git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14455 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MANYBODY/pair_comb3.cpp

@@ -604,7 +604,7 @@ void PairComb3::read_file(char *file)
 
   FILE *fp;
   if (comm->me == 0) {
-    fp = fopen(file,"r");
+    fp = force->open_potential(file);
     if (fp == NULL) {
       char str[128];
       sprintf(str,"Cannot open COMB3 potential file %s",file);

src/MANYBODY/pair_polymorphic.cpp

@@ -108,7 +108,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
   int itype,jtype,ktype;
   int iparam_ii,iparam_jj,iparam_kk,iparam_ij,iparam_ik,iparam_ijk;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
-  double rsq,rsq1,rsq2,r0,r1,r2;
+  double rsq,r0,r1,r2;
   double delr1[3],delr2[3],fi[3],fj[3],fk[3];
   double zeta_ij,prefactor,wfac,pfac,gfac,fa,fa_d,bij,bij_d;
   double costheta;
@@ -872,7 +872,8 @@ void PairPolymorphic::grab(FILE *fp, int n, double *list)
     fgets(line,MAXLINE,fp);
     ptr = strtok(line," \t\n\r\f");
     list[i++] = atof(ptr);
-    while (ptr = strtok(NULL," \t\n\r\f")) list[i++] = atof(ptr);
+    while ((ptr = strtok(NULL," \t\n\r\f")))
+      list[i++] = atof(ptr);
   }
 }
  

src/QEQ/fix_qeq.cpp

@@ -16,10 +16,10 @@
      Based on fix qeq/reax by H. Metin Aktulga
 ------------------------------------------------------------------------- */
 
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 #include "fix_qeq.h"
 #include "atom.h"
 #include "comm.h"
@@ -49,7 +49,7 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
   if (narg < 8) error->all(FLERR,"Illegal fix qeq command");
-  
+
   nevery = force->inumeric(FLERR,arg[3]);
   cutoff = force->numeric(FLERR,arg[4]);
   tolerance = force->numeric(FLERR,arg[5]);
@@ -102,7 +102,7 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) :
   s_hist = t_hist = NULL;
   grow_arrays(atom->nmax);
   atom->add_callback(0);
-  
+
   for( int i = 0; i < atom->nmax; i++ )
     for (int j = 0; j < nprev; ++j )
       s_hist[i][j] = t_hist[i][j] = atom->q[i];
@@ -625,7 +625,7 @@ double FixQEq::parallel_dot( double *v1, double *v2, int n)
     if (atom->mask[i] & groupbit)
       my_dot += v1[i] * v2[i];
   }
-  
+
   MPI_Allreduce( &my_dot, &res, 1, MPI_DOUBLE, MPI_SUM, world );
 
   return res;

src/QEQ/fix_qeq_fire.cpp

@@ -15,10 +15,10 @@
    Contributing author: Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 #include "fix_qeq_fire.h"
 #include "atom.h"
 #include "comm.h"
@@ -49,8 +49,8 @@ using namespace FixConst;
 
 /* ---------------------------------------------------------------------- */
 
-FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) : 
-  FixQEq(lmp, narg, arg) 
+FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) :
+  FixQEq(lmp, narg, arg)
 {
   qdamp = 0.20;
   qstep = 0.20;
@@ -68,7 +68,7 @@ FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) :
       iarg += 2;
     } else error->all(FLERR,"Illegal fix qeq/fire command");
   }
-  
+
   comb = NULL;
   comb3 = NULL;
 }
@@ -89,7 +89,7 @@ void FixQEqFire::init()
   neighbor->requests[irequest]->half = 1;
   neighbor->requests[irequest]->full = 0;
 
-  if (tolerance < 1e-4) 
+  if (tolerance < 1e-4)
     if (comm->me == 0)
       error->warning(FLERR,"Fix qeq/fire tolerance may be too small"
 		    " for damped fires");

src/USER-MISC/improper_distance.cpp

@@ -65,7 +65,6 @@ void ImproperDistance::compute(int eflag, int vflag)
 //  double ss1,ss2,ss3,r1,r2,r3,c0,c1,c2,s1,s2;
 //  double s12,c,s,domega,a,a11,a22,a33,a12,a13,a23;
   double domega,a;
-  double sx2,sy2,sz2;
 
   eimproper = 0.0;
   if (eflag || vflag) ev_setup(eflag,vflag);