/[escript]/trunk/escript/py_src/modelframe.py
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trunk/esys2/escript/py_src/modelframe.py revision 123 by jgs, Fri Jul 8 04:08:13 2005 UTC trunk/escript/py_src/modelframe.py revision 1312 by ksteube, Mon Sep 24 06:18:44 2007 UTC
# Line 1  Line 1 
1    #
2  # $Id$  # $Id$
3    #
4    #######################################################
5    #
6    #           Copyright 2003-2007 by ACceSS MNRF
7    #       Copyright 2007 by University of Queensland
8    #
9    #                http://esscc.uq.edu.au
10    #        Primary Business: Queensland, Australia
11    #  Licensed under the Open Software License version 3.0
12    #     http://www.opensource.org/licenses/osl-3.0.php
13    #
14    #######################################################
15    #
16    
17    """
18    Environment for implementing models in escript
19    
20    @var __author__: name of author
21    @var __copyright__: copyrights
22    @var __license__: licence agreement
23    @var __url__: url entry point on documentation
24    @var __version__: version
25    @var __date__: date of the version
26    """
27    
28    __author__="Lutz Gross, l.gross@uq.edu.au"
29    __copyright__="""  Copyright (c) 2006 by ACcESS MNRF
30                        http://www.access.edu.au
31                    Primary Business: Queensland, Australia"""
32    __license__="""Licensed under the Open Software License version 3.0
33                 http://www.opensource.org/licenses/osl-3.0.php"""
34    __url__="http://www.iservo.edu.au/esys"
35    __version__="$Revision$"
36    __date__="$Date$"
37    
38    
39  from types import StringType,IntType,FloatType,BooleanType,ListType,DictType  from types import StringType,IntType,FloatType,BooleanType,ListType,DictType
40  from sys import stdout  from sys import stdout
41    import numarray
42    import operator
43  import itertools  import itertools
44    import time
45  import modellib  import os
46    
47  # import the 'set' module if it's not defined (python2.3/2.4 difference)  # import the 'set' module if it's not defined (python2.3/2.4 difference)
48  try:  try:
# Line 14  except NameError: Line 52  except NameError:
52    
53  from xml.dom import minidom  from xml.dom import minidom
54    
 def dataNode(document, tagName, data):  
     t = document.createTextNode(str(data))  
     n = document.createElement(tagName)  
     n.appendChild(t)  
     return n  
   
 def esysDoc():  
     doc = minidom.Document()  
     esys = doc.createElement('ESys')  
     doc.appendChild(esys)  
     return doc, esys  
55    
56  def all(seq):  def all(seq):
57      for x in seq:      for x in seq:
# Line 32  def all(seq): Line 59  def all(seq):
59              return False              return False
60      return True      return True
61    
62  LinkableObjectRegistry = {}  def any(seq):
63        for x in seq:
64  def registerLinkableObject(obj_id, o):          if x:
65      LinkableObjectRegistry[obj_id] = o              return True
66        return False
67    
68    def importName(modulename, name):
69        """ Import a named object from a module in the context of this function,
70            which means you should use fully qualified module paths.
71            Return None on failure.
72    
73  LinkRegistry = []          This function from: http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/52241
74        """
75        module = __import__(modulename, globals(), locals(), [name])
76            
77        try:
78            return vars(module)[name]
79        except KeyError:
80            raise ImportError("Could not import %s from %s" % (name, modulename))
81    
82  def registerLink(obj_id, l):  class ESySXMLParser(object):
83      LinkRegistry.append((obj_id,l))      """
84        parser for ESysXML file
85  def parse(xml):      """
86      global LinkRegistry, LinkableObjectRegistry      def __init__(self,xml, debug=False):
87      LinkRegistry = []        self.__dom = minidom.parseString(xml)
88      LinkableObjectRegistry = {}        self.__linkable_object_registry= {}
89          self.__link_registry=  []
90      doc = minidom.parseString(xml)        self.__esys=self.__dom.getElementsByTagName('ESys')[0]
91          self.debug=debug
92      sim = getComponent(doc.firstChild)    
93      for obj_id, link in LinkRegistry:      def getClassPath(self, node):
94          link.target = LinkableObjectRegistry[obj_id]          type = node.getAttribute("type")
95            if (node.getAttribute("module")):
96      return sim              module = node.getAttribute("module")
97                return importName(module, type)
98  def getComponent(doc):          else:
99      for node in doc.childNodes:              return importName("__main__", type)
         if isinstance(node, minidom.Element):  
             if node.tagName == 'Simulation':  
                 if node.getAttribute("type") == 'Simulation':  
                     return Simulation.fromDom(node)  
                 elif node.getAttribute("type") == 'ExplicitSimulation':  
                     return ExplicitSimulation.fromDom(node)  
             if node.tagName == 'Model':  
                 model_type = node.getAttribute("type")  
                 model_subclasses = Model.__subclasses__()  
                 for model in model_subclasses:  
                     if model_type == model.__name__:  
                         return model.fromDom(node)  
                       
             raise "Invalid simulation type, %r" % node.getAttribute("type")  
100    
101      raise ValueError("No Simulation Found")      def setLinks(self):
102                        for obj_id, link in self.__link_registry:
103                link.target = self.__linkable_object_registry[obj_id]
104    
105        def parse(self):
106           """
107           parser method for EsysXML and returns the list of generating ParameterSets
108           """
109           found=[]
110           for node in self.__esys.childNodes:
111               if isinstance(node, minidom.Element):
112                   if node.tagName == 'Simulation':
113                            found.append(Simulation.fromDom(self, node))
114                   elif node.tagName == 'Model':
115                            found.append(self.getClassPath(node).fromDom(self, node))
116                   elif node.tagName == 'ParameterSet':
117                            found.append(self.getClassPath(node).fromDom(self, node))
118                   else:
119                      raise "Invalid type, %r" % node.getAttribute("type")
120           self.setLinks()
121           return found
122    
123        def registerLink(self,obj_id, link):
124            self.__link_registry.append((int(obj_id),link))
125    
126        def registerLinkableObject(self,obj, node):
127            id_str=node.getAttribute('id').strip()
128            if len(id_str)>0:
129               id=int(id_str)
130               if self.__linkable_object_registry.has_key(id):
131                   raise ValueError("Object id %s already exists."%id)
132               else:
133                   self.__linkable_object_registry[id]=obj
134    
135        def getComponent(self, node):
136           """
137           returns a single component + rank from a simulation
138           parser method for EsysXML and returns the list of generating ParameterSets
139           """
140           rank  = int(node.getAttribute("rank"))
141           for n in node.childNodes:
142               if isinstance(n, minidom.Element):
143                   if n.tagName == 'Simulation':
144                            return (rank, Simulation.fromDom(self, n))
145                   elif n.tagName == 'Model':
146                            return (rank, self.getClassPath(n).fromDom(self, n))
147                   elif n.tagName == 'ParameterSet':
148                            return (rank, self.getClassPath(n).fromDom(self, n))
149                   else:
150                     raise ValueError("illegal component type %s"%n.tagName)
151           raise ValueError("cannot resolve Component")
152    
153    class ESySXMLCreator(object):
154        """
155        creates an XML Dom representation
156        """
157        def __init__(self):
158           self.__dom=minidom.Document()
159           self.__esys =self.__dom.createElement('ESys')
160           self.__dom.appendChild(self.__esys)
161           self.__linkable_object_registry={}
162           self.__number_sequence = itertools.count(100)
163        def getRoot(self):
164           return self.__esys
165        def createElement(self,name):
166          return self.__dom.createElement(name)
167        def createTextNode(self,name):
168          return self.__dom.createTextNode(name)
169        def getElementById(self,name):
170          return self.__dom.getElementById(name)
171        def createDataNode(self, tagName, data):
172              """
173              C{createDataNode}s are the building blocks of the xml documents constructed in
174              this module.  
175        
176              @param tagName: the associated xml tag
177              @param data: the values in the tag
178              """
179              n = self.createElement(tagName)
180              n.appendChild(self.createTextNode(str(data)))
181              return n
182        def getLinkableObjectId(self, obj):
183            for id, o in self.__linkable_object_registry.items():
184                if o == obj: return id
185            id =self.__number_sequence.next()
186            self.__linkable_object_registry[id]=obj
187            return id
188            
189        def registerLinkableObject(self, obj, node):
190            """
191            returns a unique object id for object obj
192            """
193            id=self.getLinkableObjectId(obj)
194            node.setAttribute('id',str(id))
195            node.setIdAttribute("id")
196    
197        def includeTargets(self):
198            target_written=True
199            while target_written:
200                targetsList =self.__dom.getElementsByTagName('Target')
201                target_written=False
202                for element in targetsList:
203                   targetId = int(element.firstChild.nodeValue.strip())
204                   if self.getElementById(str(targetId)): continue
205                   targetObj = self.__linkable_object_registry[targetId]
206                   targetObj.toDom(self, self.__esys)
207                   target_written=True
208    
209        def toprettyxml(self):
210            self.includeTargets()
211            return self.__dom.toprettyxml()
212    
213  class Link:  class Link:
214      """      """
215      a Link makes an attribute of an object callable:      A Link makes an attribute of an object callable::
216    
217            o.object()            o.object()
218            o.a=8            o.a=8
219            l=Link(o,"a")            l=Link(o,"a")
# Line 85  class Link: Line 221  class Link:
221       """       """
222            
223      def __init__(self,target,attribute=None):      def __init__(self,target,attribute=None):
224          """creates a link to the object target. If attribute is given, the link is          """
225            Creates a link to the object target. If attribute is given, the link is
226          establised to this attribute of the target.  Otherwise the attribute is          establised to this attribute of the target.  Otherwise the attribute is
227          undefined."""          undefined.
228            """
229          self.target = target          self.target = target
230          self.attribute = None          self.attribute = None
231          self.setAttributeName(attribute)          self.setAttributeName(attribute)
232    
233        def getTarget(self):
234            """
235            returns the target
236            """
237            return self.target
238        def getAttributeName(self):
239            """
240            returns the name of the attribute the link is pointing to
241            """
242            return self.attribute
243            
244      def setAttributeName(self,attribute):      def setAttributeName(self,attribute):
245          """set a new attribute name to be collected from the target object. The          """
246          target object must have the attribute with name attribute."""          Set a new attribute name to be collected from the target object. The
247          if attribute and self.target and not hasattr(self.target, attribute):          target object must have the attribute with name attribute.
248              raise AttributeError("%s: target %s has no attribute %s."%(self, self.target, attribute))          """
249            if attribute and self.target:
250                if isinstance(self.target,LinkableObject):
251                   if not self.target.hasAttribute(attribute):
252                      raise AttributeError("%s: target %s has no attribute %s."%(self, self.target, attribute))
253                else:
254                   if not hasattr(self.target,attribute):
255                      raise AttributeError("%s: target %s has no attribute %s."%(self, self.target, attribute))
256          self.attribute = attribute          self.attribute = attribute
257            
258      def hasDefinedAttributeName(self):      def hasDefinedAttributeName(self):
259          """returns true if an attribute name is set"""          """
260            Returns true if an attribute name is set.
261            """
262          return self.attribute != None          return self.attribute != None
263            
264      def __repr__(self):      def __repr__(self):
265          """returns a string representation of the link"""          """
266            Returns a string representation of the link.
267            """
268          if self.hasDefinedAttributeName():          if self.hasDefinedAttributeName():
269              return "<Link to attribute %s of %s>" % (self.attribute, self.target)              return "<Link to attribute %s of %s>" % (self.attribute, self.target)
270          else:          else:
271              return "<Link to target %s>" % self.target              return "<Link to target %s>" % self.target
272            
273      def __call__(self,name=None):      def __call__(self,name=None):
274          """returns the value of the attribute of the target object. If the          """
275          atrribute is callable then the return value of the call is returned."""          Returns the value of the attribute of the target object. If the
276            atrribute is callable then the return value of the call is returned.
277            """
278          if name:          if name:
279              out=getattr(self.target, name)              out=getattr(self.target, name)
280          else:          else:
# Line 123  class Link: Line 285  class Link:
285          else:          else:
286              return out              return out
287    
288      def toDom(self, document, node):      def toDom(self, esysxml, node):
289          """ toDom method of Link. Creates a Link node and appends it to the current XML          """
290          document """          C{toDom} method of Link. Creates a Link node and appends it to the
291          link = document.createElement('Link')      current XML esysxml.
292          link.appendChild(dataNode(document, 'Target', self.target.id))          """
293            link = esysxml.createElement('Link')
294            assert (self.target != None), ("Target was none, name was %r" % self.attribute)
295            link.appendChild(esysxml.createDataNode('Target', esysxml.getLinkableObjectId(self.target)))
296          # this use of id will not work for purposes of being able to retrieve the intended          # this use of id will not work for purposes of being able to retrieve the intended
297          # target from the xml later. I need a better unique identifier.          # target from the xml later. I need a better unique identifier.
298          assert self.attribute, "You can't xmlify a Link without a target attribute"          assert self.attribute, "You can't xmlify a Link without a target attribute"
299          link.appendChild(dataNode(document, 'Attribute', self.attribute))          link.appendChild(esysxml.createDataNode('Attribute', self.attribute))
300          node.appendChild(link)          node.appendChild(link)
301    
302      def fromDom(cls, doc):      def fromDom(cls, esysxml, node):
303          targetid = doc.getElementsByTagName("Target")[0].firstChild.nodeValue.strip()          targetid = int(node.getElementsByTagName("Target")[0].firstChild.nodeValue.strip())
304          attribute = doc.getElementsByTagName("Attribute")[0].firstChild.nodeValue.strip()          attribute =str(node.getElementsByTagName("Attribute")[0].firstChild.nodeValue.strip())
305          l = cls(None, attribute)          l = cls(None, attribute)
306          registerLink(targetid, l)          esysxml.registerLink(targetid, l)
307          return l          return l
308    
309      fromDom = classmethod(fromDom)      fromDom = classmethod(fromDom)
310            
     def writeXML(self,ostream=stdout):  
         """writes an XML representation of self to the output stream ostream.  
         If ostream is nor present the standart output stream is used.  If  
         esysheader==True the esys XML header is written"""  
   
