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Fix a few more issues resulting from "nelements != atom->types" 

this also detects in a more safely fashion, whether there is data in the second part of the input file, that is still formatted for he first part.
This commit is contained in:
Axel Kohlmeyer 2019-06-05 17:11:53 -04:00 committed by GitHub
parent e9b4ab7363
commit 40a2f275c2
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GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 27 additions and 19 deletions
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46
src/USER-MISC/pair_extep.cpp
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@ -19,6 +19,7 @@
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <cctype>
#include "pair_extep.h"
#include "atom.h"
#include "neighbor.h"
@ -653,15 +654,15 @@ void PairExTeP::read_file(char *file)
// if all 3 args are in element list, then parse this line
// else skip to next line
for (ielement = 0; ielement < atom->ntypes; ielement++)
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == atom->ntypes) continue;
for (jelement = 0; jelement < atom->ntypes; jelement++)
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jelement == atom->ntypes) continue;
for (kelement = 0; kelement < atom->ntypes; kelement++)
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (strcmp(words[2],elements[kelement]) == 0) break;
if (kelement == atom->ntypes) continue;
if (kelement == nelements) continue;
// load up parameter settings and error check their values
@ -746,17 +747,24 @@ void PairExTeP::read_file(char *file)
nwords = atom->count_words(line);
if (nwords == 0) continue;
//skip a line if it is an unused single entry
if (nwords == 17) continue;
if (nwords != params_per_line)
error->all(FLERR,"Incorrect format in ExTeP 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;
while ((nwords < params_per_line)
&& (words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
// skip line if it is a leftover from the previous section,
// which can be identified by having 3 elements (instead of 2)
// as first words.
if (isupper(words[0][0]) && isupper(words[1][0]) && isupper(words[2][0]))
continue;
// need to have two elements followed by a number in each line
if (!(isupper(words[0][0]) && isupper(words[1][0])
&& !isupper(words[2][0])))
error->all(FLERR,"Incorrect format in ExTeP potential file");
// ielement,jelement = 1st args
// if all 3 args are in element list, then parse this line
@ -764,12 +772,12 @@ void PairExTeP::read_file(char *file)
// these lines set ielement and jelement to the
// integers matching the strings from the input
for (ielement = 0; ielement < atom->ntypes; ielement++)
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == atom->ntypes) continue;
for (jelement = 0; jelement < atom->ntypes; jelement++)
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jelement == atom->ntypes) continue;
if (jelement == nelements) continue;
int Ni = atoi(words[2]);
int Nj = atoi(words[3]);
@ -1077,8 +1085,8 @@ void PairExTeP::costheta_d(double *rij_hat, double rij,
// initialize spline for F_corr (based on PairLCBOP::F_conj)
void PairExTeP::spline_init() {
for ( int iel=0; iel<atom->ntypes; iel++) {
for ( int jel=0; jel<atom->ntypes; jel++) {
for ( int iel=0; iel<nelements; iel++) {
for ( int jel=0; jel<nelements; jel++) {
for ( int N_ij=0; N_ij<4; N_ij++ ) {
for ( int N_ji=0; N_ji<4; N_ji++ ) {
TF_corr_param &f = F_corr_param[iel][jel][N_ij][N_ji];