Changed NEBM old numpy declarations to the most efficient Cython typed memoryviews

Author: davidcorteso

fidimag/atomistic/lib/util.c

@@ -81,7 +81,7 @@ double skyrmion_number(double *spin, double *charge,
      *
      */
 
-	int i, j;
+	int i;
 	int index, id;
 
 	double sum = 0;

fidimag/common/neb_method/nebm_cartesian_clib.pyx

@@ -1,8 +1,3 @@
-import numpy
-cimport numpy as np
-np.import_array()
-
-
 cdef extern from "nebm_cartesian_lib.h":
 
     double compute_distance_cartesian(double * A, double * B, int n_dofs_image,
@@ -51,9 +46,9 @@ cdef extern from "nebm_lib.h":
     void normalise_images_C(double * y, int n_images, 
                             int n_dofs_image)
 
-def compute_tangents(np.ndarray[double, ndim=1, mode="c"] tangents,
-                     np.ndarray[double, ndim=1, mode="c"] y,
-                     np.ndarray[double, ndim=1, mode="c"] energies,
+def compute_tangents(double [:] tangents,
+                     double [:] y,
+                     double [:] energies,
                      n_dofs_image,
                      n_images
                      ):
@@ -62,13 +57,13 @@ def compute_tangents(np.ndarray[double, ndim=1, mode="c"] tangents,
                        n_dofs_image, n_images
                        )
 
-def compute_spring_force(np.ndarray[double, ndim=1, mode="c"] spring_force,
-                         np.ndarray[double, ndim=1, mode="c"] y,
-                         np.ndarray[double, ndim=1, mode="c"] tangents,
+def compute_spring_force(double [:] spring_force,
+                         double [:] y,
+                         double [:] tangents,
                          k,
                          n_images,
                          n_dofs_image,
-                         np.ndarray[int, ndim=1, mode="c"] material,
+                         int [:] material,
                          n_dofs_image_material
                          ):
 
@@ -78,10 +73,10 @@ def compute_spring_force(np.ndarray[double, ndim=1, mode="c"] spring_force,
                            &material[0], n_dofs_image_material
                            )
 
-def compute_effective_force(np.ndarray[double, ndim=1, mode="c"] G,
-                            np.ndarray[double, ndim=1, mode="c"] tangents,
-                            np.ndarray[double, ndim=1, mode="c"] gradientE,
-                            np.ndarray[double, ndim=1, mode="c"] spring_force,
+def compute_effective_force(double [:] G,
+                            double [:] tangents,
+                            double [:] gradientE,
+                            double [:] spring_force,
                             climbing_image,
                             n_images,
                             n_dofs_image
@@ -93,25 +88,25 @@ def compute_effective_force(np.ndarray[double, ndim=1, mode="c"] G,
                               n_images, n_dofs_image
                               )
 
-def project_images(np.ndarray[double, ndim=1, mode="c"] vector,
-                   np.ndarray[double, ndim=1, mode="c"] y,
+def project_images(double [:]  vector,
+                   double [:]  y,
                    n_images, n_dofs_image
                    ):
 
     project_images_C(&vector[0], &y[0],
                      n_images, n_dofs_image
                      )
 
-def normalise_images(np.ndarray[double, ndim=1, mode="c"] y,
+def normalise_images(double [:] y,
                      n_images, n_dofs_image
                      ):
 
     normalise_images_C(&y[0], n_images, n_dofs_image)
 
-def compute_dYdt(np.ndarray[double, ndim=1, mode="c"] y,
-                 np.ndarray[double, ndim=1, mode="c"] G,
-                 np.ndarray[double, ndim=1, mode="c"] dYdt,
-                 np.ndarray[int, ndim=1, mode="c"] pins,
+def compute_dYdt(double [:]  y,
+                 double [:]  G,
+                 double [:]  dYdt,
+                 int [:] pins,
                  n_images,
                  n_dofs_image
                  ):

fidimag/common/neb_method/nebm_clib.pyx

@@ -1,8 +1,3 @@
-import numpy
-cimport numpy as np
-np.import_array()
-
-
 cdef extern from "nebm_lib.h":
 
     void compute_tangents_C(double *tangents,
@@ -20,9 +15,9 @@ cdef extern from "nebm_lib.h":
                                    int n_images,
                                    int n_dofs_image)
 
-def compute_tangents(np.ndarray[double, ndim=1, mode="c"] tangents,
-                     np.ndarray[double, ndim=1, mode="c"] y,
-                     np.ndarray[double, ndim=1, mode="c"] energies,
+def compute_tangents(double [:] tangents,
+                     double [:] y,
+                     double [:] energies,
                      n_dofs_image,
                      n_images
                      ):
@@ -31,10 +26,10 @@ def compute_tangents(np.ndarray[double, ndim=1, mode="c"] tangents,
                        n_dofs_image, n_images
                        )
 
-def compute_effective_force(np.ndarray[double, ndim=1, mode="c"] G,
-                            np.ndarray[double, ndim=1, mode="c"] tangents,
-                            np.ndarray[double, ndim=1, mode="c"] gradientE,
-                            np.ndarray[double, ndim=1, mode="c"] spring_force,
+def compute_effective_force(double [:] G,
+                            double [:] tangents,
+                            double [:] gradientE,
+                            double [:] spring_force,
                             climbing_image,
                             n_images,
                             n_dofs_image

fidimag/common/neb_method/nebm_geodesic_lib.c

@@ -40,7 +40,6 @@ double compute_distance_geodesic(double * A, double * B, int n_dofs_image,
      *
      */
 
-    int i, j;
     int spin_i;
     double A_cross_B[3];
     double A_cross_B_norm;

fidimag/common/neb_method/nebm_spherical_clib.pyx

@@ -1,8 +1,3 @@
-import numpy
-cimport numpy as np
-np.import_array()
-
-
 cdef extern from "nebm_spherical_lib.h":
 
     void normalise_spherical(double * a, int n)
@@ -44,20 +39,20 @@ cdef extern from "nebm_lib.h":
                                    int n_images,
                                    int n_dofs_image)
 
-def normalise_images(np.ndarray[double, ndim=1, mode="c"] y,
+def normalise_images(double [:] y,
                      n_images,
                      n_dofs_image
                      ):
 
     normalise_images_spherical_C(&y[0], n_images, n_dofs_image)
 
-def compute_spring_force(np.ndarray[double, ndim=1, mode="c"] spring_force,
-                         np.ndarray[double, ndim=1, mode="c"] y,
-                         np.ndarray[double, ndim=1, mode="c"] tangents,
+def compute_spring_force(double [:] spring_force,
+                         double [:] y,
+                         double [:] tangents,
                          k,
                          n_images,
                          n_dofs_image,
-                         np.ndarray[int, ndim=1, mode="c"] material,
+                         int [:] material,
                          n_dofs_image_material
                          ):