Commit e453adaf authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

implemented parser for 1 element potential files

parent 801111a7

src/USER-MISC/pair_agni.cpp

+93 −53
Original line number Diff line number Diff line
@@ -34,6 +34,8 @@ 


using namespace LAMMPS_NS;



#define AGNI_VERSION 1



static const char cite_pair_agni[] =

  "pair agni command:\n\n"

  "@article{botu2015adaptive,\n"
@@ -60,7 +62,8 @@ static const char cite_pair_agni[] = 
  "}\n\n";





#define MAXLINE 1024

#define MAXLINE 10240

#define MAXWORD 40

#define DELTA 4



/* ---------------------------------------------------------------------- */
@@ -90,7 +93,20 @@ PairAGNI::~PairAGNI() 
  if (elements)

    for (int i = 0; i < nelements; i++) delete [] elements[i];

  delete [] elements;

  if (params) {

    for (int i = 0; i < nparams; ++i) {

      int n = params[i].numeta;

      for (int j = 0; j < n; ++j) {

        delete [] params[i].xU[j];

      }

      delete [] params[i].eta;

      delete [] params[i].alpha;

      delete [] params[i].xU;

      delete [] params[i].yU;

    }

    memory->destroy(params);

    params = NULL;

  }



  if (allocated) {

    memory->destroy(setflag);
@@ -295,9 +311,6 @@ double PairAGNI::init_one(int i, int j) 


void PairAGNI::read_file(char *file)

{

  int params_per_line = 14;

  char **words = new char*[params_per_line+1];



  memory->sfree(params);

  params = NULL;

  nparams = 0;
@@ -318,11 +331,13 @@ void PairAGNI::read_file(char *file) 
  // one set of params can span multiple lines

  // store params if all 3 element tags are in element list



  int n,nwords,ielement,jelement,kelement;

  int i,j,n,nwords,curparam,wantdata,numdata;

  char line[MAXLINE],*ptr;

  int eof = 0;

  char **words = new char*[MAXWORD+1];



  while (1) {

    n = 0;

    if (comm->me == 0) {

      ptr = fgets(line,MAXLINE,fp);

      if (ptr == NULL) {
@@ -341,59 +356,84 @@ void PairAGNI::read_file(char *file) 
    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 Stillinger-Weber potential file");

    if (nwords > MAXWORD)

      error->all(FLERR,"Increase MAXWORD and recompile");



    // 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;

    --nwords;



    if ((nwords == 2) && (strcmp(words[0],"generation") == 0)) {

      int ver = atoi(words[1]);

      if (ver != AGNI_VERSION)

        error->all(FLERR,"Incompatible AGNI potential file version");

      if ((ver == 1) && (nelements != 1))

        error->all(FLERR,"Cannot handle multi-element systems with this potential");



    } else if ((nwords == 2) && (strcmp(words[0],"n_elements") == 0)) {

      nparams = atoi(words[1]);

      if ((nparams < 1) || params) // sanity check

        error->all(FLERR,"Invalid AGNI potential file");

      params = memory->create(params,nparams,"pair:params");

      memset(params,0,nparams*sizeof(Param));

      curparam = -1;



    } else if (params && (nwords == nparams+1) && (strcmp(words[0],"element") == 0)) {

      wantdata = -1;

      for (i = 0; i < nparams; ++i) {

        for (j = 0; j < nelements; ++j)

          if (strcmp(words[i+1],elements[j]) == 0) break;

        if (j == nelements) params[nparams].ielement = params[nparams].jelement = -1;

        else params[nparams].ielement = params[nparams].jelement = j;

      }

    } else if (params && (nwords == 2) && (strcmp(words[0],"interaction") == 0)) {

      for (i = 0; i < nparams; ++i)

        if (strcmp(words[1],elements[params[i].ielement]) == 0) curparam = i;

    } else if ((curparam >=0) && (nwords == 1) && (strcmp(words[0],"endVar") == 0)) {

      int numtrain = params[curparam].numtrain;

      int numeta = params[curparam].numeta;

      params[curparam].alpha = new double[numtrain];

      params[curparam].yU = new double[numtrain];

      params[curparam].xU = new double*[numeta];

      for (i = 0; i < numeta; ++i)

        params[curparam].xU[i] = new double[numtrain];

      

      wantdata = curparam;

      curparam = -1;

    } else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"Rc") == 0)) {

      params[curparam].cut = atof(words[1]);

    } else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"Rs") == 0)) {

      ; // ignored

    } else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"neighbors") == 0)) {

      ; // ignored

    } else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"sigma") == 0)) {

      params[curparam].sigma = atof(words[1]);

    } else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"lambda") == 0)) {

      params[curparam].lambda = atof(words[1]);

    } else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"b") == 0)) {

      params[curparam].b = atof(words[1]);

    } else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"n_train") == 0)) {

      params[curparam].numtrain = atoi(words[1]);

    } else if ((curparam >=0) && (nwords > 1) && (strcmp(words[0],"eta") == 0)) {

      params[curparam].numeta = nwords-1;

      params[curparam].eta = new double[nwords-1];

      for (i = 0, j = 1 ; j < nwords; ++i, ++j)

        params[curparam].eta[i] = atof(words[j]);

    } else if (params && (wantdata >=0) && (nwords == params[wantdata].numeta+3)) {

      n = (int) atof(words[0]);

      for (i = 0; i < params[wantdata].numeta; ++i) {

        params[wantdata].xU[i][n] = atof(words[i+1]);

      }

      params[wantdata].yU[n] = atof(words[params[wantdata].numeta+1]);

      params[wantdata].alpha[n] = atof(words[params[wantdata].numeta+2]);

      

    // ielement,jelement,kelement = 1st args

    // if all 3 args are in element list, then parse this line

    // else skip to next entry in file



    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



    params[nparams].ielement = ielement;

    params[nparams].jelement = jelement;

    params[nparams].epsilon = atof(words[3]);

    params[nparams].sigma = atof(words[4]);



    if (params[nparams].epsilon < 0.0 || params[nparams].sigma < 0.0)

      error->all(FLERR,"Illegal AGNI parameter");



    nparams++;

    } else {

      if (comm->me == 0)

        error->warning(FLERR,"Ignoring unknown content in AGNI potential file.");

    }

  }



  delete [] words;

src/USER-MISC/pair_agni.h

+3 −1
Original line number Diff line number Diff line
@@ -35,8 +35,10 @@ class PairAGNI : public Pair { 
  virtual void init_style();



  struct Param {

    double epsilon,sigma;

    double cut,cutsq;

    double *eta,**xU,*yU,*alpha;

    double sigma,lambda,b;

    int numeta,numtrain;

    int ielement,jelement;

  };

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