Commit JT 042519

- moved examples/SPIN/gneb/interpolate/ toward
tools/spin/interpolate/gneb
- added gneb in the command files in doc/src
- modified the error messages in neb_spin.h/cpp

doc/src/Commands_all.txt

@@ -83,6 +83,7 @@ An alphabetic list of all general LAMMPS commands.
 "molecule"_molecule.html,
 "ndx2group"_group2ndx.html,
 "neb"_neb.html,
+"neb_spin"_neb_spin.html,
 "neigh_modify"_neigh_modify.html,
 "neighbor"_neighbor.html,
 "newton"_newton.html,

doc/src/Commands_category.txt

@@ -116,6 +116,7 @@ Actions:
 
 "minimize"_minimize.html,
 "neb"_neb.html,
+"neb_spin"_neb_spin.html,
 "prd"_prd.html,
 "rerun"_rerun.html,
 "run"_run.html,

doc/src/Commands_fix.txt

@@ -107,6 +107,7 @@ OPT.
 "mvv/edpd"_fix_mvv_dpd.html,
 "mvv/tdpd"_fix_mvv_dpd.html,
 "neb"_fix_neb.html,
+"neb_spin"_fix_neb_spin.html,
 "nph (ko)"_fix_nh.html,
 "nph/asphere (o)"_fix_nph_asphere.html,
 "nph/body"_fix_nph_body.html,

doc/src/Howto_replica.txt

@@ -17,6 +17,7 @@ periodically.
 These are the relevant commands:
 
 "neb"_neb.html for nudged elastic band calculations
+"neb_spin"_neb_spin.html for magnetic nudged elastic band calculations
 "prd"_prd.html for parallel replica dynamics
 "tad"_tad.html for temperature accelerated dynamics
 "temper"_temper.html for parallel tempering

doc/src/Packages_details.txt

@@ -918,6 +918,7 @@ src/SPIN: filenames -> commands
 "fix nve/spin"_fix_nve_spin.html
 "fix precession/spin"_fix_precession_spin.html
 "compute spin"_compute_spin.html
+"neb/spin"_neb_spin.html
 examples/SPIN :ul
 
 :line

doc/src/commands_list.txt

@@ -67,6 +67,7 @@ Commands :h1
    minimize
    molecule
    neb
+   neb/spin
    neigh_modify
    neighbor
    newton

doc/src/fixes.txt

@@ -84,6 +84,7 @@ Fixes :h1
    fix_msst
    fix_mvv_dpd
    fix_neb
+   fix_neb_spin
    fix_nh
    fix_nh_eff
    fix_nh_uef

doc/src/neb_spin.txt

@@ -345,7 +345,7 @@ calculation fails to converge properly to the MEP, and you wish to
 restart the calculation from an intermediate point with altered
 parameters.
 
-A c file script in provided in the examples/SPIN/gneb/interpolate
+A c file script in provided in the tool/spin/interpolate_gneb
 directory, that interpolates the MEP given the information provided 
 by the verbose output option (as detailed in Appendix D of
 "(BessarabA)"_#BessarabA). 

src/SPIN/neb_spin.cpp

@@ -464,7 +464,7 @@ void NEB_spin::readfile(char *file, int flag)
       open(file);
       while (1) {
         eof = fgets(line,MAXLINE,fp);
-        if (eof == NULL) error->one(FLERR,"Unexpected end of neb file");
+        if (eof == NULL) error->one(FLERR,"Unexpected end of neb/spin file");
         start = &line[strspn(line," \t\n\v\f\r")];
         if (*start != '\0' && *start != '#') break;
       }
@@ -478,7 +478,7 @@ void NEB_spin::readfile(char *file, int flag)
         open(file);
         while (1) {
           eof = fgets(line,MAXLINE,fp);
-          if (eof == NULL) error->one(FLERR,"Unexpected end of neb file");
+          if (eof == NULL) error->one(FLERR,"Unexpected end of neb/spin file");
           start = &line[strspn(line," \t\n\v\f\r")];
           if (*start != '\0' && *start != '#') break;
         }
@@ -513,7 +513,7 @@ void NEB_spin::readfile(char *file, int flag)
       eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer);
     else
       eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
-    if (eofflag) error->all(FLERR,"Unexpected end of neb file");
+    if (eofflag) error->all(FLERR,"Unexpected end of neb/spin file");
 
     buf = buffer;
     next = strchr(buf,'\n');
@@ -522,7 +522,7 @@ void NEB_spin::readfile(char *file, int flag)
     *next = '\n';
 
     if (nwords != ATTRIBUTE_PERLINE)
-      error->all(FLERR,"Incorrect atom format in neb file");
+      error->all(FLERR,"Incorrect atom format in neb/spin file");
 
     // loop over lines of atom coords
     // tokenize the line into values
@@ -614,12 +614,12 @@ void NEB_spin::readfile(char *file, int flag)
     int ntotal;
     MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,uworld);
     if (ntotal != nreplica*nlines)
-      error->universe_all(FLERR,"Invalid atom IDs in neb file");
+      error->universe_all(FLERR,"Invalid atom IDs in neb/spin file");
   } else {
     int ntotal;
     MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,world);
     if (ntotal != nlines)
-      error->all(FLERR,"Invalid atom IDs in neb file");
+      error->all(FLERR,"Invalid atom IDs in neb/spin file");
   }
 
   // clean up
@@ -700,7 +700,7 @@ int NEB_spin::initial_rotation(double *spi, double *sploc, double fraction)
     }
   }
 
-  // knormsq should not be 0 anymore
+  // knormsq should not be 0
 
   if (knormsq == 0.0)
     error->all(FLERR,"Incorrect initial rotation operation");

src/SPIN/neb_spin.h

@@ -30,7 +30,7 @@ class NEB_spin : protected Pointers {
   NEB_spin(class LAMMPS *);
   NEB_spin(class LAMMPS *, double, double, int, int, int, double *, double *);
   ~NEB_spin();
-  void command(int, char **);  // process neb command
+  void command(int, char **);  // process neb/spin command
   void run();                  // run NEB_spin
 
   double ebf,ebr;              // forward and reverse energy barriers
@@ -104,15 +104,15 @@ E: Too many timesteps
 
 The cumulative timesteps must fit in a 64-bit integer.
 
-E: Unexpected end of neb file
+E: Unexpected end of neb/spin file
 
 A read operation from the file failed.
 
-E: Incorrect atom format in neb file
+E: Incorrect atom format in neb/spin file
 
 The number of fields per line is not what expected.
 
-E: Invalid atom IDs in neb file
+E: Invalid atom IDs in neb/spin file
 
 An ID in the file was not found in the system.