Changed all non-array variables in smol/utils/cluster modules back in…

…to int and double type in order to pass compilation.

smol/utils/cluster/container.pxd

@@ -4,6 +4,8 @@
 
 __author__ = "Luis Barroso-Luque"
 
+cimport numpy as np
+
 import cython
 from smol.utils.cluster.struct cimport (
     FloatArray1D,
@@ -16,15 +18,15 @@ from smol.utils.cluster.struct cimport (
 
 cdef class OrbitContainer:
     cdef OrbitC* data
-    cdef readonly np.int32_t size
+    cdef readonly int size
     cdef tuple _orbit_data
 
     cpdef public void set_orbits(self, tuple orbit_data) except *
 
     @staticmethod
     cdef OrbitC create_struct(
-            np.int32_t orbit_id,
-            np.int32_t bit_id,
+            int orbit_id,
+            int bit_id,
             np.float64_t[:, ::1] correlation_tensors,
             np.int32_t[::1] tensor_indices,
     )
@@ -33,7 +35,7 @@ cdef class OrbitContainer:
 @cython.final
 cdef class FloatArray2DContainer:
     cdef FloatArray2D* data
-    cdef readonly np.int32_t size
+    cdef readonly int size
     cdef tuple _arrays
 
     cpdef public void set_arrays(self, tuple arrays) except *
@@ -45,7 +47,7 @@ cdef class FloatArray2DContainer:
 @cython.final
 cdef class FloatArray1DContainer:
     cdef FloatArray1D* data
-    cdef readonly np.int32_t size
+    cdef readonly int size
     cdef tuple _arrays
 
     cpdef public void set_arrays(self, tuple arrays)  except *
@@ -57,7 +59,7 @@ cdef class FloatArray1DContainer:
 @cython.final
 cdef class IntArray1DContainer:
     cdef IntArray1D* data
-    cdef readonly np.int32_t size
+    cdef readonly int size
     cdef tuple _arrays
 
     cpdef public void set_arrays(self, tuple arrays)  except *
@@ -69,7 +71,7 @@ cdef class IntArray1DContainer:
 @cython.final
 cdef class IntArray2DContainer:
     cdef IntArray2D* data
-    cdef readonly np.int32_t size
+    cdef readonly int size
     cdef tuple _arrays
 
     cpdef public void set_arrays(self, tuple arrays)  except *

smol/utils/cluster/container.pyx

@@ -46,13 +46,13 @@ cdef class OrbitContainer:
 
     cpdef public void set_orbits(self, tuple orbit_data) except *:
         """Populated data using a list of orbit data."""
-        cdef np.int32_t i
+        cdef int i
 
         # check that dataypes are correct
         for data in orbit_data:
-            if not isinstance(data[0], np.int32_t):
+            if not isinstance(data[0], int):
                 raise TypeError("id must be an integer.")
-            if not isinstance(data[1], np.int32_t):
+            if not isinstance(data[1], int):
                 raise TypeError("bit_id must be an integer.")
             if not isinstance(data[2], np.ndarray):
                 raise TypeError("correlation_tensors must be a numpy array.")
@@ -83,8 +83,8 @@ cdef class OrbitContainer:
 
     @staticmethod
     cdef OrbitC create_struct(
-            np.int32_t orbit_id,
-            np.int32_t bit_id,
+            int orbit_id,
+            int bit_id,
             np.float64_t[:, ::1] correlation_tensors,
             np.int32_t[::1] tensor_indices,
     ):
@@ -131,7 +131,7 @@ cdef class FloatArray2DContainer:
 
     cpdef public void set_arrays(self, tuple arrays) except *:
         """Populated data using a list of 2D arrays."""
-        cdef np.int32_t i
+        cdef int i
 
         for array in arrays:
             if array.ndim != 2:
@@ -190,7 +190,7 @@ cdef class FloatArray1DContainer:
 
