From 609842916cc08041127da136b0a767e25f42d232 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 25 Jul 2013 23:52:14 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10392
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/USER-OMP/pair_eam_alloy_omp.cpp.orig | 323 --------------------
src/USER-OMP/pair_eam_fs_omp.cpp.orig | 332 ---------------------
src/USER-OMP/pair_tersoff_zbl_omp.cpp.orig | 297 ------------------
3 files changed, 952 deletions(-)
delete mode 100644 src/USER-OMP/pair_eam_alloy_omp.cpp.orig
delete mode 100644 src/USER-OMP/pair_eam_fs_omp.cpp.orig
delete mode 100644 src/USER-OMP/pair_tersoff_zbl_omp.cpp.orig
diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp.orig b/src/USER-OMP/pair_eam_alloy_omp.cpp.orig
deleted file mode 100644
index 3dff868b6a..0000000000
--- a/src/USER-OMP/pair_eam_alloy_omp.cpp.orig
+++ /dev/null
@@ -1,323 +0,0 @@
-/* ----------------------------------------------------------------------
- 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.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
-------------------------------------------------------------------------- */
-
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "pair_eam_alloy_omp.h"
-#include "atom.h"
-#include "comm.h"
-#include "memory.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-#define MAXLINE 1024
-
-/* ---------------------------------------------------------------------- */
-
-PairEAMAlloyOMP::PairEAMAlloyOMP(LAMMPS *lmp) : PairEAMOMP(lmp)
-{
- one_coeff = 1;
-}
-
-/* ----------------------------------------------------------------------
- set coeffs for one or more type pairs
- read DYNAMO setfl file
-------------------------------------------------------------------------- */
-
-void PairEAMAlloyOMP::coeff(int narg, char **arg)
-{
- int i,j;
-
- if (!allocated) allocate();
-
- if (narg != 3 + atom->ntypes)
- error->all(FLERR,"Incorrect args for pair coefficients");
-
- // insure I,J args are * *
-
- if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
- error->all(FLERR,"Incorrect args for pair coefficients");
-
- // read EAM setfl file
-
- if (setfl) {
- for (i = 0; i < setfl->nelements; i++) delete [] setfl->elements[i];
- delete [] setfl->elements;
- delete [] setfl->mass;
- memory->destroy(setfl->frho);
- memory->destroy(setfl->rhor);
- memory->destroy(setfl->z2r);
- delete setfl;
- }
- setfl = new Setfl();
- read_file(arg[2]);
-
- // read args that map atom types to elements in potential file
- // map[i] = which element the Ith atom type is, -1 if NULL
-
- for (i = 3; i < narg; i++) {
- if (strcmp(arg[i],"NULL") == 0) {
- map[i-2] = -1;
- continue;
- }
- for (j = 0; j < setfl->nelements; j++)
- if (strcmp(arg[i],setfl->elements[j]) == 0) break;
- if (j < setfl->nelements) map[i-2] = j;
- else error->all(FLERR,"No matching element in EAM potential file");
- }
-
- // clear setflag since coeff() called once with I,J = * *
-
- int n = atom->ntypes;
- for (i = 1; i <= n; i++)
- for (j = i; j <= n; j++)
- setflag[i][j] = 0;
-
- // set setflag i,j for type pairs where both are mapped to elements
- // set mass of atom type if i = j
-
- int count = 0;
- for (i = 1; i <= n; i++) {
- for (j = i; j <= n; j++) {
- if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
- count++;
- }
- }
- }
-
- if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
-}
-
-/* ----------------------------------------------------------------------
- read a multi-element DYNAMO setfl file
