/[escript]/trunk/escript/py_src/modelframe.py
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trunk/esys2/escript/py_src/modelframe.py revision 147 by jgs, Fri Aug 12 01:45:47 2005 UTC trunk/escript/py_src/modelframe.py revision 939 by gross, Thu Jan 25 04:23:38 2007 UTC
# Line 1  Line 1 
1  # $Id$  # $Id$
2    
3    """
4    Environment for implementing models in escript
5    
6    @var __author__: name of author
7    @var __copyright__: copyrights
8    @var __license__: licence agreement
9    @var __url__: url entry point on documentation
10    @var __version__: version
11    @var __date__: date of the version
12    """
13    
14    __author__="Lutz Gross, l.gross@uq.edu.au"
15    __copyright__="""  Copyright (c) 2006 by ACcESS MNRF
16                        http://www.access.edu.au
17                    Primary Business: Queensland, Australia"""
18    __license__="""Licensed under the Open Software License version 3.0
19                 http://www.opensource.org/licenses/osl-3.0.php"""
20    __url__="http://www.iservo.edu.au/esys"
21    __version__="$Revision$"
22    __date__="$Date$"
23    
24    
25  from types import StringType,IntType,FloatType,BooleanType,ListType,DictType  from types import StringType,IntType,FloatType,BooleanType,ListType,DictType
26  from sys import stdout  from sys import stdout
27    import numarray
28    import operator
29  import itertools  import itertools
 # import modellib  temporarily removed!!!  
30    
31  # 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)
32  try:  try:
# Line 13  except NameError: Line 36  except NameError:
36    
37  from xml.dom import minidom  from xml.dom import minidom
38    
 def dataNode(document, tagName, data):  
     """  
     dataNodes are the building blocks of the xml documents constructed in  
     this module. document is the current xml document, tagName is the  
     associated xml tag, and data is the values in the tag.  
     """  
     t = document.createTextNode(str(data))  
     n = document.createElement(tagName)  
     n.appendChild(t)  
     return n  
   
 def esysDoc():  
     """  
     Global method for creating an instance of an EsysXML document.  
     """  
     doc = minidom.Document()  
     esys = doc.createElement('ESys')  
     doc.appendChild(esys)  
     return doc, esys  
39    
40  def all(seq):  def all(seq):
41      for x in seq:      for x in seq:
# Line 45  def any(seq): Line 49  def any(seq):
49              return True              return True
50      return False      return False
51    
52  LinkableObjectRegistry = {}  def importName(modulename, name):
53        """ Import a named object from a module in the context of this function,
54  def registerLinkableObject(obj_id, o):          which means you should use fully qualified module paths.
55      LinkableObjectRegistry[obj_id] = o          Return None on failure.
56    
57  LinkRegistry = []          This function from: http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/52241
58        """
59  def registerLink(obj_id, l):      module = __import__(modulename, globals(), locals(), [name])
60      LinkRegistry.append((obj_id,l))          
61        try:
62            return vars(module)[name]
63        except KeyError:
64            raise ImportError("Could not import %s from %s" % (name, modulename))
65    
66  def parse(xml):  class ESySXMLParser(object):
67      """      """
68      Generic parse method for EsysXML. Without this, Links don't work.      parser for ESysXML file
69      """      """
70      global LinkRegistry, LinkableObjectRegistry      def __init__(self,xml, debug=False):
71      LinkRegistry = []        self.__dom = minidom.parseString(xml)
72      LinkableObjectRegistry = {}        self.__linkable_object_registry= {}
73          self.__link_registry=  []
74      doc = minidom.parseString(xml)        self.__esys=self.__dom.firstChild
75      sim = getComponent(doc.firstChild)        self.debug=debug
76      for obj_id, link in LinkRegistry:    
77          link.target = LinkableObjectRegistry[obj_id]      def getClassPath(self, node):
78            type = node.getAttribute("type")
79            if (node.getAttribute("module")):
80                module = node.getAttribute("module")
81                return importName(module, type)
82            else:
83                return importName("__main__", type)
84    
85      return sim      def setLinks(self):
86            for obj_id, link in self.__link_registry:
87                link.target = self.__linkable_object_registry[obj_id]
88    
89        def parse(self):
90           """
91           parser method for EsysXML and returns the list of generating ParameterSets
92           """
93           found=[]
94           for node in self.__esys.childNodes:
95               if isinstance(node, minidom.Element):
96                   if node.tagName == 'Simulation':
97                            found.append(Simulation.fromDom(self, node))
98                   elif node.tagName == 'Model':
99                            found.append(self.getClassPath(node).fromDom(self, node))
100                   elif node.tagName == 'ParameterSet':
101                            found.append(self.getClassPath(node).fromDom(self, node))
102                   else:
103                      raise "Invalid type, %r" % node.getAttribute("type")
104           self.setLinks()
105           return found
106    
107        def registerLink(self,obj_id, link):
108            self.__link_registry.append((int(obj_id),link))
109    
110        def registerLinkableObject(self,obj, node):
111            id_str=node.getAttribute('id').strip()
112            if len(id_str)>0:
113               id=int(id_str)
114               if self.__linkable_object_registry.has_key(id):
115                   raise ValueError("Object id %s already exists."%id)
116               else:
117                   self.__linkable_object_registry[id]=obj
118    
119        def getComponent(self, node):
120           """
121           returns a single component + rank from a simulation
122           parser method for EsysXML and returns the list of generating ParameterSets
123           """
124           rank  = int(node.getAttribute("rank"))
125           for n in node.childNodes:
126               if isinstance(n, minidom.Element):
127                   if n.tagName == 'Simulation':
128                            return (rank, Simulation.fromDom(self, n))
129                   elif n.tagName == 'Model':
130                            return (rank, self.getClassPath(n).fromDom(self, n))
131                   elif n.tagName == 'ParameterSet':
132                            return (rank, self.getClassPath(n).fromDom(self, n))
133                   else:
134                     raise ValueError("illegal component type %s"%n.tagName)
135           raise ValueError("cannot resolve Component")
136    
137  def getComponent(doc):  class ESySXMLCreator(object):
     """  
     Used to get components of Simualtions, Models.  
138      """      """
139      for node in doc.childNodes:      creates an XML Dom representation
140                """
141          if isinstance(node, minidom.Element):      def __init__(self):
142              if node.tagName == 'Simulation':         self.__dom=minidom.Document()
143                  if node.getAttribute("type") == 'Simulation':         self.__esys =self.__dom.createElement('ESys')
144                      return Simulation.fromDom(node)         self.__dom.appendChild(self.__esys)
145              if node.tagName == 'Model':         self.__linkable_object_registry={}
146                  model_type = node.getAttribute("type")         self.__number_sequence = itertools.count(100)
147                  model_subclasses = Model.__subclasses__()      def getRoot(self):
148                  for model in model_subclasses:         return self.__esys
149                      if model_type == model.__name__:      def createElement(self,name):
150                          return Model.fromDom(node)        return self.__dom.createElement(name)
151              if node.tagName == 'ParameterSet':      def createTextNode(self,name):
152                  parameter_type = node.getAttribute("type")        return self.__dom.createTextNode(name)
153                  return ParameterSet.fromDom(node)      def getElementById(self,name):
154              raise "Invalid simulation type, %r" % node.getAttribute("type")        return self.__dom.getElementById(name)
155                def createDataNode(self, tagName, data):
156              """
157      raise ValueError("No Simulation Found")            C{createDataNode}s are the building blocks of the xml documents constructed in
158                          this module.  
