lammps-sys 0.6.0

//
// Created by charlie sievers on 6/21/18.
//

#include <mpi.h>
#include <cmath>
#include <cstring>
#include "dynamical_matrix.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "error.h"
#include "group.h"
#include "force.h"
#include "memory.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "update.h"
#include "neighbor.h"
#include "pair.h"
#include "timer.h"
#include "finish.h"
#include <algorithm>

using namespace LAMMPS_NS;
enum{REGULAR,ESKM};

/* ---------------------------------------------------------------------- */

DynamicalMatrix::DynamicalMatrix(LAMMPS *lmp) : Pointers(lmp), fp(NULL)
{
    external_force_clear = 1;
}

/* ---------------------------------------------------------------------- */

DynamicalMatrix::~DynamicalMatrix()
{
    if (fp && me == 0) fclose(fp);
    memory->destroy(groupmap);
    fp = NULL;
}

/* ----------------------------------------------------------------------
   setup without output or one-time post-init setup
   flag = 0 = just force calculation
   flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */

void DynamicalMatrix::setup()
{
    // setup domain, communication and neighboring
    // acquire ghosts
    // build neighbor lists
    if (triclinic) domain->x2lamda(atom->nlocal);
    domain->pbc();
    domain->reset_box();
    comm->setup();
    if (neighbor->style) neighbor->setup_bins();
    comm->exchange();
    comm->borders();
    if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
    domain->image_check();
    domain->box_too_small_check();
    neighbor->build(1);
    neighbor->ncalls = 0;
    neighbor->every = 2;                       // build every this many steps
    neighbor->delay = 1;
    neighbor->ago = 0;
    neighbor->ndanger = 0;

    // compute all forces
    external_force_clear = 0;
    eflag=0;
    vflag=0;
    update_force();

    //if all then skip communication groupmap population
    if (gcount == atom->natoms)
        for (bigint i=0; i<atom->natoms; i++)
            groupmap[i] = i;
    else
        create_groupmap();
}

/* ---------------------------------------------------------------------- */

void DynamicalMatrix::command(int narg, char **arg)
{
    MPI_Comm_rank(world,&me);

    if (domain->box_exist == 0)
        error->all(FLERR,"Dynamical_matrix command before simulation box is defined");
    if (narg < 2) error->all(FLERR,"Illegal dynamical_matrix command");

    lmp->init();

    // orthogonal vs triclinic simulation box

    triclinic = domain->triclinic;

    if (force->pair && force->pair->compute_flag) pair_compute_flag = 1;
    else pair_compute_flag = 0;
    if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1;
    else kspace_compute_flag = 0;

    // group and style

    igroup = group->find(arg[0]);
    if (igroup == -1) error->all(FLERR,"Could not find dynamical matrix group ID");
    groupbit = group->bitmask[igroup];
    gcount = group->count(igroup);
    dynlen = (gcount)*3;
    memory->create(groupmap,atom->natoms,"total_group_map:totalgm");
    update->setupflag = 1;

    int style = -1;
    if (strcmp(arg[1],"regular") == 0) style = REGULAR;
    else if (strcmp(arg[1],"eskm") == 0) style = ESKM;
    else error->all(FLERR,"Illegal Dynamical Matrix command");
    del = force->numeric(FLERR, arg[2]);

    // set option defaults

    binaryflag = 0;
    scaleflag = 0;
    compressed = 0;
    file_flag = 0;
    file_opened = 0;
    conversion = 1;

    // read options from end of input line
    if (style == REGULAR) options(narg-3,&arg[3]);  //COME BACK
    else if (style == ESKM) options(narg-3,&arg[3]); //COME BACK
    else if (comm->me == 0 && screen) fprintf(screen,"Illegal Dynamical Matrix command\n");

    if (atom->map_style == 0)
      error->all(FLERR,"Dynamical_matrix command requires an atom map, see atom_modify");

