update potential file parser in pair style extep
This commit is contained in:
Axel Kohlmeyer
1
examples/PACKAGES/extep/BN.extep
Symbolic link
1
examples/PACKAGES/extep/BN.extep
Symbolic link
@ -0,0 +1 @@
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../../../potentials/BN.extep
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@ -14,10 +14,10 @@ B B B 3 1.0 0.0 26617.3000 141.2000 -0.1300 1.1422470 0.01498
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N N N 3 1.0 0.0 23.5000 3.7500 -0.4000 0.6650000 0.01925100 2.6272721 2563.5603417 2.0 0.2 2.8293093 2978.9527928
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B B N 3 1.0 0.0 26617.3000 141.2000 -0.1300 1.1422470 0.01498959 2.5211820 2768.7363631 2.0 0.2 2.6857244 3376.3350735
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N N B 3 1.0 0.0 23.5000 3.7500 -0.4000 0.6650000 0.01925100 2.6272721 2563.5603417 2.0 0.2 2.8293093 2978.9527928
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B N B 3 1.0 0.0d0 306.586555205d0 10.d0 -0.7218d0 0.6576543657d0 0.0027024851d0 2.69335d0 2595.6860833266d0 2.d0 0.2d0 2.95d0 3330.0655849887d0
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B N N 3 1.0 0.0d0 306.586555205d0 10.d0 -0.7218d0 0.6576543657d0 0.0027024851d0 2.69335d0 2595.6860833266d0 2.d0 0.2d0 2.95d0 3330.0655849887d0
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N B B 3 1.0 0.0d0 306.586555205d0 10.d0 -0.7218d0 0.6576543657d0 0.0027024851d0 2.69335d0 2595.6860833266d0 2.d0 0.2d0 2.95d0 3330.0655849887d0
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N B N 3 1.0 0.0d0 306.586555205d0 10.d0 -0.7218d0 0.6576543657d0 0.0027024851d0 2.69335d0 2595.6860833266d0 2.d0 0.2d0 2.95d0 3330.0655849887d0
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B N B 3 1.0 0.0 306.586555205 10. -0.7218 0.6576543657 0.0027024851 2.69335 2595.6860833266 2. 0.2 2.95 3330.0655849887
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B N N 3 1.0 0.0 306.586555205 10. -0.7218 0.6576543657 0.0027024851 2.69335 2595.6860833266 2. 0.2 2.95 3330.0655849887
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N B B 3 1.0 0.0 306.586555205 10. -0.7218 0.6576543657 0.0027024851 2.69335 2595.6860833266 2. 0.2 2.95 3330.0655849887
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N B N 3 1.0 0.0 306.586555205 10. -0.7218 0.6576543657 0.0027024851 2.69335 2595.6860833266 2. 0.2 2.95 3330.0655849887
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#
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# 1.9925 Bicubic Splines Parameters
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#
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@ -28,6 +28,7 @@
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#include "my_page.h"
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#include "neigh_list.h"
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#include "neighbor.h"
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#include "potential_file_reader.h"
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#include <cmath>
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#include <cstring>
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@ -511,234 +512,177 @@ double PairExTeP::init_one(int i, int j)
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void PairExTeP::read_file(char *file)
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{
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int params_per_line = 17;
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char **words = new char*[params_per_line+1];
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memory->sfree(params);
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params = nullptr;
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nparams = maxparam = 0;
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// open file on proc 0
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FILE *fp;
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if (comm->me == 0) {
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fp = utils::open_potential(file,lmp,nullptr);
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if (fp == nullptr)
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error->one(FLERR,"Cannot open ExTeP potential file {}: {}",file,utils::getsyserror());
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}
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PotentialFileReader reader(lmp, file, "ExTeP", unit_convert_flag);
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char *line;
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// read each line out of file, skipping blank lines or leading '#'
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// store line of params if all 3 element tags are in element list
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// transparently convert units for supported conversions
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int n,nwords,ielement,jelement,kelement;
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char line[MAXLINE],*ptr;
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int eof = 0;
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int unit_convert = reader.get_unit_convert();
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double conversion_factor = utils::get_conversion_factor(utils::ENERGY,unit_convert);
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while (true) {
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if (comm->me == 0) {
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ptr = fgets(line,MAXLINE,fp);
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if (ptr == nullptr) {
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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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while ((line = reader.next_line(17))) {
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try {
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ValueTokenizer values(line);
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// strip comment, skip line if blank
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std::string iname = values.next_string();
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std::string jname = values.next_string();
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std::string kname = values.next_string();
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if ((ptr = strchr(line,'#'))) *ptr = '\0';
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nwords = utils::count_words(line);
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if (nwords == 0) continue;
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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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int ielement, jelement, kelement;
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// concatenate additional lines until have params_per_line words
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for (ielement = 0; ielement < nelements; ielement++)
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if (iname == elements[ielement]) break;
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if (ielement == nelements) continue;
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for (jelement = 0; jelement < nelements; jelement++)
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if (jname == elements[jelement]) break;
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if (jelement == nelements) continue;
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for (kelement = 0; kelement < nelements; kelement++)
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if (kname == elements[kelement]) break;
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if (kelement == nelements) continue;
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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 == nullptr) {
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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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// load up parameter settings and error check their values