159        
160              @param tagName: the associated xml tag
161              @param data: the values in the tag
162              """
163              n = self.createElement(tagName)
164              n.appendChild(self.createTextNode(str(data)))
165              return n
166        def getLinkableObjectId(self, obj):
167            for id, o in self.__linkable_object_registry.items():
168                if o == obj: return id
169            id =self.__number_sequence.next()
170            self.__linkable_object_registry[id]=obj
171            return id
172            
173        def registerLinkableObject(self, obj, node):
174            """
175            returns a unique object id for object obj
176            """
177            id=self.getLinkableObjectId(obj)
178            node.setAttribute('id',str(id))
179            node.setIdAttribute("id")
180    
181        def includeTargets(self):
182            target_written=True
183            while target_written:
184                targetsList =self.__dom.getElementsByTagName('Target')
185                target_written=False
186                for element in targetsList:
187                   targetId = int(element.firstChild.nodeValue.strip())
188                   if self.getElementById(str(targetId)): continue
189                   targetObj = self.__linkable_object_registry[targetId]
190                   targetObj.toDom(self, self.__esys)
191                   target_written=True
192    
193        def toprettyxml(self):
194            self.includeTargets()
195            return self.__dom.toprettyxml()
196    
197  class Link:  class Link:
198      """      """
199      a Link makes an attribute of an object callable:      A Link makes an attribute of an object callable::
200    
201            o.object()            o.object()
202            o.a=8            o.a=8
203            l=Link(o,"a")            l=Link(o,"a")
# Line 106  class Link: Line 206  class Link:
206            
207      def __init__(self,target,attribute=None):      def __init__(self,target,attribute=None):
208          """          """
209          creates a link to the object target. If attribute is given, the link is          Creates a link to the object target. If attribute is given, the link is
210          establised to this attribute of the target.  Otherwise the attribute is          establised to this attribute of the target.  Otherwise the attribute is
211          undefined.          undefined.
212          """          """
213          self.target = target          self.target = target
214          self.attribute = None          self.attribute = None
215          self.setAttributeName(attribute)          self.setAttributeName(attribute)
216    
217        def getTarget(self):
218            """
219            returns the target
220            """
221            return self.target
222        def getAttributeName(self):
223            """
224            returns the name of the attribute the link is pointing to
225            """
226            return self.attribute
227            
228      def setAttributeName(self,attribute):      def setAttributeName(self,attribute):
229          """          """
230          set a new attribute name to be collected from the target object. The          Set a new attribute name to be collected from the target object. The
231          target object must have the attribute with name attribute.          target object must have the attribute with name attribute.
232          """          """
233          if attribute and self.target:          if attribute and self.target:
# Line 130  class Link: Line 241  class Link:
241            
242      def hasDefinedAttributeName(self):      def hasDefinedAttributeName(self):
243          """          """
244          returns true if an attribute name is set          Returns true if an attribute name is set.
245          """          """
246          return self.attribute != None          return self.attribute != None
247            
248      def __repr__(self):      def __repr__(self):
249          """          """
250          returns a string representation of the link          Returns a string representation of the link.
251          """          """
252          if self.hasDefinedAttributeName():          if self.hasDefinedAttributeName():
253              return "<Link to attribute %s of %s>" % (self.attribute, self.target)              return "<Link to attribute %s of %s>" % (self.attribute, self.target)
# Line 145  class Link: Line 256  class Link:
256            
257      def __call__(self,name=None):      def __call__(self,name=None):
258          """          """
259          returns the value of the attribute of the target object. If the          Returns the value of the attribute of the target object. If the
260          atrribute is callable then the return value of the call is returned.          atrribute is callable then the return value of the call is returned.
261          """          """
262          if name:          if name:
# Line 158  class Link: Line 269  class Link:
269          else:          else:
270              return out              return out
271    
272      def toDom(self, document, node):      def toDom(self, esysxml, node):
273          """          """
274          toDom method of Link. Creates a Link node and appends it to the current XML          C{toDom} method of Link. Creates a Link node and appends it to the
275          document      current XML esysxml.
276          """          """
277          link = document.createElement('Link')          link = esysxml.createElement('Link')
278          assert (self.target != None), ("Target was none, name was %r" % self.attribute)          assert (self.target != None), ("Target was none, name was %r" % self.attribute)
279          link.appendChild(dataNode(document, 'Target', self.target.id))          link.appendChild(esysxml.createDataNode('Target', esysxml.getLinkableObjectId(self.target)))
280          # 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
281          # target from the xml later. I need a better unique identifier.          # target from the xml later. I need a better unique identifier.
282          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"
283          link.appendChild(dataNode(document, 'Attribute', self.attribute))          link.appendChild(esysxml.createDataNode('Attribute', self.attribute))
284          node.appendChild(link)          node.appendChild(link)
285    
286      def fromDom(cls, doc):      def fromDom(cls, esysxml, node):
287          targetid = doc.getElementsByTagName("Target")[0].firstChild.nodeValue.strip()          targetid = int(node.getElementsByTagName("Target")[0].firstChild.nodeValue.strip())
288          attribute = doc.getElementsByTagName("Attribute")[0].firstChild.nodeValue.strip()          attribute =str(node.getElementsByTagName("Attribute")[0].firstChild.nodeValue.strip())
289          l = cls(None, attribute)          l = cls(None, attribute)
290          registerLink(targetid, l)          esysxml.registerLink(targetid, l)
291          return l          return l
292    
293      fromDom = classmethod(fromDom)      fromDom = classmethod(fromDom)
294            
     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  
         """  
         print 'I got to the Link writeXML method'  
         document, rootnode = esysDoc()  
         self.toDom(document, rootnode)  
   
         ostream.write(document.toprettyxml())  
   
295  class LinkableObject(object):  class LinkableObject(object):
296      """      """
297      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
298      via a Link object. For instance      via a Link object. For instance::
299                        
300             p = LinkableObject()             p = LinkableObject()
301             p.x = Link(o,"name")             p.x = Link(o,"name")
302             print p.x             print p.x
303            
304      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}.
305    
306      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
307        C{o}.  
308    
309      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
310      value of the call.      the return value of the call.
