Index: /issm/trunk-jpl/src/m/qmu/preqmu.m
===================================================================
--- /issm/trunk-jpl/src/m/qmu/preqmu.m	(revision 17790)
+++ /issm/trunk-jpl/src/m/qmu/preqmu.m	(revision 17791)
@@ -13,15 +13,17 @@
 %       iparams: same thing for params
 %       overwrite: overwrite qmudir before analysis
-%       keep: keep qmudir after analysis
-%       outfiles: (John?)
-%       rstfile: backup file name
-%       rundakota: (John?)
-%       runmpi: (John?)
 
 disp('preprocessing dakota inputs');
+qmudir    = getfieldvalue(options,'qmudir',['qmu' num2str(feature('GetPid'))]);  % qmudir = ['qmu_' datestr(now,'yyyymmdd_HHMMSS')];
+qmufile   = getfieldvalue(options,'qmufile','qmu');% qmufile cannot be changed unless ????script.sh is also changed
+overwrite = getfieldvalue(options,'overwrite','n');
+ivar      = getfieldvalue(options,'ivar',1);
+iresp     = getfieldvalue(options,'iresp',1);
+imethod   = getfieldvalue(options,'imethod',1);
+iparams   = getfieldvalue(options,'iparams',1);
 
 %first create temporary directory in which we will work
-if strncmpi(options.overwrite,'y',1)
-	system(['rm -rf ' options.qmudir '/*']); 
+if strncmpi(overwrite,'y',1)
+	system(['rm -rf ' qmudir '/*']); 
 else
 	%does the directory exist? if so, then error out
@@ -34,9 +36,9 @@
 
 %when running in library mode, the in file needs to be called md.miscellaneous.name.qmu.in
-options.qmufile=[md.miscellaneous.name ];
+qmufile=[md.miscellaneous.name ];
 
 %retrieve variables and resposnes for this particular analysis.
-variables=md.qmu.variables(options.ivar);
-responses=md.qmu.responses(options.iresp);
+variables=md.qmu.variables(ivar);
+responses=md.qmu.responses(iresp);
 
 %expand variables and responses
@@ -73,13 +75,13 @@
 
 %create in file for dakota
-dakota_in_data(md.qmu.method(options.imethod),variables,responses,md.qmu.params(options.iparams),options.qmufile);
+dakota_in_data(md.qmu.method(imethod),variables,responses,md.qmu.params(iparams),qmufile);
 system(['rm -rf ' md.miscellaneous.name '.m']);
 
 %build a list of variables and responses descriptors. the list is not expanded. {{{
 variabledescriptors={};
-variable_fieldnames=fieldnames(md.qmu.variables(options.ivar));
+variable_fieldnames=fieldnames(md.qmu.variables(ivar));
 for i=1:length(variable_fieldnames),
 	field_name=variable_fieldnames{i};
-	fieldvariables=md.qmu.variables(options.ivar).(field_name);
+	fieldvariables=md.qmu.variables(ivar).(field_name);
 	for j=1:numel(fieldvariables)
 		variabledescriptors{end+1}=fieldvariables(j).descriptor;
@@ -88,8 +90,8 @@
 
 responsedescriptors={};
-response_fieldnames=fieldnames(md.qmu.responses(options.iresp));
+response_fieldnames=fieldnames(md.qmu.responses(iresp));
 for i=1:length(response_fieldnames),
 	field_name=response_fieldnames{i};
-	fieldresponses=md.qmu.responses(options.iresp).(field_name);
+	fieldresponses=md.qmu.responses(iresp).(field_name);
 	for j=1:numel(fieldresponses)
 		responsedescriptors{end+1}=fieldresponses(j).descriptor;