     cpdef public void set_arrays(self, tuple arrays) except *:
         """Populated data using a list of 1D arrays."""
-        cdef np.int32_t i
+        cdef int i
 
         for array in arrays:
             if array.ndim != 1:
@@ -247,7 +247,7 @@ cdef class IntArray1DContainer:
 
     cpdef public void set_arrays(self, tuple arrays) except *:
         """Populated data using a list of 1D arrays."""
-        cdef np.int32_t i
+        cdef int i
 
         for array in arrays:
             if array.ndim != 1:
@@ -304,7 +304,7 @@ cdef class IntArray2DContainer:
 
     cpdef public void set_arrays(self, tuple arrays)  except *:
         """Populated data using a list of 2D arrays."""
-        cdef np.int32_t i
+        cdef int i
 
         for array in arrays:
             if array.ndim != 2:

smol/utils/cluster/correlations.pyx

@@ -16,14 +16,14 @@ cimport numpy as np
 
 
 cpdef corr_from_occupancy(const np.int32_t[::1] occu,
-                          const np.int32_t num_corr_functions,
+                          const int num_corr_functions,
                           list orbit_list):
     """Computes the correlation vector for a given encoded occupancy string.
 
     Args:
         occu (ndarray):
             encoded occupancy array
-        num_corr_functions (np.int32_t):
+        num_corr_functions (int):
             total number of bit orderings in expansion.
         orbit_list:
             Information of all orbits.
@@ -33,8 +33,8 @@ cpdef corr_from_occupancy(const np.int32_t[::1] occu,
     Returns: array
         correlation vector for given occupancy
     """
-    cdef np.int32_t i, j, n, m, I, J, M, index
-    cdef np.float64_t p
+    cdef int i, j, n, m, I, J, M, index
+    cdef double p
     cdef const np.int32_t[:, ::1] indices
     cdef const np.int32_t[::1] tensor_indices
     cdef const np.int32_t[:, ::1] corr_tensors
@@ -60,7 +60,7 @@ cpdef corr_from_occupancy(const np.int32_t[::1] occu,
 
 cpdef delta_corr_single_flip(const np.int32_t[::1] occu_f,
                              const np.int32_t[::1] occu_i,
-                             const np.int32_t num_corr_functions,
+                             const int num_corr_functions,
                              list site_orbit_list):
     """Computes the correlation difference between two occupancy arrays.
 
@@ -69,7 +69,7 @@ cpdef delta_corr_single_flip(const np.int32_t[::1] occu_f,
             encoded occupancy array with flip
         occu_i (ndarray):
             encoded occupancy array without flip
-        num_corr_functions (np.int32_t):
+        num_corr_functions (int):
             total number of bit orderings in expansion.
         site_orbit_list:
             Information of all orbits that include the flip site.
@@ -80,8 +80,8 @@ cpdef delta_corr_single_flip(const np.int32_t[::1] occu_f,
     Returns:
         ndarray: correlation vector difference
     """
-    cdef np.int32_t i, j, n, m, I, J, M, ind_i, ind_f
-    cdef np.float64_t p, ratio
+    cdef int i, j, n, m, I, J, M, ind_i, ind_f
+    cdef double p, ratio
     cdef const np.int32_t[:, ::1] indices
     cdef const np.int32_t[::1] tensor_indices
     cdef const np.float64_t[:, ::1] corr_tensors
@@ -108,7 +108,7 @@ cpdef delta_corr_single_flip(const np.int32_t[::1] occu_f,
 cpdef corr_distance_single_flip(const np.int32_t[::1] occu_f,
                                 const np.int32_t[::1] occu_i,
                                 const np.float64_t[::1] ref_corr_vector,
-                                const np.int32_t num_corr_functions,
+                                const int num_corr_functions,
                                 list orbit_list):
     """Computes the absolute distance of two correlation vectors separated by a single
     flip and a given correlation vector.
@@ -122,7 +122,7 @@ cpdef corr_distance_single_flip(const np.int32_t[::1] occu_f,
             encoded occupancy array without flip
         ref_corr_vector (ndarray):
             reference correlation vector
-        num_corr_functions (np.int32_t):
+        num_corr_functions (int):
             total number of bit orderings in expansion.
         orbit_list:
             Information of all orbits.
@@ -133,8 +133,8 @@ cpdef corr_distance_single_flip(const np.int32_t[::1] occu_f,
         ndarray: 2D with correlation vector distances from reference for each of occu_i
         and occu_f
     """
-    cdef np.int32_t i, j, n, m, I, J, M, ind_i, ind_f
-    cdef np.float64_t p_i, p_f
+    cdef int i, j, n, m, I, J, M, ind_i, ind_f
+    cdef double p_i, p_f
     cdef const np.int32_t[:, ::1] indices
     cdef const np.int32_t[::1] tensor_indices
     cdef const np.float64_t[:, ::1] corr_tensors
@@ -162,17 +162,17 @@ cpdef corr_distance_single_flip(const np.int32_t[::1] occu_f,
 