311      """      """
312        
     number_sequence = itertools.count(100)  
313            
314      def __init__(self, debug=False):      def __init__(self, id = None, debug=False):
315          """ initializes LinkableObject so that we can operate on Links """          """
316        Initializes LinkableObject so that we can operate on Links
317        """
318          self.debug = debug          self.debug = debug
319          self.__linked_attributes={}          self.__linked_attributes={}
320          self.id = self.number_sequence.next()          
   
321      def trace(self, msg):      def trace(self, msg):
322          """ If debugging is on, print the message, otherwise do nothing          """
323        If debugging is on, print the message, otherwise do nothing
324          """          """
325          if self.debug:          if self.debug:
326              print "%s: %s"%(str(self),msg)              print "%s: %s"%(str(self),msg)
327            
328      def __getattr__(self,name):      def __getattr__(self,name):
329          """returns the value of attribute name. If the value is a Link object the          """
330          object is called and the return value is returned."""      Returns the value of attribute name. If the value is a Link object the
331            object is called and the return value is returned.
332        """
333          out = self.getAttributeObject(name)          out = self.getAttributeObject(name)
334          if isinstance(out,Link):          if isinstance(out,Link):
335              return out()              return out()
# Line 234  class LinkableObject(object): Line 337  class LinkableObject(object):
337              return out              return out
338            
339      def getAttributeObject(self,name):      def getAttributeObject(self,name):
340          """return the object stored for attribute name."""          """
341        Return the object stored for attribute name.
342        """
343    
344          if self.__dict__.has_key(name):          if self.__dict__.has_key(name):
345              return self.__dict__[name]              return self.__dict__[name]
# Line 248  class LinkableObject(object): Line 353  class LinkableObject(object):
353          raise AttributeError,"No attribute %s."%name          raise AttributeError,"No attribute %s."%name
354            
355      def hasAttribute(self,name):      def hasAttribute(self,name):
356          """returns True if self as attribute name"""          """
357        Returns True if self as attribute name.
358        """
359          return self.__dict__.has_key(name) or self.__linked_attributes.has_key(name) or  self.__class__.__dict__.has_key(name)          return self.__dict__.has_key(name) or self.__linked_attributes.has_key(name) or  self.__class__.__dict__.has_key(name)
360    
361      def __setattr__(self,name,value):      def __setattr__(self,name,value):
362          """sets the value for attribute name. If value is a Link the target          """
363          attribute is set to name if no attribute has been specified."""      Sets the value for attribute name. If value is a Link the target
364            attribute is set to name if no attribute has been specified.
365        """
366    
367          if self.__dict__.has_key(name):          if self.__dict__.has_key(name):
368              del self.__dict__[name]              del self.__dict__[name]
# Line 269  class LinkableObject(object): Line 377  class LinkableObject(object):
377              self.__dict__[name] = value              self.__dict__[name] = value
378            
379      def __delattr__(self,name):      def __delattr__(self,name):
380          """removes the attribute name."""          """
381        Removes the attribute name.
382        """
383    
384          if self.__linked_attributes.has_key[name]:          if self.__linked_attributes.has_key[name]:
385              del self.__linked_attributes[name]              del self.__linked_attributes[name]
# Line 292  class _ParameterIterator: Line 402  class _ParameterIterator:
402          return self          return self
403    
404  class ParameterSet(LinkableObject):  class ParameterSet(LinkableObject):
405      """a class which allows to emphazise attributes to be written and read to XML      """
406        A class which allows to emphazise attributes to be written and read to XML
407                
408         Leaves of  an ESySParameters objects can be      Leaves of an ESySParameters object can be:
409            
410              a real number       - a real number
411              a integer number       - a integer number
412              a string       - a string
413              a boolean value       - a boolean value
414              a ParameterSet object       - a ParameterSet object
415              a Simulation object       - a Simulation object
416              a Model object       - a Model object
417              any other object (not considered by writeESySXML and writeXML)       - a numarray object
418                 - a list of booleans
419             Example how to create an ESySParameters object:          - any other object (not considered by writeESySXML and writeXML)
420            
421                   p11=ParameterSet(gamma1=1.,gamma2=2.,gamma3=3.)      Example how to create an ESySParameters object::
422                   p1=ParameterSet(dim=2,tol_v=0.001,output_file="/tmp/u.%3.3d.dx",runFlag=True,parm11=p11)      
423                   parm=ParameterSet(parm1=p1,parm2=ParameterSet(alpha=Link(p11,"gamma1")))          p11=ParameterSet(gamma1=1.,gamma2=2.,gamma3=3.)
424                p1=ParameterSet(dim=2,tol_v=0.001,output_file="/tmp/u.%3.3d.dx",runFlag=True,parm11=p11)
425             This can be accessed as          parm=ParameterSet(parm1=p1,parm2=ParameterSet(alpha=Link(p11,"gamma1")))
426            
427                   parm.parm1.gamma=0.      This can be accessed as::
428                   parm.parm1.dim=2      
429                   parm.parm1.tol_v=0.001      parm.parm1.gamma=0.
430                   parm.parm1.output_file="/tmp/u.%3.3d.dx"          parm.parm1.dim=2
431                   parm.parm1.runFlag=True          parm.parm1.tol_v=0.001
432                   parm.parm1.parm11.gamma1=1.          parm.parm1.output_file="/tmp/u.%3.3d.dx"
433                   parm.parm1.parm11.gamma2=2.          parm.parm1.runFlag=True
434                   parm.parm1.parm11.gamma3=3.          parm.parm1.parm11.gamma1=1.
435                   parm.parm2.alpha=1. (value of parm.parm1.parm11.gamma1)          parm.parm1.parm11.gamma2=2.
436                        parm.parm1.parm11.gamma3=3.
437            parm.parm2.alpha=1. (value of parm.parm1.parm11.gamma1)
438      """      """
439      def __init__(self, parameters=[], **kwargs):      def __init__(self, parameters=[], **kwargs):
440          """creates a ParameterSet with parameters parameters"""          """
441        Creates a ParameterSet with parameters parameters.
442        """
443          LinkableObject.__init__(self, **kwargs)          LinkableObject.__init__(self, **kwargs)
444          self.parameters = set()          self.parameters = set()
445          self.declareParameters(parameters)          self.declareParameters(parameters)
446    
447      def __repr__(self):      def __repr__(self):
448          return "<%s %r>" % (self.__class__.__name__,          return "<%s %d>"%(self.__class__.__name__,id(self))
                             [(p, getattr(self, p, None)) for p in self.parameters])  
449            
450      def declareParameter(self,**parameters):      def declareParameter(self,**parameters):
451          """declares a new parameter(s) and its (their) inital value."""          """
452        Declares a new parameter(s) and its (their) initial value.
453        """
454          self.declareParameters(parameters)          self.declareParameters(parameters)
455            
456      def declareParameters(self,parameters):      def declareParameters(self,parameters):
457          """declares a set of parameters. parameters can be a list, a dictonary or a ParameterSet."""          """
458        Declares a set of parameters. parameters can be a list, a dictionary
459        or a ParameterSet.
