Improved interface.

Author: lauri-codes

dscribe/descriptors/acsf.py

@@ -169,14 +169,18 @@ def is_static():
 
         return output
 
-    def create_single(self, system, centers=None):
+    def create_single(
+        self, system, centers=None, return_descriptor=True, return_derivatives=False
+    ):
         """Creates the descriptor for the given system.
 
         Args:
             system (:class:`ase.Atoms` | :class:`.System`): Input system.
             centers (iterable): Indices of the atoms around which the ACSF
                 will be returned. If no centers defined, ACSF will be created
                 for all atoms in the system.
+            return_descriptor: Whether to return the descriptor
+            return_derivatives: Whether to return the derivatives
 
         Returns:
             np.ndarray: The ACSF output for the given system and centers. The

dscribe/descriptors/coulombmatrix.py

@@ -116,10 +116,12 @@ def create(self, system, n_jobs=1, only_physical_cores=False, verbose=False):
 
         return output
 
-    def create_single(self, system):
+    def create_single(self, system, return_descriptor=True, return_derivatives=False):
         """
         Args:
             system (:class:`ase.Atoms`): Input system.
+            return_descriptor: Whether to return the descriptor
+            return_derivatives: Whether to return the derivatives
 
         Returns:
             ndarray: The zero padded matrix as a flattened 1D array.
@@ -140,6 +142,8 @@ def create_single(self, system):
             atomic_numbers,
             cell,
             pbc,
+            return_descriptor,
+            return_derivatives
         )
 
         return out_des

dscribe/descriptors/descriptor.py

@@ -270,7 +270,7 @@ def create_parallel(
         """
         # If single system given, skip the parallelization overhead
         if len(inp) == 1:
-            return self.format_array(func(*inp[0]))
+            return self.format_array(func(*inp[0], return_descriptor=True, return_derivatives=False))
 
         # Determine the number of jobs
         if n_jobs < 0:
@@ -307,7 +307,7 @@ def create_multiple(arguments, func, is_sparse, index, verbose):
             n_samples = len(arguments)
 
             for i_sample, i_arg in enumerate(arguments):
-                i_out = func(*i_arg)
+                i_out = func(*i_arg, return_descriptor=True, return_derivatives=False)
                 i_out = self.format_array(i_out)
 
                 # If the shape varies, just add result into a list

dscribe/descriptors/descriptorglobal.py

@@ -246,7 +246,7 @@ def derivatives_numerical(
                     i_pos = system_disturbed.get_positions()
                     i_pos[i_atom, i_comp] += h * deltas[i_stencil]
                     system_disturbed.set_positions(i_pos)
-                    d1 = self.create_single(system_disturbed)
+                    d1 = self.create_single(system_disturbed, return_descriptor=True, return_derivatives=False)
                     derivatives_python[i_atom, i_comp, :] += coeffs[i_stencil] * d1 / h
 
         i = 0
@@ -255,4 +255,5 @@ def derivatives_numerical(
             i += 1
 
         if return_descriptor:
-            np.copyto(c, self.create_single(system))
+            np.copyto(c, self.create_single(system, return_descriptor=True, return_derivatives=False))
+

dscribe/descriptors/descriptormatrix.py

@@ -101,10 +101,12 @@ def get_matrix(self, system):
             np.ndarray: The final two-dimensional matrix for this descriptor.
         """
 
-    def create_single(self, system):
+    def create_single(self, system, return_descriptor=True, return_derivatives=False):
         """
         Args:
             system (:class:`ase.Atoms` | :class:`.System`): Input system.
+            return_descriptor: Whether to return the descriptor
+            return_derivatives: Whether to return the derivatives
 
         Returns:
             ndarray: The zero padded matrix either as a 1D array.

