implemented parser for 1 element potential files
This commit is contained in:
Axel Kohlmeyer
@ -34,6 +34,8 @@
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using namespace LAMMPS_NS;
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#define AGNI_VERSION 1
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static const char cite_pair_agni[] =
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"pair agni command:\n\n"
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"@article{botu2015adaptive,\n"
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@ -60,7 +62,8 @@ static const char cite_pair_agni[] =
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"}\n\n";
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#define MAXLINE 1024
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#define MAXLINE 10240
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#define MAXWORD 40
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#define DELTA 4
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/* ---------------------------------------------------------------------- */
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@ -90,7 +93,20 @@ PairAGNI::~PairAGNI()
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if (elements)
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for (int i = 0; i < nelements; i++) delete [] elements[i];
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delete [] elements;
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memory->destroy(params);
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if (params) {
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for (int i = 0; i < nparams; ++i) {
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int n = params[i].numeta;
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for (int j = 0; j < n; ++j) {
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delete [] params[i].xU[j];
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}
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delete [] params[i].eta;
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delete [] params[i].alpha;
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delete [] params[i].xU;
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delete [] params[i].yU;
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}
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memory->destroy(params);
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params = NULL;
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}
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if (allocated) {
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memory->destroy(setflag);
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@ -295,9 +311,6 @@ double PairAGNI::init_one(int i, int j)
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void PairAGNI::read_file(char *file)
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{
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int params_per_line = 14;
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char **words = new char*[params_per_line+1];
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memory->sfree(params);
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params = NULL;
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nparams = 0;
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@ -318,11 +331,13 @@ void PairAGNI::read_file(char *file)
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// one set of params can span multiple lines
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// store params if all 3 element tags are in element list
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int n,nwords,ielement,jelement,kelement;
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int i,j,n,nwords,curparam,wantdata,numdata;
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char line[MAXLINE],*ptr;
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int eof = 0;
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char **words = new char*[MAXWORD+1];
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while (1) {
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n = 0;
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if (comm->me == 0) {
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ptr = fgets(line,MAXLINE,fp);
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if (ptr == NULL) {
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@ -341,59 +356,84 @@ void PairAGNI::read_file(char *file)
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nwords = atom->count_words(line);
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if (nwords == 0) continue;
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// concatenate additional lines until have params_per_line words
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while (nwords < params_per_line) {
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n = strlen(line);
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if (comm->me == 0) {
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ptr = fgets(&line[n],MAXLINE-n,fp);
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if (ptr == NULL) {
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eof = 1;
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fclose(fp);
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} else n = strlen(line) + 1;
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}
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MPI_Bcast(&eof,1,MPI_INT,0,world);
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if (eof) break;
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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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if ((ptr = strchr(line,'#'))) *ptr = '\0';
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nwords = atom->count_words(line);
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}
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if (nwords != params_per_line)
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error->all(FLERR,"Incorrect format in Stillinger-Weber potential file");
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if (nwords > MAXWORD)
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error->all(FLERR,"Increase MAXWORD and recompile");
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// words = ptrs to all words in line
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nwords = 0;
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words[nwords++] = strtok(line," \t\n\r\f");
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while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
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--nwords;
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// ielement,jelement,kelement = 1st args
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// if all 3 args are in element list, then parse this line
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// else skip to next entry in file
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if ((nwords == 2) && (strcmp(words[0],"generation") == 0)) {
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int ver = atoi(words[1]);
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if (ver != AGNI_VERSION)
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error->all(FLERR,"Incompatible AGNI potential file version");
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if ((ver == 1) && (nelements != 1))
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error->all(FLERR,"Cannot handle multi-element systems with this potential");
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for (ielement = 0; ielement < nelements; ielement++)
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if (strcmp(words[0],elements[ielement]) == 0) break;
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if (ielement == nelements) continue;
