Index: /issm/trunk-jpl/src/py/classes/balancethickness.py
===================================================================
--- /issm/trunk-jpl/src/py/classes/balancethickness.py	(revision 11792)
+++ /issm/trunk-jpl/src/py/classes/balancethickness.py	(revision 11792)
@@ -0,0 +1,20 @@
+#module imports
+from fielddisplay import fielddisplay
+class balancethickness:
+	#properties
+	def __init__(self):
+		# {{{ Properties
+		self.spcthickness = float('NaN')
+		self.thickening_rate           = float('NaN')
+		self.stabilization           = 0
+		#}}}
+	def __repr__(obj):
+		# {{{ Display
+		
+		string='   balance thickness solution parameters:' 
+		
+		string="%s\n\n%s"%(string,fielddisplay(obj,'spcthickness','thickness constraints (NaN means no constraint)'))
+		string="%s\n%s"%(string,fielddisplay(obj,'thickening_rate','ice thickening rate used in the mass conservation (dh/dt)'))
+		string="%s\n%s"%(string,fielddisplay(obj,'stabilization','0: None, 1: SU, 2: MacAyeal''s artificial diffusivity, 3:DG'))
+		return string
+		#}}}
Index: /issm/trunk-jpl/src/py/classes/clusters/generic.py
===================================================================
--- /issm/trunk-jpl/src/py/classes/clusters/generic.py	(revision 11792)
+++ /issm/trunk-jpl/src/py/classes/clusters/generic.py	(revision 11792)
@@ -0,0 +1,217 @@
+#GENERIC cluster class definition
+#
+#   Usage:
+#      cluster=generic('name','astrid',);
+#      cluster=generic('name','astrid','np',3);
+#      cluster=generic('name',oshostname(),'np',3,'login','username');
+
+
+class generic:
+	#properties
+	def __init__(self):
+		# {{{ Properties
+		self.name=''
+		self.login=''
+		self.np=1
+		self.port=0
+		self.interactive=1
+		self.codepath=issmtier() + '/bin'
+		self.executionpath=issmtier() + '/execution'
+		self.valgrind=issmtier() + '/externalpackages/valgrind/install/bin/valgrind'
+		self.valgrindlib=issmtier() + '/externalpackages/valgrind/install/lib/libmpidebug.so'
+		self.valgrindsup=issmtier() + '/externalpackages/valgrind/issm.supp'
+		#}}}
+	def __repr__(obj):
+		# {{{ Display
+		
+		string="class 'generic' object:"
+		string="%s\n\n%s"%(string,"%s%s"%('    name: ',obj.name))
+		string="%s\n%s"%(string,"%s%i"%('    np: ',obj.np))
+		string="%s\n%s"%(string,"%s%i"%('    port: ',obj.port))
+		string="%s\n%s"%(string,"%s%s"%('    codepath: ',obj.codepath))
+		string="%s\n%s"%(string,"%s%s"%('    executionpath: ',obj.executionpath))
+		string="%s\n%s"%(string,"%s%s"%('    valgrind: ',obj.valgrind))
+		string="%s\n%s"%(string,"%s%s"%('    valgrindlib: ',obj.valgrindlib))
+		string="%s\n%s"%(string,"%s%s"%('    valgrindsup: ',obj.valgrindsup))
+		return string
+		#}}}
+		
+
+#old matlab
+#		function cluster=generic(varargin) % {{{1
+#
+#			 %use provided options to change fields
+#			 options=pairoptions(varargin{:});
+#
+#			 %get name
+#			 if ~exist(options,'name'), error('option ''name'' has not been provided'); end
+#			 cluster.name=getfieldvalue(options,'name');
+#
+#			 %initialize cluster using user settings if provided
+#			 if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end
+#
+#			 %OK get other fields
+#			 for i=1:size(options.list,1),
+#				 fieldname=options.list{i,1};
+#				 fieldvalue=options.list{i,2};
+#				 if ismember(fieldname,properties('generic')),
+#					 cluster.(fieldname)=fieldvalue;
+#				 else
+#					 disp(['''' fieldname ''' is not a property of cluster generic']);
+#				 end
+#			 end
+#		 end
+#		 %}}}
+#		 function checkconsistency(cluster,md,solution,analyses) % {{{1
+#			 if cluster.np<1
+#				 checkmessage(['number of processors should be at least 1']);
+#			 end
+#			 if isnan(cluster.np),
+#				 checkessage('number of processors should not be NaN!');
+#			 end
+#		 end
+#		 %}}}