-------------------------------------------------------------------------- */
-
-void PairEAMAlloyOMP::read_file(char *filename)
-{
- Setfl *file = setfl;
-
- // open potential file
-
- int me = comm->me;
- FILE *fptr;
- char line[MAXLINE];
-
- if (me == 0) {
- fptr = fopen(filename,"r");
- if (fptr == NULL) {
- char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
- error->one(FLERR,str);
- }
- }
-
- // read and broadcast header
- // extract element names from nelements line
-
- int n;
- if (me == 0) {
- fgets(line,MAXLINE,fptr);
- fgets(line,MAXLINE,fptr);
- fgets(line,MAXLINE,fptr);
- fgets(line,MAXLINE,fptr);
- n = strlen(line) + 1;
- }
- MPI_Bcast(&n,1,MPI_INT,0,world);
- MPI_Bcast(line,n,MPI_CHAR,0,world);
-
- sscanf(line,"%d",&file->nelements);
- int nwords = atom->count_words(line);
- if (nwords != file->nelements + 1)
- error->all(FLERR,"Incorrect element names in EAM potential file");
-
- char **words = new char*[file->nelements+1];
- nwords = 0;
- strtok(line," \t\n\r\f");
- while (words[nwords++] = strtok(NULL," \t\n\r\f")) continue;
-
- file->elements = new char*[file->nelements];
- for (int i = 0; i < file->nelements; i++) {
- n = strlen(words[i]) + 1;
- file->elements[i] = new char[n];
- strcpy(file->elements[i],words[i]);
- }
- delete [] words;
-
- if (me == 0) {
- fgets(line,MAXLINE,fptr);
- sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
- }
-
- MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
- MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&file->nr,1,MPI_INT,0,world);
- MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
-
- file->mass = new double[file->nelements];
- memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
- memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
- memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
- "pair:z2r");
-
- int i,j,tmp;
- for (i = 0; i < file->nelements; i++) {
- if (me == 0) {
- fgets(line,MAXLINE,fptr);
- sscanf(line,"%d %lg",&tmp,&file->mass[i]);
- }
- MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
-
- if (me == 0) grab(fptr,file->nrho,&file->frho[i][1]);
- MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
- if (me == 0) grab(fptr,file->nr,&file->rhor[i][1]);
- MPI_Bcast(&file->rhor[i][1],file->nr,MPI_DOUBLE,0,world);
- }
-
- for (i = 0; i < file->nelements; i++)
- for (j = 0; j <= i; j++) {
- if (me == 0) grab(fptr,file->nr,&file->z2r[i][j][1]);
- MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
- }
-
- // close the potential file
-
- if (me == 0) fclose(fptr);
-}
-
-/* ----------------------------------------------------------------------
- copy read-in setfl potential to standard array format
-------------------------------------------------------------------------- */
-
-void PairEAMAlloyOMP::file2array()
-{
- int i,j,m,n;
- int ntypes = atom->ntypes;
-
- // set function params directly from setfl file
-
- nrho = setfl->nrho;
- nr = setfl->nr;
- drho = setfl->drho;
- dr = setfl->dr;
-
- // ------------------------------------------------------------------
- // setup frho arrays
- // ------------------------------------------------------------------
-
- // allocate frho arrays
- // nfrho = # of setfl elements + 1 for zero array
-
- nfrho = setfl->nelements + 1;
- memory->destroy(frho);
- memory->create(frho,nfrho,nrho+1,"pair:frho");
-
- // copy each element's frho to global frho
-
- for (i = 0; i < setfl->nelements; i++)
- for (m = 1; m <= nrho; m++) frho[i][m] = setfl->frho[i][m];
-
- // add extra frho of zeroes for non-EAM types to point to (pair hybrid)