         document, rootnode = esysDoc()  
         self.toDom(document, rootnode)  
   
         ostream.write(document.toprettyxml())  
   
311  class LinkableObject(object):  class LinkableObject(object):
312      """      """
313      An object that allows to link its attributes to attributes of other objects      An object that allows to link its attributes to attributes of other objects
314      via a Link object. For instance      via a Link object. For instance::
315                        
316             p = LinkableObject()             p = LinkableObject()
317             p.x = Link(o,"name")             p.x = Link(o,"name")
318             print p.x             print p.x
319            
320      links attribute x of p to the attribute name of object o.      links attribute C{x} of C{p} to the attribute name of object C{o}.
321    
322      p.x will contain the current value of attribute name of object o.        C{p.x} will contain the current value of attribute C{name} of object
323        C{o}.  
324    
325      If the value of getattr(o, "name") is callable, p.x will rturn the return      If the value of C{getattr(o, "name")} is callable, C{p.x} will return
326      value of the call.      the return value of the call.
327      """      """
328        
     number_sequence = itertools.count(100)  
329            
330      def __init__(self, debug=False):      def __init__(self, id = None, debug=False):
331          """ initializes LinkableObject so that we can operate on Links """          """
332        Initializes LinkableObject so that we can operate on Links
333        """
334          self.debug = debug          self.debug = debug
335          self.__linked_attributes={}          self.__linked_attributes={}
336          self.id = self.number_sequence.next()          
   
337      def trace(self, msg):      def trace(self, msg):
338          """ If debugging is on, print the message, otherwise do nothing          """
339        If debugging is on, print the message, otherwise do nothing
340          """          """
341          if self.debug:          if self.debug:
342              print msg              print "%s: %s"%(str(self),msg)
343            
344      def __getattr__(self,name):      def __getattr__(self,name):
345          """returns the value of attribute name. If the value is a Link object the          """
346          object is called and the return value is returned."""      Returns the value of attribute name. If the value is a Link object the
347            object is called and the return value is returned.
348        """
349          out = self.getAttributeObject(name)          out = self.getAttributeObject(name)
350          if isinstance(out,Link):          if isinstance(out,Link):
351              return out()              return out()
# Line 194  class LinkableObject(object): Line 353  class LinkableObject(object):
353              return out              return out
354            
355      def getAttributeObject(self,name):      def getAttributeObject(self,name):
356          """return the object stored for attribute name."""          """
357        Return the object stored for attribute name.
358        """
359    
360          if self.__dict__.has_key(name):          if self.__dict__.has_key(name):
361              return self.__dict__[name]              return self.__dict__[name]
# Line 202  class LinkableObject(object): Line 363  class LinkableObject(object):
363          if self.__linked_attributes.has_key(name):          if self.__linked_attributes.has_key(name):
364              return self.__linked_attributes[name]              return self.__linked_attributes[name]
365    
366            if self.__class__.__dict__.has_key(name):
367                return self.__class.__dict__[name]
368    
369          raise AttributeError,"No attribute %s."%name          raise AttributeError,"No attribute %s."%name
370            
371      def __setattr__(self,name,value):      def hasAttribute(self,name):
372          """sets the value for attribute name. If value is a Link the target          """
373          attribute is set to name if no attribute has been specified."""      Returns True if self as attribute name.
374        """
375            return self.__dict__.has_key(name) or self.__linked_attributes.has_key(name) or  self.__class__.__dict__.has_key(name)
376    
377        def __setattr__(self,name,value):
378            """
379        Sets the value for attribute name. If value is a Link the target
380            attribute is set to name if no attribute has been specified.
381        """
382    
383          if self.__dict__.has_key(name):          if self.__dict__.has_key(name):
384              del self.__dict__[name]              del self.__dict__[name]
# Line 217  class LinkableObject(object): Line 388  class LinkableObject(object):
388                  value.setAttributeName(name)                  value.setAttributeName(name)
389              self.__linked_attributes[name] = value              self.__linked_attributes[name] = value
390    
391              self.trace("DEBUG: %s: attribute %s is now linked by %s."%(self,name,value))              self.trace("attribute %s is now linked by %s."%(name,value))
392          else:          else:
393              self.__dict__[name] = value              self.__dict__[name] = value
394            
395      def __delattr__(self,name):      def __delattr__(self,name):
396          """removes the attribute name."""          """
397        Removes the attribute name.
398        """
399    
400          if self.__linked_attributes.has_key[name]:          if self.__linked_attributes.has_key[name]:
401              del self.__linked_attributes[name]              del self.__linked_attributes[name]
# Line 231  class LinkableObject(object): Line 404  class LinkableObject(object):
404          else:          else:
405              raise AttributeError,"No attribute %s."%name              raise AttributeError,"No attribute %s."%name
406    
 class SimulationFrame(LinkableObject):  
     """A SimulationFrame objects represents a processess marching over time  
     until a finalizing condition is fullfilled.  At each time step an iterative  
     process can be performed and the time step size can be controlled  
     """  
     UNDEF_DT=1.e300  
     MAX_TIME_STEP_REDUCTION=20  
     MAX_ITER_STEPS=50  
       
     def __init__(self,*args, **kwargs):  
         """  
         Initialises a simulation  
           