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if (nparams == maxparam) {
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maxparam += DELTA;
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params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params");
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// make certain all addional allocated storage is initialized
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// to avoid false positives when checking with valgrind
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memset(params + nparams, 0, DELTA*sizeof(Param));
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}
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params[nparams].ielement = ielement;
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params[nparams].jelement = jelement;
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params[nparams].kelement = kelement;
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params[nparams].powerm = values.next_double();
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params[nparams].gamma = values.next_double();
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params[nparams].lam3 = values.next_double();
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params[nparams].c = values.next_double();
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params[nparams].d = values.next_double();
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params[nparams].h = values.next_double();
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params[nparams].powern = values.next_double();
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params[nparams].beta = values.next_double();
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params[nparams].lam2 = values.next_double();
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params[nparams].bigb = values.next_double();
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params[nparams].bigr = values.next_double();
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params[nparams].bigd = values.next_double();
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params[nparams].lam1 = values.next_double();
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params[nparams].biga = values.next_double();
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// currently only allow m exponent of 1 or 3
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params[nparams].powermint = int(params[nparams].powerm);
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if (unit_convert) {
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params[nparams].biga *= conversion_factor;
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params[nparams].bigb *= conversion_factor;
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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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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 = utils::count_words(line);
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if (params[nparams].c < 0.0 ||
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params[nparams].d < 0.0 ||
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params[nparams].powern < 0.0 ||
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params[nparams].beta < 0.0 ||
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params[nparams].lam2 < 0.0 ||
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params[nparams].bigb < 0.0 ||
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params[nparams].bigr < 0.0 ||
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params[nparams].bigd < 0.0 ||
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params[nparams].bigd > params[nparams].bigr ||
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params[nparams].lam1 < 0.0 ||
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params[nparams].biga < 0.0 ||
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params[nparams].powerm - params[nparams].powermint != 0.0 ||
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(params[nparams].powermint != 3 &&
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params[nparams].powermint != 1) ||
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params[nparams].gamma < 0.0)
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error->one(FLERR,"Illegal ExTeP parameter");
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nparams++;
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if (nparams >= pow(nelements,3)) break;
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}
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if (nwords != params_per_line)
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error->all(FLERR,"Insufficient spline parameters in potential file");
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/* F_IJ (3) */
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// initialize F_corr_data to all zeros
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for (int iel=0; iel < nelements; iel++)
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for (int jel=0; jel < nelements; jel++)
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for (int in=0; in < 4; in++)
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for (int jn=0; jn < 4; jn++)
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for (int ivar=0; ivar < 3; ivar++)
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F_corr_data[iel][jel][in][jn][ivar]=0;
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// words = ptrs to all words in line
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// read the spline coefficients
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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(nullptr," \t\n\r\f"))) continue;
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while ((line = reader.next_line(8))) {
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try {
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ValueTokenizer values(line);
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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 line
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std::string iname = values.next_string();
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std::string jname = values.next_string();
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std::string kname = values.next_string();
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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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// ielement,jelement = 1st args
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// if all 2 args are in element list, then parse this line
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// else skip to next entry in file
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int ielement, jelement;
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// load up parameter settings and error check their values
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for (ielement = 0; ielement < nelements; ielement++)
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if (iname == elements[ielement]) break;
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if (ielement == nelements) continue;
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for (jelement = 0; jelement < nelements; jelement++)
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if (jname == elements[jelement]) break;
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if (jelement == nelements) continue;
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if (nparams == maxparam) {
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maxparam += DELTA;
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params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
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"pair:params");
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// skip line if it is a leftover from the previous section,
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// which can be identified by having 3 elements (instead of 2)
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// as first words.
