Merge branch 'ion_vertical_advection' of github.com:AetherModel/Aether into ion_vertical_advection

Author: aaronjridley

share/run/UA/inputs/defaults.json

@@ -101,7 +101,8 @@
     "Sources" : {
 	"Grid" : {
 	    "Centripetal" : true,
-		"Coriolis" : true },
+		"Coriolis" : true,
+		"Cent_acc": true },
 	"Neutrals" : {
 	    "NO_cool" : false,
 	    "O_cool": false } },

src/inputs.cpp

@@ -547,10 +547,13 @@ std::vector<std::string> Inputs::get_omniweb_files() {
 
 precision_t Inputs::get_dt_output(int iOutput) {
   precision_t value = 0.0;
-  int nOutputs = settings.at("Outputs").at("type").size();
+  int nOutputs = settings.at("Outputs").at("dt").size();
 
   if (iOutput < nOutputs)
     value = settings.at("Outputs").at("dt").at(iOutput);
+  else{
+    report.error("Output Error; more output types than dt's provided.");
+  }
 
   return value;
 }

src/main/main.cpp

@@ -168,7 +168,7 @@ int main() {
       didWork = output(neutralsMag, ionsMag, mGrid, time, planet);
     }
     if (!didWork)
-      throw std::string("output failed!");
+      throw std::string("Initial output failed!");
 
     // This is advancing now... We are not coupling, so set dt_couple to the
     // end of the simulation

src/output.cpp

@@ -87,7 +87,14 @@ bool output(const Neutrals &neutrals,
 
   for (int iOutput = 0; iOutput < nOutputs; iOutput++) {
 
-    if (time.check_time_gate(input.get_dt_output(iOutput))) {
+    // make sure the output dt is set correctly. Otherwise these errors aren't caught correctly.
+    precision_t dt_output = input.get_dt_output(iOutput);
+    if (dt_output == 0.0){
+      report.exit(function);
+      return false;
+    }
+
+    if (time.check_time_gate(dt_output)) {
 
       // ------------------------------------------------------------
       // Store time in all of the files:
@@ -244,7 +251,7 @@ bool output(const Neutrals &neutrals,
                                                     grid.radius_scgc);
       }
 
-      if (type_output == "bfield") {
+      if (type_output == "bfield" || type_output == "ions") {
         AllOutputContainers[iOutput].store_variable("mlat",
                                                     "Magnetic Latitude",
                                                     "degrees",