Merge tag '1.0.4.rc4' into develop

version 1.0.4.rc4

CHANGELOG

-version 1.0.4.rc2
+version 1.0.4.rc4
+----------------
+* bug fix in coordination number analysis: some pairs were never taken into account
+* bug fix when transmutating atoms from an atom selection different to 'all'
+
+version 1.0.4.rc3
 ----------------
 * bug fix in debian packager: add the python-setuptools dependency
 * improved LAMMPS converter: the parsing of the config file is more tolerance in term of required keyword format

MDANSE/Framework/Configurators/AtomSelectionConfigurator.py

@@ -105,14 +105,17 @@ class AtomSelectionConfigurator(IConfigurator):
                 parser = AtomSelectionParser(trajConfig["instance"])
                 indexes.update(parser.parse(v))
 
-        indexes = sorted(list(indexes))
+        self["flatten_indexes"] = sorted(list(indexes))
+        
+        trajConfig = self._configurable[self._dependencies['trajectory']]
 
         atoms = sorted(trajConfig["universe"].atomList(), key = operator.attrgetter('index'))
         selectedAtoms = [atoms[idx] for idx in indexes]
 
-        self["selection_length"] = len(indexes)        
+        self["selection_length"] = len(self["flatten_indexes"])        
+        self['indexes'] = [[idx] for idx in self["flatten_indexes"]]
+
         self['elements'] = [[at.symbol] for at in selectedAtoms]
-        self['indexes'] = [[idx] for idx in indexes]
         self['names'] = [at.symbol for at in selectedAtoms]
         self['unique_names'] = sorted(set(self['names']))
         self['masses'] = [[ELEMENTS[n,'atomic_weight']] for n in self['names']]

MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py

@@ -112,12 +112,18 @@ class AtomTransmutationConfigurator(IConfigurator):
             raise ConfiguratorError("the element %r is not registered in the database" % element, self)
 
         atomSelConfigurator = self._configurable[self._dependencies['atom_selection']]
-                
+                        
         for idx in selection:
-            atomSelConfigurator["names"][idx] = element
-            atomSelConfigurator["elements"][idx] = [element]
+            try:
+                idxInSelection = atomSelConfigurator["flatten_indexes"].index(idx)
+            except ValueError:
+                pass
+            else:                 
+                atomSelConfigurator["names"][idxInSelection] = element
+                atomSelConfigurator["elements"][idxInSelection] = [element]
 
         atomSelConfigurator['unique_names'] = sorted(set(atomSelConfigurator['names']))
+        atomSelConfigurator['masses'] = [[ELEMENTS[n,'atomic_weight']] for n in atomSelConfigurator['names']]
             
     def get_information(self):
         '''

MDANSE/Framework/Jobs/CoordinationNumber.py

@@ -93,7 +93,8 @@ class CoordinationNumber(DistanceHistogram):
             self._concentrations[k] /= nFrames
 
         nAtomsPerElement = self.configuration['atom_selection'].get_natoms()
-        for at1,at2 in self._elementsPairs:
+        for pair in self._elementsPairs:
+            at1,at2 = pair 
             ni = nAtomsPerElement[at1]
             nj = nAtomsPerElement[at2]
             
@@ -120,6 +121,7 @@ class CoordinationNumber(DistanceHistogram):
             cBeta = self._concentrations[pair[1]]
                         
             invPair = pair[::-1]
+            print pair, cnIntra
             self._outputData["cn_intra_%s%s" % pair][:] = self.averageDensity*cBeta*cnIntra
             self._outputData["cn_inter_%s%s" % pair][:] = self.averageDensity*cBeta*cnInter        
             self._outputData["cn_total_%s%s" % pair][:] = self.averageDensity*cBeta*cnTotal 

MDANSE/__pkginfo__.py

-__version__ = "1.0.4.rc3"
+__version__ = "1.0.4.rc4"
 
-__date__ = "28-11-2016"
+__date__ = "29-11-2016"
 
 __author__ = "Eric Pellegrini"