         Just calls the parent constructor.  
         """  
         LinkableObject.__init__(self,*args, **kwargs)  
       
     def doInitialization(self,t):  
         """initializes the time stepping scheme. This function may be  
         overwritten."""  
         pass  
       
     def getSafeTimeStepSize(self,dt):  
         """returns a time step size which can savely be used. This function may  
         be overwritten."""  
         return self.UNDEF_DT  
       
     def finalize(self):  
         """returns True if the time stepping is finalized. This function may be  
         overwritten."""  
         return True  
         
     def doFinalization(self):  
         """finalizes the time stepping.  This function may be overwritten."""  
         pass  
       
     def doIterationInitialization(self,dt):  
         """initializes the iteration at time step t. This function may be  
         overwritten. (only called if doStep is not overwritten)"""  
         pass  
       
     def doIterationStep(self,dt):  
         """executes the iteration step. This function may be overwritten. (only  
         called if doStep is not overwritten)"""  
         pass  
       
     def terminate(self):  
         """returns True if iteration on a time step is terminated. (only called  
         if doStep is not overwritten)"""  
         return True  
         
     def doIterationFinalization(self,dt):  
         """finalalizes the iteration process. (only called if doStep is not  
         overwritten)"""  
         pass  
       
     def run(self,check_point=None):  
         """run the simulation by performing essentially  
       
             self.doInitialization()  
             while not self.finalize():  
                dt=self.getSafeTimeStepSize()  
                self.doStep(dt)  
                if n%check_point==0: self.writeXML()  
             self.doFinalization()  
       
         """  
         self.__tn=0.  
         self.__n=0  
         self.__dt=None  
         self.doInitialization(self.__tn)  
         while not self.finalize():  
             self.__n+=1  
             self.__dt=self.getSafeTimeStepSize(self.__dt)  
             if self.__dt==None: self.__dt=self.UNDEF_DT  
             if not self.__dt>0:  
                  raise NonPositiveStepSizeError("non-positive step size in step %d",self.__n)  
             self.trace("%s: %d. time step %e (step size %e.)" %  
                           (self,self.__n,self.__tn+self.__dt,self.__dt))  
             endoftimestep=False  
             failcounter=0  
             while not endoftimestep:  
                 endoftimestep=True  
                 try:  
                     self.doStep(self.__dt)  
                 except FailedTimeStepError:  
                     self.__dt=self.getSafeTimeStepSize(self.__dt)  
                     if self.__dt==None: self.__dt=self.UNDEF_DT  
                     endoftimestep=False  
                     self.trace("%s: time step is repeated with new step size %e."%(self,self.__dt))  
                 except IterationDivergenceError:  
                     self.__dt*=0.5  
                     endoftimestep=False  
                     failcounter+=1  
                     if failcounter>self.MAX_TIME_STEP_REDUCTION:  
                         raise IterationBreakDownError("reduction of time step to achieve convergence failed.")  
   
                     self.trace("%s: iteration failes. time step is repeated with new step size %e."  
                         % (self,self.__dt))  
             self.__tn+=self.__dt  
             if not check_point==None:  
                 if self.__n%check_point==0:  
                     self.trace("%s: check point is created."%self)  
                     self.writeXML()  
         self.doFinalization()  
   
     def writeXML(self):  
         raise RuntimeError, "Not implemented"  
       
     def doStep(self,dt):  
         """executes a time step by iteration. This function may be overwritten.  
             
            basicly it performs :  
       
             self.doIterationInitialization(dt)  
             while not self.terminate(): self.doIterationStep(dt)  
             self.doIterationFinalization(dt)  
       
         """  
         self.doIterationInitialization(dt)  
         self.__iter=0  
         while not self.terminate():  
             self.trace("%s: iteration step %d"%(self,self.__iter))  
             self.doIterationStep(dt)  
             self.__iter+=1  
             if self.__iter>self.MAX_ITER_STEPS:  
                 raise IterationDivergenceError("%s: divergence in step %d"%(self,self.__iter))  
         self.doIterationFinalization(dt)  
   
 class Simulation(SimulationFrame):  
     """A Simulation object is comprised by SimulationFrame(s) called subsimulations."""  
       
     def __init__(self, subsimulations=[], *args, **kwargs):  
         """initiates a simulation from a list of subsimulations. """  
         SimulationFrame.__init__(self, *args, **kwargs)  
         self.__subsimulations=[]  
   
         for i in range(len(subsimulations)):  
             self[i] = subsimulations[i]  
       
     def iterSubsimulations(self):  
         """returns an iterator over the subsimulations"""  
         return self.__subsimulations  
       
     def __getitem__(self,i):  
         """returns the i-th subsimulation"""  
         return self.__subsimulations[i]  
       
     def __setitem__(self,i,value):  
         """sets the i-th subsimulation"""  
         if not isinstance(value,SimulationFrame):  
             raise ValueError("assigned value is not a Simulation")  
         for j in range(max(i-len(self.__subsimulations)+1,0)): self.__subsimulations.append(None)  
         self.__subsimulations[i]=value  
       
     def __len__(self):  
         """returns the number of subsimulations"""  
         return len(self.__subsimulations)  
   
     def toDom(self, document, node):  
         """ toDom method of Simulation class """  
         simulation = document.createElement('Simulation')  
         simulation.setAttribute('type', self.__class__.__name__)  
   
         for rank, sim in enumerate(self.iterSubsimulations()):  
             component = document.createElement('Component')  
             component.setAttribute('rank', str(rank))  
   
             sim.toDom(document, component)  
   
             simulation.appendChild(component)  
   
         node.appendChild(simulation)  
   
     def writeXML(self,ostream=stdout):  
         """writes the object as an XML object into an output stream"""  
         document, rootnode = esysDoc()  
         self.toDom(document, rootnode)  
         ostream.write(document.toprettyxml())  
       
     def getSafeTimeStepSize(self,dt):  
         """returns a time step size which can safely be used by all subsimulations"""  
         out=self.UNDEF_DT  
         for o in self.iterSubsimulations():  
             dt_new = o.getSafeTimeStepSize(dt)  
             if dt_new != None:  
                 out = min(out,dt_new)  
   
         return out  
       
     def doInitialization(self,dt):  
         """initializes all subsimulations """  
         for o in self.iterSubsimulations():  
             o.doInitialization(dt)  
       
     def finalize(self):  
         """returns True if all subsimulations are finalized"""  
         return all([o.finalize() for o in self.iterSubsimulations()])  
         
     def doFinalization(self):  
         """finalalizes the time stepping for all subsimulations."""  
         for i in self.iterSubsimulations(): i.doFinalization()  
       
     def doIterationInitialization(self,dt):  
         """initializes the iteration at time t for all subsimulations."""  
         self.__iter=0  
         self.trace("%s: iteration starts"%self)  
   
         for o in self.iterSubsimulations():  
             o.doIterationInitialization(dt)  
       
     def terminate(self):  
         """returns True if all iterations for all subsimulations are terminated."""  
         return all([o.terminate() for o in self.iterSubsimulations()])  
         
     def doIterationFinalization(self,dt):  
         """finalalizes the iteration process for each of the subsimulations."""  
         for o in self.iterSubsimulations():  
             o.doIterationFinalization(dt)  
         self.trace("%s: iteration finalized after %s steps"%(self,self.__iter+1))  
       
     def doIterationStep(self,dt):  
         """executes the iteration step at time step for each subsimulation"""  
         self.__iter+=1  
         self.trace("%s: iteration step %d"%(self,self.__iter))  
         for o in self.iterSubsimulations():  
             o.doIterationStep(dt)  
   
     def fromDom(cls, doc):  
         """  
         Needs to be filled out.  
         """  
         sims = []  
         for node in doc.childNodes:  
             if isinstance(node, minidom.Text):  
                 continue  
   
             sims.append(getComponent(node))  
   
   
         return cls(sims)  
   
   
               
   
   
     fromDom = classmethod(fromDom)  
   
 class ExplicitSimulation(Simulation):  
     """This is a modified form of the Simulation class. In fact it overwrites  
     the doStep method by executing the doStep method of all subsimulations  
     rather then iterating over all subsimulations."""  
   
     def doStep(self,dt):  
         """executes the time step for all subsimulation"""  
         for i in self.iterSubsimulations():  
             i.doStep(dt)  
   
