From 9cd994f57c701c7e28cc82c38c20edfd0a5cedc2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 9 May 2017 15:35:48 -0400
Subject: [PATCH] fix issues with potential file parser
- use Force::open_potential()
- replace ftell()/fseek() with rewind()/fgets() which is safer on windows and other platforms with automatic CR/LF to LF conversion on text files
- make parser use properly NULL terminated strings through using strtok()
---
src/USER-MISC/pair_meam_spline.cpp | 52 ++++++++++++++++--------------
1 file changed, 27 insertions(+), 25 deletions(-)
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index 6fbff31753..e2f9209685 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -45,9 +45,6 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
-#include <iostream>
-
-using namespace std;
using namespace LAMMPS_NS;
@@ -449,7 +446,7 @@ void PairMEAMSpline::read_file(const char* filename)
int nmultichoose2; // = (n+1)*n/2;
if(comm->me == 0) {
- FILE *fp = fopen(filename, "r");
+ FILE *fp = force->open_potential(filename);
if(fp == NULL) {
char str[1024];
sprintf(str,"Cannot open spline MEAM potential file %s", filename);
@@ -458,31 +455,35 @@ void PairMEAMSpline::read_file(const char* filename)
// Skip first line of file. It's a comment.
char line[MAXLINE];
+ char *ptr;
fgets(line, MAXLINE, fp);
- // Second line holds potential type ("meam/spline") in new potential format.
- bool isNewFormat;
- long loc = ftell(fp);
+ // Second line holds potential type ("meam/spline")
+ // in new potential format.
+
+ bool isNewFormat = false;
fgets(line, MAXLINE, fp);
- if (strncmp(line, "meam/spline", 11) == 0) {
+ ptr = strtok(line, " \t\n\r\f");
+
+ if (strcmp(ptr, "meam/spline") == 0) {
isNewFormat = true;
// parse the rest of the line!
- char *linep = line+12, *word;
- const char *sep = " ,;:-\t\n"; // overkill, but safe
- word = strsep(&linep, sep);
- if (! *word)
- error->one(FLERR, "Need to include number of atomic species on meam/spline line in potential file");
- int n = atoi(word);
- if (n<1)
- error->one(FLERR, "Invalid number of atomic species on meam/spline line in potential file");
- nelements = n;
- elements = new char*[n];
- for (int i=0; i<n; ++i) {
- word = strsep(&linep, sep);
- if (! *word)
- error->one(FLERR, "Not enough atomic species in meam/spline\n");
- elements[i] = new char[strlen(word)+1];
- strcpy(elements[i], word);
+ ptr = strtok(NULL," \t\n\r\f");
+ if (ptr == NULL)
+ error->one(FLERR,"Need to include number of atomic species on"
+ " meam/spline line in multi-element potential file");
+ nelements = atoi(ptr);
+ if (nelements < 1)
+ error->one(FLERR, "Invalid number of atomic species on"
+ " meam/spline line in potential file");
+ elements = new char*[nelements];
+ for (int i=0; i<nelements; ++i) {
+ ptr = strtok(NULL," \t\n\r\f");
+ if (ptr == NULL)
+ error->one(FLERR, "Not enough atomic species in meam/spline"
+ " line of multi-element potential file");
+ elements[i] = new char[strlen(ptr)+1];
+ strcpy(elements[i], ptr);
}
} else {
isNewFormat = false;
@@ -490,7 +491,8 @@ void PairMEAMSpline::read_file(const char* filename)
elements = new char*[1];
elements[0] = new char[1];
strcpy(elements[0], "");
- fseek(fp, loc, SEEK_SET);
+ rewind(fp);
+ fgets(line, MAXLINE, fp);
}
nmultichoose2 = ((nelements+1)*nelements)/2;
--
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