+#		 function BuildQueueScript(cluster,md) % {{{1
+#		 
+#			 %retrieve parameters
+#			 modelname=md.miscellaneous.name;
+#			 solution=md.private.solution;
+#			 isvalgrind=md.debug.valgrind;
+#			 isgprof=md.debug.gprof;
+#
+#			 %open file for writing: 
+#			 if ~ispc,
+#				 fid=fopen([modelname '.queue'],'w');
+#			 else
+#				 fid=fopen([modelname '.bat'],'w');
+#			 end
+#
+#			 %write instructions for launching a job on the cluster
+#			 if ~ispc,
+#				 fprintf(fid,'#!/bin/sh\n');
+#			 else
+#				 fprintf(fid,'@echo off\n');
+#			 end
+#			 
+#			 if ~isvalgrind,
+#				 if cluster.interactive
+#					 if ~ispc,
+#						 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s ',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+#					 else
+#						 fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+#					 end
+#				 else
+#					 if ~ispc,
+#						 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname);
+#					 else
+#						 fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog ',cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname);
+#					 end
+#				 end
+#			 else
+#				 if ~ispc,
+#					 %Add --gen-suppressions=all to get suppression lines
+#					 fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib);
+#					 fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
+#					 cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname);
+#				 else
+#					 error('valgrind not supported on windows platforms');
+#				 end
+#			 end
+#
+#			 if isgprof,
+#				 if ~ispc,
+#					 fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname);
+#				 else
+#					 error('gprof not supported on windows platforms');
+#				 end
+#
+#			 end
+#
+#			 if ~md.settings.io_gather,
+#				 if ~ispc,
+#					 %concatenate the output files:
+#					 fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
+#				 else
+#					 error('iogather not supported on windows platforms');
+#				 end
+#
+#			 end
+#			 
+#			 %close file: 
+#			 fclose(fid);
+#
+#			 %in interactive mode, create a run file, and errlog and outlog file
+#			 if cluster.interactive,
+#				 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
+#				 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
+#			 end
+#
+#
+#		 end
+#		 %}}}
+#		 function LaunchQueueJob(cluster,md,options)% {{{1
+#			 
+#			 if ~ispc,
+#					 %lauch command, to be executed via ssh
+#					 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.private.runtimename ' && mkdir ' md.private.runtimename ...
+#					 ' && cd ' md.private.runtimename ' && mv ../' md.private.runtimename '.tar.gz ./ && tar -zxf ' md.private.runtimename '.tar.gz  && source  ' md.miscellaneous.name '.queue '];
+#
+#					 if ~strcmpi(options.batch,'yes'),
+#
+#						 %compress the files into one zip.
+#						 compressstring=['tar -zcf ' md.private.runtimename '.tar.gz ' md.miscellaneous.name '.bin ' md.miscellaneous.name '.queue '  md.miscellaneous.name '.petsc '];
+#						 if md.qmu.isdakota,
+#							 compressstring=[compressstring md.miscellaneous.name '.qmu.in'];
+#					end
+#					if cluster.interactive,
+#						compressstring=[compressstring ' ' md.miscellaneous.name '.errlog ' md.miscellaneous.name '.outlog '];
+#					end
+#					system(compressstring);
+#
+#					disp('uploading input file and queueing script');
+#					issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[md.private.runtimename '.tar.gz']});
+#
+#					disp('launching solution sequence on remote cluster');
+#					issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
+#				else
+#					disp('batch mode requested: not launching job interactively');
+#					disp('launch solution sequence on remote cluster by hand');
+#				end
+#			else
+#				%launch right here, do not compress or archive.
