Merge pull request #716 from akohlmey/collected-small-changes

Collected small changes and bugfixes for next patch

doc/src/Section_commands.txt

@@ -637,10 +637,10 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "rigid/nve (o)"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph (o)"_fix_rigid.html,
-"rigid/small/npt (o)"_fix_rigid.html,
-"rigid/small/nve (o)"_fix_rigid.html,
-"rigid/small/nvt (o)"_fix_rigid.html,
+"rigid/small/nph"_fix_rigid.html,
+"rigid/small/npt"_fix_rigid.html,
+"rigid/small/nve"_fix_rigid.html,
+"rigid/small/nvt"_fix_rigid.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "spring"_fix_spring.html,

doc/src/compute_dihedral_local.txt

@@ -27,8 +27,8 @@ compute 1 all dihedral/local phi :pre
 
 Define a computation that calculates properties of individual dihedral
 interactions.  The number of datums generated, aggregated across all
-processors, equals the number of angles in the system, modified by the
-group parameter as explained below.
+processors, equals the number of dihedral angles in the system, modified
+by the group parameter as explained below.
 
 The value {phi} is the dihedral angle, as defined in the diagram on
 the "dihedral_style"_dihedral_style.html doc page.

doc/src/create_atoms.txt

@@ -227,16 +227,18 @@ the sinusoid would appear to be "smoother".  Also note the use of the
 converts lattice spacings to distance.  Click on the image for a
 larger version.
 
+dimension       2
 variable        x equal 100
 variable        y equal 25
 lattice         hex 0.8442
 region          box block 0 $x 0 $y -0.5 0.5
 create_box      1 box :pre
 
-variable        xx equal 0.0
-variable        yy equal 0.0
+variable        xx internal 0.0
+variable        yy internal 0.0
 variable        v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
-create_atoms    1 box var v set x xx set y yy :pre
+create_atoms    1 box var v set x xx set y yy
+write_dump      all atom sinusoid.lammpstrj :pre
 
 :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
 

doc/src/fix_rigid.txt

@@ -7,11 +7,17 @@
 :line
 
 fix rigid command :h3
+fix rigid/omp command :h3
 fix rigid/nve command :h3
+fix rigid/nve/omp command :h3
 fix rigid/nvt command :h3
+fix rigid/nvt/omp command :h3
 fix rigid/npt command :h3
+fix rigid/npt/omp command :h3
 fix rigid/nph command :h3
+fix rigid/nph/omp command :h3
 fix rigid/small command :h3
+fix rigid/small/omp command :h3
 fix rigid/nve/small command :h3
 fix rigid/nvt/small command :h3
 fix rigid/npt/small command :h3
@@ -28,7 +34,7 @@ bodystyle = {single} or {molecule} or {group} :l
   {molecule} args = none
   {custom} args = {i_propname} or {v_varname}
     i_propname = an integer property defined via fix property/atom
-    v_varname  = an atom-style or atomfile-style variable 
+    v_varname  = an atom-style or atomfile-style variable
   {group} args = N groupID1 groupID2 ...
     N = # of groups
     groupID1, groupID2, ... = list of N group IDs :pre
@@ -93,7 +99,7 @@ fix 1 clump rigid custom v_bodyid :pre
 fix 0 all property/atom i_bodyid
 read_restart data.rigid fix 0 NULL Bodies
 fix 1 clump rigid/small custom i_bodyid :pre
-	
+
 [Description:]
 
 Treat one or more sets of atoms as independent rigid bodies.  This

doc/src/print.txt

@@ -14,10 +14,11 @@ print string keyword value :pre
 
 string = text string to print, which may contain variables :ulb,l
 zero or more keyword/value pairs may be appended :l
-keyword = {file} or {append} or {screen} :l
+keyword = {file} or {append} or {screen} or {universe} :l
   {file} value = filename
   {append} value = filename
-  {screen} value = {yes} or {no} :pre
+  {screen} value = {yes} or {no}
+  {universe} value = {yes} or {no} :pre
 :ule
 
 [Examples:]
@@ -26,6 +27,7 @@ print "Done with equilibration" file info.dat
 print Vol=$v append info.dat screen no
 print "The system volume is now $v"
 print 'The system volume is now $v'
+print "NEB calculation 1 complete" screen no universe yes
 print """
 System volume = $v
 System temperature = $t
@@ -49,6 +51,11 @@ it does not exist.
 If the {screen} keyword is used, output to the screen and logfile can
 be turned on or off as desired.
 
+If the {universe} keyword is used, output to the global screen and
+logfile can be turned on or off as desired. In multi-partition
+calculations, the {screen} option and the corresponding output only
+apply to the screen and logfile of the individual partition.
+
 If you want the print command to be executed multiple times (with
 changing variable values), there are 3 options.  First, consider using
 the "fix print"_fix_print.html command, which will print a string
@@ -74,4 +81,4 @@ thermodynamic properties, global values calculated by a
 
 [Default:]
 
-The option defaults are no file output and screen = yes.
+The option defaults are no file output, screen = yes, and universe = no.

