigint j=1; j<=natoms; j++){
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local_jdx = atom->map(j);
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if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal
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&& gm[j-1] >= 0){
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for (bigint beta=0; beta<3; beta++){
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if (atom->rmass_flag == 1)
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imass = sqrt(m[local_idx] * m[local_jdx]);
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else
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imass = sqrt(m[type[local_idx]] * m[type[local_jdx]]);
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dynmat[alpha][gm[j-1]*3+beta] -= -f[local_jdx][beta];
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dynmat[alpha][gm[j-1]*3+beta] /= (2 * del * imass);
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dynmat[alpha][gm[j-1]*3+beta] *= conversion;
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}
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}
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}
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displace_atom(local_idx,alpha,1);
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}
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for (int k=0; k<3; k++)
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MPI_Reduce(dynmat[k],fdynmat[k],dynlen,MPI_DOUBLE,MPI_SUM,0,world);
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if (me == 0)
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writeMatrix(fdynmat);
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dynmat_clear(dynmat);
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if (comm->me == 0 && screen) {
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int p = 10 * gm[i-1] / gcount;
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if (p > prog) {
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prog = p;
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fprintf(screen," %d%%",p*10);
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fflush(screen);
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}
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}
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}
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if (comm->me == 0 && screen) fprintf(screen,"\n");
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for (int i=0; i < 3; i++)
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delete [] dynmat[i];
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delete [] dynmat;
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for (int i=0; i < 3; i++)
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delete [] fdynmat[i];
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delete [] fdynmat;
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if (screen && me ==0 ) fprintf(screen,"Finished Calculating Dynamical Matrix\n");
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}
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/* ----------------------------------------------------------------------
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write dynamical matrix
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------------------------------------------------------------------------- */
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void DynamicalMatrix::writeMatrix(double **dynmat)
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{
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if (me != 0 || !fp)
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return;
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clearerr(fp);
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if (binaryflag) {
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for (int i=0; i<3; i++)
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fwrite(dynmat[i], sizeof(double), dynlen, fp);
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if (ferror(fp))
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error->one(FLERR, "Error writing to binary file");
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} else {
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for (int i = 0; i < 3; i++) {
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for (bigint j = 0; j < dynlen; j++) {
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if ((j+1)%3==0) fprintf(fp, "%4.8f\n", dynmat[i][j]);
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else fprintf(fp, "%4.8f ",dynmat[i][j]);
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}
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}
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if (ferror(fp))
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error->one(FLERR,"Error writing to file");
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}
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}
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/* ----------------------------------------------------------------------
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Displace atoms
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---------------------------------------------------------------------- */
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void DynamicalMatrix::displace_atom(int local_idx, int direction, int magnitude)
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{
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if (local_idx < 0) return;
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double **x = atom->x;
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int *sametag = atom->sametag;
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int j = local_idx;
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x[local_idx][direction] += del*magnitude;
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while (sametag[j] >= 0){
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j = sametag[j];
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x[j][direction] += del*magnitude;
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}
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}
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/* ----------------------------------------------------------------------
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evaluate potential energy and forces
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may migrate atoms due to reneighboring
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return new energy, which should include nextra_global dof
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return negative gradient stored in atom->f
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return negative gradient for nextra_global dof in fextra
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------------------------------------------------------------------------- */
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void DynamicalMatrix::update_force()
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{
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force_clear();
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if (pair_compute_flag) {
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force->pair->compute(eflag,vflag);
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timer->stamp(Timer::PAIR);
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}
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if (atom->molecular) {
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if (force->bond) force->bond->compute(eflag,vflag);
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if (force->angle) force->angle->compute(eflag,vflag);
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if (force->dihedral) force->dihedral->compute(eflag,vflag);
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if (force->improper) force->improper->compute(eflag,vflag);
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timer->stamp(Timer::BOND);
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}
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if (kspace_compute_flag) {
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force->kspace->compute(eflag,vflag);
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timer->stamp(Timer::KSPACE);
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}
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if (force->newton) {
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comm->reverse_comm();
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timer->stamp(Timer::COMM);
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}
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++ update->nsteps;
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}