+#				system([md.miscellaneous.name '.bat']);
+#			end
+#
+#		end %}}}
+#		 function Download(cluster,md)% {{{1
+#
+#			if ~ispc,
+#				%some check
+#				if isempty(md.private.runtimename),
+#					error('supply runtime name for results to be loaded!');
+#				end
+#
+#				%Figure out the  directory where all the files are in: 
+#				directory=[cluster.executionpath '/' md.private.runtimename '/'];
+#
+#				%What packages are we picking up from remote cluster
+#				packages={[md.miscellaneous.name '.outlog'],[md.miscellaneous.name '.errlog']};
+#				if md.qmu.isdakota,
+#					packages{end+1}=[md.miscellaneous.name '.qmu.err'];
+#					packages{end+1}=[md.miscellaneous.name '.qmu.out'];
+#					if isfield(md.qmu.params,'tabular_graphics_data'),
+#						if md.qmu.params.tabular_graphics_data==true,
+#							packages{end+1}='dakota_tabular.dat'; 
+#						end
+#					end
+#				else
+#					packages{end+1}=[md.miscellaneous.name '.outbin'];
+#				end
+#
+#				%copy files from cluster to present directory
+#				issmscpin(cluster.name, cluster.login, cluster.port, directory, packages);
+#			else
+#				%do nothing!
+#			end
+#		end %}}}
+#
Index: /issm/trunk-jpl/src/py/classes/clusters/none.py
===================================================================
--- /issm/trunk-jpl/src/py/classes/clusters/none.py	(revision 11792)
+++ /issm/trunk-jpl/src/py/classes/clusters/none.py	(revision 11792)
@@ -0,0 +1,24 @@
+#NONE cluster class definition
+#
+#   Usage:
+#      cluster=none();
+#      cluster=none('np',3);
+#      cluster=none('np',3,'login','username');
+
+class none:
+	#properties
+	def __init__(self):
+		# {{{ Properties
+		self.name='none'
+		#}}}
+	def __repr__(obj):
+		# {{{ Display
+		
+		string="class 'none' object:"
+		string="%s\n\n%s"%(string,"%s%s"%('    name: ',obj.name))
+		return string
+		#}}}
+	def checkconsistency(cluster,md,solution,analyses):
+		pass
+	def BuildQueueScript(cluster,md):
+			 raise RuntimeError('none.BuildQueueScript error message: serial cluster cannot build queue script')
Index: /issm/trunk-jpl/src/py/classes/diagnostic.py
===================================================================
--- /issm/trunk-jpl/src/py/classes/diagnostic.py	(revision 11792)
+++ /issm/trunk-jpl/src/py/classes/diagnostic.py	(revision 11792)
@@ -0,0 +1,63 @@
+#module imports
+from fielddisplay import fielddisplay
+
+class diagnostic:
+	#properties
+	def __init__(self):
+		# {{{ Properties
+		self.spcvx                    = float('NaN')
+		self.spcvy                    = float('NaN')
+		self.spcvz                    = float('NaN')
+		self.restol                   = 0
+		self.reltol                   = 0
+		self.abstol                   = 0
+		self.isnewton                 = 0
+		self.stokesreconditioning     = 0
+		self.viscosity_overshoot      = 0
+		self.icefront                 = float('NaN')
+		self.maxiter                  = 0
+		self.shelf_dampening          = 0
+		self.vertex_pairing           = float('NaN')
+		self.penalty_factor           = float('NaN')
+		self.rift_penalty_lock        = float('NaN')
+		self.rift_penalty_threshold   = 0
+		self.referential              = float('NaN')
+		self.requested_outputs        = float('NaN')
+		#}}}
+	def __repr__(obj):
