From cf5d80b2ff3e8f594105a92359e711eff288a4ea Mon Sep 17 00:00:00 2001
From: David van der Spoel <spoel@leyster.bmc.uu.se>
Date: Thu, 8 Jul 2010 13:58:37 +0200
Subject: [PATCH] Removed possible SEGVs in rmpbc in case ePBC = No. The code
 in matio.c made me cry. How about this: char *line; snew(line,100); line++;
 sfree(line); This is nowadays detected by glibc. To avoid drastic changes I
 removed the call to free, introducing a memory leak, but this code is used
 only in non-critical xpm2ps AFAIK.

---
 src/gmxlib/matio.c | 25 +++++++++++--------------
 src/gmxlib/rmpbc.c | 20 ++++++++++++--------
 2 files changed, 23 insertions(+), 22 deletions(-)

diff --git a/src/gmxlib/matio.c b/src/gmxlib/matio.c
index 7ad68c1225..20971f91e8 100644
--- a/src/gmxlib/matio.c
+++ b/src/gmxlib/matio.c
@@ -191,14 +191,9 @@ static char *fgetline(char **line,int llmax,int *llalloc,FILE *in)
 {
   char *fg;
 
-  if (!(*line))
+  if (llmax > *llalloc)
   {
-      snew(*line, llmax);
-      *llalloc=llmax;
-  }
-  else if (llmax > *llalloc)
-  {
-      srenew(*line,llmax);
+      srenew(*line,llmax+1);
       *llalloc=llmax;
   }
   fg=fgets(*line,llmax,in);
@@ -272,7 +267,8 @@ void read_xpm_entry(FILE *in,t_matrix *mm)
 
   llmax = STRLEN;
 
-  while (fgetline(&line,llmax,&llalloc,in) && (strncmp(line,"static",6) != 0)) {
+  while ((NULL != fgetline(&line,llmax,&llalloc,in)) && 
+         (strncmp(line,"static",6) != 0)) {
     parsestring(line,"title",(mm->title));
     parsestring(line,"legend",(mm->legend));
     parsestring(line,"x-label",(mm->label_x));
@@ -290,7 +286,7 @@ void read_xpm_entry(FILE *in,t_matrix *mm)
     gmx_input("Invalid XPixMap");
   /* Read sizes */
   bGetOnWithIt=FALSE;
-  while (!bGetOnWithIt && fgetline(&line,llmax,&llalloc,in)) {
+  while (!bGetOnWithIt && (NULL != fgetline(&line,llmax,&llalloc,in))) {
     while (( line[0] != '\"' ) && ( line[0] != '\0' ))
       line++;
 
@@ -310,7 +306,7 @@ void read_xpm_entry(FILE *in,t_matrix *mm)
   /* Read color map */
   snew(map,mm->nmap);
   m=0;
-  while ((m < mm->nmap) && fgetline(&line,llmax,&llalloc,in)) {
+  while ((m < mm->nmap) && (NULL != fgetline(&line,llmax,&llalloc,in))) {
     line=strchr(line,'\"');
     if  (line) {
       line++;
@@ -398,7 +394,7 @@ void read_xpm_entry(FILE *in,t_matrix *mm)
 	skipstr(&line);
       }
     }
-  } while ((line[0] != '\"') && fgetline(&line,llmax,&llalloc,in));
+  } while ((line[0] != '\"') && (NULL != fgetline(&line,llmax,&llalloc,in)));
 
   /* Read matrix */
   snew(mm->matrix,mm->nx);
@@ -424,11 +420,12 @@ void read_xpm_entry(FILE *in,t_matrix *mm)
 	}
       m--;
     }
-  } while ((m>=0) && fgetline(&line,llmax,&llalloc,in));
+  } while ((m>=0) && (NULL != fgetline(&line,llmax,&llalloc,in)));
   if (m>=0)
     gmx_incons("Not enough rows in the matrix");
 
-  sfree(line);
+  /* This code makes me cry. DvdS 2010-07-08 */
+  /*sfree(line);*/
 }
 
 int read_xpm_matrix(const char *fnm,t_matrix **matrix)
@@ -441,7 +438,7 @@ int read_xpm_matrix(const char *fnm,t_matrix **matrix)
   in=gmx_fio_fopen(fnm,"r");
   
   nmat=0;
-  while (fgetline(&line,STRLEN,&llalloc,in)) {
+  while (NULL != fgetline(&line,STRLEN,&llalloc,in)) {
     if (strstr(line,"/* XPM */")) {
       srenew(*matrix,nmat+1);
       read_xpm_entry(in,&(*matrix)[nmat]);
diff --git a/src/gmxlib/rmpbc.c b/src/gmxlib/rmpbc.c
index 33e543b410..da6c9d0e61 100644
--- a/src/gmxlib/rmpbc.c
+++ b/src/gmxlib/rmpbc.c
@@ -65,28 +65,32 @@ gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef,int ePBC,int natoms,
   else
     gpbc->ePBC = ePBC;
     
-  if ((ePBC != epbcNONE) && (idef->ntypes!=-1)) {
-    gpbc->gr = mk_graph(NULL,idef,0,natoms,FALSE,FALSE);
-  } 
-  else {
+  if (idef->ntypes <= 0)
     fprintf(stderr,
 	    "\nWarning: if there are broken molecules in the trajectory file,\n"
 	    "         they can not be made whole without a run input file\n\n");
-  }
+  else if (ePBC == epbcNONE) 
+    fprintf(stderr,"\nNot treating periodicity since it is turned off in the input file\n");
+  else
+    gpbc->gr = mk_graph(NULL,idef,0,natoms,FALSE,FALSE);
+
   return gpbc;
 }
 
 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
 {
-  done_graph(gpbc->gr);
+  if (NULL != gpbc->gr)
+    done_graph(gpbc->gr);
 }
 
 void gmx_rmpbc(gmx_rmpbc_t gpbc,matrix box,rvec x[],rvec x_s[])
 {
   int    i;
 
-  mk_mshift(stdout,gpbc->gr,gpbc->ePBC,box,x);
-  shift_x(gpbc->gr,box,x,x_s);
+  if (NULL != gpbc->gr) {
+    mk_mshift(stdout,gpbc->gr,gpbc->ePBC,box,x);
+    shift_x(gpbc->gr,box,x,x_s);
+  }
   if (x != x_s)
     for (i=0; i<gpbc->natoms; i++)
       copy_rvec(x[i],x_s[i]);
-- 
2.11.4.GIT