Index: /issm/trunk/src/m/solutions/dakota/qmu.m
===================================================================
--- /issm/trunk/src/m/solutions/dakota/qmu.m	(revision 267)
+++ /issm/trunk/src/m/solutions/dakota/qmu.m	(revision 268)
@@ -1,3 +1,3 @@
-function md=qmu(md,package)
+function md=qmu(md,package,varargin)
 %INPUT function md=qmu(md,package)
 %Deal with coupled ISSM or Cielo/ Dakota runs, to do sensitivity analyses.
@@ -5,7 +5,33 @@
 global ISSM_DIR;
 
+% qmudir =['qmu_' datestr(now,'yyyymmdd_HHMMSS')];
+qmudir ='qmu';
+%  qmufile can not be changed unless cielo_ice_script.sh is
+qmufile='qmu';
+ivar   =1;
+iresp  =1;
+imethod=1;
+iparams=1;
+
+%  process any extra input arguments
+
+for i=1:2:nargin-2
+    switch varargin{i}
+        case 'qmudir'
+            qmudir =varargin{i+1};
+        case 'qmufile'
+            qmufile=varargin{i+1};
+        case 'ivar'
+            ivar   =varargin{i+1};
+        case 'iresp'
+            iresp  =varargin{i+1};
+        case 'imethod'
+            imethod=varargin{i+1};
+        case 'iparams'
+            iparams=varargin{i+1};
+    end
+end
+
 %first create temporary directory in which we will work
-% qmudir=['qmu_' datestr(now,'yyyymmdd_HHMMSS')];
-qmudir='qmu';
 if exist(qmudir,'dir')
     overwrite=input(['Overwrite existing ''' qmudir ''' directory? Y/N [N]: '], 's');
@@ -21,34 +47,31 @@
 
 %save our model in qmu so that it can be repeatedly used by Dakota.
-save Qmu.model md
+save('Qmu.model','md')
 
 %create m and in files for dakota
-if ~isfield(md.qmu_params,'analysis_driver') || ...
-    isempty(md.qmu_params.analysis_driver)
-    md.qmu_params.analysis_driver=[ISSM_DIR '/src/m/solutions/dakota/cielo_ice_script.sh'];
+if ~isfield(md.qmu_params(iparams),'analysis_driver') || ...
+    isempty(md.qmu_params(iparams).analysis_driver)
+    md.qmu_params(iparams).analysis_driver=[ISSM_DIR '/src/m/solutions/dakota/cielo_ice_script.sh'];
 end
 
-if (numel(md.qmu_method) > 1)
-    imeth=input('Which method? ');
-else
-    imeth=1;
+dakota_in_data(md.qmu_method(imethod),md.variables(ivar),md.responses(iresp),md.qmu_params(iparams),qmufile,package,md);
+rundak=input(['Run Dakota analysis ''' qmufile '''? Y/N [N]: '], 's');
+if ~strncmpi(rundak,'y',1)
+    cd ..
+    return
 end
-dakota_in_data(md.qmu_method(imeth),md.variables,md.responses,md.qmu_params,'qmu',package,md);
-cd ..
-return
 
 %call dakota
-system('dakota -i qmu.in -o qmu.out -e qmu.err');
-% system('export MPIRUN_NPROCS=8;mpirun -np 4 dakota -i qmu.in -o qmu.out -e qmu.err');
+system(['dakota -i ' qmufile '.in -o ' qmufile '.out -e ' qmufile '.err']);
+% system(['export MPIRUN_NPROCS=8;mpirun -np 4 dakota -i ' qmufile '.in -o ' qmufile '.out -e ' qmufile '.err']);
 
 %parse inputs and results from dakota
-[method,dvar,dresp_in]=dakota_in_parse('qmu.in');
+[method,dvar,dresp_in]=dakota_in_parse([qmufile '.in']);
 md.dakotaresults.method   =method;
 md.dakotaresults.dvar     =dvar;
 md.dakotaresults.dresp_in =dresp_in;
-[method,dresp_out,scm,pcm,srcm,prcm]=dakota_out_parse('qmu.out');
+
+[method,dresp_out,scm,pcm,srcm,prcm]=dakota_out_parse([qmufile '.out']);
 md.dakotaresults.dresp_out=dresp_out;
-[method,dresp_dat                  ]=dakota_out_parse('dakota_tabular.dat');
-md.dakotaresults.dresp_dat=dresp_dat;
 md.dakotaresults.scm      =scm;
 md.dakotaresults.pcm      =pcm;
@@ -56,9 +79,20 @@
 md.dakotaresults.prcm     =prcm;
 
+if exist('dakota_tabular.dat','file')
+    [method,dresp_dat                  ]=dakota_out_parse('dakota_tabular.dat');
+    md.dakotaresults.dresp_dat=dresp_dat;
+end
+
 %save input and output files into model
-md.dakotain =readfile('qmu.in');
-md.dakotaout=readfile('qmu.out');
-md.dakotadat=readfile('dakota_tabular.dat');
-	
+md.dakotain =readfile([qmufile '.in']);
+md.dakotaout=readfile([qmufile '.out']);
+if exist('dakota_tabular.dat','file')
+	md.dakotadat=readfile('dakota_tabular.dat');
+end
+
+system('zip -mq params.in.zip params.in.[1-9]*');
+system('zip -mq results.out.zip results.out.[1-9]*');
+system('zip -mq matlab.out.zip matlab*.out.[1-9]*');
+
 %get out of local directory and erase
 cd ../