Fixes #262

Two changes have been made.
  - In run.c:parseInput(), a warning is generated if (!par->lte_only && par->nSolveIters<=par->nSolveItersDone && !allBitsSet(par->dataFlags, DS_mask_populations)). I.e. if the user has neither set pops values via a submitted grid file, nor requested any solver iterations.
  - In run.c:run(), gp[gi].mol[si].pops is malloc'd and filled with zeros whether par->doSolveRTE is set or not.

Upshot of the changes are that, where previous the code would seg fault if the user left par->nSolveIters at default, now it will proceed, with a warning message. Any output images will contain zero contribution from line emission.

An additional change: in run.c:run(), formerly the decision to set par->doSolveRTE depended on (par->nSolveIters>0 || par->lte_only), now it depends on (par->nSolveIters>par->nSolveItersDone || par->lte_only).

Author: imckstewart

src/run.c

@@ -978,8 +978,14 @@ exit(1);
 
   par->edgeVelsAvailable=0; /* default value, this is set within getEdgeVelocities(). */
 
-  if(!silent && par->nSolveIters>0 && par->lte_only)
-    warning("Requesting par.nSolveIters>0 will have no effect if LTE calculation is also requested.");
+  if(!silent){
+    if(par->lte_only){
+      if(par->nSolveIters>0)
+        warning("Requesting par->nSolveIters>0 will have no effect if LTE calculation is also requested.");
+    }else if(par->nSolveIters<=par->nSolveItersDone && !allBitsSet(par->dataFlags, DS_mask_populations)){
+      warning("No supplied pops values, and par->nSolveIters <= par->nSolveItersDone.");
+    }
+  }
 
   /* Allocate moldata array.
   */
@@ -1085,7 +1091,8 @@ exit(1);
     par.doMolCalcs = (par.nLineImages>0);
 
   }else{
-    if(par.nSolveIters>0 || par.lte_only) /* To save the user having to set par.doSolveRTE as well as par.nSolveIters>0 or par.lte_only. */
+//    if(par.nSolveIters>0 || par.lte_only) /* To save the user having to set par.doSolveRTE as well as par.nSolveIters>0 or par.lte_only. */
+    if(par.nSolveIters>par.nSolveItersDone || par.lte_only) /* To save the user having to set par->doSolveRTE as well as par->nSolveIters>0 or par->lte_only. */
       par.doSolveRTE = TRUE;
 
     par.doMolCalcs = par.doSolveRTE || par.nLineImages>0;
@@ -1146,8 +1153,10 @@ exit(1);
     for(gi=0;gi<par.ncell;gi++){
       for(si=0;si<par.nSpecies;si++){
         gp[gi].mol[si].specNumDens = malloc(sizeof(double)*md[si].nlev);
+        gp[gi].mol[si].pops        = malloc(sizeof(double)*md[si].nlev);
         for(ei=0;ei<md[si].nlev;ei++){
           gp[gi].mol[si].specNumDens[ei] = 0.0;
+          gp[gi].mol[si].pops[ei] = 0.0;
         }
       }
     }