Modification of source file to compel with new scientific and MMTK ILL version

Extensions/mic_fast_calc.pyx

@@ -103,7 +103,7 @@ def mic_generator_2D(double[:,:] pts not None, double border, double[:] box_para
         
 def mic_generator_3D(double[:,:] pts not None, double border, double[:] box_param):
     
-    cdef int i, m, new_id, nb_init_points
+    cdef int i, j_int, m, new_id, nb_init_points
     cdef double x, y, z, Xmin, Xmax, Ymin, Ymax, Zmin, Zmax, j, k, l, n0, n1, n2
     cdef vector[equiv_t] equivalence
     cdef vector[point] new_points
@@ -168,8 +168,9 @@ def mic_generator_3D(double[:,:] pts not None, double border, double[:] box_para
     
     for i in range(new_points.size()):
         j = i + nb_init_points
-        res[j,0] = new_points[i][0]
-        res[j,1] = new_points[i][1]
-        res[j,2] = new_points[i][2]
+        j_int = int(j)
+        res[j_int,0] = new_points[i][0]
+        res[j_int,1] = new_points[i][1]
+        res[j_int,2] = new_points[i][2]
     
     return res, d

Extensions/mt_fast_calc.pyx

@@ -13,8 +13,8 @@ def mt(ndarray[np.float64_t, ndim = 2] config not None,
        ndarray[np.int32_t, ndim = 3] grid not None,
        double resolution,ndarray[np.float64_t, ndim = 1] mini not None): 
     
-    cdef int at, nbatom , atom
-    cdef double Xpos, Ypos, Zpos, i, j, k , mx, my, mz
+    cdef int at, nbatom, atom, i, j, k
+    cdef double Xpos, Ypos, Zpos, mx, my, mz
     
     mx = mini[0] 
     my = mini[1]
@@ -23,7 +23,7 @@ def mt(ndarray[np.float64_t, ndim = 2] config not None,
     nbatom = config.shape[0]
     for atom in range(nbatom):
         # The  of atoms |i| in the current configuration.
-        i = floor((config[atom,0]-mx)/resolution)
-        j = floor((config[atom,1]-my)/resolution)
-        k = floor((config[atom,2]-mz)/resolution)
-        grid[i,j,k] += 1
+        i = int(floor((config[atom,0]-mx)/resolution))
+        j = int(floor((config[atom,1]-my)/resolution))
+        k = int(floor((config[atom,2]-mz)/resolution))
+        grid[i][j][k] += 1

MDANSE/Framework/Jobs/DipoleAutoCorrelationFunction.py

@@ -96,8 +96,12 @@ class DipoleAutoCorrelationFunction(IJob):
         conf = self.configuration['trajectory']['instance'].universe.contiguousObjectConfiguration()
 
         dipoleMoment = numpy.zeros((3,),dtype=numpy.float64)
-        for idx in self._indexes: 
-            dipoleMoment += self.configuration["atom_charges"]["charges"][idx]*conf[idx]
+        for idx in self._indexes:
+            temp = self.configuration["atom_charges"]["charges"][idx]*conf[idx]
+            # Loop to sum temp because MMTK redefines __add__ operator, leading to a crash
+            #dipoleMoment = dipoleMoment + self.configuration["atom_charges"]["charges"][idx]*conf[idx]
+            for k in range(len(temp)):
+                dipoleMoment[k] = dipoleMoment[k] + temp[k]
                 
         return index, dipoleMoment
 

MDANSE/Framework/Jobs/MolecularTrace.py

@@ -107,12 +107,12 @@ class MolecularTrace(IJob):
         self.min = numpy.array([minx, miny, minz], dtype = numpy.float64)
         self._outputData.add('origin',"line", self.min, units = 'nm')
         