- // this is necessary b/c fp is still computed for non-EAM atoms
-
- for (m = 1; m <= nrho; m++) frho[nfrho-1][m] = 0.0;
-
- // type2frho[i] = which frho array (0 to nfrho-1) each atom type maps to
- // if atom type doesn't point to element (non-EAM atom in pair hybrid)
- // then map it to last frho array of zeroes
-
- for (i = 1; i <= ntypes; i++)
- if (map[i] >= 0) type2frho[i] = map[i];
- else type2frho[i] = nfrho-1;
-
- // ------------------------------------------------------------------
- // setup rhor arrays
- // ------------------------------------------------------------------
-
- // allocate rhor arrays
- // nrhor = # of setfl elements
-
- nrhor = setfl->nelements;
- memory->destroy(rhor);
- memory->create(rhor,nrhor,nr+1,"pair:rhor");
-
- // copy each element's rhor to global rhor
-
- for (i = 0; i < setfl->nelements; i++)
- for (m = 1; m <= nr; m++) rhor[i][m] = setfl->rhor[i][m];
-
- // type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
- // for setfl files, I,J mapping only depends on I
- // OK if map = -1 (non-EAM atom in pair hybrid) b/c type2rhor not used
-
- for (i = 1; i <= ntypes; i++)
- for (j = 1; j <= ntypes; j++)
- type2rhor[i][j] = map[i];
-
- // ------------------------------------------------------------------
- // setup z2r arrays
- // ------------------------------------------------------------------
-
- // allocate z2r arrays
- // nz2r = N*(N+1)/2 where N = # of setfl elements
-
- nz2r = setfl->nelements * (setfl->nelements+1) / 2;
- memory->destroy(z2r);
- memory->create(z2r,nz2r,nr+1,"pair:z2r");
-
- // copy each element pair z2r to global z2r, only for I >= J
-
- n = 0;
- for (i = 0; i < setfl->nelements; i++)
- for (j = 0; j <= i; j++) {
- for (m = 1; m <= nr; m++) z2r[n][m] = setfl->z2r[i][j][m];
- n++;
- }
-
- // type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
- // set of z2r arrays only fill lower triangular Nelement matrix
- // value = n = sum over rows of lower-triangular matrix until reach irow,icol
- // swap indices when irow < icol to stay lower triangular
- // if map = -1 (non-EAM atom in pair hybrid):
- // type2z2r is not used by non-opt
- // but set type2z2r to 0 since accessed by opt
-
- int irow,icol;
- for (i = 1; i <= ntypes; i++) {
- for (j = 1; j <= ntypes; j++) {
- irow = map[i];
- icol = map[j];
- if (irow == -1 || icol == -1) {
- type2z2r[i][j] = 0;
- continue;
- }
- if (irow < icol) {
- irow = map[j];
- icol = map[i];
- }
- n = 0;
- for (m = 0; m < irow; m++) n += m + 1;
- n += icol;
- type2z2r[i][j] = n;
- }
- }
-}
diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp.orig b/src/USER-OMP/pair_eam_fs_omp.cpp.orig
deleted file mode 100644
index 84101913c5..0000000000
--- a/src/USER-OMP/pair_eam_fs_omp.cpp.orig
+++ /dev/null
@@ -1,332 +0,0 @@
-/* ----------------------------------------------------------------------
- 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.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing authors: Tim Lau (MIT)
-------------------------------------------------------------------------- */
-
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "pair_eam_fs_omp.h"
-#include "atom.h"
-#include "comm.h"
-#include "memory.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-#define MAXLINE 1024
-
-/* ---------------------------------------------------------------------- */
-
-PairEAMFSOMP::PairEAMFSOMP(LAMMPS *lmp) : PairEAMOMP(lmp)
-{
- one_coeff = 1;
-}
-
-/* ----------------------------------------------------------------------