460        """
461          if isinstance(parameters,ListType):          if isinstance(parameters,ListType):
462              parameters = zip(parameters, itertools.repeat(None))              parameters = zip(parameters, itertools.repeat(None))
463          if isinstance(parameters,DictType):          if isinstance(parameters,DictType):
# Line 352  class ParameterSet(LinkableObject): Line 470  class ParameterSet(LinkableObject):
470              self.trace("parameter %s has been declared."%prm)              self.trace("parameter %s has been declared."%prm)
471    
472      def releaseParameters(self,name):      def releaseParameters(self,name):
473          """removes parameter name from the paramameters"""          """
474        Removes parameter name from the paramameters.
475        """
476          if self.isParameter(name):          if self.isParameter(name):
477              self.parameters.remove(name)              self.parameters.remove(name)
478              self.trace("parameter %s has been removed."%name)              self.trace("parameter %s has been removed."%name)
479            
480      def __iter__(self):      def __iter__(self):
481          """creates an iterator over the parameter and their values"""          """
482        Creates an iterator over the parameter and their values.
483        """
484          return _ParameterIterator(self)          return _ParameterIterator(self)
485            
486      def showParameters(self):      def showParameters(self):
487          """returns a descrition of the parameters"""                  """
488        Returns a descrition of the parameters.
489        """        
490          out="{"          out="{"
491          notfirst=False          notfirst=False
492          for i,v in self:          for i,v in self:
# Line 375  class ParameterSet(LinkableObject): Line 499  class ParameterSet(LinkableObject):
499          return out+"}"          return out+"}"
500            
501      def __delattr__(self,name):      def __delattr__(self,name):
502          """removes the attribute name."""          """
503        Removes the attribute name.
504        """
505          LinkableObject.__delattr__(self,name)          LinkableObject.__delattr__(self,name)
506          try:          try:
507              self.releaseParameter(name)              self.releaseParameter(name)
508          except:          except:
509              pass              pass
510    
511      def toDom(self, document, node):      def toDom(self, esysxml, node):
512          """ toDom method of ParameterSet class """          """
513          pset = document.createElement('ParameterSet')      C{toDom} method of Model class
514        """
515            pset = esysxml.createElement('ParameterSet')
516            pset.setAttribute('type', self.__class__.__name__)
517            pset.setAttribute('module', self.__class__.__module__)
518            esysxml.registerLinkableObject(self, pset)
519            self._parametersToDom(esysxml, pset)
520          node.appendChild(pset)          node.appendChild(pset)
         self._parametersToDom(document, pset)  
521    
522      def _parametersToDom(self, document, node):      def _parametersToDom(self, esysxml, node):
         node.setAttribute ('id', str(self.id))  
523          for name,value in self:          for name,value in self:
524              param = document.createElement('Parameter')              # convert list to numarray when possible:
525              param.setAttribute('type', value.__class__.__name__)              if isinstance (value, list):
526                    elem_type=-1
527                    for i in value:
528                        if isinstance(i, bool):
529                            elem_type = max(elem_type,0)
530                        if isinstance(i, int) and not isinstance(i, bool):
531                            elem_type = max(elem_type,1)
532                        if isinstance(i, float):
533                            elem_type = max(elem_type,2)
534                    if elem_type == 0: value = numarray.array(value,numarray.Bool)
535                    if elem_type == 1: value = numarray.array(value,numarray.Int)
536                    if elem_type == 2: value = numarray.array(value,numarray.Float)
537    
538              param.appendChild(dataNode(document, 'Name', name))              param = esysxml.createElement('Parameter')
539                param.setAttribute('type', value.__class__.__name__)
540    
541              val = document.createElement('Value')              param.appendChild(esysxml.createDataNode('Name', name))
542    
543              if isinstance(value,ParameterSet):              val = esysxml.createElement('Value')
544                  value.toDom(document, val)              if isinstance(value,(ParameterSet,Link,DataSource)):
545                    value.toDom(esysxml, val)
546                  param.appendChild(val)                  param.appendChild(val)
547              elif isinstance(value, Link):              elif isinstance(value, numarray.NumArray):
548                  value.toDom(document, val)                  shape = value.getshape()
549                    if isinstance(shape, tuple):
550                        size = reduce(operator.mul, shape)
551                        shape = ' '.join(map(str, shape))
552                    else:
553                        size = shape
554                        shape = str(shape)
555    
556                    arraytype = value.type()
557                    if isinstance(arraytype, numarray.BooleanType):
558                          arraytype_str="Bool"
559                    elif isinstance(arraytype, numarray.IntegralType):
560                          arraytype_str="Int"
561                    elif isinstance(arraytype, numarray.FloatingType):
562                          arraytype_str="Float"
563                    elif isinstance(arraytype, numarray.ComplexType):
564                          arraytype_str="Complex"
565                    else:
566                          arraytype_str=str(arraytype)
567                    numarrayElement = esysxml.createElement('NumArray')
568                    numarrayElement.appendChild(esysxml.createDataNode('ArrayType', arraytype_str))
569                    numarrayElement.appendChild(esysxml.createDataNode('Shape', shape))
570                    numarrayElement.appendChild(esysxml.createDataNode('Data', ' '.join(
571                        [str(x) for x in numarray.reshape(value, size)])))
572                    val.appendChild(numarrayElement)
573                  param.appendChild(val)                  param.appendChild(val)
574              elif isinstance(value,StringType):              elif isinstance(value, list):
575                  param.appendChild(dataNode(document, 'Value', value))                  param.appendChild(esysxml.createDataNode('Value', ' '.join([str(x) for x in value]) ))
576                elif isinstance(value, (str, bool, int, float, type(None))):
577                    param.appendChild(esysxml.createDataNode('Value', str(value)))
578                elif isinstance(value, dict):
579                     dic = esysxml.createElement('dictionary')
580                     if len(value.keys())>0:
581                         dic.setAttribute('key_type', value.keys()[0].__class__.__name__)
582                         dic.setAttribute('value_type', value[value.keys()[0]].__class__.__name__)
583                     for k,v in value.items():
584                        i=esysxml.createElement('item')
585                        i.appendChild(esysxml.createDataNode('key', k))
586                        i.appendChild(esysxml.createDataNode('value', v))
587                        dic.appendChild(i)
588                     param.appendChild(dic)
589              else:              else:
590                  param.appendChild(dataNode(document, 'Value', str(value)))                  print value
591                    raise ValueError("cannot serialize %s type to XML."%str(value.__class__))
592    
593              node.appendChild(param)              node.appendChild(param)
594    
595      def fromDom(cls, doc):      def fromDom(cls, esysxml, node):
   
596          # Define a host of helper functions to assist us.          # Define a host of helper functions to assist us.
597          def _children(node):          def _children(node):
598              """              """
599              Remove the empty nodes from the children of this node              Remove the empty nodes from the children of this node.
