Index: sm/trunk/src/m/solutions/dakota/cielo_ice_script.sh
===================================================================
--- /issm/trunk/src/m/solutions/dakota/cielo_ice_script.sh	(revision 2141)
+++ 	(revision )
@@ -1,65 +1,0 @@
-#!/bin/bash -f
-# Sample simulator to Dakota system call script
-# See User Manual for instructions
-
-# $argv[1] is params.in.(fn_eval_num) FROM Dakota
-# $argv[2] is results.out.(fn_eval_num) returned to Dakota
-
-if [ -e $2 ]
-then
-    exit
-fi
-
-#check ISSM_DIR global variable is defined!
-if [[ "$ISSM_DIR" == "" ]]
-then
-	echo "Dakota could not find the ISSM_DIR global variable ! Aborting..."
-	exit 1
-fi
-
-# ------------------------
-# Set up working directory
-# ------------------------
-num=`echo $1 | sed 's/params.in.//g'`
-
-mkdir workdir.$num
-cp Qmu.model workdir.$num
-cp $ISSM_DIR/startup.m workdir.$num
-cd workdir.$num
-echo -n "$num" > number
-
-
-# --------------
-# PRE-PROCESSING
-# --------------
-# Use the following line if SNL's APREPRO utility is used instead of DPrePro.
-# ../aprepro -c '*' -q --nowarning modal.bdf.template modal.bdf
-
-#Preprocess 
-dprepro ../$1 ../qmu.m cielo_ice_run.m
-
-# --------
-# ANALYSIS
-# --------
-
-#nast707 jid=modal.bdf mem=2m scr=yes bat=no >&! nastran.out
-#cp -p ../cielo_ice_run.m .
-echo "Submitting function evaluation $num to Matlab."
-matlab -nodisplay -r "cielo_ice_run('Qmu.model','$2');exit;" >& matlab.out.$num
-echo "Receiving function evaluation $num from Matlab."
-
-# ---------------
-# POST-PROCESSING
-# ---------------
-
-#grep '                                  X           ' modal.f06 | cut -c 46-60 > $2
-#grep '        7        ' modal.f06 | cut -c 66-80 >> $2
-mv $2 ../.
-mv matlab.out.$num ../.
-
-# --------
-# Clean up
-# --------
-
-cd ..
-rm -rf workdir.$num
Index: /issm/trunk/src/m/solutions/dakota/dakota_in_data.m
===================================================================
--- /issm/trunk/src/m/solutions/dakota/dakota_in_data.m	(revision 2141)
+++ /issm/trunk/src/m/solutions/dakota/dakota_in_data.m	(revision 2142)
@@ -109,8 +109,9 @@
         for j=1:length(variables.(fnames{i}))
             %call setupdesign
-            dvar.(fnames{i})=QmuSetupDesign(dvar.(fnames{i}),variables.(fnames{i})(j),params,varargin{:}); 
+            dvar.(fnames{i})=QmuSetupDesign(dvar.(fnames{i}),variables.(fnames{i})(j),params,varargin{:});
         end
     end
 end
+
 
 %%  responses
@@ -135,6 +136,3 @@
 dakota_in_write(dmeth.method,dmeth,dvar,dresp,params,filei,varargin{:});
 
-%Write m file
-%dakota_m_write(dmeth.method,dmeth,dvar,dresp,params,filei,package,varargin{:});
-
 end
Index: sm/trunk/src/m/solutions/dakota/dakota_m_write.m
===================================================================
--- /issm/trunk/src/m/solutions/dakota/dakota_m_write.m	(revision 2141)
+++ 	(revision )
@@ -1,296 +1,0 @@
-%
-%  write a Matlab .m function file to be called by Dakota for
-%  the Matlab direct or external driver.
-%
-%  []=dakota_m_write(method,dmeth,dvar,dresp,params,filem,package,varargin)
-%
-%  where the required input is:
-%    method        (character, dakota method name)
-%    dmeth         (dakota_method, method class object)
-%    dvar          (structure array, variable class objects)
-%    dresp         (structure array, response class objects)
-%    params        (structure array, method-independent parameters)
-%    filem         (character, name of .m file)
-%    package       (character, analysis package)
-%
-%  the method, dmeth, and filem will be prompted if empty.