407  class _ParameterIterator:  class _ParameterIterator:
408      def __init__(self,parameterset):      def __init__(self,parameterset):
409    
# Line 503  class _ParameterIterator: Line 418  class _ParameterIterator:
418          return self          return self
419    
420  class ParameterSet(LinkableObject):  class ParameterSet(LinkableObject):
421      """a class which allows to emphazise attributes to be written and read to XML      """
422        A class which allows to emphazise attributes to be written and read to XML
423                
424         Leaves of  an ESySParameters objects can be      Leaves of an ESySParameters object can be:
425            
426              a real number       - a real number
427              a integer number       - a integer number
428              a string       - a string
429              a boolean value       - a boolean value
430              a ParameterSet object       - a ParameterSet object
431              a Simulation object       - a Simulation object
432              a Model object       - a Model object
433              any other object (not considered by writeESySXML and writeXML)       - a numarray object
434                 - a list of booleans
435             Example how to create an ESySParameters object:          - any other object (not considered by writeESySXML and writeXML)
436            
437                   p11=ParameterSet(gamma1=1.,gamma2=2.,gamma3=3.)      Example how to create an ESySParameters object::
438                   p1=ParameterSet(dim=2,tol_v=0.001,output_file="/tmp/u.%3.3d.dx",runFlag=True,parm11=p11)      
439                   parm=ParameterSet(parm1=p1,parm2=ParameterSet(alpha=Link(p11,"gamma1")))          p11=ParameterSet(gamma1=1.,gamma2=2.,gamma3=3.)
440                p1=ParameterSet(dim=2,tol_v=0.001,output_file="/tmp/u.%3.3d.dx",runFlag=True,parm11=p11)
441             This can be accessed as          parm=ParameterSet(parm1=p1,parm2=ParameterSet(alpha=Link(p11,"gamma1")))
442            
443                   parm.parm1.gamma=0.      This can be accessed as::
444                   parm.parm1.dim=2      
445                   parm.parm1.tol_v=0.001      parm.parm1.gamma=0.
446                   parm.parm1.output_file="/tmp/u.%3.3d.dx"          parm.parm1.dim=2
447                   parm.parm1.runFlag=True          parm.parm1.tol_v=0.001
448                   parm.parm1.parm11.gamma1=1.          parm.parm1.output_file="/tmp/u.%3.3d.dx"
449                   parm.parm1.parm11.gamma2=2.          parm.parm1.runFlag=True
450                   parm.parm1.parm11.gamma3=3.          parm.parm1.parm11.gamma1=1.
451                   parm.parm2.alpha=1. (value of parm.parm1.parm11.gamma1)          parm.parm1.parm11.gamma2=2.
452                        parm.parm1.parm11.gamma3=3.
453            parm.parm2.alpha=1. (value of parm.parm1.parm11.gamma1)
454      """      """
455      def __init__(self, parameters=[], **kwargs):      def __init__(self, parameters=[], **kwargs):
456          """creates a ParameterSet with parameters parameters"""          """
457        Creates a ParameterSet with parameters parameters.
458        """
459          LinkableObject.__init__(self, **kwargs)          LinkableObject.__init__(self, **kwargs)
460          self.parameters = set()          self.parameters = set()
461          self.declareParameters(parameters)          self.declareParameters(parameters)
462    
463        def __repr__(self):
464            return "<%s %d>"%(self.__class__.__name__,id(self))
465            
466      def declareParameter(self,**parameters):      def declareParameter(self,**parameters):
467          """declares a new parameter(s) and its (their) inital value."""          """
468        Declares a new parameter(s) and its (their) initial value.
469        """
470          self.declareParameters(parameters)          self.declareParameters(parameters)
471            
472      def declareParameters(self,parameters):      def declareParameters(self,parameters):
473          """declares a set of parameters. parameters can be a list, a dictonary or a ParameterSet."""          """
474        Declares a set of parameters. parameters can be a list, a dictionary
475        or a ParameterSet.
476        """
477          if isinstance(parameters,ListType):          if isinstance(parameters,ListType):
478              parameters = zip(parameters, itertools.repeat(None))              parameters = zip(parameters, itertools.repeat(None))
479          if isinstance(parameters,DictType):          if isinstance(parameters,DictType):
# Line 556  class ParameterSet(LinkableObject): Line 483  class ParameterSet(LinkableObject):
483              setattr(self,prm,value)              setattr(self,prm,value)
484              self.parameters.add(prm)              self.parameters.add(prm)
485    
             self.trace("%s: parameter %s has been declared."%(self,prm))  
   
486      def releaseParameters(self,name):      def releaseParameters(self,name):
487          """removes parameter name from the paramameters"""          """
488        Removes parameter name from the paramameters.
489        """
490          if self.isParameter(name):          if self.isParameter(name):
491              self.parameters.remove(name)              self.parameters.remove(name)
492              self.debug("%s: parameter %s has been removed."%(self, name))              self.trace("parameter %s has been removed."%name)
493    
494        def checkLinkTargets(self, models, hash):
495            """
496            returns a set of tuples ("<self>(<name>)", <target model>) if the parameter <name> is linked to model <target model>
497            but <target model> is not in the list models. If the a parameter is linked to another parameter set which is not in the hash list
498            the parameter set is checked for its models. hash gives the call history.
499            """
500            out=set()
501            for name, value in self:
502                if isinstance(value, Link):
503                   m=value.getTarget()
504                   if isinstance(m, Model):
505                       if not m in models: out.add( (str(self)+"("+name+")",m) )
506                   elif isinstance(m, ParameterSet) and not m in hash:
507                         out|=set( [ (str(self)+"("+name+")."+f[0],f[1]) for f in m.checkLinkTargets(models, hash+[ self ] ) ] )
508            return out
509            
510      def __iter__(self):      def __iter__(self):
511          """creates an iterator over the parameter and their values"""          """
512        Creates an iterator over the parameter and their values.
513        """
514          return _ParameterIterator(self)          return _ParameterIterator(self)
515            
516      def showParameters(self):      def showParameters(self):
517          """returns a descrition of the parameters"""                  """
518        Returns a descrition of the parameters.
519        """        
520          out="{"          out="{"
521          notfirst=False          notfirst=False
522          for i,v in self:          for i,v in self:
# Line 582  class ParameterSet(LinkableObject): Line 529  class ParameterSet(LinkableObject):
529          return out+"}"          return out+"}"
530            
531      def __delattr__(self,name):      def __delattr__(self,name):
532          """removes the attribute name."""          """
533        Removes the attribute name.
534        """
535          LinkableObject.__delattr__(self,name)          LinkableObject.__delattr__(self,name)
536          try:          try:
537              self.releaseParameter(name)              self.releaseParameter(name)
538          except:          except:
539              pass              pass
540    
541      def toDom(self, document, node):      def toDom(self, esysxml, node):
542          """ toDom method of ParameterSet class """          """
543          pset = document.createElement('ParameterSet')      C{toDom} method of Model class
544        """
545            pset = esysxml.createElement('ParameterSet')
546            pset.setAttribute('type', self.__class__.__name__)
547            pset.setAttribute('module', self.__class__.__module__)
548            esysxml.registerLinkableObject(self, pset)
549            self._parametersToDom(esysxml, pset)
550          node.appendChild(pset)          node.appendChild(pset)
         self._parametersToDom(document, pset)  
551    
552      def _parametersToDom(self, document, node):      def _parametersToDom(self, esysxml, node):
         node.setAttribute ('id', str(self.id))  
553          for name,value in self:          for name,value in self:
554              param = document.createElement('Parameter')              # convert list to numarray when possible:
555              param.setAttribute('type', value.__class__.__name__)              if isinstance (value, list):
556                    elem_type=-1
557                    for i in value:
558                        if isinstance(i, bool):
559                            elem_type = max(elem_type,0)
560                        elif isinstance(i, int):
561                            elem_type = max(elem_type,1)
562                        elif isinstance(i, float):
563                            elem_type = max(elem_type,2)
564                    if elem_type == 0: value = numarray.array(value,numarray.Bool)
565                    if elem_type == 1: value = numarray.array(value,numarray.Int)
566                    if elem_type == 2: value = numarray.array(value,numarray.Float)
567    
568              param.appendChild(dataNode(document, 'Name', name))              param = esysxml.createElement('Parameter')
569                param.setAttribute('type', value.__class__.__name__)
570    
571              val = document.createElement('Value')              param.appendChild(esysxml.createDataNode('Name', name))
572    
573              if isinstance(value,ParameterSet):              val = esysxml.createElement('Value')
574                  value.toDom(document, val)              if isinstance(value,(ParameterSet,Link,DataSource)):
575                    value.toDom(esysxml, val)
576                  param.appendChild(val)                  param.appendChild(val)
577              elif isinstance(value, Link):              elif isinstance(value, numarray.NumArray):
578                  value.toDom(document, val)                  shape = value.getshape()
579                    if isinstance(shape, tuple):
580                        size = reduce(operator.mul, shape)
581                        shape = ' '.join(map(str, shape))
582                    else:
583                        size = shape
584                        shape = str(shape)
585    
586                    arraytype = value.type()
587                    if isinstance(arraytype, numarray.BooleanType):
588                          arraytype_str="Bool"
589                    elif isinstance(arraytype, numarray.IntegralType):
590                          arraytype_str="Int"
591                    elif isinstance(arraytype, numarray.FloatingType):
592                          arraytype_str="Float"
593                    elif isinstance(arraytype, numarray.ComplexType):
594                          arraytype_str="Complex"
595                    else:
596                          arraytype_str=str(arraytype)
597                    numarrayElement = esysxml.createElement('NumArray')
598                    numarrayElement.appendChild(esysxml.createDataNode('ArrayType', arraytype_str))
599                    numarrayElement.appendChild(esysxml.createDataNode('Shape', shape))
600                    numarrayElement.appendChild(esysxml.createDataNode('Data', ' '.join(
601                        [str(x) for x in numarray.reshape(value, size)])))
602                    val.appendChild(numarrayElement)
603                  param.appendChild(val)                  param.appendChild(val)
604              elif isinstance(value,StringType):              elif isinstance(value, list):
605                  param.appendChild(dataNode(document, 'Value', value))                  param.appendChild(esysxml.createDataNode('Value', ' '.join([str(x) for x in value]) ))
606                elif isinstance(value, (str, bool, int, float, type(None))):
607                    param.appendChild(esysxml.createDataNode('Value', str(value)))
608                elif isinstance(value, dict):
609                     dic = esysxml.createElement('dictionary')
610                     if len(value.keys())>0:
611                         dic.setAttribute('key_type', value.keys()[0].__class__.__name__)
612                         dic.setAttribute('value_type', value[value.keys()[0]].__class__.__name__)
613                     for k,v in value.items():
614                        i=esysxml.createElement('item')
615                        i.appendChild(esysxml.createDataNode('key', k))
616                        i.appendChild(esysxml.createDataNode('value', v))
617                        dic.appendChild(i)
618                     param.appendChild(dic)
619              else:              else:
620                  param.appendChild(dataNode(document, 'Value', str(value)))                  raise ValueError("cannot serialize %s type to XML."%str(value.__class__))
621    
622              node.appendChild(param)              node.appendChild(param)
623    
624          def fromDom(cls, esysxml, node):
     def fromDom(cls, doc):  
   