+		# {{{ Display
+		
+		
+		string='\n   Diagnostic solution parameters:'
+		string="%s\n\n%s"%(string,'      Convergence criteria:')
+			
+		string="%s\n%s"%(string,fielddisplay(obj,'restol','mechanical equilibrium residual convergence criterion'))
+		string="%s\n%s"%(string,fielddisplay(obj,'reltol','velocity relative convergence criterion, NaN -> not applied'))
+		string="%s\n%s"%(string,fielddisplay(obj,'abstol','velocity absolute convergence criterion, NaN -> not applied'))
+		string="%s\n%s"%(string,fielddisplay(obj,'isnewton','Apply Newton''s method instead of a Picard fixed point method'))
+		string="%s\n%s"%(string,fielddisplay(obj,'maxiter','maximum number of nonlinear iterations'))
+		string="%s\n%s"%(string,fielddisplay(obj,'viscosity_overshoot','over-shooting constant new=new+C*(new-old)'))
+
+		string="%s\n%s"%(string,'      boundary conditions:')
+
+		string="%s\n%s"%(string,fielddisplay(obj,'spcvx','x-axis velocity constraint (NaN means no constraint)'))
+		string="%s\n%s"%(string,fielddisplay(obj,'spcvy','y-axis velocity constraint (NaN means no constraint)'))
+		string="%s\n%s"%(string,fielddisplay(obj,'spcvz','z-axis velocity constraint (NaN means no constraint)'))
+		string="%s\n%s"%(string,fielddisplay(obj,'icefront','segments on ice front list (last column 0-> Air, 1-> Water, 2->Ice'))
+
+		string="%s\n%s"%(string,'      Rift options:')
+		string="%s\n%s"%(string,fielddisplay(obj,'rift_penalty_threshold','threshold for instability of mechanical constraints'))
+		string="%s\n%s"%(string,fielddisplay(obj,'rift_penalty_lock','number of iterations before rift penalties are locked'))
+
+		string="%s\n%s"%(string,'      Penalty options:')
+		string="%s\n%s"%(string,fielddisplay(obj,'penalty_factor','offset used by penalties: penalty = Kmax*10^offset'))
+		string="%s\n%s"%(string,fielddisplay(obj,'vertex_pairing','pairs of vertices that are penalized'))
+
+		string="%s\n%s"%(string,'      Other:')
+		string="%s\n%s"%(string,fielddisplay(obj,'shelf_dampening','use dampening for floating ice ? Only for Stokes model'))
+		string="%s\n%s"%(string,fielddisplay(obj,'stokesreconditioning','multiplier for incompressibility equation. Only for Stokes model'))
+		string="%s\n%s"%(string,fielddisplay(obj,'referential','local referential'))
+		string="%s\n%s"%(string,fielddisplay(obj,'requested_outputs','additional outputs requested'))
+
+		return string
+		#}}}
Index: /issm/trunk-jpl/src/py/classes/model.py
===================================================================
--- /issm/trunk-jpl/src/py/classes/model.py	(revision 11791)
+++ /issm/trunk-jpl/src/py/classes/model.py	(revision 11792)
@@ -16,4 +16,7 @@
 from settings import settings
 from solver import solver
+from none import none
+from balancethickness import balancethickness
+from diagnostic import diagnostic
 #}}}
 class model:
@@ -38,8 +41,8 @@
 		self.settings         = settings()
 		self.solver           = solver()
-		self.cluster          = [];
+		self.cluster          = none()
 
-		self.balancethickness = [];
-		self.diagnostic       = [];
+		self.balancethickness = balancethickness()
+		self.diagnostic       = diagnostic()
 		self.groundingline    = [];
 		self.hydrology        = [];