dscribe/descriptors/ewaldsummatrix.py

@@ -177,7 +177,17 @@ def create(
 
         return output
 
-    def create_single(self, system, accuracy=1e-5, w=1, r_cut=None, g_cut=None, a=None):
+    def create_single(
+        self,
+        system,
+        accuracy=1e-5,
+        w=1,
+        r_cut=None,
+        g_cut=None,
+        a=None,
+        return_descriptor=True,
+        return_derivatives=False,
+    ):
         """
         Args:
             system (:class:`ase.Atoms` | :class:`.System`): Input system.
@@ -198,6 +208,8 @@ def create_single(self, system, accuracy=1e-5, w=1, r_cut=None, g_cut=None, a=No
                 Gaussians. If not provided, a default value of :math:`\\alpha =
                 \\sqrt{\\pi}\\left(\\frac{N}{V^2}\\right)^{1/6}` is used.
                 Corresponds to the standard deviation of the Gaussians.
+            return_descriptor: Whether to return the descriptor
+            return_derivatives: Whether to return the derivatives
         """
         self.q = system.get_atomic_numbers()
         self.q_squared = self.q**2
@@ -213,6 +225,7 @@ def create_single(self, system, accuracy=1e-5, w=1, r_cut=None, g_cut=None, a=No
         # specified, use the accuracy and the weighting w to determine default
         # similarly as in https://doi.org/10.1080/08927022.2013.840898
         if r_cut is None and g_cut is None:
+
             f = np.sqrt(-np.log(accuracy))
             r_cut = f / a
             g_cut = 2 * a * f

dscribe/descriptors/lmbtr.py

@@ -374,6 +374,8 @@ def create_single(
         self,
         system,
         centers=None,
+        return_descriptor=True,
+        return_derivatives=False
     ):
         """Return the local many-body tensor representation for the given
         system and centers.
@@ -386,6 +388,8 @@ def create_single(
                 If cartesian positions are provided, new atoms are added at that
                 position. If no centers are provided, all atoms in the system
                 will be used as centers.
+            return_descriptor: Whether to return the descriptor
+            return_derivatives: Whether to return the derivatives
 
         Returns:
             1D ndarray: The local many-body tensor representations of given

dscribe/descriptors/mbtr.py

@@ -388,11 +388,13 @@ def create(self, system, n_jobs=1, only_physical_cores=False, verbose=False):
 
         return output
 
-    def create_single(self, system):
+    def create_single(self, system, return_descriptor=True, return_derivatives=False):
         """Return the many-body tensor representation for the given system.
 
         Args:
             system (:class:`ase.Atoms` | :class:`.System`): Input system.
+            return_descriptor: Whether to return the descriptor
+            return_derivatives: Whether to return the derivatives
 
         Returns:
             np.ndarray | sparse.COO: A single concatenated output vector is

dscribe/descriptors/soap.py

@@ -486,7 +486,9 @@ def is_static():
 
         return output
 
-    def create_single(self, system, centers=None):
+    def create_single(
+        self, system, centers=None, return_descriptor=True, return_derivatives=False
+    ):
         """Return the SOAP output for the given system and given centers.
 
         Args:
@@ -495,6 +497,8 @@ def create_single(self, system, centers=None):
                 specified, the SOAP spectrum will be created for these points.
                 If no centers are defined, the SOAP output will be created
                 for all atoms in the system.
+            return_descriptor: Whether to return the descriptor
+            return_derivatives: Whether to return the derivatives
 
         Returns:
             np.ndarray | sparse.COO: The SOAP output for the

dscribe/ext/coulombmatrix.cpp

@@ -39,15 +39,16 @@ CoulombMatrix::CoulombMatrix(
 
 void CoulombMatrix::create(
     py::array_t<double> out, 
-    py::array_t<double> positions,
-    py::array_t<int> atomic_numbers,
-    CellList cell_list
+    System &system,
+    CellList cell_list,
+    bool return_descriptor,
+    bool return_derivatives
 )
 {
     // Calculate all pairwise distances.
     auto out_mu = out.mutable_unchecked<1>();
-    auto atomic_numbers_u = atomic_numbers.unchecked<1>();
-    auto positions_u = positions.unchecked<2>();
+    auto atomic_numbers_u = system.atomic_numbers.unchecked<1>();
+    auto positions_u = system.positions.unchecked<2>();
     int n_atoms = atomic_numbers_u.shape(0);
     MatrixXd matrix = distancesEigen(positions_u);