625          # Define a host of helper functions to assist us.          # Define a host of helper functions to assist us.
626          def _children(node):          def _children(node):
627              """              """
628              Remove the empty nodes from the children of this node              Remove the empty nodes from the children of this node.
629              """              """
630              return [x for x in node.childNodes              ret = []
631                      if not isinstance(x, minidom.Text) or x.nodeValue.strip()]              for x in node.childNodes:
632                    if isinstance(x, minidom.Text):
633                        if x.nodeValue.strip():
634                            ret.append(x)
635                    else:
636                        ret.append(x)
637                return ret
638    
639          def _floatfromValue(doc):          def _floatfromValue(esysxml, node):
640              return float(doc.nodeValue.strip())              return float(node.nodeValue.strip())
641    
642          def _stringfromValue(doc):          def _stringfromValue(esysxml, node):
643              return str(doc.nodeValue.strip())              return str(node.nodeValue.strip())
644                  
645            def _intfromValue(esysxml, node):
646                return int(node.nodeValue.strip())
647    
648            def _boolfromValue(esysxml, node):
649                return _boolfromstring(node.nodeValue.strip())
650    
651            def _nonefromValue(esysxml, node):
652                return None
653    
654            def _numarrayfromValue(esysxml, node):
655                for node in _children(node):
656                    if node.tagName == 'ArrayType':
657                        arraytype = node.firstChild.nodeValue.strip()
658                    if node.tagName == 'Shape':
659                        shape = node.firstChild.nodeValue.strip()
660                        shape = [int(x) for x in shape.split()]
661                    if node.tagName == 'Data':
662                        data = node.firstChild.nodeValue.strip()
663                        data = [float(x) for x in data.split()]
664                return numarray.reshape(numarray.array(data, type=getattr(numarray, arraytype)),
665                                        shape)
666          
667            def _listfromValue(esysxml, node):
668                return [x for x in node.nodeValue.split()]
669    
670            def _boolfromstring(s):
671                if s == 'True':
672                    return True
673                else:
674                    return False
675          # Mapping from text types in the xml to methods used to process trees of that type          # Mapping from text types in the xml to methods used to process trees of that type
676          ptypemap = {"Simulation": Simulation.fromDom,          ptypemap = {"Simulation": Simulation.fromDom,
677                      "Model":Model.fromDom,                      "Model":Model.fromDom,
678                      "ParameterSet":ParameterSet.fromDom,                      "ParameterSet":ParameterSet.fromDom,
679                      "Link":Link.fromDom,                      "Link":Link.fromDom,
680                        "DataSource":DataSource.fromDom,
681                      "float":_floatfromValue,                      "float":_floatfromValue,
682                      #"int":_intfromValue,                      "int":_intfromValue,
683                      "str":_stringfromValue,                      "str":_stringfromValue,
684                      #"bool":_boolfromValue                      "bool":_boolfromValue,
685                        "list":_listfromValue,
686                        "NumArray":_numarrayfromValue,
687                        "NoneType":_nonefromValue,
688                      }                      }
689    
690          parameters = {}          parameters = {}
691          for node in _children(doc):          for n in _children(node):
692              ptype = node.getAttribute("type")              ptype = n.getAttribute("type")
693                if not ptypemap.has_key(ptype):
694                   raise KeyError("cannot handle parameter type %s."%ptype)
695    
696              pname = pvalue = None              pname = pvalue = None
697              for childnode in _children(node):              for childnode in _children(n):
   
698                  if childnode.tagName == "Name":                  if childnode.tagName == "Name":
699                      pname = childnode.firstChild.nodeValue.strip()                      pname = childnode.firstChild.nodeValue.strip()
700    
701                  if childnode.tagName == "Value":                  if childnode.tagName == "Value":
702                      nodes = _children(childnode)                      nodes = _children(childnode)
703                      pvalue = ptypemap[ptype](nodes[0])                      pvalue = ptypemap[ptype](esysxml, nodes[0])
704    
705              parameters[pname] = pvalue              parameters[pname] = pvalue
706    
707          # Create the instance of ParameterSet          # Create the instance of ParameterSet
708          o = cls()          try:
709               o = cls(debug=esysxml.debug)
710            except TypeError, inst:
711               print inst.args[0]
712               if inst.args[0]=="__init__() got an unexpected keyword argument 'debug'":
713                  raise TypeError("The Model class %s __init__ needs to have argument 'debug'.")
714               else:
715                  raise inst
716          o.declareParameters(parameters)          o.declareParameters(parameters)
717          registerLinkableObject(doc.getAttribute("id"), o)          esysxml.registerLinkableObject(o, node)
718          return o          return o
719            
720      fromDom = classmethod(fromDom)      fromDom = classmethod(fromDom)
       
     def writeXML(self,ostream=stdout):  
         """writes the object as an XML object into an output stream"""  
         # ParameterSet(d) with d[Name]=Value  
         document, node = esysDoc()  
         self.toDom(document, node)  
         ostream.write(document.toprettyxml())  
   
 class Model(ParameterSet,SimulationFrame):  
     """a Model is a SimulationFrame which is also a ParameterSet."""  
   
     def __init__(self,parameters=[],*args,**kwargs):  
         """creates a model"""  
         ParameterSet.__init__(self, parameters=parameters)  
         SimulationFrame.__init__(self,*args,**kwargs)  
   
     def toDom(self, document, node):  
         """ toDom method of Model class """  
         pset = document.createElement('Model')  
         pset.setAttribute('type', self.__class__.__name__)  
         node.appendChild(pset)  
         self._parametersToDom(document, pset)  
   
721    
722  class IterationDivergenceError(Exception):      def writeXML(self,ostream=stdout):
723      """excpetion which should be thrown if there is no convergence of the iteration process at a time step but there is a chance taht a smaller step could help          """
724         to reach convergence."""      Writes the object as an XML object into an output stream.
725      pass      """
726            esysxml=ESySXMLCreator()
727  class IterationBreakDownError(Exception):          self.toDom(esysxml, esysxml.getRoot())
728      """excpetion which should be thrown if there is no conevregence and there is no chance that a time step reduction would help"""          ostream.write(esysxml.toprettyxml())
729      pass      
730    class Model(ParameterSet):
731  class FailedTimeStepError(Exception):      """
732      """excpetion which should be thrown if the time step fails because of a step size that have been choosen to be to large"""      A Model object represents a processess marching over time until a
733      pass      finalizing condition is fullfilled. At each time step an iterative
734        process can be performed and the time step size can be controlled. A
735  class NonPositiveStepSizeError(Exception):      Model has the following work flow::
736      """excpetion which is thrown if the step size is not positive"""            
737      pass            doInitialization()
738              while not terminateInitialIteration(): doInitializationiStep()
739              doInitialPostprocessing()
740              while not finalize():
741                   dt=getSafeTimeStepSize(dt)
742                   doStepPreprocessing(dt)
743                   while not terminateIteration(): doStep(dt)
744                   doStepPostprocessing(dt)
745              doFinalization()
746    
747        where C{doInitialization}, C{finalize}, C{getSafeTimeStepSize},
748        C{doStepPreprocessing}, C{terminateIteration}, C{doStepPostprocessing},
749        C{doFinalization} are methods of the particular instance of a Model. The
750        default implementations of these methods have to be overwritten by the
751        subclass implementing a Model.
752        """
753    
754  #      UNDEF_DT=1.e300
 #   ignore this text:  
 #  
 """ the Model class provides a framework to run a time-dependent simulation. A  
 Model has a set of parameter which may be fixed or altered by the Model itself  
 or other Models over time.    
755    
756         The parameters of a models are declared at instantion, e.g.      def __init__(self,parameters=[],**kwargs):
757            """
758        Creates a model.
759    
760             m=Model({"message" : "none" })          Just calls the parent constructor.
761            """
762            ParameterSet.__init__(self, parameters=parameters,**kwargs)
763    
764         creates a Model with parameters p1 and p2 with inital values 1 and 2.      def __str__(self):
765         Typically a particular model is defined as a subclass of Model:         return "<%s %d>"%(self.__class__.__name__,id(self))
766    
         class Messenger(Model):  
             def __init__(self):  
                Model.__init__(self,parameters={"message" : "none" })  
767    
768          m=MyModel()      def setUp(self):
769            """
770            Sets up the model.
771    
772         There are various ways how model parameters can be changed:          This function may be overwritten.
773            """
774            pass
775    
776         1) use object attributes:      def doInitialization(self):
777            """
778        Initializes the time stepping scheme. This method is not called in case of a restart.
779        
780        This function may be overwritten.
781        """
782            pass
783        def doInitialStep(self):
784            """
785        performs an iteration step in the initialization phase. This method is not called in case of a restart.
786    
787            m.message="Hello World!"      This function may be overwritten.
788        """
789            pass
790    
791         2) use setParamter method      def terminateInitialIteration(self):
792                    """
793                  Returns True if iteration at the inital phase is terminated.
794            m.setParameters(message="Hello World!")      """
795            return True
796    
797         3) or dictonaries      def doInitialPostprocessing(self):
798              """
799             d={ message : "Hello World!" }      finalises the initialization iteration process. This method is not called in case of a restart.
            m.setParameters(**d)  
800    
801        This function may be overwritten.
802        """
803            pass
804        
805        def getSafeTimeStepSize(self,dt):
806            """
807        Returns a time step size which can safely be used.
808    
809         A model executed buy staring the run method of the model:          C{dt} gives the previously used step size.
   