600              """              """
601              return [x for x in node.childNodes              ret = []
602                      if not isinstance(x, minidom.Text) or x.nodeValue.strip()]              for x in node.childNodes:
603                    if isinstance(x, minidom.Text):
604                        if x.nodeValue.strip():
605                            ret.append(x)
606                    else:
607                        ret.append(x)
608                return ret
609    
610          def _floatfromValue(doc):          def _floatfromValue(esysxml, node):
611              return float(doc.nodeValue.strip())              return float(node.nodeValue.strip())
612    
613          def _stringfromValue(doc):          def _stringfromValue(esysxml, node):
614              return str(doc.nodeValue.strip())              return str(node.nodeValue.strip())
615                
616          def _intfromValue(doc):          def _intfromValue(esysxml, node):
617              return int(doc.nodeValue.strip())              return int(node.nodeValue.strip())
618    
619          def _boolfromValue(doc):          def _boolfromValue(esysxml, node):
620              return bool(doc.nodeValue.strip())              return _boolfromstring(node.nodeValue.strip())
621          
622            def _nonefromValue(esysxml, node):
623                return None
624    
625            def _numarrayfromValue(esysxml, node):
626                for node in _children(node):
627                    if node.tagName == 'ArrayType':
628                        arraytype = node.firstChild.nodeValue.strip()
629                    if node.tagName == 'Shape':
630                        shape = node.firstChild.nodeValue.strip()
631                        shape = [int(x) for x in shape.split()]
632                    if node.tagName == 'Data':
633                        data = node.firstChild.nodeValue.strip()
634                        data = [float(x) for x in data.split()]
635                return numarray.reshape(numarray.array(data, type=getattr(numarray, arraytype)),
636                                        shape)
637          
638            def _listfromValue(esysxml, node):
639                return [x for x in node.nodeValue.split()]
640    
641            def _boolfromstring(s):
642                if s == 'True':
643                    return True
644                else:
645                    return False
646          # 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
647          ptypemap = {"Simulation": Simulation.fromDom,          ptypemap = {"Simulation": Simulation.fromDom,
648                      "Model":Model.fromDom,                      "Model":Model.fromDom,
649                      "ParameterSet":ParameterSet.fromDom,                      "ParameterSet":ParameterSet.fromDom,
650                      "Link":Link.fromDom,                      "Link":Link.fromDom,
651                        "DataSource":DataSource.fromDom,
652                      "float":_floatfromValue,                      "float":_floatfromValue,
653                      "int":_intfromValue,                      "int":_intfromValue,
654                      "str":_stringfromValue,                      "str":_stringfromValue,
655                      "bool":_boolfromValue                      "bool":_boolfromValue,
656                        "list":_listfromValue,
657                        "NumArray":_numarrayfromValue,
658                        "NoneType":_nonefromValue,
659                      }                      }
660    
 #        print doc.toxml()  
   
661          parameters = {}          parameters = {}
662          for node in _children(doc):          for n in _children(node):
663              ptype = node.getAttribute("type")              ptype = n.getAttribute("type")
664                if not ptypemap.has_key(ptype):
665                   raise KeyError("cannot handle parameter type %s."%ptype)
666    
667              pname = pvalue = None              pname = pvalue = None
668              for childnode in _children(node):              for childnode in _children(n):
   
669                  if childnode.tagName == "Name":                  if childnode.tagName == "Name":
670                      pname = childnode.firstChild.nodeValue.strip()                      pname = childnode.firstChild.nodeValue.strip()
671    
672                  if childnode.tagName == "Value":                  if childnode.tagName == "Value":
673                      nodes = _children(childnode)                      nodes = _children(childnode)
674                      pvalue = ptypemap[ptype](nodes[0])                      pvalue = ptypemap[ptype](esysxml, nodes[0])
675    
676              parameters[pname] = pvalue              parameters[pname] = pvalue
677    
678          # Create the instance of ParameterSet          # Create the instance of ParameterSet
679          o = cls()          o = cls(debug=esysxml.debug)
680          o.declareParameters(parameters)          o.declareParameters(parameters)
681          registerLinkableObject(doc.getAttribute("id"), o)          esysxml.registerLinkableObject(o, node)
682          return o          return o
683            
684      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())  
685    
686        def writeXML(self,ostream=stdout):
687            """
688        Writes the object as an XML object into an output stream.
689        """
690            esysxml=ESySXMLCreator()
691            self.toDom(esysxml, esysxml.getRoot())
692            ostream.write(esysxml.toprettyxml())
693        
694  class Model(ParameterSet):  class Model(ParameterSet):
695      """      """
696        A Model object represents a processess marching over time until a
697      A Model object represents a processess marching over time      finalizing condition is fullfilled. At each time step an iterative
698      until a finalizing condition is fullfilled. At each time step an iterative      process can be performed and the time step size can be controlled. A
699      process can be performed and the time step size can be controlled. A Model has      Model has the following work flow::
700      the following work flow:            
   
701            doInitialization()            doInitialization()
702              while not terminateInitialIteration(): doInitializationiStep()
703              doInitialPostprocessing()
704            while not finalize():            while not finalize():
705                 dt=getSafeTimeStepSize(dt)                 dt=getSafeTimeStepSize(dt)
706                 doStepPreprocessing(dt)                 doStepPreprocessing(dt)
# Line 493  class Model(ParameterSet): Line 708  class Model(ParameterSet):
708                 doStepPostprocessing(dt)                 doStepPostprocessing(dt)
709            doFinalization()            doFinalization()
710    
711            where doInitialization,finalize, getSafeTimeStepSize, doStepPreprocessing, terminateIteration, doStepPostprocessing, doFinalization      where C{doInitialization}, C{finalize}, C{getSafeTimeStepSize},
712            are methods of the particular instance of a Model. The default implementations of these methods have to be overwritten by      C{doStepPreprocessing}, C{terminateIteration}, C{doStepPostprocessing},
713            the subclass implementinf a Model.      C{doFinalization} are methods of the particular instance of a Model. The
714        default implementations of these methods have to be overwritten by the
715        subclass implementing a Model.
716      """      """
717    
718      UNDEF_DT=1.e300      UNDEF_DT=1.e300
719    
720      def __init__(self,parameters=[],**kwarg):      def __init__(self,parameters=[],**kwargs):
721          """creates a model          """
722        Creates a model.
723    
724              Just calls the parent constructor.          Just calls the parent constructor.
725          """          """
726          ParameterSet.__init__(self, parameters=parameters,**kwarg)          ParameterSet.__init__(self, parameters=parameters,**kwargs)
727    
728      def __str__(self):      def __str__(self):
729         return "<%s %d>"%(self.__class__,id(self))         return "<%s %d>"%(self.__class__.__name__,id(self))
730    
     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)  
731    
732      def doInitialization(self):      def doInitialization(self):
733          """initializes the time stepping scheme. This function may be overwritten."""          """
734        Initializes the time stepping scheme.  
735        
736        This function may be overwritten.
737        """
738            pass
739        def doInitialStep(self):
740            """
741        performs an iteration step in the initialization phase
742    
743        This function may be overwritten.
744        """
745            pass
746    
747        def terminateInitialIteration(self):
748            """
749        Returns True if iteration at the inital phase is terminated.
750        """
751            return True
752    
753        def doInitialPostprocessing(self):
754            """
755        finalises the initialization iteration process
756    
757        This function may be overwritten.
758        """
759          pass          pass
760            
761      def getSafeTimeStepSize(self,dt):      def getSafeTimeStepSize(self,dt):
762          """returns a time step size which can safely be used.          """
763             dt gives the previously used step size.      Returns a time step size which can safely be used.
