Improved base classes.

SINGROUP · Aug 14, 2023 · d50cefa · d50cefa
1 parent c5284a5
commit d50cefa
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Showing 9 changed files with 77 additions and 53 deletions.
diff --git a/dscribe/ext/coulombmatrix.cpp b/dscribe/ext/coulombmatrix.cpp
@@ -37,14 +37,17 @@ CoulombMatrix::CoulombMatrix(
 {
 }
 
-void CoulombMatrix::create_raw(
- py::detail::unchecked_mutable_reference<double, 1> &out_mu, 
- py::detail::unchecked_reference<double, 2> &positions_u, 
- py::detail::unchecked_reference<int, 1> &atomic_numbers_u,
- CellList &cell_list
+void CoulombMatrix::create(
+ py::array_t<double> out, 
+ py::array_t<double> positions,
+ py::array_t<int> atomic_numbers,
+ CellList cell_list
 )
 {
  // 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>();
  int n_atoms = atomic_numbers_u.shape(0);
  MatrixXd matrix = distancesEigen(positions_u);
 

diff --git a/dscribe/ext/coulombmatrix.h b/dscribe/ext/coulombmatrix.h
@@ -44,11 +44,11 @@ class CoulombMatrix: public DescriptorGlobal {
  /**
  * For creating feature vectors.
  */
- void create_raw(
- py::detail::unchecked_mutable_reference<double, 1> &out_mu, 
- py::detail::unchecked_reference<double, 2> &positions_u, 
- py::detail::unchecked_reference<int, 1> &atomic_numbers_u,
- CellList &cell_list
+ void create(
+ py::array_t<double> out, 
+ py::array_t<double> positions,
+ py::array_t<int> atomic_numbers,
+ CellList cell_list
  );
 
  /**

diff --git a/dscribe/ext/descriptorglobal.cpp b/dscribe/ext/descriptorglobal.cpp
@@ -42,13 +42,18 @@ void DescriptorGlobal::create(
  positions = system_extended.positions;
  atomic_numbers = system_extended.atomic_numbers;
  }
+ this->create(out, positions, atomic_numbers);
+}
 
+void DescriptorGlobal::create(
+ py::array_t<double> out, 
+ py::array_t<double> positions,
+ py::array_t<int> atomic_numbers
+)
+{
  // Calculate neighbours with a cell list
  CellList cell_list(positions, this->cutoff);
- auto out_mu = out.mutable_unchecked<1>();
- auto positions_u = positions.unchecked<2>();
- auto atomic_numbers_u = atomic_numbers.unchecked<1>();
- this->create_raw(out_mu, positions_u, atomic_numbers_u, cell_list);
+ this->create(out, positions, atomic_numbers, cell_list);
 }
 
 void DescriptorGlobal::derivatives_numerical(
@@ -66,7 +71,6 @@ void DescriptorGlobal::derivatives_numerical(
  int n_atoms = atomic_numbers.size();
  int n_features = this->get_number_of_features();
  auto derivatives_mu = derivatives.mutable_unchecked<3>();
- auto descriptor_mu = descriptor.mutable_unchecked<1>();
  auto indices_u = indices.unchecked<1>();
  auto pbc_u = pbc.unchecked<1>();
 
@@ -79,15 +83,13 @@ void DescriptorGlobal::derivatives_numerical(
  atomic_numbers = system_extension.atomic_numbers;
  }
  auto positions_mu = positions.mutable_unchecked<2>();
- auto positions_u = positions.unchecked<2>();
- auto atomic_numbers_u = atomic_numbers.unchecked<1>();
 
  // Pre-calculate cell list for atoms
  CellList cell_list_atoms(positions, this->cutoff);
 
  // Calculate the desciptor value if requested
  if (return_descriptor) {
- this->create_raw(descriptor_mu, positions_u, atomic_numbers_u, cell_list_atoms);
+ this->create(descriptor, positions, atomic_numbers, cell_list_atoms);
  }
 
  // Central finite difference with error O(h^2)
@@ -134,7 +136,7 @@ void DescriptorGlobal::derivatives_numerical(
  auto d_mu = d.mutable_unchecked<1>();
 
  // Calculate descriptor value
- this->create_raw(d_mu, positions_u, atomic_numbers_u, cell_list_atoms);
+ this->create(d, positions, atomic_numbers, cell_list_atoms);
 