           m=Messenger()  
           m.run()  
810    
811         The run methods marches through time. It first calls the          This function may be overwritten.
812         doInitialization() method of the Model to set up the process. In each      """
813         time step the doStep() method is called to get from the current to the          return self.UNDEF_DT
814         next time step. The step size is defined by calling the      
815         getSafeTimeStepSize() method.  the time integration process is      def finalize(self):
816         terminated when the finalize() methods return true. Final the          """
817         doFinalization() method is called to finalize the process. To implement      Returns False if the time stepping is finalized.
818         a particular model a subclass of the Model class is defined. The      
819         subclass overwrites the default methods of Model.      This function may be overwritten.
820        """
821         The following class defines a messenger printing in the doStep method          return False
822         what ever the current value of its parameter message is:        
823        def doFinalization(self):
824         class Messenger(Model):          """
825              def __init__(self):      Finalizes the time stepping.
826                 Model.__init__(self,parameters={"message" : "none" })      
827        This function may be overwritten.
828        """
829            pass
830        
831        def doStepPreprocessing(self,dt):
832            """
833        Sets up a time step of step size dt.
834        
835        This function may be overwritten.
836        """
837            pass
838        
839        def doStep(self,dt):
840            """
841        Executes an iteration step at a time step.
842    
843              def doInitialization(self):          C{dt} is the currently used time step size.
                print "I start talking now!"  
844    
845              def doStep(self,t):          This function may be overwritten.
846                 print "Message (time %e) : %s "%(t,self.message)      """
847            pass
848        
849        def terminateIteration(self):
850            """
851        Returns True if iteration on a time step is terminated.
852        """
853            return True
854    
             def doFinalization(self):  
                print "I have no more to say!"  
855                
856         If a instance of the Messenger class is run, it will print the      def doStepPostprocessing(self,dt):
857         initialization and finalization message only.  This is because the          """
858         default method for finalize() does always returns True and therefore the      finalises the time step.
        transition is terminated startcht away.  
           
        Following example for solving the ODE using a forward euler scheme:  
859    
860                  u(t=0)=u0          dt is the currently used time step size.
                 u_t=a*u**2       for all 0<t<=ten  
861    
862        exact solution is given by u(t)=1/(1/u0-a*t)          This function may be overwritten.
863        """
864            pass
865    
866        class  Ode1(Model):      def toDom(self, esysxml, node):
867           def __init__(self,**args):          """
868              Model.__init__(self,parameters={"tend" : 1., "dt" : 0.0001 ,"a" : 0.1 ,"u" : 1. },name="test",debug=True)      C{toDom} method of Model class
869        """
870           def doInitialization(self):          pset = esysxml.createElement('Model')
871               self._tn=0          pset.setAttribute('type', self.__class__.__name__)
872            pset.setAttribute('module', self.__class__.__module__)
873           def doStep(self,t):          esysxml.registerLinkableObject(self, pset)
874               self.u=self.u+(t-self._tn)*self.a*self.u**2          node.appendChild(pset)
875               self._tn=t          self._parametersToDom(esysxml, pset)
876        
877           def doFinalization(self):  class Simulation(Model):
878               print "all done final error = ",abs(self.u-1./(1./3.-self.a*self._tn))      """
879        A Simulation object is special Model which runs a sequence of Models.
          def getSafeTimeStepSize(self):  
              return self.dt  
   
          def finalize(self):  
              return self._tn>=self.tend  
   
        In some cases at a given time step an iteration process has to be  
        performed to get the state of the Model for the next time step. ` In  
        this case the doStep() method is replaced by a sequance of methods which  
        implements this iterative process.  The method then will control the  
        iteration process by initializing the iteration through calling the  
        doIterationInitialization() method. The iteration is preformed by  
        calling the doIterationStep() method until the terminate() method  
        returns True. The doIterationFinalization() method is called to end the  
        iteration.  
        For a particular model these methods have to overwritten by a suitable  
        subclass without touching the doStep() method.  
880    
881         following example is a modification of the example above. Here an      The methods C{doInitialization}, C{finalize}, C{getSafeTimeStepSize},
882         implicit euler scheme is used. in each time step the problem      C{doStepPreprocessing}, C{terminateIteration}, C{doStepPostprocessing},
883                  C{doFinalization} are executing the corresponding methods of the models in
884             0= u_{n+1}-u_{n}+a*dt*u_{n+1}**2      the simulation.
885        """
886        
887        FAILED_TIME_STEPS_MAX=20
888        MAX_ITER_STEPS=50
889        MAX_CHANGE_OF_DT=2.
890        
891        def __init__(self, models=[], **kwargs):
892            """
893        Initiates a simulation from a list of models.
894        """
895            super(Simulation, self).__init__(**kwargs)
896            self.declareParameter(time=0.,
897                                  time_step=0,
898                                  dt = self.UNDEF_DT)
899            for m in models:
900                if not isinstance(m, Model):
901                     raise TypeError("%s is not a subclass of Model."%m)
902            self.__models=[]
903            for i in range(len(models)):
904                self[i] = models[i]
905                
906    
907         has to be solved for u_{n+1}. The Newton scheme is used to solve this non-linear problem.      def __repr__(self):
908            """
909            Returns a string representation of the Simulation.
910            """
911            return "<Simulation %r>" % self.__models
912    
913        def __str__(self):
914        class  Ode2(Model):          """
915            Returning Simulation as a string.
916            """
917            return "<Simulation %d>"%id(self)
918        
919        def iterModels(self):
920            """
921        Returns an iterator over the models.
922        """
923            return self.__models
924        
925        def __getitem__(self,i):
926            """
927        Returns the i-th model.
928        """
929            return self.__models[i]
930        
931        def __setitem__(self,i,value):
932            """
933        Sets the i-th model.
934        """
935            if not isinstance(value,Model):
936                raise ValueError,"assigned value is not a Model but instance of %s"%(value.__class__.__name__,)
937            for j in range(max(i-len(self.__models)+1,0)):
938                self.__models.append(None)
939            self.__models[i]=value
940        
941        def __len__(self):
942            """
943        Returns the number of models.
944        """
945            return len(self.__models)
946    
947         def __init__(self,**args):      def getAllModels(self):
948             Model.__init__(self,{"tend" : 1., "dt" : 0.1 ,"a" : 10. ,"u" : 1. , "tol " : 1.e-8},"test","bla",None,True)          """
949            returns a list of all models used in the Simulation including subsimulations
950            """
951            out=[]
952            for m in self.iterModels():
953                if isinstance(m, Simulation):
954                   out+=m.getAllModels()
955                else:
956                   out.append(m)
957            return list(set(out))
958    
959         def doInitialization(self):      def checkModels(self, models, hash):
960             self.__tn=0          """
961            returns a list of (model,parameter, target model ) if the the parameter of model
962            is linking to the target_model which is not in list of models.
963            """
964            out=self.checkLinkTargets(models, hash + [self])
965            for m in self.iterModels():
966                if isinstance(m, Simulation):
967                     out|=m.checkModels(models, hash)
968                else:
969                     out|=m.checkLinkTargets(models, hash + [self])
970            return set( [ (str(self)+"."+f[0],f[1]) for f in out ] )
971    
972         def doIterationInitialization(self,t):      
973              self.__iter=0      def getSafeTimeStepSize(self,dt):
974              self.u_last=self.u                      """
975              self.current_dt=t-self.tn      Returns a time step size which can safely be used by all models.
             self.__tn=t  
   
        def doIterationStep(self):  
           self.__iter+=1  
           self.u_old=self.u  
           self.u=(self.current_dt*self.a*self.u**2-self.u_last)/(2*self.current_dt*self.a*self.u-1.)  
   
        def terminate(self):  
            return abs(self.u_old-self.u)<self.tol*abs(self.u)  
   
        def doIterationFinalization(self)  
            print "all done"  
   
        def getSafeTimeStepSize(self):  
            return self.dt  
   
        def finalize(self):  
             return self.__tn>self.tend  
   
        A model can be composed from subsimulations. Subsimulations are treated  
        as model parameters. If a model parameter is set or a value of a model  
        parameter is requested, the model will search for this parameter its  
        subsimulations in the case the model does not have this parameter  
        itself. The order in which the subsimulations are searched is critical.  
        By default a Model initializes all its subsimulations, is finalized when  
        all its subsimulations are finalized and finalizes all its  
        subsimulations. In the case an iterative process is applied on a  
        particular time step the iteration is initialized for all  
        subsimulations, then the iteration step is performed for each  
        subsimulation until all subsimulations indicate termination. Then the  
        iteration is finalized for all subsimulations. Finally teh doStop()  
        method for all submethods is called.  
   