    // move atoms by 3-vector or specified variable(s)

    if (style == REGULAR) {
        setup();
        timer->init();
        timer->barrier_start();
        calculateMatrix();
        timer->barrier_stop();
    }

    if (style == ESKM) {
        setup();
        convert_units(update->unit_style);
        conversion = conv_energy/conv_distance/conv_mass;
        timer->init();
        timer->barrier_start();
        calculateMatrix();
        timer->barrier_stop();
    }

    Finish finish(lmp);
    finish.end(1);
}

/* ----------------------------------------------------------------------
   parse optional parameters
------------------------------------------------------------------------- */

void DynamicalMatrix::options(int narg, char **arg)
{
    if (narg < 0) error->all(FLERR,"Illegal dynamical_matrix command");
    int iarg = 0;
    const char* filename = "dynmat.dyn";
    while (iarg < narg) {
        if (strcmp(arg[iarg],"binary") == 0) {
            if (iarg + 2 > narg) error->all(FLERR, "Illegal dynamical_matrix command");
            if (strcmp(arg[iarg+1],"gzip") == 0) {
                compressed = 1;
            }
            else if (strcmp(arg[iarg+1],"yes") == 0) {
                binaryflag = 1;
            }
            iarg += 2;
        }
        else if (strcmp(arg[iarg],"file") == 0) {
            if (iarg+2 > narg) error->all(FLERR, "Illegal dynamical_matrix command");
            filename = arg[iarg + 1];
            file_flag = 1;
            iarg += 2;
        } else error->all(FLERR,"Illegal dynamical_matrix command");
    }
    if (file_flag == 1) {
        openfile(filename);
    }
}

/* ----------------------------------------------------------------------
   generic opening of a file
   ASCII or binary or gzipped
   some derived classes override this function
------------------------------------------------------------------------- */

void DynamicalMatrix::openfile(const char* filename)
{
    // if file already opened, return
    //if (me!=0) return;
    if (file_opened) return;

    if (compressed) {
#ifdef LAMMPS_GZIP
        char gzip[128];
    sprintf(gzip,"gzip -6 > %s",filename);
#ifdef _WIN32
    fp = _popen(gzip,"wb");
#else
    fp = popen(gzip,"w");
#endif
#else
        error->one(FLERR,"Cannot open gzipped file");
#endif
    } else if (binaryflag) {
        fp = fopen(filename,"wb");
    } else {
        fp = fopen(filename,"w");
    }

    if (fp == NULL) error->one(FLERR,"Cannot open dump file");

    file_opened = 1;
}

/* ----------------------------------------------------------------------
   create dynamical matrix
------------------------------------------------------------------------- */

void DynamicalMatrix::calculateMatrix()
{
    int local_idx; // local index
    int local_jdx; // second local index
    int nlocal = atom->nlocal;
    bigint natoms = atom->natoms;
    int *type = atom->type;
    bigint *gm = groupmap;
    double imass; // dynamical matrix element
    double *m = atom->mass;
    double **f = atom->f;

    double **dynmat = new double*[3];
    for (int i=0; i<3; i++)
        dynmat[i] = new double[dynlen];

    double **fdynmat = new double*[3];
    for (int i=0; i<3; i++)
        fdynmat[i] = new double[dynlen];

    //initialize dynmat to all zeros
    dynmat_clear(dynmat);

    if (comm->me == 0 && screen) {
        fprintf(screen,"Calculating Dynamical Matrix ...\n");
        fprintf(screen,"  Total # of atoms = " BIGINT_FORMAT "\n", natoms);
        fprintf(screen,"  Atoms in group = " BIGINT_FORMAT "\n", gcount);
        fprintf(screen,"  Total dynamical matrix elements = " BIGINT_FORMAT "\n", (dynlen*dynlen) );
    }
    