lib/gpu/lal_lj_expand_ext.cpp

@@ -92,7 +92,7 @@ int lje_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
 // ---------------------------------------------------------------------------
 // Copy updated coeffs from host to device
 // ---------------------------------------------------------------------------
-int lje_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
+void lje_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
                    double **host_lj2, double **host_lj3, double **host_lj4,
                    double **offset, double **shift) {
   int world_me=LJEMF.device->world_me();

src/GPU/pair_gauss_gpu.cpp

@@ -43,7 +43,7 @@ int gauss_gpu_init(const int ntypes, double **cutsq, double **host_a,
                    double **b, double **offset, double *special_lj, const int nlocal,
                    const int nall, const int max_nbors, const int maxspecial,
                    const double cell_size, int &gpu_mode, FILE *screen);
-int gauss_gpu_reinit(const int ntypes, double **cutsq, double **host_a,
+void gauss_gpu_reinit(const int ntypes, double **cutsq, double **host_a,
                    double **b, double **offset);
 void gauss_gpu_clear();
 int ** gauss_gpu_compute_n(const int ago, const int inum,

src/GPU/pair_lj_cut_coul_long_gpu.cpp

@@ -56,7 +56,7 @@ int ljcl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
                   double **host_cut_ljsq, double host_cut_coulsq,
                   double *host_special_coul, const double qqrd2e,
                   const double g_ewald);
-int ljcl_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
+void ljcl_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
                     double **host_lj2, double **host_lj3, double **host_lj4,
                     double **offset, double **host_lj_cutsq);
 void ljcl_gpu_clear();

src/GPU/pair_lj_cut_gpu.cpp

@@ -45,7 +45,7 @@ int ljl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
                  const int nall, const int max_nbors, const int maxspecial,
                  const double cell_size, int &gpu_mode, FILE *screen);
 
-int ljl_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
+void ljl_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
                    double **host_lj2, double **host_lj3, double **host_lj4,
                    double **offset);
 

src/GPU/pair_lj_expand_gpu.cpp

@@ -45,7 +45,7 @@ int lje_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
                  const int nlocal, const int nall, const int max_nbors,
                  const int maxspecial, const double cell_size, int &gpu_mode,
                  FILE *screen);
-int lje_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
+void lje_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
                    double **host_lj2, double **host_lj3, double **host_lj4,
                    double **offset, double **shift);
 void lje_gpu_clear();

src/dump_image.cpp

@@ -1345,7 +1345,7 @@ int DumpImage::modify_param(int narg, char **arg)
     if (atom->nbondtypes == 0)
       error->all(FLERR,"Dump modify bdiam not allowed with no bond types");
     int nlo,nhi;
-    force->bounds(FLERR,arg[1],atom->ntypes,nlo,nhi);
+    force->bounds(FLERR,arg[1],atom->nbondtypes,nlo,nhi);
     double diam = force->numeric(FLERR,arg[2]);
     if (diam <= 0.0) error->all(FLERR,"Illegal dump_modify command");
     for (int i = nlo; i <= nhi; i++) bdiamtype[i] = diam;

src/error.cpp

@@ -115,10 +115,10 @@ void Error::all(const char *file, int line, const char *str)
   if (me == 0) {
     if (input && input->line) lastcmd = input->line;
     if (screen) fprintf(screen,"ERROR: %s (%s:%d)\n"
-		        "Last command: %s\n",
+                        "Last command: %s\n",
                         str,file,line,lastcmd);
     if (logfile) fprintf(logfile,"ERROR: %s (%s:%d)\n"
-		         "Last command: %s\n",
+                         "Last command: %s\n",
                          str,file,line,lastcmd);
   }
 
@@ -152,9 +152,17 @@ void Error::all(const char *file, int line, const char *str)
 void Error::one(const char *file, int line, const char *str)
 {
   int me;
+  const char *lastcmd = (const char*)"(unknown)";
   MPI_Comm_rank(world,&me);
-  if (screen) fprintf(screen,"ERROR on proc %d: %s (%s:%d)\n",
-                      me,str,file,line);
+
+  if (input && input->line) lastcmd = input->line;
+  if (screen) fprintf(screen,"ERROR on proc %d: %s (%s:%d)\n"
+                      "Last command: %s\n",
+                      me,str,file,line,lastcmd);
+  if (logfile) fprintf(logfile,"ERROR on proc %d: %s (%s:%d)\n"
+                       "Last command: %s\n",
+                       me,str,file,line,lastcmd);
+
   if (universe->nworlds > 1)
     if (universe->uscreen)
       fprintf(universe->uscreen,"ERROR on proc %d: %s (%s:%d)\n",

src/input.cpp

@@ -530,8 +530,11 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
         value = variable->retrieve(var);
       }
 
-      if (value == NULL) error->one(FLERR,"Substitution for illegal variable");
-
+      if (value == NULL) {
+        char str[128];
+        sprintf(str,"Substitution for illegal variable %s",var);
+        error->one(FLERR,str);
+      }
       // check if storage in str2 needs to be expanded
       // re-initialize ptr and ptr2 to the point beyond the variable.
 
@@ -1172,6 +1175,7 @@ void Input::print()
 
   FILE *fp = NULL;
   int screenflag = 1;
+  int universeflag = 0;
 
   int iarg = 1;
   while (iarg < narg) {
@@ -1194,6 +1198,12 @@ void Input::print()
       else if (strcmp(arg[iarg+1],"no") == 0) screenflag = 0;
       else error->all(FLERR,"Illegal print command");
       iarg += 2;
+    } else if (strcmp(arg[iarg],"universe") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal print command");
+      if (strcmp(arg[iarg+1],"yes") == 0) universeflag = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) universeflag = 0;
+      else error->all(FLERR,"Illegal print command");
+      iarg += 2;
     } else error->all(FLERR,"Illegal print command");
   }
 
@@ -1205,6 +1215,10 @@ void Input::print()
       fclose(fp);
     }
   }
+  if (universeflag && (universe->me == 0)) {
+    if (universe->uscreen)  fprintf(universe->uscreen, "%s\n",line);
+    if (universe->ulogfile) fprintf(universe->ulogfile,"%s\n",line);
+  }
 }
 
 /* ---------------------------------------------------------------------- */