  // Add value to final derivative array
  double coeff = coefficients[i_stencil];

diff --git a/dscribe/ext/descriptorglobal.h b/dscribe/ext/descriptorglobal.h
@@ -30,14 +30,15 @@ using namespace std;
 class DescriptorGlobal : public Descriptor {
  public:
  /**
- * Calculates the feature vector.
- *
- * @param out Numpy output array for the descriptor.
- * @param positions Atomic positions as [n_atoms, 3] numpy array.
- * @param atomic_numbers Atomic numbers as [n_atoms] numpy array.
- * @param cell Simulation cell as [3, 3] numpy array.
- * @param pbc Simulation cell periodicity as [3] numpy array.
- */
+ * @brief Version of 'create' that automatically extends the system
+ * based on PBC and calculates celllist.
+ * 
+ * @param out 
+ * @param positions 
+ * @param atomic_numbers 
+ * @param cell 
+ * @param pbc 
+ */
  void create(
  py::array_t<double> out, 
  py::array_t<double> positions,
@@ -47,15 +48,32 @@ class DescriptorGlobal : public Descriptor {
  );
 
  /**
- * Called internally. The system should already be extended
- * periodically and CellList should be available.
+ * @brief Version of 'create' that automatically calculates celllist.
+ * 
+ * @param out 
+ * @param positions 
+ * @param atomic_numbers 
  */
- virtual void create_raw(
- py::detail::unchecked_mutable_reference<double, 1> &out_mu, 
- py::detail::unchecked_reference<double, 2> &positions_u,
- py::detail::unchecked_reference<int, 1> &atomic_numbers_u,
- CellList &cell_list
- ) = 0; 
+ void create(
+ py::array_t<double> out, 
+ py::array_t<double> positions,
+ py::array_t<int> atomic_numbers
+ );
+
+ /**
+ * @brief Pure virtual function for calculating the feature vectors.
+ * 
+ * @param out 
+ * @param positions 
+ * @param atomic_numbers 
+ * @param cell_list 
+ */
+ virtual void create(
+ py::array_t<double> out, 
+ py::array_t<double> positions,
+ py::array_t<int> atomic_numbers,
+ CellList cell_list
+ ) = 0;
 
  /**
  * Calculates the numerical derivates with central finite difference.

diff --git a/dscribe/ext/descriptorlocal.cpp b/dscribe/ext/descriptorlocal.cpp
@@ -34,7 +34,7 @@ void DescriptorLocal::create(
  py::array_t<double> cell,
  py::array_t<bool> pbc,
  py::array_t<double> centers
-) const
+)
 {
  // Extend system if periodicity is requested.
  auto pbc_u = pbc.unchecked<1>();
@@ -52,7 +52,7 @@ void DescriptorLocal::create(
  py::array_t<double> positions,
  py::array_t<int> atomic_numbers,
  py::array_t<double> centers
-) const
+)
 {
  // Calculate neighbours with a cell list
  CellList cell_list(positions, this->cutoff);
@@ -93,7 +93,7 @@ void DescriptorLocal::derivatives_numerical(
  py::array_t<int> indices,
  bool attach,
  bool return_descriptor
-) const
+)
 {
  int n_copies = 1;
  int n_atoms = atomic_numbers.size();

diff --git a/dscribe/ext/descriptorlocal.h b/dscribe/ext/descriptorlocal.h
@@ -47,7 +47,7 @@ class DescriptorLocal : public Descriptor {
  py::array_t<double> cell,
  py::array_t<bool> pbc,
  py::array_t<double> centers
- ) const;
+ );
 
  /**
  * @brief Version of 'create' that automatically calculates celllist.
@@ -62,7 +62,7 @@ class DescriptorLocal : public Descriptor {
  py::array_t<double> positions,
  py::array_t<int> atomic_numbers,
  py::array_t<double> centers
- ) const;
+ );
 
  /**
  * @brief Pure virtual function for calculating the feature vectors.
@@ -79,7 +79,7 @@ class DescriptorLocal : public Descriptor {
  py::array_t<int> atomic_numbers,
  py::array_t<double> centers,
  CellList cell_list
- ) const = 0;
+ ) = 0;
 