-        self.gdim = numpy.ceil(numpy.array([dimx, dimy, dimz])/self.resolution)
+        self.gdim = numpy.ceil(numpy.array([dimx, dimy, dimz])/self.resolution).astype(numpy.int)
         spacing = self.configuration['spatial_resolution']['value']
         self._outputData.add('spacing',"line",numpy.array([spacing, spacing, spacing]), units = 'nm')
         self.grid = numpy.zeros(self.gdim, dtype = numpy.int32)
 
-        self._outputData.add('molecular_trace',"volume", tuple(numpy.ceil(numpy.array([dimx, dimy, dimz])/self.resolution)))
+        self._outputData.add('molecular_trace',"volume", tuple(numpy.ceil(numpy.array([dimx, dimy, dimz])/self.resolution).astype(numpy.int)))
         
         self._indexes  = [idx for idxs in self.configuration['atom_selection']['indexes'] for idx in idxs]
         

MDANSE/Framework/QVectors/SphericalLatticeQVectors.py

-#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
-#------------------------------------------------------------------------------------------
-#Copyright (C)
-#2015- Eric C. Pellegrini Institut Laue-Langevin
-#BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
-#France
-#pellegrini[at]ill.fr
-#goret[at]ill.fr
-#aoun[at]ill.fr
-#
-#This library is free software; you can redistribute it and/or
-#modify it under the terms of the GNU Lesser General Public
-#License as published by the Free Software Foundation; either
-#version 2.1 of the License, or (at your option) any later version.
-#
-#This library is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#Lesser General Public License for more details.
-#
-#You should have received a copy of the GNU Lesser General Public
-#License along with this library; if not, write to the Free Software
-#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-
-''' 
-Created on Mar 30, 2015
-
-:author: Eric C. Pellegrini
-'''
-
-import collections
-import random
-
-import numpy
-
-from MDANSE import REGISTRY
-from MDANSE.Framework.QVectors.LatticeQvectors import LatticeQVectors
-
-class SphericalLatticeQVectors(LatticeQVectors):
-    """
-    """
-
-    settings = collections.OrderedDict()
-    settings['seed'] = ('integer', {"mini":0, "default":0})
-    settings['shells'] = ('range', {"valueType":float, "includeLast":True, "mini":0.0})
-    settings['n_vectors'] = ('integer', {"mini":1, "default":50})
-    settings['width'] = ('float', {"mini":1.0e-6, "default":1.0})
-
-    def _generate(self):
-                     
-        if self._configuration["seed"]["value"] != 0:           
-            numpy.random.seed(self._configuration["seed"]["value"])
-            random.seed(self._configuration["seed"]["value"])
-                
-        qMax = self._configuration["shells"]["last"] + 0.5*self._configuration["width"]["value"]
-        
-        hklMax = numpy.ceil([qMax/v.length()for v in self._reciprocalBasis]) + 1
-                
-        vects = numpy.mgrid[-hklMax[0]:hklMax[0]+1,-hklMax[1]:hklMax[1]+1,-hklMax[2]:hklMax[2]+1]
-                
-        vects = vects.reshape(3,(2*hklMax[0]+1)*(2*hklMax[1]+1)*(2*hklMax[2]+1))
-                    
-        vects = numpy.dot(self._reciprocalMatrix,vects)
-                
-        dists2 = numpy.sum(vects**2,axis=0)
-                
-        halfWidth = self._configuration["width"]["value"]/2
-        
-        nVectors = self._configuration["n_vectors"]["value"]
-
-        if self._status is not None:
-            self._status.start(self._configuration["shells"]['number'])
-
-        self._configuration["q_vectors"] = collections.OrderedDict()
-
-        for q in self._configuration["shells"]["value"]:
-                                    
-            qmin = max(0,q - halfWidth)
-                                    
-            q2low = qmin*qmin
-            q2up = (q + halfWidth)*(q + halfWidth)
-            
-            hits = numpy.where((dists2 >= q2low) & (dists2 <= q2up))[0]            
-
-            nHits = len(hits)
-                                    
-            if nHits != 0:
-
-                n = min(nHits,nVectors)
