Unverified Commit 0abbc590 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

multiple changes to integrate into LAMMPS more smoothly 

- indentation at 2 blanks
- use BIGINT_FORMAT consistently
- use MathSpecial::square() instead of pow(x,2)
parent fddc164d

src/USER-PHONON/third_order.cpp

+416 −415
Original line number Diff line number Diff line
@@ -2,10 +2,10 @@ 
// Created by charlie sievers on 7/5/18.

//



#include "third_order.h"

#include <mpi.h>

#include <cmath>

#include <cstring>

#include "third_order.h"

#include "atom.h"

#include "domain.h"

#include "comm.h"
@@ -23,12 +23,12 @@ 
#include "pair.h"

#include "timer.h"

#include "finish.h"

#include "math_special.h"

#include <algorithm>

#include "complex"





#include <complex>



using namespace LAMMPS_NS;

using namespace MathSpecial;

enum{REGULAR,BALLISTICO};



/* ---------------------------------------------------------------------- */
@@ -179,13 +179,11 @@ void ThirdOrder::options(int narg, char **arg) 
      filename = fss.str().c_str();

      file_flag = 1;

      iarg += 2;

        }

        else if (strcmp(arg[iarg],"binary") == 0) {

    } else if (strcmp(arg[iarg],"binary") == 0) {

      if (iarg + 2 > narg) error->all(FLERR, "Illegal third_order command");

      if (strcmp(arg[iarg+1],"gzip") == 0) {

        compressed = 1;

            }

            else if (strcmp(arg[iarg+1],"yes") == 0) {

      } else if (strcmp(arg[iarg+1],"yes") == 0) {

        binaryflag = 1;

      }

      iarg += 2;
@@ -253,7 +251,8 @@ void ThirdOrder::calculateMatrix() 
    fprintf(screen,"Calculating Third Order ...\n");

    fprintf(screen,"  Total # of atoms = " BIGINT_FORMAT "\n", natoms);

    fprintf(screen,"  Atoms in group = " BIGINT_FORMAT "\n", gcount);

        fprintf(screen,"  Total third order elements = " BIGINT_FORMAT "\n", (dynlen*dynlen*dynlen) );

    fprintf(screen,"  Total third order elements = "

            BIGINT_FORMAT "\n", (dynlen*dynlen*dynlen) );

  }



  update->nsteps = 0;
@@ -339,8 +338,8 @@ void ThirdOrder::calculateMatrix() 
  delete [] dynmat;

  delete [] fdynmat;



    if (screen && me ==0 ) fprintf(screen,"Finished Calculating Third Order Tensor\n");



  if (screen && me ==0 )

    fprintf(screen,"Finished Calculating Third Order Tensor\n");

}



/* ----------------------------------------------------------------------
@@ -356,19 +355,19 @@ void ThirdOrder::writeMatrix(double *dynmat, bigint i, int a, bigint j, int b) 
  if (!binaryflag && fp) {

    clearerr(fp);

    for (int k = 0; k < gcount; k++){

            norm = pow(dynmat[k*3], 2)+

                pow(dynmat[k*3+1], 2)+

                pow(dynmat[k*3+2], 2);

      norm = square(dynmat[k*3])+

        square(dynmat[k*3+1])+

        square(dynmat[k*3+2]);

      if (norm > 1.0e-16)

        fprintf(fp,

                        "%llu %d %llu %d %llu %7.8f %7.8f %7.8f\n",

                BIGINT_FORMAT " %d " BIGINT_FORMAT " %d " BIGINT_FORMAT

                " %7.8f %7.8f %7.8f\n",

                i+1, a + 1, j+1, b + 1, groupmap[k]+1,

                dynmat[k*3] * conversion,

                dynmat[k*3+1] * conversion,

                dynmat[k*3+2] * conversion);

    }

    }

    else if (binaryflag && fp){

  } else if (binaryflag && fp){

    clearerr(fp);

    fwrite(&dynmat[0], sizeof(double), dynlen, fp);

  }
@@ -534,7 +533,8 @@ void ThirdOrder::create_groupmap() 
  //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){

    if ((local_idx >= 0) && (local_idx < nlocal)

        && (mask[local_idx] & groupbit)){

      sub_groupmap[gid] = i;

      gid += 1;

    }
@@ -553,7 +553,8 @@ void ThirdOrder::create_groupmap() 
  }



  //combine subgroup maps into total temporary groupmap

    MPI_Allgatherv(sub_groupmap,gid,MPI_LMP_BIGINT,temp_groupmap,recv,displs,MPI_LMP_BIGINT,world);

  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

src/USER-PHONON/third_order.h

+52 −52

File changed.

Contains only whitespace changes.

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