- set coeffs for one or more type pairs
- read EAM Finnis-Sinclair file
-------------------------------------------------------------------------- */
-
-void PairEAMFSOMP::coeff(int narg, char **arg)
-{
- int i,j;
-
- if (!allocated) allocate();
-
- if (narg != 3 + atom->ntypes)
- error->all(FLERR,"Incorrect args for pair coefficients");
-
- // insure I,J args are * *
-
- if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
- error->all(FLERR,"Incorrect args for pair coefficients");
-
- // read EAM Finnis-Sinclair file
-
- if (fs) {
- for (i = 0; i < fs->nelements; i++) delete [] fs->elements[i];
- delete [] fs->elements;
- delete [] fs->mass;
- memory->destroy(fs->frho);
- memory->destroy(fs->rhor);
- memory->destroy(fs->z2r);
- delete fs;
- }
- fs = new Fs();
- read_file(arg[2]);
-
- // read args that map atom types to elements in potential file
- // map[i] = which element the Ith atom type is, -1 if NULL
-
- for (i = 3; i < narg; i++) {
- if (strcmp(arg[i],"NULL") == 0) {
- map[i-2] = -1;
- continue;
- }
- for (j = 0; j < fs->nelements; j++)
- if (strcmp(arg[i],fs->elements[j]) == 0) break;
- if (j < fs->nelements) map[i-2] = j;
- else error->all(FLERR,"No matching element in EAM potential file");
- }
-
- // clear setflag since coeff() called once with I,J = * *
-
- int n = atom->ntypes;
- for (i = 1; i <= n; i++)
- for (j = i; j <= n; j++)
- setflag[i][j] = 0;
-
- // set setflag i,j for type pairs where both are mapped to elements
- // set mass of atom type if i = j
-
- int count = 0;
- for (i = 1; i <= n; i++) {
- for (j = i; j <= n; j++) {
- if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(i,fs->mass[map[i]]);
- count++;
- }
- }
- }
-
- if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
-}
-
-/* ----------------------------------------------------------------------
- read a multi-element DYNAMO setfl file
-------------------------------------------------------------------------- */
-
-void PairEAMFSOMP::read_file(char *filename)
-{
- Fs *file = fs;
-
- // open potential file
-
- int me = comm->me;
- FILE *fptr;
- char line[MAXLINE];
-
- if (me == 0) {
- fptr = fopen(filename,"r");
- if (fptr == NULL) {
- char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
- error->one(FLERR,str);
- }
- }
-
- // read and broadcast header
- // extract element names from nelements line
-
- int n;
- if (me == 0) {
- fgets(line,MAXLINE,fptr);
- fgets(line,MAXLINE,fptr);
- fgets(line,MAXLINE,fptr);
- fgets(line,MAXLINE,fptr);
- n = strlen(line) + 1;
- }
- MPI_Bcast(&n,1,MPI_INT,0,world);
- MPI_Bcast(line,n,MPI_CHAR,0,world);
-
- sscanf(line,"%d",&file->nelements);
- int nwords = atom->count_words(line);
- if (nwords != file->nelements + 1)
- error->all(FLERR,"Incorrect element names in EAM potential file");
-
- char **words = new char*[file->nelements+1];
- nwords = 0;
- strtok(line," \t\n\r\f");
- while (words[nwords++] = strtok(NULL," \t\n\r\f")) continue;
-
- file->elements = new char*[file->nelements];
- for (int i = 0; i < file->nelements; i++) {
- n = strlen(words[i]) + 1;
- file->elements[i] = new char[n];
- strcpy(file->elements[i],words[i]);
- }
- delete [] words;
-
- if (me == 0) {
- fgets(line,MAXLINE,fptr);
- sscanf(line,"%d %lg %d %lg %lg",
- &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
- }
-
- MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
- MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&file->nr,1,MPI_INT,0,world);
- MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
- MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
-
- file->mass = new double[file->nelements];
- memory->create(file->frho,file->nelements,file->nrho+1,
- "pair:frho");
- memory->create(file->rhor,file->nelements,file->nelements,
- file->nr+1,"pair:rhor");
- memory->create(file->z2r,file->nelements,file->nelements,
- file->nr+1,"pair:z2r");
-
- int i,j,tmp;
- for (i = 0; i < file->nelements; i++) {
- if (me == 0) {
- fgets(line,MAXLINE,fptr);
- sscanf(line,"%d %lg",&tmp,&file->mass[i]);
- }
- MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
-
- if (me == 0) grab(fptr,file->nrho,&file->frho[i][1]);
- MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
-
- for (j = 0; j < file->nelements; j++) {
- if (me == 0) grab(fptr,file->nr,&file->rhor[i][j][1]);
- MPI_Bcast(&file->rhor[i][j][1],file->nr,MPI_DOUBLE,0,world);
- }
- }
-
- for (i = 0; i < file->nelements; i++)
- for (j = 0; j <= i; j++) {
- if (me == 0) grab(fptr,file->nr,&file->z2r[i][j][1]);
- MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
- }
-
- // close the potential file
-
- if (me == 0) fclose(fptr);
-}
-
-/* ----------------------------------------------------------------------
- copy read-in setfl potential to standard array format
-------------------------------------------------------------------------- */
-
-void PairEAMFSOMP::file2array()
-{
- int i,j,m,n;
- int ntypes = atom->ntypes;
-
- // set function params directly from fs file
-
- nrho = fs->nrho;
- nr = fs->nr;
- drho = fs->drho;
- dr = fs->dr;
-
- // ------------------------------------------------------------------
- // setup frho arrays
- // ------------------------------------------------------------------
-
- // allocate frho arrays
- // nfrho = # of fs elements + 1 for zero array
-
- nfrho = fs->nelements + 1;
- memory->destroy(frho);
- memory->create(frho,nfrho,nrho+1,"pair:frho");
-
- // copy each element's frho to global frho
-
- for (i = 0; i < fs->nelements; i++)
- for (m = 1; m <= nrho; m++) frho[i][m] = fs->frho[i][m];
-
- // add extra frho of zeroes for non-EAM types to point to (pair hybrid)
- // this is necessary b/c fp is still computed for non-EAM atoms
-
- for (m = 1; m <= nrho; m++) frho[nfrho-1][m] = 0.0;
-
- // type2frho[i] = which frho array (0 to nfrho-1) each atom type maps to
- // if atom type doesn't point to element (non-EAM atom in pair hybrid)
- // then map it to last frho array of zeroes
-
- for (i = 1; i <= ntypes; i++)
- if (map[i] >= 0) type2frho[i] = map[i];
- else type2frho[i] = nfrho-1;
-
- // ------------------------------------------------------------------
- // setup rhor arrays
- // ------------------------------------------------------------------
-
- // allocate rhor arrays
- // nrhor = square of # of fs elements
-
- nrhor = fs->nelements * fs->nelements;
- memory->destroy(rhor);
- memory->create(rhor,nrhor,nr+1,"pair:rhor");
-
- // copy each element pair rhor to global rhor
-
- n = 0;
- for (i = 0; i < fs->nelements; i++)
- for (j = 0; j < fs->nelements; j++) {
- for (m = 1; m <= nr; m++) rhor[n][m] = fs->rhor[i][j][m];
- n++;
- }
-
- // type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
- // for fs files, there is a full NxN set of rhor arrays
- // OK if map = -1 (non-EAM atom in pair hybrid) b/c type2rhor not used
-
- for (i = 1; i <= ntypes; i++)
- for (j = 1; j <= ntypes; j++)
- type2rhor[i][j] = map[i] * fs->nelements + map[j];
-
- // ------------------------------------------------------------------
- // setup z2r arrays