    // emit dynlen rows of dimalpha*dynlen*dimbeta elements

    update->nsteps = 0;
    int prog = 0;
    for (bigint i=1; i<=natoms; i++){
        local_idx = atom->map(i);
        if (gm[i-1] < 0)
            continue;
        for (bigint alpha=0; alpha<3; alpha++){
            displace_atom(local_idx, alpha, 1);
            update_force();
            for (bigint j=1; j<=natoms; j++){
                local_jdx = atom->map(j);
                if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal
                    && gm[j-1] >= 0){
                    for (int beta=0; beta<3; beta++){
                        dynmat[alpha][gm[j-1]*3+beta] -= f[local_jdx][beta];
                    }
                }
            }
            displace_atom(local_idx,alpha,-2);
            update_force();
            for (bigint j=1; j<=natoms; j++){
                local_jdx = atom->map(j);
                if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal
                    && gm[j-1] >= 0){
                    for (bigint beta=0; beta<3; beta++){
                        if (atom->rmass_flag == 1)
                            imass = sqrt(m[local_idx] * m[local_jdx]);
                        else
                            imass = sqrt(m[type[local_idx]] * m[type[local_jdx]]);
                        dynmat[alpha][gm[j-1]*3+beta] -= -f[local_jdx][beta];
                        dynmat[alpha][gm[j-1]*3+beta] /= (2 * del * imass);
                        dynmat[alpha][gm[j-1]*3+beta] *= conversion;
                    }
                }
            }
            displace_atom(local_idx,alpha,1);
        }
        for (int k=0; k<3; k++)
            MPI_Reduce(dynmat[k],fdynmat[k],dynlen,MPI_DOUBLE,MPI_SUM,0,world);
        if (me == 0)
            writeMatrix(fdynmat);
        dynmat_clear(dynmat);
        if (comm->me == 0 && screen) {
            int p = 10 * gm[i-1] / gcount;
            if (p > prog) {
              prog = p;
              fprintf(screen," %d%%",p*10);
              fflush(screen);
            }
        }
    }
    if (comm->me == 0 && screen) fprintf(screen,"\n");

    for (int i=0; i < 3; i++)
        delete [] dynmat[i];
    delete [] dynmat;

    for (int i=0; i < 3; i++)
        delete [] fdynmat[i];
    delete [] fdynmat;

    if (screen && me ==0 ) fprintf(screen,"Finished Calculating Dynamical Matrix\n");
}

/* ----------------------------------------------------------------------
   write dynamical matrix
------------------------------------------------------------------------- */

void DynamicalMatrix::writeMatrix(double **dynmat)
{
    if (me != 0 || !fp)
        return;

    clearerr(fp);
    if (binaryflag) {
        for (int i=0; i<3; i++)
            fwrite(dynmat[i], sizeof(double), dynlen, fp);
        if (ferror(fp))
            error->one(FLERR, "Error writing to binary file");
    } else {
        for (int i = 0; i < 3; i++) {
            for (bigint j = 0; j < dynlen; j++) {
                if ((j+1)%3==0) fprintf(fp, "%4.8f\n", dynmat[i][j]);
                else fprintf(fp, "%4.8f ",dynmat[i][j]);
            }
        }
        if (ferror(fp))
            error->one(FLERR,"Error writing to file");
    }
}

/* ----------------------------------------------------------------------
  Displace atoms
   ---------------------------------------------------------------------- */

void DynamicalMatrix::displace_atom(int local_idx, int direction, int magnitude)
{
    if (local_idx < 0) return;

    double **x = atom->x;
    int *sametag = atom->sametag;
    int j = local_idx;

    x[local_idx][direction] += del*magnitude;

    while (sametag[j] >= 0){
        j = sametag[j];
        x[j][direction] += del*magnitude;
    }
}


/* ----------------------------------------------------------------------
   evaluate potential energy and forces
   may migrate atoms due to reneighboring
   return new energy, which should include nextra_global dof
   return negative gradient stored in atom->f
   return negative gradient for nextra_global dof in fextra
------------------------------------------------------------------------- */

void DynamicalMatrix::update_force()
{
    force_clear();

    if (pair_compute_flag) {
        force->pair->compute(eflag,vflag);
        timer->stamp(Timer::PAIR);
    }
    if (atom->molecular) {
        if (force->bond) force->bond->compute(eflag,vflag);
        if (force->angle) force->angle->compute(eflag,vflag);
        if (force->dihedral) force->dihedral->compute(eflag,vflag);
        if (force->improper) force->improper->compute(eflag,vflag);
        timer->stamp(Timer::BOND);
    }
    if (kspace_compute_flag) {
        force->kspace->compute(eflag,vflag);
        timer->stamp(Timer::KSPACE);
    }
    if (force->newton) {
        comm->reverse_comm();
        timer->stamp(Timer::COMM);
    }
    ++ update->nsteps;
}