        Here we are creating a model which groups ab instantiation of the Ode2 and the Messenger Model  
   
        o=Ode2()  
        m=Messenger()  
        om=Model(subsimulations=[o,m],debug=True)  
        om.dt=0.01  
        om.u=1.  
        m.message="it's me!"  
        om.run()  
   
        Notice that dt and u are parameters of class Ode2 and message is a  
        parameter of the Messenger class. The Model formed from these models  
        automatically hand the assignment of new values down to the  
        subsimulation. om.run() starts this combined model where now the  
        soStep() method of the Messenger object printing the value of its  
        parameter message together with a time stamp is executed in each time  
        step introduced by the Ode2 model.  
976    
977         A parameter of a Model can be linked to an attribute of onother object,          This is the minimum over the time step sizes of all models.
978         typically an parameter of another Model object.          """
979                  out=min([o.getSafeTimeStepSize(dt) for o in self.iterModels()])
980                  return out
        which is comprised by a set of subsimulations.  
        The simulation is run through its run method which in the simplest case has the form:  
981    
982            s=Model()      def setUp(self):
983            s.run()          """
984            performs the setup for all models
985            """
986            for o in self.iterModels():
987                 o.setUp()
988        
989        def doInitialization(self):
990            """
991        Initializes all models.
992        """
993            for o in self.iterModels():
994                 o.doInitialization()
995        def doInitialStep(self):
996            """
997        performs an iteration step in the initialization step for all models
998        """
999            iter=0
1000            while not self.terminateInitialIteration():
1001                if iter==0: self.trace("iteration for initialization starts")
1002                iter+=1
1003                self.trace("iteration step %d"%(iter))
1004                for o in self.iterModels():
1005                     o.doInitialStep()
1006                if iter>self.MAX_ITER_STEPS:
1007                     raise IterationDivergenceError("initial iteration did not converge after %s steps."%iter)
1008            self.trace("Initialization finalized after %s iteration steps."%iter)
1009    
1010         The run has an initializion and finalization phase. The latter is called      def doInitialPostprocessing(self):
1011         if all subsimulations are to be finalized. The simulation is processing          """
1012         in time through calling the stepForward methods which updates the      finalises the initialization iteration process for all models.
1013         observables of each subsimulation.  A time steps size which is save for      """
1014         all subsimulation is choosen.          for o in self.iterModels():
1015                o.doInitialPostprocessing()
1016        def finalize(self):
1017            """
1018        Returns True if any of the models is to be finalized.
1019        """
1020            return any([o.finalize() for o in self.iterModels()])
1021          
1022        def doFinalization(self):
1023            """
1024        finalises the time stepping for all models.
1025        """
1026            for i in self.iterModels(): i.doFinalization()
1027            self.trace("end of time integation.")
1028        
1029        def doStepPreprocessing(self,dt):
1030            """
1031        Initializes the time step for all models.
1032        """
1033            for o in self.iterModels():
1034                o.doStepPreprocessing(dt)
1035        
1036        def terminateIteration(self):
1037            """
1038        Returns True if all iterations for all models are terminated.
1039        """
1040            out=all([o.terminateIteration() for o in self.iterModels()])
1041            return out
1042    
1043         At given time step an iterative process may be performed to make sure      def terminateInitialIteration(self):
1044         that all observables are consistent across all subsimulations.  In this          """
1045         case, similar the time dependence, an initialization and finalization of      Returns True if all initial iterations for all models are terminated.
1046         the iteration is performed.      """
1047            out=all([o.terminateInitialIteration() for o in self.iterModels()])
1048            return out
1049          
1050        def doStepPostprocessing(self,dt):
1051            """
1052        finalises the iteration process for all models.
1053        """
1054            for o in self.iterModels():
1055                o.doStepPostprocessing(dt)
1056            self.time_step+=1
1057            self.time+=dt
1058            self.dt=dt
1059        
1060        def doStep(self,dt):
1061            """
1062        Executes the iteration step at a time step for all model::
1063    
1064                self.doStepPreprocessing(dt)
1065                while not self.terminateIteration():
1066                for all models:
1067                self.doStep(dt)
1068                    self.doStepPostprocessing(dt)
1069            """
1070            self.iter=0
1071            while not self.terminateIteration():
1072                if self.iter==0: self.trace("iteration at %d-th time step %e starts"%(self.time_step+1,self.time+dt))
1073                self.iter+=1
1074                self.trace("iteration step %d"%(self.iter))
1075                for o in self.iterModels():
1076                      o.doStep(dt)
1077            if self.iter>0: self.trace("iteration at %d-th time step %e finalized."%(self.time_step+1,self.time+dt))
1078    
1079         A Model has input and output parameters where each input parameter can      def run(self,check_pointing=None):
1080         be constant, time dependent or may depend on an output parameter of          """
1081         another model or the model itself. To create a parameter name of a model      Run the simulation by performing essentially::
1082         and to assign a value to it one can use the statement      
1083                self.setUp()
1084                if not restart:
1085                self.doInitialization()
1086                    while not self.terminateInitialIteration(): self.doInitialStep()
1087                    self.doInitialPostprocessing()
1088            while not self.finalize():
1089                dt=self.getSafeTimeStepSize()
1090                    self.doStepPreprocessing(dt_new)
1091                    self.doStep(dt_new)
1092                    self.doStepPostprocessing(dt_new)
1093            self.doFinalization()
1094    
1095            If one of the models in throws a C{FailedTimeStepError} exception a
1096        new time step size is computed through getSafeTimeStepSize() and the
1097        time step is repeated.
1098      
1099            If one of the models in throws a C{IterationDivergenceError}
1100        exception the time step size is halved and the time step is repeated.
1101    
1102             model.name=object          In both cases the time integration is given up after
1103        C{Simulation.FAILED_TIME_STEPS_MAX} attempts.
1104            """
1105            # check the completness of the models:
1106            # first a list of all the models involved in the simulation including subsimulations:
1107            #
1108            missing=self.checkModels(self.getAllModels(), [])
1109            if len(missing)>0:
1110                msg=""
1111                for l in missing:
1112                     msg+="\n\t"+str(l[1])+" at "+l[0]
1113                raise MissingLink("link targets missing in the Simulation: %s"%msg)
1114            #==============================
1115            self.setUp()
1116            if self.time_step < 1:
1117               self.doInitialization()
1118               self.doInitialStep()
1119               self.doInitialPostprocessing()
1120            while not self.finalize():
1121                step_fail_counter=0
1122                iteration_fail_counter=0
1123                if self.time_step==0:
1124                    dt_new=self.getSafeTimeStepSize(self.dt)
1125                else:
1126                    dt_new=min(max(self.getSafeTimeStepSize(self.dt),self.dt/self.MAX_CHANGE_OF_DT),self.dt*self.MAX_CHANGE_OF_DT)
1127                self.trace("%d. time step %e (step size %e.)" % (self.time_step+1,self.time+dt_new,dt_new))
1128                end_of_step=False
1129                while not end_of_step:
1130                   end_of_step=True
1131                   if not dt_new>0:
1132                      raise NonPositiveStepSizeError("non-positive step size in step %d"%(self.time_step+1))
1133                   try:
1134                      self.doStepPreprocessing(dt_new)
1135                      self.doStep(dt_new)
1136                      self.doStepPostprocessing(dt_new)
1137                   except IterationDivergenceError:
1138                      dt_new*=0.5
1139                      end_of_step=False
1140                      iteration_fail_counter+=1
1141                      if iteration_fail_counter>self.FAILED_TIME_STEPS_MAX:
1142                               raise SimulationBreakDownError("reduction of time step to achieve convergence failed after %s steps."%self.FAILED_TIME_STEPS_MAX)
1143                      self.trace("Iteration failed. Time step is repeated with new step size %s."%dt_new)
1144                   except FailedTimeStepError:
1145                      dt_new=self.getSafeTimeStepSize(self.dt)
1146                      end_of_step=False
1147                      step_fail_counter+=1
1148                      self.trace("Time step is repeated with new time step size %s."%dt_new)
1149                      if step_fail_counter>self.FAILED_TIME_STEPS_MAX:
1150                            raise SimulationBreakDownError("Time integration is given up after %d attempts."%step_fail_counter)
1151                if not check_pointing==None:
1152                   if check_pointing.doDump():
1153                        self.trace("check point is created.")
1154                        self.writeXML()
1155            self.doFinalization()
1156    
1157    
1158         At any time the current value of the parameter name can be obtained by      def toDom(self, esysxml, node):
1159            """
1160        C{toDom} method of Simulation class.
1161        """
1162            simulation = esysxml.createElement('Simulation')
1163            esysxml.registerLinkableObject(self, simulation)
1164            for rank, sim in enumerate(self.iterModels()):
1165                component = esysxml.createElement('Component')
1166                component.setAttribute('rank', str(rank))
1167                sim.toDom(esysxml, component)
1168                simulation.appendChild(component)
1169            node.appendChild(simulation)
1170    
                value=model.name  
1171    
1172         If the object that has been assigned to the paramter/attribute name has      def fromDom(cls, esysxml, node):
1173         the attribute/parameter name isself the current value of this attribute          sims = []
1174         of the object is returned (e.g. for model.name=object where object has          for n in node.childNodes:
1175         an attribute name, the statement value=model.name whould assign the              if isinstance(n, minidom.Text):
1176         value object.name to value.). If the name of the parameters of a model                  continue
1177         and an object don't match the setParameter method of model can be used.              sims.append(esysxml.getComponent(n))
1178         So          sims.sort(_comp)
1179            sim=cls([s[1] for s in sims], debug=esysxml.debug)
1180            esysxml.registerLinkableObject(sim, node)
1181            return sim
1182    
1183             model.setParameter(name,object,name_for_object)      fromDom = classmethod(fromDom)
1184    
1185         links the parameter name of model with the parameter name_for_object of  def _comp(a,b):
1186         object.      if a[0]<a[1]:
1187          return 1
1188        elif a[0]>a[1]:
1189          return -1
1190        else:
1191          return 0
1192    
1193         The run method initiates checkpointing (it is not clear how to do this  class IterationDivergenceError(Exception):
1194         yet)      """
1195     =====      Exception which is thrown if there is no convergence of the iteration
1196                    process at a time step.
    """  
1197    
1198        But there is a chance that a smaller step could help to reach convergence.
1199        """
1200        pass
1201    
1202    class FailedTimeStepError(Exception):
1203        """
1204        Exception which is thrown if the time step fails because of a step
1205        size that have been choosen to be too large.
1206        """
1207        pass
1208    
1209  if __name__=="__main__":  class SimulationBreakDownError(Exception):
1210      import math      """
1211      #      Exception which is thrown if the simulation does not manage to
1212      # test for parameter set      progress in time.
1213      #      """
1214      p11=ParameterSet()      pass
     p11.declareParameter(gamma1=1.,gamma2=2.,gamma3=3.)  
     p1=ParameterSet()  
     p1.declareParameter(dim=2,tol_v=0.001,output_file="/tmp/u.%3.3d.dx",runFlag=True,parm11=p11)  
     parm=ParameterSet({ "parm1" : p1 , "parm2" : ParameterSet(["alpha"])})  
     parm.parm2.alpha=Link(p11,"gamma1")  
     parm.x="that should not be here!"  
     print parm.showParameters()  
     # should be something like: {"parm2" : {"alpha" : reference to attribute  
     # gamma1 of <__main__.ParameterSet instance at 0xf6db51cc>},"parm1" : {"dim"  
     # : 2,"runFlag" : True,"tol_v": 0.001,"parm11" : {"gamma3" : 3.0,"gamma2" :  
     # 2.0,"gamma1" : 1.0},"output_file" : /tmp/u.%3.3d.dx}}  
     assert parm.parm2.alpha==1.  
     parm.writeXML()  
       
