Merge pull request #98 from computationalmodelling/cvode_bug

Cvode bug

Author: rpep

fidimag/common/sundials/cvode.pxd

@@ -9,7 +9,7 @@ cdef extern from "sundials/sundials_nvector.h":
 
     ctypedef _generic_N_Vector *N_Vector
     N_Vector N_VNew_Serial(long int vec_length)
-    N_Vector N_VNew_OpenMP(long int vec_length)
+    N_Vector N_VNew_OpenMP(long int vec_length, int num_threads)
     void N_VDestroy_Serial(N_Vector v)
     void N_VDestroy_OpenMP(N_Vector v)
     void N_VPrint_Serial(N_Vector v)

fidimag/common/sundials/cvode.pyx

@@ -4,6 +4,7 @@ cimport numpy as np  # import special compile-time information about numpy
 cimport openmp
 np.import_array()  # don't remove or you'll segfault
 from libc.string cimport memcpy
+import sys
 
 cdef extern from "../../atomistic/lib/clib.h":
     void normalise(double * m, int nxyz)
@@ -179,6 +180,9 @@ cdef class CvodeSolver(object):
         self.check_flag(flag, "CVodeSetUserData")
 
         self.cvode_already_initialised = 0
+
+        self.u_y = N_VMake_Serial(self.y.size, <realtype *> self.y.data)
+
         self.set_initial_value(spins, self.t)
         self.set_options(rtol, atol)
 
@@ -191,7 +195,7 @@ cdef class CvodeSolver(object):
         self.y[:] = spin[:]
 
         cdef np.ndarray[double, ndim = 1, mode = "c"] y = self.y
-        self.u_y = N_VMake_Serial(y.size, & y[0])
+        copy_arr2nv(self.y, self.u_y)
 
         if self.cvode_already_initialised:
             flag = CVodeReInit(self.cvode_mem, t, self.u_y)
@@ -363,6 +367,9 @@ cdef class CvodeSolver_OpenMP(object):
         self.check_flag(flag, "CVodeSetUserData")
 
         self.cvode_already_initialised = 0
+
+        self.u_y = N_VMake_OpenMP(self.y.size, <realtype *> self.y.data, self.num_threads)
+
         self.set_initial_value(spins, self.t)
         self.set_options(rtol, atol)
 
@@ -375,7 +382,7 @@ cdef class CvodeSolver_OpenMP(object):
         self.y[:] = spin[:]
 
         cdef np.ndarray[double, ndim = 1, mode = "c"] y = self.y
-        self.u_y = N_VMake_OpenMP(y.size, &y[0], self.num_threads)
+        copy_arr2nv_openmp(self.y, self.u_y)
 
         if self.cvode_already_initialised:
             flag = CVodeReInit(self.cvode_mem, t, self.u_y)

fidimag/common/vtk.py

@@ -21,7 +21,6 @@ def __init__(self, mesh, header="", directory=".", filename="unnamed"):
             # for keyword argument dimensions: if the mesh is made up of
             # nx * ny * nz cells, it has (nx + 1) * (ny + 1) * (nz + 1)
             # vertices.
-            print(mesh.grid)
             structure = pyvtk.RectilinearGrid(* mesh.grid)
         else:
             raise NotImplementedError(