-
-                if nHits > nVectors:
-                    hits = random.sample(hits,nVectors)
-
-                self._configuration["q_vectors"][q] = {}
-                self._configuration["q_vectors"][q]['q_vectors'] = vects[:,hits]
-                self._configuration["q_vectors"][q]['n_q_vectors'] = n
-                self._configuration["q_vectors"][q]['q'] = q
-                self._configuration["q_vectors"][q]['hkls'] = numpy.rint(numpy.dot(self._invReciprocalMatrix,
-                                                                                self._configuration["q_vectors"][q]['q_vectors']))
-
-            if self._status is not None:
-                if self._status.is_stopped():
-                    return None
-                else:
-                    self._status.update()
-
-REGISTRY["spherical_lattice"] = SphericalLatticeQVectors
+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on Mar 30, 2015
+
+:author: Eric C. Pellegrini
+'''
+
+import collections
+import random
+
+import numpy
+
+from MDANSE import REGISTRY
+from MDANSE.Framework.QVectors.LatticeQvectors import LatticeQVectors
+
+class SphericalLatticeQVectors(LatticeQVectors):
+    """
+    """
+
+    settings = collections.OrderedDict()
+    settings['seed'] = ('integer', {"mini":0, "default":0})
+    settings['shells'] = ('range', {"valueType":float, "includeLast":True, "mini":0.0})
+    settings['n_vectors'] = ('integer', {"mini":1, "default":50})
+    settings['width'] = ('float', {"mini":1.0e-6, "default":1.0})
+
+    def _generate(self):
+                     
+        if self._configuration["seed"]["value"] != 0:           
+            numpy.random.seed(self._configuration["seed"]["value"])
+            random.seed(self._configuration["seed"]["value"])
+                
+        qMax = self._configuration["shells"]["last"] + 0.5*self._configuration["width"]["value"]
+        
+        hklMax = numpy.ceil([qMax/v.length()for v in self._reciprocalBasis]) + 1
+                
+        vects = numpy.mgrid[-hklMax[0]:hklMax[0]+1,-hklMax[1]:hklMax[1]+1,-hklMax[2]:hklMax[2]+1]
+                
+        vects = vects.reshape(3,int(2*hklMax[0]+1)*int(2*hklMax[1]+1)*int(2*hklMax[2]+1))
+                    
+        vects = numpy.dot(self._reciprocalMatrix,vects)
+                
+        dists2 = numpy.sum(vects**2,axis=0)
+                
+        halfWidth = self._configuration["width"]["value"]/2
+        
+        nVectors = self._configuration["n_vectors"]["value"]
+
+        if self._status is not None:
+            self._status.start(self._configuration["shells"]['number'])
+
+        self._configuration["q_vectors"] = collections.OrderedDict()
+
+        for q in self._configuration["shells"]["value"]:
+                                    
+            qmin = max(0,q - halfWidth)
+                                    
+            q2low = qmin*qmin
+            q2up = (q + halfWidth)*(q + halfWidth)
+            
+            hits = numpy.where((dists2 >= q2low) & (dists2 <= q2up))[0]            
+
+            nHits = len(hits)
+                                    
+            if nHits != 0:
+
+                n = min(nHits,nVectors)
+
+                if nHits > nVectors:
+                    hits = random.sample(hits,nVectors)
+
+                self._configuration["q_vectors"][q] = {}
+                self._configuration["q_vectors"][q]['q_vectors'] = vects[:,hits]
+                self._configuration["q_vectors"][q]['n_q_vectors'] = n
+                self._configuration["q_vectors"][q]['q'] = q
+                self._configuration["q_vectors"][q]['hkls'] = numpy.rint(numpy.dot(self._invReciprocalMatrix,
+                                                                                self._configuration["q_vectors"][q]['q_vectors']))
+
+            if self._status is not None:
+                if self._status.is_stopped():
+                    return None
+                else:
+                    self._status.update()
+
+REGISTRY["spherical_lattice"] = SphericalLatticeQVectors