remove class member name clashes. Pointers contains infile so we rename other uses to inpfile

src/MISC/fix_orient_bcc.cpp

@@ -115,25 +115,25 @@ FixOrientBCC::FixOrientBCC(LAMMPS *lmp, int narg, char **arg) :
     char *result;
     int count;
 
-    FILE *infile = fopen(xifilename,"r");
+    FILE *inpfile = fopen(xifilename,"r");
-    if (infile == NULL) error->one(FLERR,"Fix orient/bcc file open failed");
+    if (inpfile == NULL) error->one(FLERR,"Fix orient/bcc file open failed");
     for (int i = 0; i < 4; i++) {
-      result = fgets(line,IMGMAX,infile);
+      result = fgets(line,IMGMAX,inpfile);
       if (!result) error->one(FLERR,"Fix orient/bcc file read failed");
       count = sscanf(line,"%lg %lg %lg",&Rxi[i][0],&Rxi[i][1],&Rxi[i][2]);
       if (count != 3) error->one(FLERR,"Fix orient/bcc file read failed");
     }
-    fclose(infile);
+    fclose(inpfile);
 
-    infile = fopen(chifilename,"r");
+    inpfile = fopen(chifilename,"r");
-    if (infile == NULL) error->one(FLERR,"Fix orient/bcc file open failed");
+    if (inpfile == NULL) error->one(FLERR,"Fix orient/bcc file open failed");
     for (int i = 0; i < 4; i++) {
-      result = fgets(line,IMGMAX,infile);
+      result = fgets(line,IMGMAX,inpfile);
       if (!result) error->one(FLERR,"Fix orient/bcc file read failed");
       count = sscanf(line,"%lg %lg %lg",&Rchi[i][0],&Rchi[i][1],&Rchi[i][2]);
       if (count != 3) error->one(FLERR,"Fix orient/bcc file read failed");
     }
-    fclose(infile);
+    fclose(inpfile);
   }
 
   MPI_Bcast(&Rxi[0][0],18,MPI_DOUBLE,0,world);

src/MISC/fix_orient_fcc.cpp

@@ -113,25 +113,25 @@ FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
     char *result;
     int count;
 
-    FILE *infile = fopen(xifilename,"r");
+    FILE *inpfile = fopen(xifilename,"r");
-    if (infile == NULL) error->one(FLERR,"Fix orient/fcc file open failed");
+    if (inpfile == NULL) error->one(FLERR,"Fix orient/fcc file open failed");
     for (int i = 0; i < 6; i++) {
-      result = fgets(line,IMGMAX,infile);
+      result = fgets(line,IMGMAX,inpfile);
       if (!result) error->one(FLERR,"Fix orient/fcc file read failed");
       count = sscanf(line,"%lg %lg %lg",&Rxi[i][0],&Rxi[i][1],&Rxi[i][2]);
       if (count != 3) error->one(FLERR,"Fix orient/fcc file read failed");
     }
-    fclose(infile);
+    fclose(inpfile);
 
-    infile = fopen(chifilename,"r");
+    inpfile = fopen(chifilename,"r");
-    if (infile == NULL) error->one(FLERR,"Fix orient/fcc file open failed");
+    if (inpfile == NULL) error->one(FLERR,"Fix orient/fcc file open failed");
     for (int i = 0; i < 6; i++) {
-      result = fgets(line,IMGMAX,infile);
+      result = fgets(line,IMGMAX,inpfile);
       if (!result) error->one(FLERR,"Fix orient/fcc file read failed");
       count = sscanf(line,"%lg %lg %lg",&Rchi[i][0],&Rchi[i][1],&Rchi[i][2]);
       if (count != 3) error->one(FLERR,"Fix orient/fcc file read failed");
     }
-    fclose(infile);
+    fclose(inpfile);
   }
 
   MPI_Bcast(&Rxi[0][0],18,MPI_DOUBLE,0,world);

src/REPLICA/neb.cpp

@@ -146,12 +146,12 @@ void NEB::command(int narg, char **arg)
 
   if (strcmp(arg[5],"final") == 0) {
     if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEB command");
-    infile = arg[6];
+    inpfile = arg[6];
-    readfile(infile,0);
+    readfile(inpfile,0);
   } else if (strcmp(arg[5],"each") == 0) {
     if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEB command");
-    infile = arg[6];
+    inpfile = arg[6];
-    readfile(infile,1);
+    readfile(inpfile,1);
   } else if (strcmp(arg[5],"none") == 0) {
     if (narg != 6 && narg !=7) error->universe_all(FLERR,"Illegal NEB command");
   } else error->universe_all(FLERR,"Illegal NEB command");