764             This function may be overwritten."""  
765            C{dt} gives the previously used step size.
766    
767            This function may be overwritten.
768        """
769          return self.UNDEF_DT          return self.UNDEF_DT
770            
771      def finalize(self):      def finalize(self):
772          """returns False if the time stepping is finalized. This function may be          """
773          overwritten."""      Returns False if the time stepping is finalized.
774        
775        This function may be overwritten.
776        """
777          return False          return False
778                
779      def doFinalization(self):      def doFinalization(self):
780          """finalizes the time stepping. This function may be overwritten."""          """
781        Finalizes the time stepping.
782        
783        This function may be overwritten.
784        """
785          pass          pass
786            
787      def doStepPreprocessing(self,dt):      def doStepPreprocessing(self,dt):
788          """sets up a time step of step size dt. This function may be overwritten."""          """
789        Sets up a time step of step size dt.
790        
791        This function may be overwritten.
792        """
793          pass          pass
794            
795      def doStep(self,dt):      def doStep(self,dt):
796          """executes an iteration step at a time step.          """
797             dt is the currently used time step size.      Executes an iteration step at a time step.
798             This function may be overwritten."""  
799            C{dt} is the currently used time step size.
800    
801            This function may be overwritten.
802        """
803          pass          pass
804            
805      def terminateIteration(self):      def terminateIteration(self):
806          """returns True if iteration on a time step is terminated."""          """
807        Returns True if iteration on a time step is terminated.
808        """
809          return True          return True
810    
811                
812      def doStepPostprocessing(self,dt):      def doStepPostprocessing(self,dt):
813          """finalalizes the time step.          """
814             dt is the currently used time step size.      finalises the time step.
815             This function may be overwritten."""  
816            dt is the currently used time step size.
817    
818            This function may be overwritten.
819        """
820          pass          pass
       
     def writeXML(self, ostream=stdout):  
         document, node = esysDoc()  
         self.toDom(document, node)  
         ostream.write(document.toprettyxml())  
       
       
821    
822        def toDom(self, esysxml, node):
823            """
824        C{toDom} method of Model class
825        """
826            pset = esysxml.createElement('Model')
827            pset.setAttribute('type', self.__class__.__name__)
828            pset.setAttribute('module', self.__class__.__module__)
829            esysxml.registerLinkableObject(self, pset)
830            node.appendChild(pset)
831            self._parametersToDom(esysxml, pset)
832        
833  class Simulation(Model):  class Simulation(Model):
834      """      """
835            A Simulation object is special Model which runs a sequence of Models.      A Simulation object is special Model which runs a sequence of Models.
836    
837            The methods doInitialization,finalize, getSafeTimeStepSize, doStepPreprocessing,      The methods C{doInitialization}, C{finalize}, C{getSafeTimeStepSize},
838            terminateIteration, doStepPostprocessing, doFinalization      C{doStepPreprocessing}, C{terminateIteration}, C{doStepPostprocessing},
839            are executing the corresponding methods of the models in the simulation.      C{doFinalization} are executing the corresponding methods of the models in
840                  the simulation.
841      """      """
842            
843      FAILED_TIME_STEPS_MAX=20      FAILED_TIME_STEPS_MAX=20
844      MAX_ITER_STEPS=50      MAX_ITER_STEPS=50
845        MAX_CHANGE_OF_DT=2.
846            
847      def __init__(self, models=[], **kwargs):      def __init__(self, models=[], **kwargs):
848          """initiates a simulation from a list of models. """          """
849          Model.__init__(self, **kwargs)      Initiates a simulation from a list of models.
850        """
851            super(Simulation, self).__init__(**kwargs)
852            for m in models:
853                if not isinstance(m, Model):
854                     raise TypeError("%s is not a subclass of Model."%m)
855          self.__models=[]          self.__models=[]
   
856          for i in range(len(models)):          for i in range(len(models)):
857              self[i] = models[i]              self[i] = models[i]
858                
859    
860      def __repr__(self):      def __repr__(self):
861          """          """
862          returns a string representation of the Simulation          Returns a string representation of the Simulation.
863          """          """
864          return "<Simulation %r>" % self.__models          return "<Simulation %r>" % self.__models
865    
866      def __str__(self):      def __str__(self):
867          """          """
868          returning Simulation as a string          Returning Simulation as a string.
869          """          """
870          return "<Simulation %d>"%id(self)          return "<Simulation %d>"%id(self)
871            
872      def iterModels(self):      def iterModels(self):
873          """returns an iterator over the models"""          """
874        Returns an iterator over the models.
875        """
876          return self.__models          return self.__models
877            
878      def __getitem__(self,i):      def __getitem__(self,i):
879          """returns the i-th model"""          """
880        Returns the i-th model.
881        """
882          return self.__models[i]          return self.__models[i]
883            
884      def __setitem__(self,i,value):      def __setitem__(self,i,value):
885          """sets the i-th model"""          """
886        Sets the i-th model.
887        """
888          if not isinstance(value,Model):          if not isinstance(value,Model):
889              raise ValueError("assigned value is not a Model")              raise ValueError,"assigned value is not a Model but instance of %s"%(value.__class__.__name__,)
890          for j in range(max(i-len(self.__models)+1,0)): self.__models.append(None)          for j in range(max(i-len(self.__models)+1,0)):
891                self.__models.append(None)
892          self.__models[i]=value          self.__models[i]=value
893            
894      def __len__(self):      def __len__(self):
895          """returns the number of models"""          """
896        Returns the number of models.
897        """
898          return len(self.__models)          return len(self.__models)
899    
900      def toDom(self, document, node):      def getAllModels(self):
901          """ toDom method of Simulation class """          """
902          simulation = document.createElement('Simulation')          returns a list of all models used in the Simulation including subsimulations
903          simulation.setAttribute('type', self.__class__.__name__)          """
904            out=[]
905          for rank, sim in enumerate(self.iterModels()):          for m in self.iterModels():
906              component = document.createElement('Component')              if isinstance(m, Simulation):
907              component.setAttribute('rank', str(rank))                 out+=m.getAllModels()
908                else:
909              sim.toDom(document, component)                 out.append(m)
910            return list(set(out))
             simulation.appendChild(component)  
911    
912          node.appendChild(simulation)      def checkModelLinks(self, models):
913            """
914            returns a list of (model,parameter, target model ) if the the parameter of model
915            is linking to the target_model which is not in list of models.
916            """
917            out=[]
918            for m in self.iterModels():
919                if isinstance(m, Simulation):
920                   out+=[ (m,) + f for f in  m.checkModelLinks(models) ]
921                else:
922                  for p in m:
923                     if isinstance(p[1], Link):
924                        l_m=p[1].getTarget()
925                        if isinstance(l_m, Model) and not l_m in models: out.append( (m,p[0],l_m) )
926            return out
927    
     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())  
928            
929      def getSafeTimeStepSize(self,dt):      def getSafeTimeStepSize(self,dt):
930          """returns a time step size which can safely be used by all models.          """
931             This is the minimum over the time step sizes of all models."""      Returns a time step size which can safely be used by all models.