- // ------------------------------------------------------------------
-
- // allocate z2r arrays
- // nz2r = N*(N+1)/2 where N = # of fs elements
-
- nz2r = fs->nelements * (fs->nelements+1) / 2;
- memory->destroy(z2r);
- memory->create(z2r,nz2r,nr+1,"pair:z2r");
-
- // copy each element pair z2r to global z2r, only for I >= J
-
- n = 0;
- for (i = 0; i < fs->nelements; i++)
- for (j = 0; j <= i; j++) {
- for (m = 1; m <= nr; m++) z2r[n][m] = fs->z2r[i][j][m];
- n++;
- }
-
- // type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
- // set of z2r arrays only fill lower triangular Nelement matrix
- // value = n = sum over rows of lower-triangular matrix until reach irow,icol
- // swap indices when irow < icol to stay lower triangular
- // if map = -1 (non-EAM atom in pair hybrid):
- // type2z2r is not used by non-opt
- // but set type2z2r to 0 since accessed by opt
-
- int irow,icol;
- for (i = 1; i <= ntypes; i++) {
- for (j = 1; j <= ntypes; j++) {
- irow = map[i];
- icol = map[j];
- if (irow == -1 || icol == -1) {
- type2z2r[i][j] = 0;
- continue;
- }
- if (irow < icol) {
- irow = map[j];
- icol = map[i];
- }
- n = 0;
- for (m = 0; m < irow; m++) n += m + 1;
- n += icol;
- type2z2r[i][j] = n;
- }
- }
-}
diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp.orig b/src/USER-OMP/pair_tersoff_zbl_omp.cpp.orig
deleted file mode 100644
index 9c0f397118..0000000000
--- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp.orig
+++ /dev/null
@@ -1,297 +0,0 @@
-/* ----------------------------------------------------------------------
- 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.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing author: Aidan Thompson (SNL) - original Tersoff implementation
- David Farrell (NWU) - ZBL addition
-------------------------------------------------------------------------- */
-
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "pair_tersoff_zbl_omp.h"
-#include "atom.h"
-#include "update.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "force.h"
-#include "comm.h"
-#include "memory.h"
-#include "error.h"
-
-#include "math_const.h"
-#include "math_special.h"
-using namespace LAMMPS_NS;
-using namespace MathConst;
-using namespace MathSpecial;
-
-#define MAXLINE 1024
-#define DELTA 4
-
-/* ----------------------------------------------------------------------
- Fermi-like smoothing function
-------------------------------------------------------------------------- */
-
-static double F_fermi(const double r, const double expsc, const double cut)
-{
- return 1.0 / (1.0 + exp(-expsc*(r-cut)));
-}
-
-/* ----------------------------------------------------------------------
- Fermi-like smoothing function derivative with respect to r
-------------------------------------------------------------------------- */
-
-static double F_fermi_d(const double r, const double expsc, const double cut)
-{
- return expsc*exp(-expsc*(r-cut)) / square(1.0 + exp(-expsc*(r-cut)));
-}
-
-/* ---------------------------------------------------------------------- */
-
-PairTersoffZBLOMP::PairTersoffZBLOMP(LAMMPS *lmp) : PairTersoffOMP(lmp)
-{
- // hard-wired constants in metal or real units
- // a0 = Bohr radius
- // epsilon0 = permittivity of vacuum = q / energy-distance units
- // e = unit charge
- // 1 Kcal/mole = 0.043365121 eV
-
- if (strcmp(update->unit_style,"metal") == 0) {
- global_a_0 = 0.529;
- global_epsilon_0 = 0.00552635;
- global_e = 1.0;
- } else if (strcmp(update->unit_style,"real") == 0) {
- global_a_0 = 0.529;