src/REPLICA/neb.h

@@ -47,7 +47,7 @@ class NEB : protected Pointers {
   double ftol;                 // force tolerance convergence criterion
   int n1steps, n2steps;        // number of steps in stage 1 and 2
   int nevery;                  // output interval
-  char *infile;                // name of file containing final state
+  char *inpfile;                // name of file containing final state
 
   class FixNEB *fneb;
   int numall;                  // per-replica dimension of array all

src/RIGID/fix_rigid.cpp

@@ -59,7 +59,7 @@ enum{ISO,ANISO,TRICLINIC};
 
 FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg), step_respa(NULL),
-  infile(NULL), nrigid(NULL), mol2body(NULL), body2mol(NULL),
+  inpfile(NULL), nrigid(NULL), mol2body(NULL), body2mol(NULL),
   body(NULL), displace(NULL), masstotal(NULL), xcm(NULL),
   vcm(NULL), fcm(NULL), inertia(NULL), ex_space(NULL),
   ey_space(NULL), ez_space(NULL), angmom(NULL), omega(NULL),
@@ -327,7 +327,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   t_iter = 1;
   t_order = 3;
   p_chain = 10;
-  infile = NULL;
+  inpfile = NULL;
 
   pcouple = NONE;
   pstyle = ANISO;
@@ -546,12 +546,12 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
       p_chain = force->inumeric(FLERR,arg[iarg+1]);
       iarg += 2;
 
-    } else if (strcmp(arg[iarg],"infile") == 0) {
+    } else if (strcmp(arg[iarg],"inpfile") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
-      delete [] infile;
+      delete [] inpfile;
       int n = strlen(arg[iarg+1]) + 1;
-      infile = new char[n];
+      inpfile = new char[n];
-      strcpy(infile,arg[iarg+1]);
+      strcpy(inpfile,arg[iarg+1]);
       restart_file = 1;
       reinitflag = 0;
       iarg += 2;
@@ -649,7 +649,7 @@ FixRigid::~FixRigid()
   atom->delete_callback(id,0);
 
   delete random;
-  delete [] infile;
+  delete [] inpfile;
   memory->destroy(mol2body);
   memory->destroy(body2mol);
 
@@ -760,14 +760,14 @@ void FixRigid::init()
   // setup rigid bodies, using current atom info. if reinitflag is not set,
   // do the initialization only once, b/c properties may not be re-computable
   // especially if overlapping particles.
-  //   do not do dynamic init if read body properties from infile.
+  //   do not do dynamic init if read body properties from inpfile.
-  // this is b/c the infile defines the static and dynamic properties and may
+  // this is b/c the inpfile defines the static and dynamic properties and may
   // not be computable if contain overlapping particles.
-  //   setup_bodies_static() reads infile itself
+  //   setup_bodies_static() reads inpfile itself
 
   if (reinitflag || !setupflag) {
     setup_bodies_static();
-    if (!infile) setup_bodies_dynamic();
+    if (!inpfile) setup_bodies_dynamic();
     setupflag = 1;
   }
 
@@ -1640,7 +1640,7 @@ void FixRigid::set_v()
    sets extended flags, masstotal, center-of-mass
    sets Cartesian and diagonalized inertia tensor
    sets body image flags
-   may read some properties from infile
+   may read some properties from inpfile
 ------------------------------------------------------------------------- */
 
 void FixRigid::setup_bodies_static()
@@ -1791,7 +1791,7 @@ void FixRigid::setup_bodies_static()
     xcm[ibody][2] = all[ibody][2]/masstotal[ibody];
   }
 
-  // set vcm, angmom = 0.0 in case infile is used
+  // set vcm, angmom = 0.0 in case inpfile is used
   // and doesn't overwrite all body's values
   // since setup_bodies_dynamic() will not be called
 
@@ -1810,7 +1810,7 @@ void FixRigid::setup_bodies_static()
   // inbody[i] = 0/1 if Ith rigid body is initialized by file
 
   int *inbody;
-  if (infile) {
+  if (inpfile) {
     memory->create(inbody,nbody,"rigid:inbody");
     for (ibody = 0; ibody < nbody; ibody++) inbody[ibody] = 0;
     readfile(0,masstotal,xcm,vcm,angmom,imagebody,inbody);
@@ -1918,7 +1918,7 @@ void FixRigid::setup_bodies_static()
 