932    
933            This is the minimum over the time step sizes of all models.
934        """
935          out=min([o.getSafeTimeStepSize(dt) for o in self.iterModels()])          out=min([o.getSafeTimeStepSize(dt) for o in self.iterModels()])
         print "%s: safe step size is %e."%(str(self),out)  
936          return out          return out
937            
938      def doInitialization(self):      def doInitialization(self):
939          """initializes all models """          """
940        Initializes all models.
941        """
942          self.n=0          self.n=0
943          self.tn=0.          self.tn=0.
944          for o in self.iterModels():          for o in self.iterModels():
945              o.doInitialization()               o.doInitialization()
946            def doInitialStep(self):
947            """
948        performs an iteration step in the initialization step for all models
949        """
950            iter=0
951            while not self.terminateInitialIteration():
952                if iter==0: self.trace("iteration for initialization starts")
953                iter+=1
954                self.trace("iteration step %d"%(iter))
955                for o in self.iterModels():
956                     o.doInitialStep()
957                if iter>self.MAX_ITER_STEPS:
958                     raise IterationDivergenceError("initial iteration did not converge after %s steps."%iter)
959            self.trace("Initialization finalized after %s iteration steps."%iter)
960    
961        def doInitialPostprocessing(self):
962            """
963        finalises the initialization iteration process for all models.
964        """
965            for o in self.iterModels():
966                o.doInitialPostprocessing()
967      def finalize(self):      def finalize(self):
968          """returns True if any of the models is to be finalized"""          """
969        Returns True if any of the models is to be finalized.
970        """
971          return any([o.finalize() for o in self.iterModels()])          return any([o.finalize() for o in self.iterModels()])
972                
973      def doFinalization(self):      def doFinalization(self):
974          """finalalizes the time stepping for all models."""          """
975        finalises the time stepping for all models.
976        """
977          for i in self.iterModels(): i.doFinalization()          for i in self.iterModels(): i.doFinalization()
978          self.trace("end of time integation.")          self.trace("end of time integation.")
979            
980      def doStepPreprocessing(self,dt):      def doStepPreprocessing(self,dt):
981          """initializes the time step for all models."""          """
982        Initializes the time step for all models.
983        """
984          for o in self.iterModels():          for o in self.iterModels():
985              o.doStepPreprocessing(dt)              o.doStepPreprocessing(dt)
986            
987      def terminateIteration(self):      def terminateIteration(self):
988          """returns True if all iterations for all models are terminated."""          """
989        Returns True if all iterations for all models are terminated.
990        """
991          out=all([o.terminateIteration() for o in self.iterModels()])          out=all([o.terminateIteration() for o in self.iterModels()])
992          return out          return out
993    
994        def terminateInitialIteration(self):
995            """
996        Returns True if all initial iterations for all models are terminated.
997        """
998            out=all([o.terminateInitialIteration() for o in self.iterModels()])
999            return out
1000                
1001      def doStepPostprocessing(self,dt):      def doStepPostprocessing(self,dt):
1002          """finalalizes the iteration process for all models."""          """
1003        finalises the iteration process for all models.
1004        """
1005          for o in self.iterModels():          for o in self.iterModels():
1006              o.doStepPostprocessing(dt)              o.doStepPostprocessing(dt)
1007          self.n+=1          self.n+=1
# Line 679  class Simulation(Model): Line 1009  class Simulation(Model):
1009            
1010      def doStep(self,dt):      def doStep(self,dt):
1011          """          """
1012               executes the iteration step at a time step for all model:      Executes the iteration step at a time step for all model::
1013    
1014                    self.doStepPreprocessing(dt)              self.doStepPreprocessing(dt)
1015                    while not self.terminateIteration(): for all models: self.doStep(dt)              while not self.terminateIteration():
1016                    self.doStepPostprocessing(dt)              for all models:
1017                self.doStep(dt)
1018                    self.doStepPostprocessing(dt)
1019          """          """
1020          self.iter=0          self.iter=0
1021          while not self.terminateIteration():          while not self.terminateIteration():
# Line 697  class Simulation(Model): Line 1028  class Simulation(Model):
1028    
1029      def run(self,check_point=None):      def run(self,check_point=None):
1030          """          """
1031        Run the simulation by performing essentially::
            run the simulation by performing essentially  
1032            
1033                 self.doInitialization()          self.doInitialization()
1034                 while not self.finalize():              while not self.terminateInitialIteration(): self.doInitialStep()
1035                    dt=self.getSafeTimeStepSize()              self.doInitialPostprocessing()
1036                    self.doStep(dt)          while not self.finalize():
1037                    if n%check_point==0: self.writeXML()              dt=self.getSafeTimeStepSize()
1038                 self.doFinalization()              self.doStep(dt)
1039                if n%check_point==0:
1040             If one of the models in throws a FailedTimeStepError exception a new time step size is              self.writeXML()
1041             computed through getSafeTimeStepSize() and the time step is repeated.          self.doFinalization()
1042    
1043            If one of the models in throws a C{FailedTimeStepError} exception a
1044        new time step size is computed through getSafeTimeStepSize() and the
1045        time step is repeated.
1046        
1047             If one of the models in throws a IterationDivergenceError exception the time step size          If one of the models in throws a C{IterationDivergenceError}
1048             is halved and the time step is repeated.      exception the time step size is halved and the time step is repeated.
1049    
1050             In both cases the time integration is given up after Simulation.FAILED_TIME_STEPS_MAX          In both cases the time integration is given up after
1051             attempts.      C{Simulation.FAILED_TIME_STEPS_MAX} attempts.