 
 cpdef interactions_from_occupancy(const np.int32_t[::1] occu,
-                                  const np.int32_t num_interactions,
-                                  const np.float64_t offset,
+                                  const int num_interactions,
+                                  const double offset,
                                   list orbit_list):
     """Computes the cluster interaction vector for a given encoded occupancy string.
 
     Args:
         occu (ndarray):
             encoded occupancy vector
-        num_interactions (np.int32_t):
+        num_interactions (int):
             total number of cluster interactions (orbits in cluster subspace).
-        offset (np.float64_t):
+        offset (double):
             eci value for the constant term.
         orbit_list:
             Information of all orbits.
@@ -181,8 +181,8 @@ cpdef interactions_from_occupancy(const np.int32_t[::1] occu,
     Returns: array
         cluster interaction vector for given occupancy
     """
-    cdef np.int32_t n, i, j, I, J, index
-    cdef np.float64_t p
+    cdef int n, i, j, I, J, index
+    cdef double p
     cdef const np.int32_t[:, ::1] indices
     cdef const np.int32_t[::1] tensor_indices
     cdef const np.float64_t[::1] interaction_tensor
@@ -208,7 +208,7 @@ cpdef interactions_from_occupancy(const np.int32_t[::1] occu,
 
 cpdef delta_interactions_single_flip(const np.int32_t[::1] occu_f,
                                      const np.int32_t[::1] occu_i,
-                                     const np.int32_t num_interactions,
+                                     const int num_interactions,
                                      list site_orbit_list):
     """Computes the cluster interaction vector difference between two occupancy
     strings.
@@ -217,7 +217,7 @@ cpdef delta_interactions_single_flip(const np.int32_t[::1] occu_f,
             encoded occupancy vector with flip
         occu_i (ndarray):
             encoded occupancy vector without flip
-        num_interactions (np.int32_t):
+        num_interactions (int):
             total number of cluster interactions (orbits in cluster subspace).
         site_orbit_list:
             Information of all orbits that include the flip site.
@@ -227,8 +227,8 @@ cpdef delta_interactions_single_flip(const np.int32_t[::1] occu_f,
     Returns:
         ndarray: cluster interaction vector difference
     """
-    cdef np.int32_t i, j, n, I, J, ind_i, ind_f
-    cdef np.float64_t p, ratio
+    cdef int i, j, n, I, J, ind_i, ind_f
+    cdef double p, ratio
     cdef const np.int32_t[:, ::1] indices
     cdef const np.int32_t[::1] tensor_indices
     cdef const np.float64_t[::1] interaction_tensor
@@ -252,7 +252,7 @@ cpdef delta_interactions_single_flip(const np.int32_t[::1] occu_f,
 cpdef interaction_distance_single_flip(const np.int32_t[::1] occu_f,
                                        const np.int32_t[::1] occu_i,
                                        const np.float64_t[::1] ref_interaction_vector,
-                                       const np.int32_t num_interactions,
+                                       const int num_interactions,
                                        list orbit_list):
     """Computes the absolute distance of two cluster interaction vectors separated by a
     single flip and a given correlation vector.
@@ -266,7 +266,7 @@ cpdef interaction_distance_single_flip(const np.int32_t[::1] occu_f,