   // overwrite Cartesian inertia tensor with file values
 
-  if (infile) readfile(1,NULL,all,NULL,NULL,NULL,inbody);
+  if (inpfile) readfile(1,NULL,all,NULL,NULL,NULL,inbody);
 
   // diagonalize inertia tensor for each body via Jacobi rotations
   // inertia = 3 eigenvalues = principal moments of inertia
@@ -2116,11 +2116,11 @@ void FixRigid::setup_bodies_static()
   MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
 
   // error check that re-computed moments of inertia match diagonalized ones
-  // do not do test for bodies with params read from infile
+  // do not do test for bodies with params read from inpfile
 
   double norm;
   for (ibody = 0; ibody < nbody; ibody++) {
-    if (infile && inbody[ibody]) continue;
+    if (inpfile && inbody[ibody]) continue;
     if (inertia[ibody][0] == 0.0) {
       if (fabs(all[ibody][0]) > TOLERANCE)
         error->all(FLERR,"Fix rigid: Bad principal moments");
@@ -2149,7 +2149,7 @@ void FixRigid::setup_bodies_static()
       error->all(FLERR,"Fix rigid: Bad principal moments");
   }
 
-  if (infile) memory->destroy(inbody);
+  if (inpfile) memory->destroy(inbody);
 }
 
 /* ----------------------------------------------------------------------
@@ -2268,10 +2268,10 @@ void FixRigid::readfile(int which, double *vec,
   char line[MAXLINE];
 
   if (me == 0) {
-    fp = fopen(infile,"r");
+    fp = fopen(inpfile,"r");
     if (fp == NULL) {
       char str[128];
-      snprintf(str,128,"Cannot open fix rigid infile %s",infile);
+      snprintf(str,128,"Cannot open fix rigid inpfile %s",inpfile);
       error->one(FLERR,str);
     }
 
@@ -2371,7 +2371,7 @@ void FixRigid::readfile(int which, double *vec,
 
 /* ----------------------------------------------------------------------
    write out restart info for mass, COM, inertia tensor, image flags to file
-   identical format to infile option, so info can be read in when restarting
+   identical format to inpfile option, so info can be read in when restarting
    only proc 0 writes list of global bodies to file
 ------------------------------------------------------------------------- */
 

src/RIGID/fix_rigid.h

@@ -67,7 +67,7 @@ class FixRigid : public Fix {
   int triclinic;
   double MINUSPI,TWOPI;
 
-  char *infile;             // file to read rigid body attributes from
+  char *inpfile;             // file to read rigid body attributes from
   int rstyle;               // SINGLE,MOLECULE,GROUP
   int setupflag;            // 1 if body properties are setup, else 0
   int earlyflag;            // 1 if forces/torques computed at post_force()
@@ -261,7 +261,7 @@ E: Fix rigid: Bad principal moments
 The principal moments of inertia computed for a rigid body
 are not within the required tolerances.
 
-E: Cannot open fix rigid infile %s
+E: Cannot open fix rigid inpfile %s
 
 The specified file cannot be opened.  Check that the path and name are
 correct.

src/RIGID/fix_rigid_small.cpp

@@ -70,7 +70,7 @@ enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF};
 
 FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg), step_respa(NULL),
-  infile(NULL), body(NULL), bodyown(NULL), bodytag(NULL), atom2body(NULL),
+  inpfile(NULL), body(NULL), bodyown(NULL), bodytag(NULL), atom2body(NULL),
   xcmimage(NULL), displace(NULL), eflags(NULL), orient(NULL), dorient(NULL),
   avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL), counts(NULL),
   itensor(NULL), mass_body(NULL), langextra(NULL), random(NULL),
@@ -191,7 +191,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
 
   int seed;
   langflag = 0;
-  infile = NULL;
+  inpfile = NULL;
   onemols = NULL;
   reinitflag = 1;
 
@@ -232,12 +232,12 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
       if (seed <= 0) error->all(FLERR,"Illegal fix rigid/small command");
       iarg += 5;
 
