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

@@ -97,7 +97,11 @@ class DipoleAutoCorrelationFunction(IJob):
 
         dipoleMoment = numpy.zeros((3,),dtype=numpy.float64)
         for idx in self._indexes:
-            dipoleMoment += self.configuration["atom_charges"]["charges"][idx]*conf[idx]
+            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

@@ -60,7 +60,7 @@ class SphericalLatticeQVectors(LatticeQVectors):
                 
         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 = vects.reshape(3,int(2*hklMax[0]+1)*int(2*hklMax[1]+1)*int(2*hklMax[2]+1))
                     
         vects = numpy.dot(self._reciprocalMatrix,vects)