     #=======================  
     class Messenger(Model):  
         def __init__(self):  
             Model.__init__(self)  
             self.declareParameter(message="none")  
   
         def doInitialization(self,t):  
             self.__t=t  
             print "I start talking now!"  
   
         def doStep(self,dt):  
             self.__t+=dt  
             print "Message (time %e) : %s "%(self.__t,self.message)  
1215    
1216          def doFinalization(self):  class NonPositiveStepSizeError(Exception):
1217              print "I have no more to say!"      """
1218          Exception which is thrown if the step size is not positive.
1219      class ODETEST(Model):      """
1220          """ implements a solver for the ODE      pass
1221    
1222                du/dt=a*u+f(t)  class MissingLink(Exception):
1223        """
1224        Exception thrown when a link is missing
1225        """
1226        pass
1227    
1228             we use a implicit euler scheme :  class DataSource(object):
1229        """
1230        Class for handling data sources, including local and remote files. This class is under development.
1231        """
1232    
1233                u_n-u_{n-1}= dt*a u_n + st*f(t_n)      def __init__(self, uri="file.ext", fileformat="unknown"):
1234            self.uri = uri
1235            self.fileformat = fileformat
1236    
1237             to get u_n we run an iterative process      def toDom(self, esysxml, node):
1238            """
1239                 u_{n.k}=u_{n-1}+dt*(a u_{n.i-1} + f(t_n))          C{toDom} method of DataSource. Creates a DataSource node and appends it to the
1240        current XML esysxml.
1241            """
1242            ds = esysxml.createElement('DataSource')
1243            ds.appendChild(esysxml.createDataNode('URI', self.uri))
1244            ds.appendChild(esysxml.createDataNode('FileFormat', self.fileformat))
1245            node.appendChild(ds)
1246    
1247        def fromDom(cls, esysxml, node):
1248            uri= str(node.getElementsByTagName("URI")[0].firstChild.nodeValue.strip())
1249            fileformat= str(node.getElementsByTagName("FileFormat")[0].firstChild.nodeValue.strip())
1250            ds = cls(uri, fileformat)
1251            return ds
1252    
1253        def getLocalFileName(self):
1254            return self.uri
1255    
1256             input for this model are step size dt, end time tend and a value for      fromDom = classmethod(fromDom)
            a, f and initial value for u. we need also a tolerance tol for a  
            stopping criterion.  
1257    
1258    class RestartManager(object):
1259         """
1260         A restart manager which does two things: it decides when restart files have created (when doDump returns true) and
1261         manages directories for restart files. The method getNewDumper creates a new directory and returns its name.
1262        
1263         This restart manager will decide to dump restart files if every dump_step calls of doDump or
1264         if more than dump_time since the last dump has elapsed. The restart manager controls two directories for dumping restart data, namely
1265         for the current and previous dump. This way the previous dump can be used for restart in the case the current dump failed.
1266    
1267         @cvar SEC: unit of seconds, for instance for 5*RestartManager.SEC to define 5 seconds.
1268         @cvar MIN: unit of minutes, for instance for 5*RestartManager.MIN to define 5 minutes.
1269         @cvar H: unit of hours, for instance for 5*RestartManager.H to define 5 hours.
1270         @cvar D: unit of days, for instance for 5*RestartManager.D to define 5 days.
1271         """
1272         SEC=1.
1273         MIN=60.
1274         H=360.
1275         D=8640.
1276         def __init__(self,dump_time=1080., dump_step=None, dumper=None):
1277             """
1278             initializes the RestartManager.
1279    
1280             @param dump_time: defines the minimum time interval in SEC between to dumps. If None, time is not used as criterion.
1281             @param dump_step: defines the number of calls of doDump between to dump events. If None, the call counter is not used as criterion.
1282             @param dumper: defines the directory for dumping restart files. Additionally the directories dumper+"_bkp" and dumper+"_bkp2" are used.
1283                            if the directory does not exist it is created. If dumper is not present a unique directory within the current
1284                            working directory is used.
1285             """
1286             self.__dump_step=dump_time
1287             self.__dump_time=dump_step
1288             self.__counter=0
1289             self.__saveMarker()
1290             if dumper == None:
1291                self.__dumper="restart"+str(os.getpid())
1292             else:
1293                self.__dumper=dumper
1294             self.__dumper_bkp=self.__dumper+"_bkp"
1295             self.__dumper_bkp2=self.__dumper+"_bkp2"
1296             self.__current_dumper=None
1297         def __saveMarker(self):
1298             self.__last_restart_time=time.time()
1299             self.__last_restart_counter=self.__counter
1300         def getCurrentDumper(self):
1301             """
1302             returns the name of the currently used dumper
1303             """
1304             return self.__current_dumper
1305         def doDump(self):
1306          """          """
1307            returns true the restart should be dumped. use C{getNewDumper} to get the directory name to be used.
1308          def __init__(self):          """
1309              Model.__init__(self,debug=True)          if self.__dump_step == None:
1310              self.declareParameter(tend=1.,dt=0.1,a=0.9,u=10.,f=0.,message="",tol=1.e-8)             if self.__dump_step == None:
1311                  out = False
1312          def doInitialization(self,t):             else:
1313              self.__tn=t                out = (self.__dump_step + self.__last_restart_counter) <= self.__counter
1314              self.__iter=0          else:
1315                         if dump_step == None:
1316          def doIterationInitialization(self,dt):                out = (self.__last_restart_time + self.__dump_time) <= time.time()
1317              self.__iter=0             else:
1318              self.__u_last=self.u                            out =    ( (self.__dump_step + self.__last_restart_counter) <= self.__counter)  \
1319                        or ( (self.__last_restart_time + self.__dump_time) <= time.time() )
1320          def doIterationStep(self,dt):          if out: self.__saveMarker()
1321              self.__iter+=1          self__counter+=1
1322              self.__u_old=self.u       def getNewDumper(self):
1323              self.u=self.__u_last+dt*(self.a*self.__u_old+self.f)         """
1324           creates a new directory to be used for dumping and returns its name.
1325           """
1326           if os.access(self.__dumper_bkp,os.F_OK):
1327              if os.access(self.__dumper_bkp2, os.F_OK):
1328                 raise RunTimeError("please remove %s."%self.__dumper_bkp2)
1329              try:
1330                 os.rename(self.__dumper_bkp, self.__dumper_bkp2)
1331              except:
1332                 self.__current_dumper=self.__dumper
1333                 raise RunTimeError("renaming back-up directory %s failed. Use %s for restart."%(self.__dumper_bkp,self.__dumper))
1334           if os.access(self.__dumper,os.F_OK):
1335              if os.access(self.__dumper_bkp, os.F_OK):
1336                 raise RunTimeError("please remove %s."%self.__dumper_bkp)
1337              try:
1338                 os.rename(self.__dumper, self.__dumper_bkp)
1339              except:
1340                 self.__current_dumper=self.__dumper_bkp2
1341                 raise RunTimeError("moving directory %s to back-up failed. Use %s for restart."%(self.__dumper,self.__dumper_bkp2))
1342           try:
1343              os.mkdir(self.__dumper)
1344           except:
1345              self.__current_dumper=self.__dumper_bkp
1346              raise RunTimeError("creating a new restart directory %s failed. Use %s for restart."%(self.__dumper,self.__dumper_bkp))
1347           if os.access(self.__dumper_bkp2, os.F_OK): os.rmdir(self.__dumper_bkp2)
1348           return self.getCurrentDumper()
1349                    
1350          def terminate(self):      
1351              if self.__iter<1:  # vim: expandtab shiftwidth=4:
                 return False  
             else:  
                 return abs(self.__u_old-self.u)<self.tol*abs(self.u)  
   
         def doIterationFinalization(self,dt):  
             self.__tn+=dt  
             self.message="current error = %e"%abs(self.u-10.*math.exp((self.a-1.)*self.__tn))  
   
         def getSafeTimeStepSize(self,dt):  
             return min(self.dt,1./(abs(self.a)+1.))  
   
         def finalize(self):  
             return self.__tn>=self.tend  
   
     #  
     #   s solves the coupled ODE:  
     #  
     #     du/dt=a*u+  v  
     #     dv/dt=  u+a*v  
     #    
     #   each equation is treated through the ODETEST class. The equations are  
     #   linked and iteration over each time step is performed.  the current  
     #   error of v is reported by the Messenger class.  
     #  
     o1=ODETEST()  
     o1.u=10  
     o2=ODETEST()  
     o2.u=-10.  
     o1.f=Link(o2,"u")  
     o2.f=Link(o1,"u")  
     m=Messenger()  
     o1.dt=0.01  
     m.message=Link(o1)  
     s=ExplicitSimulation([Simulation([o1,o2],debug=True),m],debug=True)  
     s.run()  
     s.writeXML()  

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