forked from lijiext/lammps
Update pair eam alloy
This commit is contained in:
Richard Berger
parent
e08404f53c
commit
fac7b864fc
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@ -24,11 +24,11 @@
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#include "memory.h"
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#include "error.h"
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#include "utils.h"
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#include "tokenizer.h"
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#include "potential_file_reader.h"
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using namespace LAMMPS_NS;
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#define MAXLINE 1024
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/* ---------------------------------------------------------------------- */
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PairEAMAlloy::PairEAMAlloy(LAMMPS *lmp) : PairEAM(lmp)
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@ -61,7 +61,7 @@ void PairEAMAlloy::coeff(int narg, char **arg)
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if (setfl) {
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for (i = 0; i < setfl->nelements; i++) delete [] setfl->elements[i];
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delete [] setfl->elements;
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delete [] setfl->mass;
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memory->destroy(setfl->mass);
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memory->destroy(setfl->frho);
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memory->destroy(setfl->rhor);
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memory->destroy(setfl->z2r);
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@ -117,98 +117,111 @@ void PairEAMAlloy::read_file(char *filename)
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{
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Setfl *file = setfl;
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// open potential file
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// read potential file
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if(comm->me == 0) {
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PotentialFileReader reader(lmp, filename, "EAM");
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int me = comm->me;
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FILE *fptr;
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char line[MAXLINE];
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try {
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char * line = nullptr;
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if (me == 0) {
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fptr = force->open_potential(filename);
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if (fptr == NULL) {
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char str[128];
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snprintf(str,128,"Cannot open EAM potential file %s",filename);
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error->one(FLERR,str);
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reader.skip_line();
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reader.skip_line();
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reader.skip_line();
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// extract element names from nelements line
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line = reader.next_line(1);
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ValueTokenizer values(line);
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file->nelements = values.next_int();
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if (values.count() != file->nelements + 1)
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error->one(FLERR,"Incorrect element names in EAM potential file");
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file->elements = new char*[file->nelements];
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for (int i = 0; i < file->nelements; i++) {
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const std::string word = values.next_string();
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const int n = word.length() + 1;
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file->elements[i] = new char[n];
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strcpy(file->elements[i], word.c_str());
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}
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//
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line = reader.next_line(5);
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values = ValueTokenizer(line);
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file->nrho = values.next_int();
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file->drho = values.next_double();
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file->nr = values.next_int();
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file->dr = values.next_double();
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file->cut = values.next_double();
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if ((file->nrho <= 0) || (file->nr <= 0) || (file->dr <= 0.0))
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error->one(FLERR,"Invalid EAM potential file");
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memory->create(file->mass, file->nelements, "pair:mass");
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memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
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memory->create(file->rhor, file->nelements, file->nr + 1, "pair:rhor");
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memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
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for (int i = 0; i < file->nelements; i++) {
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line = reader.next_line(2);
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values = ValueTokenizer(line);
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values.next_int(); // ignore
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file->mass[i] = values.next_double();
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reader.next_dvector(file->nrho, &file->frho[i][1]);
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reader.next_dvector(file->nr, &file->rhor[i][1]);
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}
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for (int i = 0; i < file->nelements; i++) {
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for (int j = 0; j <= i; j++) {
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reader.next_dvector(file->nr, &file->z2r[i][j][1]);
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}
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}
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} catch (TokenizerException & e) {
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error->one(FLERR, e.what());
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}
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}
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// read and broadcast header
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// extract element names from nelements line
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// broadcast potential information
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MPI_Bcast(&file->nelements, 1, MPI_INT, 0, world);
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int n;
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if (me == 0) {
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utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
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utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
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n = strlen(line) + 1;
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MPI_Bcast(&file->nrho, 1, MPI_INT, 0, world);
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MPI_Bcast(&file->drho, 1, MPI_DOUBLE, 0, world);
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MPI_Bcast(&file->nr, 1, MPI_INT, 0, world);
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MPI_Bcast(&file->dr, 1, MPI_DOUBLE, 0, world);
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MPI_Bcast(&file->cut, 1, MPI_DOUBLE, 0, world);
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// allocate memory on other procs
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if (comm->me != 0) {
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file->elements = new char*[file->nelements];
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for (int i = 0; i < file->nelements; i++) file->elements[i] = nullptr;
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memory->create(file->mass, file->nelements, "pair:mass");
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memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
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memory->create(file->rhor, file->nelements, file->nr + 1, "pair:rhor");
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memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
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}
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MPI_Bcast(&n,1,MPI_INT,0,world);
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MPI_Bcast(line,n,MPI_CHAR,0,world);
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sscanf(line,"%d",&file->nelements);
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int nwords = utils::count_words(line);
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if (nwords != file->nelements + 1)
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error->all(FLERR,"Incorrect element names in EAM potential file");
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char **words = new char*[file->nelements+1];
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nwords = 0;
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strtok(line," \t\n\r\f");
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while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
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file->elements = new char*[file->nelements];
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// broadcast file->elements string array
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for (int i = 0; i < file->nelements; i++) {
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n = strlen(words[i]) + 1;
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file->elements[i] = new char[n];
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strcpy(file->elements[i],words[i]);
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}
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delete [] words;
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if (me == 0) {
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utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
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nwords = sscanf(line,"%d %lg %d %lg %lg",
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&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
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int n = strlen(file->elements[i]) + 1;
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MPI_Bcast(&n, 1, MPI_INT, 0, world);
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if (comm->me != 0) file->elements[i] = new char[n];
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MPI_Bcast(file->elements[i], n, MPI_CHAR, 0, world);
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}
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MPI_Bcast(&nwords,1,MPI_INT,0,world);
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MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
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MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&file->nr,1,MPI_INT,0,world);
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MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
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// broadcast file->mass, frho, rhor
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for (int i = 0; i < file->nelements; i++) {
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MPI_Bcast(&file->mass[i], 1, MPI_DOUBLE, 0, world);
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MPI_Bcast(&file->frho[i][1], file->nrho, MPI_DOUBLE, 0, world);
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MPI_Bcast(&file->rhor[i][1], file->nr, MPI_DOUBLE, 0, world);
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}
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if ((nwords != 5) || (file->nrho <= 0) || (file->nr <= 0) || (file->dr <= 0.0))
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error->all(FLERR,"Invalid EAM potential file");
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file->mass = new double[file->nelements];
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memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
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memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
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memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
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"pair:z2r");
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int i,j,tmp;
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for (i = 0; i < file->nelements; i++) {
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if (me == 0) {
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utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
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sscanf(line,"%d %lg",&tmp,&file->mass[i]);
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// broadcast file->z2r
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for (int i = 0; i < file->nelements; i++) {
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for (int j = 0; j <= i; j++) {
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MPI_Bcast(&file->z2r[i][j][1], file->nr, MPI_DOUBLE, 0, world);
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}
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MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
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if (me == 0) grab(fptr,file->nrho,&file->frho[i][1]);
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MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
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if (me == 0) grab(fptr,file->nr,&file->rhor[i][1]);
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MPI_Bcast(&file->rhor[i][1],file->nr,MPI_DOUBLE,0,world);
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}
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for (i = 0; i < file->nelements; i++)
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for (j = 0; j <= i; j++) {
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if (me == 0) grab(fptr,file->nr,&file->z2r[i][j][1]);
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MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
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}
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// close the potential file
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if (me == 0) fclose(fptr);
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}
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/* ----------------------------------------------------------------------
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