/* ----------------------------------------------------------------------
   clear force on own & ghost atoms
   clear other arrays as needed
------------------------------------------------------------------------- */

void DynamicalMatrix::force_clear()
{
    if (external_force_clear) return;

    // clear global force array
    // if either newton flag is set, also include ghosts

    size_t nbytes = sizeof(double) * atom->nlocal;
    if (force->newton) nbytes += sizeof(double) * atom->nghost;

    if (nbytes) {
        memset(&atom->f[0][0],0,3*nbytes);
    }
}

/* ----------------------------------------------------------------------
   clear dynmat needed
------------------------------------------------------------------------- */

void DynamicalMatrix::dynmat_clear(double **dynmat)
{

    size_t nbytes = sizeof(double) * dynlen;

    if (nbytes) {
        for (int i=0; i<3; i++)
            memset(&dynmat[i][0],0,nbytes);
    }
}

/* ---------------------------------------------------------------------- */

void DynamicalMatrix::convert_units(const char *style)
{
    // physical constants from:
    // http://physics.nist.gov/cuu/Constants/Table/allascii.txt
    // using thermochemical calorie = 4.184 J

    if (strcmp(style,"lj") == 0) {
        error->all(FLERR,"Conversion Not Set");
        //conversion = 1; // lj -> 10 J/mol

    } else if (strcmp(style,"real") == 0) {
        conv_energy = 418.4; // kcal/mol -> 10 J/mol
        conv_mass = 1; // g/mol -> g/mol
        conv_distance = 1; // angstrom -> angstrom

    } else if (strcmp(style,"metal") == 0) {
        conv_energy = 9648.5; // eV -> 10 J/mol
        conv_mass = 1; // g/mol -> g/mol
        conv_distance = 1; // angstrom -> angstrom

    } else if (strcmp(style,"si") == 0) {
        if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float");
        conv_energy = 6.022E22; // J -> 10 J/mol
        conv_mass = 6.022E26; // kg -> g/mol
        conv_distance = 1E-10; // meter -> angstrom

    } else if (strcmp(style,"cgs") == 0) {
        if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float");
        conv_energy = 6.022E12; // Erg -> 10 J/mol
        conv_mass = 6.022E23; // g -> g/mol
        conv_distance = 1E-7; // centimeter -> angstrom

    } else if (strcmp(style,"electron") == 0) {
        conv_energy = 262550; // Hartree -> 10 J/mol
        conv_mass = 1; // amu -> g/mol
        conv_distance = 0.529177249; // bohr -> angstrom

    } else if (strcmp(style,"micro") == 0) {
        if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion");
        conv_energy = 6.022E10; // picogram-micrometer^2/microsecond^2 -> 10 J/mol
        conv_mass = 6.022E11; // pg -> g/mol
        conv_distance = 1E-4; // micrometer -> angstrom

    } else if (strcmp(style,"nano") == 0) {
        if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion");
        conv_energy = 6.022E4; // attogram-nanometer^2/nanosecond^2 -> 10 J/mol
        conv_mass = 6.022E5; // ag -> g/mol
        conv_distance = 0.1; // angstrom -> angstrom

    } else error->all(FLERR,"Units Type Conversion Not Found");

}

/* ---------------------------------------------------------------------- */

void DynamicalMatrix::create_groupmap()
{
    //Create a group map which maps atom order onto group
    // groupmap[global atom index-1] = output column/row

    int local_idx; // local index
    int gid = 0; //group index
    int nlocal = atom->nlocal;
    int *mask = atom->mask;
    bigint natoms = atom->natoms;
    int *recv = new int[comm->nprocs];
    int *displs = new int[comm->nprocs];
    bigint *temp_groupmap = new bigint[natoms];

    //find number of local atoms in the group (final_gid)
    for (bigint i=1; i<=natoms; i++){
        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;
}