-%  params may be empty, in which case defaults will be used.
-%
-%  the optional varargin are passed directly through to the
-%  QmuUpdateFunctions brancher to be used by the analysis
-%  package.  for example, this could be model information.
-%
-%  this function writes a matlab .m function file to be called
-%  by dakota for the matlab direct or external driver.  for
-%  the direct driver, dakota is linked with matlab and
-%  automatically starts a matlab session, passing the variables
-%  and responses through the function; for the external driver,
-%  dakota calls a shell script to start the matlab session,
-%  passing the variables and responses through text files.
-%  this function must be tailored to the particular analysis
-%  package.
-%
-%  this data would typically be generated by a matlab script
-%  for a specific model, using the method, variable, and
-%  response class objects.  this function may be called by
-%  dakota_in_data.
-%
-%  "Copyright 2009, by the California Institute of Technology.
-%  ALL RIGHTS RESERVED. United States Government Sponsorship
-%  acknowledged. Any commercial use must be negotiated with
-%  the Office of Technology Transfer at the California Institute
-%  of Technology.  (NTR 47078)
-%
-%  This software may be subject to U.S. export control laws.
-%  By accepting this  software, the user agrees to comply with
-%  all applicable U.S. export laws and regulations. User has the
-%  responsibility to obtain export licenses, or other export
-%  authority as may be required before exporting such information
-%  to foreign countries or providing access to foreign persons."
-%
-function []=dakota_m_write(method,dmeth,dvar,dresp,params,filem,package,varargin)
-
-if ~nargin
-    help dakota_m_write
-    return
-end
-
-%  process the input parameters
-
-if ~exist('method','var') || isempty(method)
-    method=input('Method?  ','s');
-end
-
-if ~exist('dmeth' ,'var') || isempty(dmeth)
-    dmeth=dakota_method(method);
-end
-
-if ~exist('params','var')
-    params=[];
-end
-
-if ~exist('filem' ,'var') || isempty(filem)
-    filem=input('Matlab m-file to write?  ','s');
-end
-[pathstr,name,ext,versn] = fileparts(filem);
-if isempty(ext)
-    ext='.m';
-end
-filem2=fullfile(pathstr,[name ext versn]);
-
-display(sprintf('Opening Matlab m-file ''%s''.',filem2));
-fidm=fopen(sprintf('%s',filem2),'w');
-if (fidm < 0)
-    error('''%s'' could not be opened.',filem2);
-end
-
-%  write beginning of the Matlab m-file
-
-begin_write(fidm,name,params);
-
-%  write variables into the Matlab m-file
-
-variables_write(fidm,dmeth,dvar,params,varargin{:});
-
-%  write solution into the Matlab m-file
-
-solution_write(fidm,package);
-
-%  write responses into the Matlab m-file
-
-responses_write(fidm,dmeth,params,dresp);
-
-%  write end of the Matlab m-file
-
-end_write(fidm,name,params);
-
-fclose(fidm);
-display('End of file successfully written.');
-
-end
-
-%%  function to write beginning of the Matlab m-file
-
-function []=begin_write(fidm,name,params)
-
-display('Writing beginning of Matlab m-file.');
-
-fprintf(fidm,'%%\n');
-if strcmpi(params.analysis_driver,'matlab')
-    fprintf(fidm,'%%  Run the specified input variables and return the output responses.\n');
