Index: /issm/trunk/src/m/solutions/dakota/dakota_in_data.m =================================================================== --- /issm/trunk/src/m/solutions/dakota/dakota_in_data.m (revision 1013) +++ /issm/trunk/src/m/solutions/dakota/dakota_in_data.m (revision 1014) @@ -1,6 +1,49 @@ % -% define the data to write the dakota .in file +% define the data to write the dakota .in and .m files. % -% []=dakota_in_data(variables,responses,dmeth,dparams,filei,package,varargin) +% []=dakota_in_data(dmeth,variables,responses,dparams,filei,package,varargin) +% +% where the required input is: +% dmeth (dakota_method, method class object) +% variables (structure array, variable class objects) +% responses (structure array, response class objects) +% dparams (structure array, method-independent parameters) +% filei (character, name of .in and .m files) +% package (character, analysis package) +% +% 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 defines the data to write the dakota .in and +% .m files. it is necessary for multiple reasons. first, +% it collects the parameters and applies some defaults that +% are unique to the environment. second, some analysis package +% variables and/or responses may be treated differently by +% dakota. for example, an analysis package variable may be +% defined as an array, so the QmuSetupDesign brancher will +% create dakota variables for each element of the array. +% finally it calls the functions to write the .in and .m files. +% this function is independent of 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. +% +% "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_in_data(dmeth,variables,responses,dparams,filei,package,varargin) @@ -55,6 +98,6 @@ % for linear constraints, just copy - if strcmp(class(variables.(fnames{i})),'linear_inequality_constraint') || ... - strcmp(class(variables.(fnames{i})),'linear_equality_constraint' ) + if isa(variables.(fnames{i}),'linear_inequality_constraint') || ... + isa(variables.(fnames{i}),'linear_equality_constraint' ) dvar.(fnames{i})=variables.(fnames{i}); Index: /issm/trunk/src/m/solutions/dakota/dakota_in_params.m =================================================================== --- /issm/trunk/src/m/solutions/dakota/dakota_in_params.m (revision 1013) +++ /issm/trunk/src/m/solutions/dakota/dakota_in_params.m (revision 1014) @@ -3,4 +3,35 @@ % % [params]=dakota_in_params(params) +% +% where the optional input is: +% params (structure array, method-independent parameters) +% +% and the output is the same. +% +% this function takes a structure of method-independent dakota +% parameters, which may be empty, and adds default parameters +% for those parameters which do not exist. +% +% the field names of the structure are identical to the dakota +% parameter names (and are in fact used to write them to the +% files). logical values are used for parameters which have +% no associated data and are determined only by their presence +% or absence. +% +% note that the method-dependent parameters are contained in +% the dakota_method class object. +% +% "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 [params]=dakota_in_params(params) Index: /issm/trunk/src/m/solutions/dakota/dakota_in_parse.m =================================================================== --- /issm/trunk/src/m/solutions/dakota/dakota_in_parse.m (revision 1013) +++ /issm/trunk/src/m/solutions/dakota/dakota_in_parse.m (revision 1014) @@ -1,6 +1,43 @@ % -% read a Dakota .in file and parse it. +% read a Dakota .in input file and parse it. % % [method,dvar,dresp]=dakota_in_parse(filei) +% +% where the required input is: +% filei (character, name of .in file) +% +% the required output is: +% method (character, dakota method name) +% dvar (structure array, variables) +% dresp (structure array, responses) +% +% the filei will be prompted if empty. the fields of dvar and +% dresp are particular to the data contained within the file. +% +% this function reads a dakota .in input file and parses it +% into the matlab workspace. it operates in a content-driven +% fashion, where it parses whatever input data it encounters +% in the file, rather than searching for data based on the +% particular method. (this makes it independent of method.) +% +% as of now, parameters are generally not parsed. also, the +% variable and response classes are not used for output. +% +% this data would typically be used for modifying and submitting +% a subsequent dakota run. it could also be used with output +% data for post-processing or annotation purposes. +% +% "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 [method,dvar,dresp]=dakota_in_parse(filei) @@ -233,5 +270,5 @@ function [dresp]=responses_parse(fidi,tokens,itoken) -display('Reading Dakota response functions.'); +display('Reading Dakota responses.'); dresp=[]; nof =0; @@ -515,5 +552,5 @@ strncmpi(tokens{1}{itoken},'responses',9) -% assemble the lists by response function +% assemble the lists by response if exist('nrespl','var') && isfield(dresp,'rf') Index: /issm/trunk/src/m/solutions/dakota/dakota_in_write.m =================================================================== --- /issm/trunk/src/m/solutions/dakota/dakota_in_write.m (revision 1013) +++ /issm/trunk/src/m/solutions/dakota/dakota_in_write.m (revision 1014) @@ -1,6 +1,41 @@ % -% write a Dakota .in file. +% write a Dakota .in input file. % % []=dakota_in_write(method,dmeth,dvar,dresp,params,filei,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) +% filei (character, name of .in file) +% +% the method, dmeth, and filei will be prompted if empty. +% params may be empty, in which case defaults will be used. +% +% the optional varargin are not yet used. +% +% this function writes a dakota .in input file to be used +% by dakota. this file is independent of 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_in_write(method,dmeth,dvar,dresp,params,filei,varargin) @@ -26,4 +61,5 @@ [pathstr,name,ext,versn] = fileparts(filei); if isempty(ext) +% fileparts only considers '.in' to be the extension, not '.qmu.in' ext='.qmu.in'; end Index: /issm/trunk/src/m/solutions/dakota/dakota_m_write.m =================================================================== --- /issm/trunk/src/m/solutions/dakota/dakota_m_write.m (revision 1013) +++ /issm/trunk/src/m/solutions/dakota/dakota_m_write.m (revision 1014) @@ -1,7 +1,51 @@ % -% write a Dakota .m file for the Matlab direct or external -% driver. -% -% []=dakota_m_write(method,dmeth,dvar,dresp,params,filem,package) +% 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) @@ -99,5 +143,5 @@ end -%% function to write design variables into the Matlab m-file +%% function to write variables into the Matlab m-file function []=variables_write(fidm,dmeth,dvar,params,varargin) @@ -145,5 +189,5 @@ eval([descriptor '_lock=1;']); - %now, we need a string to put in the matlab file, which will update all the design variables + %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{:}); Index: /issm/trunk/src/m/solutions/dakota/dakota_out_parse.m =================================================================== --- /issm/trunk/src/m/solutions/dakota/dakota_out_parse.m (revision 1013) +++ /issm/trunk/src/m/solutions/dakota/dakota_out_parse.m (revision 1014) @@ -1,6 +1,48 @@ % -% read a Dakota .out file and parse it. +% read a Dakota .out or .dat output file and parse it. % % [method,dresp,scm,pcm,srcm,prcm]=dakota_out_parse(filei) +% +% where the required input is: +% filei (character, name of .out file) +% +% the required output is: +% method (character, dakota method name) +% dresp (structure array, responses) +% +% and the optional output is: +% scm (double array, simple correlation matrix) +% pcm (double array, partial correlation matrix) +% srcm (double array, simple rank correlation matrix) +% prcm (double array, partial rank correlation matrix) +% +% the filei will be prompted if empty. the fields of dresp +% are particular to the data contained within the file. the +% scm, pcm, srcm, and prcm are output by dakota only for the +% sampling methods. +% +% this function reads a dakota .out output file and parses it +% into the matlab workspace. it operates in a content-driven +% fashion, where it skips the intermediate data and then parses +% whatever output data it encounters in the order in which it +% exists in the file, rather than searching for data based on +% the particular method. (this makes it independent of method.) +% it also can read and parse the .dat tabular_output file. +% +% this data would typically be used for plotting and other +% post-processing within matlab or excel. +% +% "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 [method,dresp,scm,pcm,srcm,prcm]=dakota_out_parse(filei) @@ -183,12 +225,12 @@ % draw box plot -%figure -%subplot(2,1,1) -%plot_boxplot(dresp); +% figure +% subplot(2,1,1) +% plot_boxplot(dresp); % draw normal probability plot -%subplot(2,1,2) -%plot_normplot(dresp); +% subplot(2,1,2) +% plot_normplot(dresp); end @@ -483,5 +525,5 @@ [ntokens,tokens]=fltokens(fline); idvar=idvar+1; - dresp(end).desvar(idvar,1)=cellstr(tokens{1}{5}); + dresp(end).var (idvar,1)=cellstr(tokens{1}{5}); dresp(end).impfac(idvar,1)= tokens{1}{7}; @@ -497,5 +539,5 @@ if ~idvar display(' Importance Factors not available.'); - dresp(end).desvar={}; + dresp(end).var ={}; dresp(end).impfac=[]; while ~ieof && ...