- global_epsilon_0 = 0.00552635 * 0.043365121;
- global_e = 1.0;
- } else error->all(FLERR,"Pair tersoff/zbl requires metal or real units");
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairTersoffZBLOMP::read_file(char *file)
-{
- int params_per_line = 21;
- char **words = new char*[params_per_line+1];
-
- memory->sfree(params);
- params = NULL;
- nparams = 0;
-
- // open file on proc 0
-
- FILE *fp;
- if (comm->me == 0) {
- fp = fopen(file,"r");
- if (fp == NULL) {
- char str[128];
- sprintf(str,"Cannot open Tersoff potential file %s",file);
- error->one(FLERR,str);
- }
- }
-
- // read each line out of file, skipping blank lines or leading '#'
- // store line of params if all 3 element tags are in element list
-
- int n,nwords,ielement,jelement,kelement;
- char line[MAXLINE],*ptr;
- int eof = 0;
-
- while (1) {
- if (comm->me == 0) {
- ptr = fgets(line,MAXLINE,fp);
- if (ptr == NULL) {
- eof = 1;
- fclose(fp);
- } else n = strlen(line) + 1;
- }
- MPI_Bcast(&eof,1,MPI_INT,0,world);
- if (eof) break;
- MPI_Bcast(&n,1,MPI_INT,0,world);
- MPI_Bcast(line,n,MPI_CHAR,0,world);
-
- // strip comment, skip line if blank
-
- if (ptr = strchr(line,'#')) *ptr = '\0';
- nwords = atom->count_words(line);
- if (nwords == 0) continue;
-
- // concatenate additional lines until have params_per_line words
-
- while (nwords < params_per_line) {
- n = strlen(line);
- if (comm->me == 0) {
- ptr = fgets(&line[n],MAXLINE-n,fp);
- if (ptr == NULL) {
- eof = 1;
- fclose(fp);
- } else n = strlen(line) + 1;
- }
- MPI_Bcast(&eof,1,MPI_INT,0,world);
- if (eof) break;
- MPI_Bcast(&n,1,MPI_INT,0,world);
- MPI_Bcast(line,n,MPI_CHAR,0,world);
- if (ptr = strchr(line,'#')) *ptr = '\0';
- nwords = atom->count_words(line);
- }
-
- if (nwords != params_per_line)
- error->all(FLERR,"Incorrect format in Tersoff potential file");
-
- // words = ptrs to all words in line
-
- nwords = 0;
- words[nwords++] = strtok(line," \t\n\r\f");
- while (words[nwords++] = strtok(NULL," \t\n\r\f")) continue;
-
- // ielement,jelement,kelement = 1st args
- // if all 3 args are in element list, then parse this line
- // else skip to next line
-
- for (ielement = 0; ielement < nelements; ielement++)
- if (strcmp(words[0],elements[ielement]) == 0) break;
- if (ielement == nelements) continue;
- for (jelement = 0; jelement < nelements; jelement++)
- if (strcmp(words[1],elements[jelement]) == 0) break;
- if (jelement == nelements) continue;
- for (kelement = 0; kelement < nelements; kelement++)
- if (strcmp(words[2],elements[kelement]) == 0) break;
- if (kelement == nelements) continue;
-
- // load up parameter settings and error check their values
-
- if (nparams == maxparam) {
- maxparam += DELTA;
- params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
- }
-
- params[nparams].ielement = ielement;
- params[nparams].jelement = jelement;
- params[nparams].kelement = kelement;
- params[nparams].powerm = atof(words[3]);
- params[nparams].gamma = atof(words[4]);
- params[nparams].lam3 = atof(words[5]);
- params[nparams].c = atof(words[6]);
- params[nparams].d = atof(words[7]);
- params[nparams].h = atof(words[8]);
- params[nparams].powern = atof(words[9]);
- params[nparams].beta = atof(words[10]);
- params[nparams].lam2 = atof(words[11]);
- params[nparams].bigb = atof(words[12]);
- params[nparams].bigr = atof(words[13]);
- params[nparams].bigd = atof(words[14]);
- params[nparams].lam1 = atof(words[15]);
- params[nparams].biga = atof(words[16]);
- params[nparams].Z_i = atof(words[17]);