-    fprintf(fidm,'%%\n');
-    fprintf(fidm,'function Dakota=%s(Dakota)\n\n',name);
-    fprintf(fidm,'clk=clock;\n');
-    fprintf(fidm,'cpu=cputime;\n\n');
-    fprintf(fidm,'%% Dakota\n\n');
-    fprintf(fidm,'infile=''%s'';\n','Qmu.model');
-else
-    fprintf(fidm,'%%  Run the specified input file and return the output file.\n');
-    fprintf(fidm,'%%\n');
-    fprintf(fidm,'function %s(infile,outfile)\n\n',name);
-    fprintf(fidm,'clk=clock;\n');
-    fprintf(fidm,'cpu=cputime;\n\n');
-end
-fprintf(fidm,'try\n');
-fprintf(fidm,'\tloadmodel(infile);\n\n');
-
-if strcmpi(params.analysis_driver,'matlab')
-	fprintf(fidm,'\tmd=qmuname(md,Dakota.fnEvalId);\n\n');
-else
-	fprintf(fidm,'\tmd=qmuname(md);\n\n');
-end
-
-end
-
-%%  function to write variables into the Matlab m-file
-
-function []=variables_write(fidm,dmeth,dvar,params,varargin)
-
-display('Writing variables for Matlab m-file.');
-
-fprintf(fidm,'%%  Apply the variables.\n\n');
-ixc=0;
-
-%  variables vary by method
-
-ixc=vsets_write(fidm,ixc,dvar,dmeth.variables,params,varargin{:});
-
-end
-
-%%  function to write variable sets into the Matlab m-file
-
-function [ixc]=vsets_write(fidm,ixc,dvar,variables,params,varargin)
-
-for i=1:length(variables)
-    if isfield(dvar,variables{i})
-        ixc=vlist_write(fidm,ixc,variables{i},dvar.(variables{i}),params,varargin{:});
-    end
-end
-
-end
-
-%%  function to write variable list into the Matlab m-file
-
-function [ixc]=vlist_write(fidm,ixc,vtype,dvar,params,varargin)
-
-disp(sprintf('  Writing %d %s variables.',length(dvar),class(dvar)));
-
-for i=1:length(dvar)
-
-	%first find descriptor, without sample number on it.
-	descriptor=discardnum(dvar(i).descriptor);
-
-	%is there a lock on this variable? We don't want to update the variable twice!
-	if exist([descriptor '_lock'],'var'),
-		%lock is in place, do not update! continue;
-		continue;
-	else
-		%first things first, put lock in place
-		eval([descriptor '_lock=1;']);
-
-		%now, we need a string to put in the matlab file, which will update all the variables 
-		%for  this descriptor.
-		[string,ixc]=QmuUpdateFunctions(ixc,descriptor,dvar,params,i,varargin{:});
-
-		%dump this string in the matlab file.
-        fprintf(fidm,'%s',string);
-	end
-end
-
-end
-
-%%  function to write solution into the Matlab m-file
-
-function []=solution_write(fidm,package)
-
-display('Writing solution for Matlab m-file.');
-fprintf(fidm,'%%  Run the solution.\n\n');
-
-fprintf(fidm,['\tmd=solve(md,''diagnostic'',''' package ''');\n\n']);
-
-end
-
-%%  function to write responses into the Matlab m-file
-
-function []=responses_write(fidm,dmeth,params,dresp)
-
-display('Writing responses for Matlab m-file.');
-
-fprintf(fidm,'%%  Calculate the responses.\n\n');
-ifnvals=0;
-
-if ~strcmpi(params.analysis_driver,'matlab')
-    fprintf(fidm,'\tfid=fopen(outfile,''w'');\n\n');
-end
-
-%  responses vary by method
-
-ifnvals=rsets_write(fidm,ifnvals,params,dresp,dmeth.responses);
-
-fprintf(fidm,'\n');
-if ~strcmpi(params.analysis_driver,'matlab')
-    fprintf(fidm,'\tstatus=fclose(fid);\n\n');
-end
-
-end
-
-%%  function to write response sets into the Matlab m-file
-
-function [ifnvals]=rsets_write(fidm,ifnvals,params,dresp,responses)