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for (jelement = 0; jelement < nelements; jelement++)
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if (strcmp(words[1],elements[jelement]) == 0) break;
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if (jelement == nelements) continue;
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for (kelement = 0; kelement < nelements; kelement++)
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if (strcmp(words[2],elements[kelement]) == 0) break;
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if (kelement == nelements) continue;
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} else if ((nwords == 2) && (strcmp(words[0],"n_elements") == 0)) {
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nparams = atoi(words[1]);
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if ((nparams < 1) || params) // sanity check
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error->all(FLERR,"Invalid AGNI potential file");
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params = memory->create(params,nparams,"pair:params");
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memset(params,0,nparams*sizeof(Param));
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curparam = -1;
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// load up parameter settings and error check their values
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params[nparams].ielement = ielement;
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params[nparams].jelement = jelement;
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params[nparams].epsilon = atof(words[3]);
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params[nparams].sigma = atof(words[4]);
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if (params[nparams].epsilon < 0.0 || params[nparams].sigma < 0.0)
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error->all(FLERR,"Illegal AGNI parameter");
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nparams++;
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} else if (params && (nwords == nparams+1) && (strcmp(words[0],"element") == 0)) {
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wantdata = -1;
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for (i = 0; i < nparams; ++i) {
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for (j = 0; j < nelements; ++j)
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if (strcmp(words[i+1],elements[j]) == 0) break;
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if (j == nelements) params[nparams].ielement = params[nparams].jelement = -1;
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else params[nparams].ielement = params[nparams].jelement = j;
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}
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} else if (params && (nwords == 2) && (strcmp(words[0],"interaction") == 0)) {
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for (i = 0; i < nparams; ++i)
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if (strcmp(words[1],elements[params[i].ielement]) == 0) curparam = i;
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} else if ((curparam >=0) && (nwords == 1) && (strcmp(words[0],"endVar") == 0)) {
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int numtrain = params[curparam].numtrain;
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int numeta = params[curparam].numeta;
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params[curparam].alpha = new double[numtrain];
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params[curparam].yU = new double[numtrain];
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params[curparam].xU = new double*[numeta];
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for (i = 0; i < numeta; ++i)
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params[curparam].xU[i] = new double[numtrain];
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wantdata = curparam;
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curparam = -1;
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} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"Rc") == 0)) {
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params[curparam].cut = atof(words[1]);
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} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"Rs") == 0)) {
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; // ignored
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} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"neighbors") == 0)) {
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; // ignored
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} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"sigma") == 0)) {
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params[curparam].sigma = atof(words[1]);
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} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"lambda") == 0)) {
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params[curparam].lambda = atof(words[1]);
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} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"b") == 0)) {
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params[curparam].b = atof(words[1]);
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} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"n_train") == 0)) {
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params[curparam].numtrain = atoi(words[1]);
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} else if ((curparam >=0) && (nwords > 1) && (strcmp(words[0],"eta") == 0)) {
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params[curparam].numeta = nwords-1;
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params[curparam].eta = new double[nwords-1];
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for (i = 0, j = 1 ; j < nwords; ++i, ++j)
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params[curparam].eta[i] = atof(words[j]);
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} else if (params && (wantdata >=0) && (nwords == params[wantdata].numeta+3)) {
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n = (int) atof(words[0]);
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for (i = 0; i < params[wantdata].numeta; ++i) {
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params[wantdata].xU[i][n] = atof(words[i+1]);
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}
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params[wantdata].yU[n] = atof(words[params[wantdata].numeta+1]);
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params[wantdata].alpha[n] = atof(words[params[wantdata].numeta+2]);
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} else {
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if (comm->me == 0)
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error->warning(FLERR,"Ignoring unknown content in AGNI potential file.");
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}
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}
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delete [] words;
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@ -35,8 +35,10 @@ class PairAGNI : public Pair {
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virtual void init_style();
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struct Param {
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double epsilon,sigma;
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double cut,cutsq;
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double *eta,**xU,*yU,*alpha;
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double sigma,lambda,b;
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int numeta,numtrain;
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int ielement,jelement;
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};
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