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/* ----------------------------------------------------------------------
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clear force on own & ghost atoms
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clear other arrays as needed
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------------------------------------------------------------------------- */
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void DynamicalMatrix::force_clear()
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{
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if (external_force_clear) return;
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// clear global force array
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// if either newton flag is set, also include ghosts
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size_t nbytes = sizeof(double) * atom->nlocal;
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if (force->newton) nbytes += sizeof(double) * atom->nghost;
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if (nbytes) {
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memset(&atom->f[0][0],0,3*nbytes);
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}
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}
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/* ----------------------------------------------------------------------
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clear dynmat needed
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------------------------------------------------------------------------- */
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void DynamicalMatrix::dynmat_clear(double **dynmat)
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{
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size_t nbytes = sizeof(double) * dynlen;
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if (nbytes) {
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for (int i=0; i<3; i++)
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memset(&dynmat[i][0],0,nbytes);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DynamicalMatrix::convert_units(const char *style)
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{
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// physical constants from:
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// http://physics.nist.gov/cuu/Constants/Table/allascii.txt
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// using thermochemical calorie = 4.184 J
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if (strcmp(style,"lj") == 0) {
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error->all(FLERR,"Conversion Not Set");
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//conversion = 1; // lj -> 10 J/mol
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} else if (strcmp(style,"real") == 0) {
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conv_energy = 418.4; // kcal/mol -> 10 J/mol
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conv_mass = 1; // g/mol -> g/mol
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conv_distance = 1; // angstrom -> angstrom
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} else if (strcmp(style,"metal") == 0) {
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conv_energy = 9648.5; // eV -> 10 J/mol
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conv_mass = 1; // g/mol -> g/mol
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conv_distance = 1; // angstrom -> angstrom
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} else if (strcmp(style,"si") == 0) {
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if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float");
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conv_energy = 6.022E22; // J -> 10 J/mol
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conv_mass = 6.022E26; // kg -> g/mol
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conv_distance = 1E-10; // meter -> angstrom
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} else if (strcmp(style,"cgs") == 0) {
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if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float");
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conv_energy = 6.022E12; // Erg -> 10 J/mol
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conv_mass = 6.022E23; // g -> g/mol
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conv_distance = 1E-7; // centimeter -> angstrom
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} else if (strcmp(style,"electron") == 0) {
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conv_energy = 262550; // Hartree -> 10 J/mol
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conv_mass = 1; // amu -> g/mol
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conv_distance = 0.529177249; // bohr -> angstrom
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} else if (strcmp(style,"micro") == 0) {
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if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion");
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conv_energy = 6.022E10; // picogram-micrometer^2/microsecond^2 -> 10 J/mol
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conv_mass = 6.022E11; // pg -> g/mol
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conv_distance = 1E-4; // micrometer -> angstrom
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} else if (strcmp(style,"nano") == 0) {
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if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion");
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conv_energy = 6.022E4; // attogram-nanometer^2/nanosecond^2 -> 10 J/mol
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conv_mass = 6.022E5; // ag -> g/mol
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conv_distance = 0.1; // angstrom -> angstrom
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} else error->all(FLERR,"Units Type Conversion Not Found");
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}
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/* ---------------------------------------------------------------------- */
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void DynamicalMatrix::create_groupmap()
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{
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//Create a group map which maps atom order onto group
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// groupmap[global atom index-1] = output column/row
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int local_idx; // local index
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int gid = 0; //group index
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int nlocal = atom->nlocal;
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int *mask = atom->mask;
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bigint natoms = atom->natoms;
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int *recv = new int[comm->nprocs];
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int *displs = new int[comm->nprocs];
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bigint *temp_groupmap = new bigint[natoms];
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//find number of local atoms in the group (final_gid)
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for (bigint i=1; i<=natoms; i++){
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|
local_idx = atom->map(i);
|
|
if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit)
|
|
gid += 1; // gid at the end of loop is final_Gid
|
|
}
|
|
//create an array of length final_gid
|
|
bigint *sub_groupmap = new bigint[gid];
|
|
|
|
gid = 0;
|
|
//create a map between global atom id and group atom id for each proc
|
|
for (bigint i=1; i<=natoms; i++){
|
|
local_idx = atom->map(i);
|
|
if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit){
|
|
sub_groupmap[gid] = i;
|
|
gid += 1;
|
|
}
|
|
}
|
|
|
|
//populate arrays for Allgatherv
|
|
for (int i=0; i<comm->nprocs; i++){
|
|
recv[i] = 0;
|
|
}
|
|
recv[comm->me] = gid;
|
|
MPI_Allreduce(recv,displs,comm->nprocs,MPI_INT,MPI_SUM,world);
|
|
for (int i=0; i<comm->nprocs; i++){
|
|
recv[i]=displs[i];
|
|
if (i>0) displs[i] = displs[i-1]+recv[i-1];
|
|
else displs[i] = 0;
|
|
}
|
|
|
|
//combine subgroup maps into total temporary groupmap
|
|
MPI_Allgatherv(sub_groupmap,gid,MPI_LMP_BIGINT,temp_groupmap,recv,displs,MPI_LMP_BIGINT,world);
|
|
std::sort(temp_groupmap,temp_groupmap+gcount);
|
|
|
|
//populate member groupmap based on temp groupmap
|
|
bigint j = 0;
|
|
for (bigint i=1; i<=natoms; i++){
|
|
// flag groupmap contents that are in temp_groupmap
|
|
if (j < gcount && i == temp_groupmap[j])
|
|
groupmap[i-1] = j++;
|
|
else
|
|
groupmap[i-1] = -1;
|
|
}
|
|
|
|
//free that memory!
|
|
delete[] recv;
|
|
delete[] displs;
|
|
delete[] sub_groupmap;
|
|
delete[] temp_groupmap;
|
|
}
|