-    } else if (strcmp(arg[iarg],"infile") == 0) {
+    } else if (strcmp(arg[iarg],"inpfile") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
-      delete [] infile;
+      delete [] inpfile;
       int n = strlen(arg[iarg+1]) + 1;
-      infile = new char[n];
+      inpfile = new char[n];
-      strcpy(infile,arg[iarg+1]);
+      strcpy(inpfile,arg[iarg+1]);
       restart_file = 1;
       reinitflag = 0;
       iarg += 2;
@@ -546,7 +546,7 @@ FixRigidSmall::~FixRigidSmall()
   memory->destroy(dorient);
 
   delete random;
-  delete [] infile;
+  delete [] inpfile;
 
   memory->destroy(langextra);
   memory->destroy(mass_body);
@@ -622,10 +622,10 @@ void FixRigidSmall::init()
    if reinitflag is not set, do the initialization only once, b/c properties
    may not be re-computable especially if overlapping particles or bodies
    are inserted from mol template.
-     do not do dynamic init if read body properties from infile. this
+     do not do dynamic init if read body properties from inpfile. this
-   is b/c the infile defines the static and dynamic properties and may not
+   is b/c the inpfile defines the static and dynamic properties and may not
    be computable if contain overlapping particles setup_bodies_static()
-   reads infile itself.
+   reads inpfile itself.
      cannot do this until now, b/c requires comm->setup() to have setup stencil
    invoke pre_neighbor() to insure body xcmimage flags are reset
      needed if Verlet::setup::pbc() has remapped/migrated atoms for 2nd run
@@ -638,7 +638,7 @@ void FixRigidSmall::setup_pre_neighbor()
     setup_bodies_static();
   else pre_neighbor();
 
-  if ((reinitflag || !setupflag) && !infile)
+  if ((reinitflag || !setupflag) && !inpfile)
     setup_bodies_dynamic();
 
   setupflag = 1;
@@ -1775,7 +1775,7 @@ int FixRigidSmall::rendezvous_body(int n, char *inbuf,
    sets extended flags, masstotal, center-of-mass
    sets Cartesian and diagonalized inertia tensor
    sets body image flags
-   may read some properties from infile
+   may read some properties from inpfile
 ------------------------------------------------------------------------- */
 
 void FixRigidSmall::setup_bodies_static()
@@ -1932,7 +1932,7 @@ void FixRigidSmall::setup_bodies_static()
     xcm[2] /= body[ibody].mass;
   }
 
-  // set vcm, angmom = 0.0 in case infile is used
+  // set vcm, angmom = 0.0 in case inpfile is used
   // and doesn't overwrite all body's values
   // since setup_bodies_dynamic() will not be called
 
@@ -1955,7 +1955,7 @@ void FixRigidSmall::setup_bodies_static()
   // inbody[i] = 0/1 if Ith rigid body is initialized by file
 
   int *inbody;
-  if (infile) {
+  if (inpfile) {
     memory->create(inbody,nlocal_body,"rigid/small:inbody");
     for (ibody = 0; ibody < nlocal_body; ibody++) inbody[ibody] = 0;
     readfile(0,NULL,inbody);
@@ -2058,7 +2058,7 @@ void FixRigidSmall::setup_bodies_static()
 
   // overwrite Cartesian inertia tensor with file values
 
-  if (infile) readfile(1,itensor,inbody);
+  if (inpfile) readfile(1,itensor,inbody);
 
   // diagonalize inertia tensor for each body via Jacobi rotations
   // inertia = 3 eigenvalues = principal moments of inertia
@@ -2257,11 +2257,11 @@ void FixRigidSmall::setup_bodies_static()
   comm->reverse_comm_fix(this,6);
 
   // error check that re-computed moments of inertia match diagonalized ones
-  // do not do test for bodies with params read from infile
+  // do not do test for bodies with params read from inpfile
 
   double norm;
   for (ibody = 0; ibody < nlocal_body; ibody++) {
-    if (infile && inbody[ibody]) continue;
+    if (inpfile && inbody[ibody]) continue;
     inertia = body[ibody].inertia;
 
     if (inertia[0] == 0.0) {
@@ -2295,7 +2295,7 @@ void FixRigidSmall::setup_bodies_static()
   // clean up
 
   memory->destroy(itensor);
-  if (infile) memory->destroy(inbody);
+  if (inpfile) memory->destroy(inbody);
 }
 
 /* ----------------------------------------------------------------------
@@ -2437,10 +2437,10 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
   // open file and read header
 
   if (me == 0) {
-    fp = fopen(infile,"r");
+    fp = fopen(inpfile,"r");
     if (fp == NULL) {
       char str[128];
-      snprintf(str,128,"Cannot open fix rigid/small infile %s",infile);
+      snprintf(str,128,"Cannot open fix rigid/small inpfile %s",inpfile);
       error->one(FLERR,str);
     }
 
@@ -2538,7 +2538,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
 
 /* ----------------------------------------------------------------------
    write out restart info for mass, COM, inertia tensor to file
-   identical format to infile option, so info can be read in when restarting
+   identical format to inpfile option, so info can be read in when restarting
    each proc contributes info for rigid bodies it owns
 ------------------------------------------------------------------------- */
 

src/RIGID/fix_rigid_small.h

@@ -74,7 +74,7 @@ class FixRigidSmall : public Fix {
   int triclinic;
   double MINUSPI,TWOPI;
 