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// make certain all addional allocated storage is initialized
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// to avoid false positives when checking with valgrind
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if (!utils::is_integer(kname))
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continue;
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memset(params + nparams, 0, DELTA*sizeof(Param));
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}
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int Ni = atoi(kname.c_str());
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int Nj = values.next_int();
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double spline_val = values.next_double();
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double spline_derx = values.next_double();
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double spline_dery = values.next_double();
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params[nparams].ielement = ielement;
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params[nparams].jelement = jelement;
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params[nparams].kelement = kelement;
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params[nparams].powerm = atof(words[3]);
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params[nparams].gamma = atof(words[4]);
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params[nparams].lam3 = atof(words[5]);
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params[nparams].c = atof(words[6]);
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params[nparams].d = atof(words[7]);
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params[nparams].h = atof(words[8]);
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params[nparams].powern = atof(words[9]);
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params[nparams].beta = atof(words[10]);
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params[nparams].lam2 = atof(words[11]);
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params[nparams].bigb = atof(words[12]);
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params[nparams].bigr = atof(words[13]);
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params[nparams].bigd = atof(words[14]);
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params[nparams].lam1 = atof(words[15]);
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params[nparams].biga = atof(words[16]);
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// Set value for all pairs of ielement,jelement (any kelement)
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for (int iparam = 0; iparam < nparams; iparam++) {
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if ( ielement == params[iparam].ielement && jelement == params[iparam].jelement) {
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F_corr_data[ielement][jelement][Ni][Nj][0] = spline_val;
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F_corr_data[ielement][jelement][Ni][Nj][1] = spline_derx;
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F_corr_data[ielement][jelement][Ni][Nj][2] = spline_dery;
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// currently only allow m exponent of 1 or 3
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params[nparams].powermint = int(params[nparams].powerm);
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if (params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
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params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
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params[nparams].lam2 < 0.0 || params[nparams].bigb < 0.0 ||
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params[nparams].bigr < 0.0 ||params[nparams].bigd < 0.0 ||
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params[nparams].bigd > params[nparams].bigr ||
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params[nparams].lam1 < 0.0 || params[nparams].biga < 0.0 ||
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params[nparams].powerm - params[nparams].powermint != 0.0 ||
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(params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
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params[nparams].gamma < 0.0)
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error->all(FLERR,"Illegal ExTeP parameter");
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nparams++;
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if (nparams >= pow(nelements,3)) break;
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}
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// deallocate words array
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delete[] words;
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/* F_IJ (3) */
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// read the spline coefficients
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params_per_line = 8;
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// reallocate with new size
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words = new char*[params_per_line+1];
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// initialize F_corr_data to all zeros
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for (int iel=0;iel<nelements;iel++)
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for (int jel=0;jel<nelements;jel++)
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for (int in=0;in<4;in++)
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for (int jn=0;jn<4;jn++)
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for (int ivar=0;ivar<3;ivar++)
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F_corr_data[iel][jel][in][jn][ivar]=0;
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// loop until EOF
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while (true) {
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if (comm->me == 0) {
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ptr = fgets(line,MAXLINE,fp);
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//fputs(line,stdout);
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if (ptr == nullptr) {
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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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// strip comment, skip line if blank
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if ((ptr = strchr(line,'#'))) *ptr = '\0';
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nwords = utils::count_words(line);
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if (nwords == 0) continue;
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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 ((nwords < params_per_line)
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&& (words[nwords++] = strtok(nullptr," \t\n\r\f"))) continue;
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|
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// skip line if it is a leftover from the previous section,
|
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// which can be identified by having 3 elements (instead of 2)
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// as first words.