- params[nparams].Z_j = atof(words[18]);
- params[nparams].ZBLcut = atof(words[19]);
- params[nparams].ZBLexpscale = atof(words[20]);
-
- // currently only allow m exponent of 1 or 3
-
- params[nparams].powermint = int(params[nparams].powerm);
-
- if (
- params[nparams].lam3 < 0.0 || params[nparams].c < 0.0 ||
- params[nparams].d < 0.0 || params[nparams].powern < 0.0 ||
- params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
- params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
- params[nparams].bigd < 0.0 ||
- params[nparams].bigd > params[nparams].bigr ||
- params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
- params[nparams].powerm - params[nparams].powermint != 0.0 ||
- (params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
- params[nparams].gamma < 0.0 ||
- params[nparams].Z_i < 1.0 || params[nparams].Z_j < 1.0 ||
- params[nparams].ZBLcut < 0.0 || params[nparams].ZBLexpscale < 0.0)
- error->all(FLERR,"Illegal Tersoff parameter");
-
- nparams++;
- }
-
- delete [] words;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairTersoffZBLOMP::force_zeta(Param *param, double rsq, double zeta_ij,
- double &fforce, double &prefactor,
- int eflag, double &eng)
-{
- double r,fa,fa_d,bij;
-
- r = sqrt(rsq);
-
- fa = (r > param->bigr + param->bigd) ? 0.0 :
- -param->bigb * exp(-param->lam2 * r) * ters_fc(r,param) *
- F_fermi(r,param->ZBLexpscale,param->ZBLcut);
-
- fa_d = (r > param->bigr + param->bigd) ? 0.0 :
- param->bigb * exp(-param->lam2 * r) *
- (param->lam2 * ters_fc(r,param) *
- F_fermi(r,param->ZBLexpscale,param->ZBLcut) -
- ters_fc_d(r,param) * F_fermi(r,param->ZBLexpscale,param->ZBLcut)
- - ters_fc(r,param) * F_fermi_d(r,param->ZBLexpscale,param->ZBLcut));
-
- bij = ters_bij(zeta_ij,param);
- fforce = 0.5*bij*fa_d / r;
- prefactor = -0.5*fa * ters_bij_d(zeta_ij,param);
- if (eflag) eng = 0.5*bij*fa;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairTersoffZBLOMP::repulsive(Param *param, double rsq, double &fforce,
- int eflag, double &eng)
-{
- double r,tmp_fc,tmp_fc_d,tmp_exp;
-
- // Tersoff repulsive portion
-
- r = sqrt(rsq);
- tmp_fc = ters_fc(r,param);
- tmp_fc_d = ters_fc_d(r,param);
- tmp_exp = exp(-param->lam1 * r);
- double fforce_ters = param->biga * tmp_exp * (tmp_fc_d - tmp_fc*param->lam1);
- double eng_ters = tmp_fc * param->biga * tmp_exp;
-
- // ZBL repulsive portion
-
- double esq = square(global_e);
- double a_ij = (0.8854*global_a_0) /
- (pow(param->Z_i,0.23) + pow(param->Z_j,0.23));
- double premult = (param->Z_i * param->Z_j * esq)/(4.0*MY_PI*global_epsilon_0);
- double r_ov_a = r/a_ij;
- double phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
- 0.2802*exp(-0.4029*r_ov_a) + 0.02817*exp(-0.2016*r_ov_a);
- double dphi = (1.0/a_ij) * (-3.2*0.1818*exp(-3.2*r_ov_a) -
- 0.9423*0.5099*exp(-0.9423*r_ov_a) -
- 0.4029*0.2802*exp(-0.4029*r_ov_a) -
- 0.2016*0.02817*exp(-0.2016*r_ov_a));
- double fforce_ZBL = premult*-rsq* phi + premult/r*dphi;
- double eng_ZBL = premult/r*phi;
-
- // combine two parts with smoothing by Fermi-like function
-
- fforce = -(-F_fermi_d(r,param->ZBLexpscale,param->ZBLcut) * eng_ZBL +
- (1.0 - F_fermi(r,param->ZBLexpscale,param->ZBLcut))*fforce_ZBL +
- F_fermi_d(r,param->ZBLexpscale,param->ZBLcut)*eng_ters +
- F_fermi(r,param->ZBLexpscale,param->ZBLcut)*fforce_ters) / r;
-
- if (eflag)
- eng = (1.0 - F_fermi(r,param->ZBLexpscale,param->ZBLcut))*eng_ZBL +
- F_fermi(r,param->ZBLexpscale,param->ZBLcut)*eng_ters;
-}
--
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