  /**
  * Calculates the numerical derivates with central finite difference.
@@ -109,7 +109,7 @@ class DescriptorLocal : public Descriptor {
  py::array_t<int> indices,
  bool attach,
  bool return_descriptor
- ) const;
+ );
 
  protected:
  DescriptorLocal(bool periodic, string average="", double cutoff=0);

diff --git a/dscribe/ext/ext.cpp b/dscribe/ext/ext.cpp
@@ -17,6 +17,7 @@ limitations under the License.
 #include <pybind11/numpy.h> // Enables easy access to numpy arrays
 #include <pybind11/stl.h> // Enables automatic type conversion from C++ containers to python
 #include "descriptorlocal.h"
+#include "descriptorglobal.h"
 #include "celllist.h"
 #include "coulombmatrix.h"
 #include "soap.h"
@@ -36,7 +37,7 @@ PYBIND11_MODULE(ext, m) {
  // CoulombMatrix
  py::class_<CoulombMatrix>(m, "CoulombMatrix")
  .def(py::init<unsigned int, string, double, int>())
- .def("create", &CoulombMatrix::create)
+ .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double>, py::array_t<bool> >()(&DescriptorGlobal::create))
  .def("derivatives_numerical", &CoulombMatrix::derivatives_numerical)
  .def(py::pickle(
  [](const CoulombMatrix &p) {
@@ -58,16 +59,16 @@ PYBIND11_MODULE(ext, m) {
  // SOAP
  py::class_<SOAPGTO>(m, "SOAPGTO")
  .def(py::init<double, int, int, double, py::dict, string, double, py::array_t<int>, py::array_t<double>, bool, string, py::array_t<double>, py::array_t<double> >())
- .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double> >()(&DescriptorLocal::create, py::const_))
- .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double>, py::array_t<bool>, py::array_t<double> >()(&DescriptorLocal::create, py::const_))
- .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double>, CellList>()(&SOAPGTO::create, py::const_))
+ .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double> >()(&DescriptorLocal::create))
+ .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double>, py::array_t<bool>, py::array_t<double> >()(&DescriptorLocal::create))
+ .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double>, CellList>()(&SOAPGTO::create))
  .def("derivatives_numerical", &SOAPGTO::derivatives_numerical)
  .def("derivatives_analytical", &SOAPGTO::derivatives_analytical);
  py::class_<SOAPPolynomial>(m, "SOAPPolynomial")
  .def(py::init<double, int, int, double, py::dict, string, double, py::array_t<int>, py::array_t<double>, bool, string, py::array_t<double>, py::array_t<double> >())
- .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double> >()(&DescriptorLocal::create, py::const_))
- .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double>, py::array_t<bool>, py::array_t<double> >()(&DescriptorLocal::create, py::const_))
- .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double>, CellList>()(&SOAPPolynomial::create, py::const_))
+ .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double> >()(&DescriptorLocal::create))
+ .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double>, py::array_t<bool>, py::array_t<double> >()(&DescriptorLocal::create))
+ .def("create", overload_cast_<py::array_t<double>, py::array_t<double>, py::array_t<int>, py::array_t<double>, CellList>()(&SOAPPolynomial::create))
  .def("derivatives_numerical", &SOAPPolynomial::derivatives_numerical);
 
  // ACSF

diff --git a/dscribe/ext/soap.cpp b/dscribe/ext/soap.cpp
@@ -55,7 +55,7 @@ void SOAPGTO::create(
  py::array_t<int> atomic_numbers,
  py::array_t<double> centers,
  CellList cell_list
-) const
+)
 {
  // Empty mock arrays since we are not calculating the derivatives
  py::array_t<double> xd({1, 1, 1, 1, 1});
@@ -204,7 +204,7 @@ void SOAPPolynomial::create(
  py::array_t<int> atomic_numbers,
  py::array_t<double> centers,
  CellList cell_list
-) const
+)
 {
  soapGeneral(
  out,

diff --git a/dscribe/ext/soap.h b/dscribe/ext/soap.h
@@ -51,7 +51,7 @@ class SOAPGTO: public DescriptorLocal {
  py::array_t<int> atomic_numbers,
  py::array_t<double> centers,
  CellList cell_list
- ) const;
+ );
 
  int get_number_of_features() const;
 
@@ -113,7 +113,7 @@ class SOAPPolynomial: public DescriptorLocal {
  py::array_t<int> atomic_numbers,
  py::array_t<double> centers,
  CellList cell_list
- ) const;
+ );
 
  int get_number_of_features() const;