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if (isupper(words[0][0]) && isupper(words[1][0]) && isupper(words[2][0]))
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continue;
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// need to have two elements followed by a number in each line
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if (!(isupper(words[0][0]) && isupper(words[1][0])
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&& !isupper(words[2][0])))
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error->all(FLERR,"Incorrect format in ExTeP potential file");
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// ielement,jelement = 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 line
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// these lines set ielement and jelement to the
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// integers matching the strings from the input
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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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int Ni = atoi(words[2]);
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int Nj = atoi(words[3]);
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double spline_val = atof(words[4]);
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double spline_derx = atof(words[5]);
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double spline_dery = atof(words[6]);
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// Set value for all pairs of ielement,jelement (any kelement)
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for (int iparam = 0; iparam < nparams; iparam++) {
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if ( ielement == params[iparam].ielement
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&& jelement == params[iparam].jelement) {
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F_corr_data[ielement][jelement][Ni][Nj][0] = spline_val;
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F_corr_data[ielement][jelement][Ni][Nj][1] = spline_derx;
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F_corr_data[ielement][jelement][Ni][Nj][2] = spline_dery;
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F_corr_data[jelement][ielement][Nj][Ni][0] = spline_val;
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F_corr_data[jelement][ielement][Nj][Ni][1] = spline_dery;
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F_corr_data[jelement][ielement][Nj][Ni][2] = spline_derx;
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F_corr_data[jelement][ielement][Nj][Ni][0] = spline_val;
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F_corr_data[jelement][ielement][Nj][Ni][1] = spline_dery;
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F_corr_data[jelement][ielement][Nj][Ni][2] = spline_derx;
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}
|
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}
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} catch (TokenizerException &e) {
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||||
error->one(FLERR, e.what());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
delete[] words;
|
||||
/* END F_IJ (3) */
|
||||
MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
|
||||
MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
|
||||
|
||||
if (comm->me != 0) {
|
||||
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params");
|
||||
}
|
||||
MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);
|
||||
MPI_Bcast(&F_corr_data[0][0][0][0][0], MAXTYPES*MAXTYPES*NSPLINE*NSPLINE*3, MPI_DOUBLE, 0, world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -428,6 +428,7 @@ void PairTersoff::read_file(char *file)
|
||||
|
||||
int unit_convert = reader.get_unit_convert();
|
||||
double conversion_factor = utils::get_conversion_factor(utils::ENERGY,unit_convert);
|
||||
|
||||
while ((line = reader.next_line(NPARAMS_PER_LINE))) {
|
||||
try {
|
||||
ValueTokenizer values(line);
|
||||
@ -455,8 +456,7 @@ void PairTersoff::read_file(char *file)
|
||||
|
||||
if (nparams == maxparam) {
|
||||
maxparam += DELTA;
|
||||
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
|
||||
"pair:params");
|
||||
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params");
|
||||
|
||||
// make certain all addional allocated storage is initialized
|
||||
// to avoid false positives when checking with valgrind
|
||||
@ -505,7 +505,7 @@ void PairTersoff::read_file(char *file)
|
||||
params[nparams].biga < 0.0 ||
|
||||
params[nparams].powerm - params[nparams].powermint != 0.0 ||
|
||||
(params[nparams].powermint != 3 &&
|
||||
params[nparams].powermint != 1) ||
|
||||
params[nparams].powermint != 1) ||
|
||||
params[nparams].gamma < 0.0)
|
||||
error->one(FLERR,"Illegal Tersoff parameter");
|
||||
|
||||
|
||||
Reference in New Issue
Block a user