             encoded occupancy array without flip
         ref_interaction_vector (ndarray):
             reference cluster interaction vector
-        num_interactions (np.int32_t):
+        num_interactions (int):
             total number of cluster interactions (orbits in cluster subspace).
         site_orbit_list:
             Information of all orbits that include the flip site.
@@ -278,8 +278,8 @@ cpdef interaction_distance_single_flip(const np.int32_t[::1] occu_f,
         ndarray: 2D with cluster interaction vector distances from reference for each of
         occu_i and occu_f
     """
-    cdef np.int32_t n, i, j, I, J, ind_i, ind_f
-    cdef np.float64_t p_i, p_f
+    cdef int n, i, j, I, J, ind_i, ind_f
+    cdef double p_i, p_f
     cdef const np.int32_t[:, ::1] indices
     cdef const np.int32_t[::1] tensor_indices
     cdef const np.float64_t[::1] interaction_tensor
@@ -309,7 +309,7 @@ cpdef delta_ewald_single_flip(const np.int32_t[::1] occu_f,
                               const np.int32_t[::1] occu_i,
                               const np.float64_t[:, ::1] ewald_matrix,
                               const np.int32_t[:, ::1] ewald_indices,
-                              const np.int32_t site_ind):
+                              const int site_ind):
     """Compute the change in electrostatic interaction energy from a flip.
 
     Args:
@@ -322,16 +322,16 @@ cpdef delta_ewald_single_flip(const np.int32_t[::1] occu_f,
         ewald_indices (ndarray):
             2D array of indices corresponding to a specific site occupation
             in the ewald matrix
-        site_ind (np.int32_t):
+        site_ind (int):
             site index for site being flipped
 
     Returns:
-        np.float64_t: electrostatic interaction energy difference
+        double: electrostatic interaction energy difference
     """
-    cdef np.int32_t i, j, k, add, sub
+    cdef int i, j, k, add, sub
     cdef bint ok
-    cdef np.float64_t out = 0
-    cdef np.float64_t out_k
+    cdef double out = 0
+    cdef double out_k
 
     # values of -1 are vacancies and hence don't have ewald indices
     add = ewald_indices[site_ind, occu_f[site_ind]]

smol/utils/cluster/evaluator.pxd

@@ -15,21 +15,21 @@ from smol.utils.cluster.container cimport (
 
 @cython.final
 cdef class ClusterSpaceEvaluator(OrbitContainer):
-    cdef np.int32_t num_corr  # total number of correlation functions
-    cdef np.int32_t num_orbits  # total number of orbits
-    cdef public np.float64_t offset  # offset for the interaction tensor
+    cdef int num_corr  # total number of correlation functions
+    cdef int num_orbits  # total number of orbits
+    cdef public double offset  # offset for the interaction tensor
     cdef FloatArray1DContainer cluster_interactions
-    cdef public np.int32_t num_threads
+    cdef public int num_threads
 
     cpdef public void reset_data(
             self,
             tuple orbit_data,
-            np.int32_t num_orbits,
-            np.int32_t num_corr_functions,
+            int num_orbits,
+            int num_corr_functions,
     )
 
     cpdef public void set_cluster_interactions(
-            self, tuple cluster_interaction_tensors, np.float64_t offset
+            self, tuple cluster_interaction_tensors, double offset
     )
 
     cpdef np.ndarray[np.float64_t, ndim=1] correlations_from_occupancy(