Defining systems¶

class System¶

A System deals with the storage of atoms and related information, as well as the computation of neighbor lists.

This class only defines a pure virtual interface for System. In order to provide access to new system, users must create a child class implementing all virtual member functions.

Subclassed by featomic::SimpleSystem, featomic_torch::SystemAdapter

Public Types

using CellMatrix = std::array<std::array<double, 3>, 3>¶: Unit cell representation as a 3x3 matrix. The cell should be written in row major order, i.e. {{ax ay az}, {bx by bz}, {cx cy cz}}, where a/b/c are the unit cell vectors.

Public Functions

System(const System&) = default¶: System is copy-constructible.

System(System&&) = default¶: System is move-constructible.

System &operator=(const System&) = default¶: System can be copy-assigned.

System &operator=(System&&) = default¶: System can be move-assigned.

virtual uintptr_t size() const = 0¶: Get the number of atoms in this system.

virtual const int32_t *types() const = 0¶: Get a pointer to the first element a contiguous array (typically std::vector or memory allocated with new[]) containing the atomic type of each atom in this system. Different atomics types should be identified with a different value. These values are usually the atomic number, but don’t have to be. The array should contain System::size() elements.

virtual const double *positions() const = 0¶: Get a pointer to the first element of a contiguous array containing the atomic cartesian coordinates. positions[0], positions[1], positions[2] must contain the x, y, z cartesian coordinates of the first atom, and so on. The array should contain 3 x System::size() elements.

virtual CellMatrix cell() const = 0¶: Get the matrix describing the unit cell.

virtual void compute_neighbors(double cutoff) = 0¶: Compute the neighbor list with the given cutoff, and store it for later access using System::pairs or System::pairs_containing.

virtual const std::vector<featomic_pair_t> &pairs() const = 0¶

Get the list of pairs in this system

This list of pair should only contain each pair once (and not twice as i-j and j-i), should not contain self pairs (i-i); and should only contains pairs where the distance between atoms is actually bellow the cutoff passed in the last call to System::compute_neighbors. This function is only valid to call after a call to System::compute_neighbors.

virtual const std::vector<featomic_pair_t> &pairs_containing(uintptr_t atom) const = 0¶

Get the list of pairs in this system containing the atom at the given index.

The same restrictions on the list of pairs as System::pairs applies, with the additional condition that the pair i-j should be included both in the return of System::pairs_containing(i) and System::pairs_containing(j).

inline featomic_system_t as_featomic_system_t()¶

Convert a child instance of the System class to a featomic_system_t to be passed to the featomic functions.

This is an advanced function that most users don’t need to call directly.

class SimpleSystem : public featomic::System ¶

A very minimal implementation of the System interface, only providing data and no neighbor list calculation. This class must thus be used with use_native_system=true in the calculation options.

Public Functions

inline SimpleSystem(CellMatrix cell = {{0}})¶: Create a new SimpleSystem, with the atoms contained in the give cell.

inline void add_atom(int32_t type, std::array<double, 3> position)¶: Add an atom with the given type and position to this system.

inline virtual uintptr_t size() const override¶: Get the number of atoms in this system.

inline virtual const int32_t *types() const override¶: Get a pointer to the first element a contiguous array (typically std::vector or memory allocated with new[]) containing the atomic type of each atom in this system. Different atomics types should be identified with a different value. These values are usually the atomic number, but don’t have to be. The array should contain System::size() elements.

inline virtual const double *positions() const override¶: Get a pointer to the first element of a contiguous array containing the atomic cartesian coordinates. positions[0], positions[1], positions[2] must contain the x, y, z cartesian coordinates of the first atom, and so on. The array should contain 3 x System::size() elements.

inline virtual CellMatrix cell() const override¶: Get the matrix describing the unit cell.

inline virtual void compute_neighbors(double) override¶: Compute the neighbor list with the given cutoff, and store it for later access using System::pairs or System::pairs_containing.

inline virtual const std::vector<featomic_pair_t> &pairs() const override¶

Get the list of pairs in this system

inline virtual const std::vector<featomic_pair_t> &pairs_containing(uintptr_t) const override¶

Get the list of pairs in this system containing the atom at the given index.