-  char *infile;             // file to read rigid body attributes from
+  char *inpfile;             // file to read rigid body attributes from
   int setupflag;            // 1 if body properties are setup, else 0
   int earlyflag;            // 1 if forces/torques are computed at post_force()
   int commflag;             // various modes of forward/reverse comm
@@ -318,7 +318,7 @@ E: Fix rigid: Bad principal moments
 The principal moments of inertia computed for a rigid body
 are not within the required tolerances.
 
-E: Cannot open fix rigid/small infile %s
+E: Cannot open fix rigid/small inpfile %s
 
 The specified file cannot be opened.  Check that the path and name are
 correct.

src/SPIN/neb_spin.cpp

@@ -139,12 +139,12 @@ void NEBSpin::command(int narg, char **arg)
 
   if (strcmp(arg[5],"final") == 0) {
     if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEBSpin command");
-    infile = arg[6];
+    inpfile = arg[6];
-    readfile(infile,0);
+    readfile(inpfile,0);
   } else if (strcmp(arg[5],"each") == 0) {
     if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEBSpin command");
-    infile = arg[6];
+    inpfile = arg[6];
-    readfile(infile,1);
+    readfile(inpfile,1);
   } else if (strcmp(arg[5],"none") == 0) {
     if (narg != 6 && narg !=7) error->universe_all(FLERR,"Illegal NEBSpin command");
   } else error->universe_all(FLERR,"Illegal NEBSpin command");

src/SPIN/neb_spin.h

@@ -46,7 +46,7 @@ class NEBSpin : protected Pointers {
   double ttol;                 // torque tolerance convergence criterion
   int n1steps, n2steps;        // number of steps in stage 1 and 2
   int nevery;                  // output interval
-  char *infile;                // name of file containing final state
+  char *inpfile;                // name of file containing final state
 
   class FixNEBSpin *fneb;
   int numall;                  // per-replica dimension of array all

src/read_restart.cpp

@@ -580,32 +580,32 @@ void ReadRestart::command(int narg, char **arg)
 }
 
 /* ----------------------------------------------------------------------
-   infile contains a "*"
+   inpfile contains a "*"
-   search for all files which match the infile pattern
+   search for all files which match the inpfile pattern
    replace "*" with latest timestep value to create outfile name
    search dir referenced by initial pathname of file
-   if infile also contains "%", use "base" when searching directory
+   if inpfile also contains "%", use "base" when searching directory
    only called by proc 0
 ------------------------------------------------------------------------- */
 
-void ReadRestart::file_search(char *infile, char *outfile)
+void ReadRestart::file_search(char *inpfile, char *outfile)
 {
   char *ptr;
 
-  // separate infile into dir + filename
+  // separate inpfile into dir + filename
 
-  char *dirname = new char[strlen(infile) + 1];
+  char *dirname = new char[strlen(inpfile) + 1];
-  char *filename = new char[strlen(infile) + 1];
+  char *filename = new char[strlen(inpfile) + 1];
 
-  if (strchr(infile,'/')) {
+  if (strchr(inpfile,'/')) {
-    ptr = strrchr(infile,'/');
+    ptr = strrchr(inpfile,'/');
     *ptr = '\0';
-    strcpy(dirname,infile);
+    strcpy(dirname,inpfile);
     strcpy(filename,ptr+1);
     *ptr = '/';
   } else {
     strcpy(dirname,"./");
-    strcpy(filename,infile);
+    strcpy(filename,inpfile);
   }
 
   // if filename contains "%" replace "%" with "base"
@@ -651,11 +651,11 @@ void ReadRestart::file_search(char *infile, char *outfile)
   if (maxnum < 0) error->one(FLERR,"Found no restart file matching pattern");
 
   // create outfile with maxint substituted for "*"
-  // use original infile, not pattern, since need to retain "%" in filename
+  // use original inpfile, not pattern, since need to retain "%" in filename
 
-  ptr = strchr(infile,'*');
+  ptr = strchr(inpfile,'*');
   *ptr = '\0';
-  sprintf(outfile,"%s" BIGINT_FORMAT "%s",infile,maxnum,ptr+1);
+  sprintf(outfile,"%s" BIGINT_FORMAT "%s",inpfile,maxnum,ptr+1);
   *ptr = '*';
 
   // clean up