   
       
1052          """          """
1053          dt=self.UNDEF_DT          # check the completness of the models:
1054            # first a list of all the models involved in the simulation including subsimulations:
1055            #
1056            missing=self.checkModelLinks(self.getAllModels())
1057            if len(missing)>0:
1058                msg=""
1059                for l in missing:
1060                     msg+="\n\t"+str(l[-1])+" at "+str(self)
1061                     for i in xrange(len(l)-1): msg+="."+str(l[i])
1062                raise MissingLink("link targets missing in the Simulation: %s"%msg)
1063            #==============================
1064          self.doInitialization()          self.doInitialization()
1065            self.doInitialStep()
1066            self.doInitialPostprocessing()
1067            dt=self.UNDEF_DT
1068          while not self.finalize():          while not self.finalize():
1069              step_fail_counter=0              step_fail_counter=0
1070              iteration_fail_counter=0              iteration_fail_counter=0
1071              dt_new=self.getSafeTimeStepSize(dt)              if self.n==0:
1072                    dt_new=self.getSafeTimeStepSize(dt)
1073                else:
1074                    dt_new=min(max(self.getSafeTimeStepSize(dt),dt/self.MAX_CHANGE_OF_DT),dt*self.MAX_CHANGE_OF_DT)
1075              self.trace("%d. time step %e (step size %e.)" % (self.n+1,self.tn+dt_new,dt_new))              self.trace("%d. time step %e (step size %e.)" % (self.n+1,self.tn+dt_new,dt_new))
1076              end_of_step=False              end_of_step=False
1077              while not end_of_step:              while not end_of_step:
1078                 end_of_step=True                 end_of_step=True
1079                 if not dt_new>0:                 if not dt_new>0:
1080                    raise NonPositiveStepSizeError("non-positive step size in step %d",self.n+1)                    raise NonPositiveStepSizeError("non-positive step size in step %d"%(self.n+1))
1081                 try:                 try:
1082                    self.doStepPreprocessing(dt_new)                    self.doStepPreprocessing(dt_new)
1083                    self.doStep(dt_new)                    self.doStep(dt_new)
# Line 739  class Simulation(Model): Line 1087  class Simulation(Model):
1087                    end_of_step=False                    end_of_step=False
1088                    iteration_fail_counter+=1                    iteration_fail_counter+=1
1089                    if iteration_fail_counter>self.FAILED_TIME_STEPS_MAX:                    if iteration_fail_counter>self.FAILED_TIME_STEPS_MAX:
1090                             raise SimulationBreakDownError("reduction of time step to achieve convergence failed.")                             raise SimulationBreakDownError("reduction of time step to achieve convergence failed after %s steps."%self.FAILED_TIME_STEPS_MAX)
1091                    self.trace("iteration fails. time step is repeated with new step size.")                    self.trace("Iteration failed. Time step is repeated with new step size %s."%dt_new)
1092                 except FailedTimeStepError:                 except FailedTimeStepError:
1093                    dt_new=self.getSafeTimeStepSize(dt)                    dt_new=self.getSafeTimeStepSize(dt)
1094                    end_of_step=False                    end_of_step=False
1095                    step_fail_counter+=1                    step_fail_counter+=1
1096                    self.trace("time step is repeated.")                    self.trace("Time step is repeated with new time step size %s."%dt_new)
1097                    if step_fail_counter>self.FAILED_TIME_STEPS_MAX:                    if step_fail_counter>self.FAILED_TIME_STEPS_MAX:
1098                          raise SimulationBreakDownError("time integration is given up after %d attempts."%step_fail_counter)                          raise SimulationBreakDownError("Time integration is given up after %d attempts."%step_fail_counter)
1099              dt=dt_new              dt=dt_new
1100              if not check_point==None:              if not check_point==None:
1101                  if n%check_point==0:                  if n%check_point==0:
# Line 755  class Simulation(Model): Line 1103  class Simulation(Model):
1103                      self.writeXML()                      self.writeXML()
1104          self.doFinalization()          self.doFinalization()
1105    
     def fromDom(cls, doc):  
         sims = []  
         for node in doc.childNodes:  
             if isinstance(node, minidom.Text):  
                 continue  
1106    
1107              sims.append(getComponent(node))      def toDom(self, esysxml, node):
1108            """
1109        C{toDom} method of Simulation class.
1110        """
1111            simulation = esysxml.createElement('Simulation')
1112            esysxml.registerLinkableObject(self, simulation)
1113            for rank, sim in enumerate(self.iterModels()):
1114                component = esysxml.createElement('Component')
1115                component.setAttribute('rank', str(rank))
1116                sim.toDom(esysxml, component)
1117                simulation.appendChild(component)
1118            node.appendChild(simulation)
1119    
1120    
1121          return cls(sims)      def fromDom(cls, esysxml, node):
1122            sims = []
1123            for n in node.childNodes:
1124                if isinstance(n, minidom.Text):
1125                    continue
1126                sims.append(esysxml.getComponent(n))
1127            sims.sort(cmp=_comp)
1128            sim=cls([s[1] for s in sims], debug=esysxml.debug)
1129            esysxml.registerLinkableObject(sim, node)
1130            return sim
1131    
1132      fromDom = classmethod(fromDom)      fromDom = classmethod(fromDom)
1133    
1134    def _comp(a,b):
1135        if a[0]<a[1]:
1136          return 1
1137        elif a[0]>a[1]:
1138          return -1
1139        else:
1140          return 0
1141    
1142  class IterationDivergenceError(Exception):  class IterationDivergenceError(Exception):
1143      """      """
1144         excpetion which is thrown if there is no convergence of the iteration process at a time step      Exception which is thrown if there is no convergence of the iteration
1145         but there is a chance taht a smaller step could help to reach convergence.      process at a time step.
1146    
1147        But there is a chance that a smaller step could help to reach convergence.
1148      """      """
1149      pass      pass
1150    
1151  class FailedTimeStepError(Exception):  class FailedTimeStepError(Exception):
1152      """excpetion which is thrown if the time step fails because of a step size that have been choosen to be too large"""      """
1153        Exception which is thrown if the time step fails because of a step
1154        size that have been choosen to be too large.
1155        """
1156      pass      pass
1157    
1158  class SimulationBreakDownError(Exception):  class SimulationBreakDownError(Exception):
1159      """excpetion which is thrown if the simulation does not manage to progress in time."""      """
1160        Exception which is thrown if the simulation does not manage to
1161        progress in time.
1162        """
1163      pass      pass
1164    
1165  class NonPositiveStepSizeError(Exception):  class NonPositiveStepSizeError(Exception):
1166      """excpetion which is thrown if the step size is not positive"""      """
1167        Exception which is thrown if the step size is not positive.
1168        """
1169        pass
1170    
1171    class MissingLink(Exception):
1172        """
1173        Exception thrown when a link is missing
1174        """
1175      pass      pass
1176    
1177    class DataSource(object):
1178        """
1179        Class for handling data sources, including local and remote files. This class is under development.
1180        """
1181    
1182        def __init__(self, uri="file.ext", fileformat="unknown"):
1183            self.uri = uri
1184            self.fileformat = fileformat
1185    
1186        def toDom(self, esysxml, node):
1187            """
1188            C{toDom} method of DataSource. Creates a DataSource node and appends it to the
1189        current XML esysxml.
1190            """
1191            ds = esysxml.createElement('DataSource')
1192            ds.appendChild(esysxml.createDataNode('URI', self.uri))
1193            ds.appendChild(esysxml.createDataNode('FileFormat', self.fileformat))
1194            node.appendChild(ds)
1195    
1196        def fromDom(cls, esysxml, node):
1197            uri= str(node.getElementsByTagName("URI")[0].firstChild.nodeValue.strip())
1198            fileformat= str(node.getElementsByTagName("FileFormat")[0].firstChild.nodeValue.strip())
1199            ds = cls(uri, fileformat)
1200            return ds
1201    
1202        def getLocalFileName(self):
1203            return self.uri
1204    
1205        fromDom = classmethod(fromDom)
1206        
1207    # vim: expandtab shiftwidth=4:

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