-
-for i=1:length(responses)
-    if isfield(dresp,responses{i})
-        ifnvals=rlist_write(fidm,ifnvals,params,responses{i},dresp.(responses{i}));
-    end
-end
-
-end
-
-%%  function to write response list into the Matlab m-file
-
-function [ifnvals]=rlist_write(fidm,ifnvals,params,rtype,dresp)
-
-disp(sprintf('  Writing %d %s responses.',length(dresp),class(dresp)));
-for i=1:length(dresp)
-    ifnvals=ifnvals+1;
-    if strcmpi(params.analysis_driver,'matlab')
-        fprintf(fidm,'\tDakota.fnVals(%d)=QmuResponseValue(md,''%s'');\n',ifnvals,dresp(i).descriptor);
-    else
-        fprintf(fidm,'\tfprintf(fid,''%%f\\n'',QmuResponseValue(md,''%s''));\n',dresp(i).descriptor);
-    end
-end
-
-end
-
-%%  function to write end of the Matlab m-file
-
-function []=end_write(fidm,name,params)
-
-display('Writing end of Matlab m-file.');
-
-fprintf(fidm,'%%  Error condition.\n\n');
-
-fprintf(fidm,'catch ME\n');
-fprintf(fidm,'\tME\n');
-fprintf(fidm,'\tfor i=1:length(ME.stack)\n');
-fprintf(fidm,'\t\tdisplay(sprintf(''    file(%%d): %%s'',  i,ME.stack(i).file));\n');
-fprintf(fidm,'\t\tdisplay(sprintf(''    name(%%d): %%s'',  i,ME.stack(i).name));\n');
-fprintf(fidm,'\t\tdisplay(sprintf(''    line(%%d): %%d\\n'',i,ME.stack(i).line));\n');
-fprintf(fidm,'\tend\n');
-if strcmpi(params.analysis_driver,'matlab')
-    fprintf(fidm,'\tDakota.failure=1;\n');
-else
-    fprintf(fidm,'\tif exist(''fid'',''var'')\n');
-    fprintf(fidm,'\t\tstatus=fclose(fid);\n');
-    fprintf(fidm,'\tend\n');
-    fprintf(fidm,'\tfid=fopen(outfile,''w'');\n');
-    fprintf(fidm,'\tfprintf(fid,''fail\\n'');\n');
-    fprintf(fidm,'\tstatus=fclose(fid);\n');
-end
-fprintf(fidm,'end\n\n');
-
-fprintf(fidm,'disp(sprintf(''%s -- %%f CPU seconds; %%f clock seconds\\n'',...\n',name);
-fprintf(fidm,'    cputime-cpu,etime(clock,clk)))\n\n');
-fprintf(fidm,'end\n\n');
-
-end
Index: /issm/trunk/src/m/solutions/dakota/preqmu.m
===================================================================
--- /issm/trunk/src/m/solutions/dakota/preqmu.m	(revision 2141)
+++ /issm/trunk/src/m/solutions/dakota/preqmu.m	(revision 2142)
@@ -41,12 +41,4 @@
 %when running in library mode, the in file needs to be called md.name.qmu.in
 options.qmufile=[md.name ];
-
-%create m and in files for dakota
-if (~isfield(md.qmu_params(options.iparams),'direct') || ...
-    ~md.qmu_params(options.iparams).direct) && ...
-   (~isfield(md.qmu_params(options.iparams),'analysis_driver') || ...
-    isempty(md.qmu_params(options.iparams).analysis_driver))
-    md.qmu_params(options.iparams).analysis_driver=[ISSM_DIR '/src/m/solutions/dakota/cielo_ice_script.sh'];
-end
 
 %retrieve variables and resposnes for this particular analysis.
Index: /issm/trunk/src/m/solutions/dakota/process_qmu_options.m
===================================================================
--- /issm/trunk/src/m/solutions/dakota/process_qmu_options.m	(revision 2141)
+++ /issm/trunk/src/m/solutions/dakota/process_qmu_options.m	(revision 2142)
@@ -86,5 +86,5 @@
 %first, the defaults
 qmudir ='qmu';% qmudir =['qmu_' datestr(now,'yyyymmdd_HHMMSS')];
-qmufile='qmu';%  qmufile can not be changed unless cielo_ice_script.sh is also changed
+qmufile='qmu';
 ivar   =1;
 iresp  =1;