Index: /issm/trunk/src/c/solutions/diagnostic_core.cpp
===================================================================
--- /issm/trunk/src/c/solutions/diagnostic_core.cpp	(revision 10649)
+++ /issm/trunk/src/c/solutions/diagnostic_core.cpp	(revision 10650)
@@ -40,5 +40,5 @@
 
 	/*for qmu analysis, reinitialize velocity so that fake sensitivities do not show up as a result of a different restart of the convergence at each trial.*/
-	if(dakota_analysis){
+	if(dakota_analysis && solution_type==DiagnosticSolutionEnum){
 		InputDuplicatex(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,QmuVxEnum,VxEnum);
 		InputDuplicatex(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,QmuVyEnum,VyEnum);
Index: /issm/trunk/src/c/solutions/transient_core.cpp
===================================================================
--- /issm/trunk/src/c/solutions/transient_core.cpp	(revision 10649)
+++ /issm/trunk/src/c/solutions/transient_core.cpp	(revision 10650)
@@ -25,4 +25,5 @@
 	double finaltime,dt,yts;
 	bool   control_analysis,isdiagnostic,isprognostic,isthermal,isgroundingline;
+	bool   dakota_analysis=false;
 	bool   time_adapt=false;
 	int    solution_type;
@@ -42,4 +43,5 @@
 	femmodel->parameters->FindParam(&yts,ConstantsYtsEnum);
 	femmodel->parameters->FindParam(&control_analysis,InversionIscontrolEnum);
+	femmodel->parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum);
 	femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum);
 	femmodel->parameters->FindParam(&output_frequency,SettingsOutputFrequencyEnum);
@@ -56,4 +58,19 @@
 	step=0;
 	time=0;
+
+	/*for qmu analysis, reinitialize velocity so that fake sensitivities do not show up as a result of a different restart of the convergence at each trial.*/
+	if(dakota_analysis){
+		InputDuplicatex(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,QmuVxEnum,VxEnum);
+		InputDuplicatex(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,QmuVyEnum,VyEnum);
+		InputDuplicatex(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,QmuVzEnum,VzEnum);
+		InputDuplicatex(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,QmuPressureEnum,PressureEnum);
+		InputDuplicatex(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,QmuThicknessEnum,ThicknessEnum);
+		InputDuplicatex(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,QmuSurfaceEnum,SurfaceEnum);
+		InputDuplicatex(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,QmuBedEnum,BedEnum);
+		if(isthermal && dim==3){
+			InputDuplicatex(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,QmuTemperatureEnum,TemperatureEnum);
+			InputDuplicatex(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,QmuMeltingEnum,BasalforcingsMeltingRateEnum);
+		}
+	}
 
 	while(time < finaltime - (yts*DBL_EPSILON)){ //make sure we run up to finaltime.