Class SystemClass#

Defined in File systemclass.hpp

Class Documentation#

class SystemClass#

SystemClass is the base class which is the core of PyMembrane.

Public Functions

inline SystemClass()#

inline SystemClass(const BoxType &box)#: Create a particles from given vectors

inline ~SystemClass()#

inline std::string get_mesh_info(void)#

const BoxType &get_box(void)#

get the box

Parameters:: void –
Returns:: const BoxType&

void set_box(const BoxType &box)#

Set the box object.

Parameters:: box –

void set_box_length(const double &Lx, const double &Ly, const double &Lz)#

set the the box

Parameters:: double –

real3 minImage(const real3 &a, const real3 &b)#

bool need_wrapping(const real3 &a, const real3 &b)#

void enforce_periodic_boundary_conditions(void)#

inline void read_mesh_from_files(std::map<std::string, std::string> &files)#

read the mesh from a file

Parameters:: std::map<std::string, std::string>& – files

inline void read_mesh_from_json(std::string &json_file)#

inline pymemb::vector<HE_HalfEdge<PropertyEdges>> get_halfedges(void)#

get the halfedges loaded in the system

Parameters:: void –
Returns:: pymemb::vector<HE_HalfEdge<PropertyEdges>>

inline pymemb::vector<HE_Vertex<PropertyVertices>> get_vertices(void)#

get the vertices loaded in the system

Parameters:: void –
Returns:: pymemb::vector<HE_Vertex<PropertyVertices>>

inline pymemb::vector<HE_Edge<PropertyEdges>> get_edges(void)#

get the edges loaded in the system

Parameters:: void –
Returns:: pymemb::vector<HE_Edge<PropertyEdges>>

inline pymemb::vector<HE_Face<PropertyFaces>> get_faces(void)#

get the faces loaded in the system

Parameters:: void –
Returns:: pymemb::vector<HE_Face<PropertyFaces>>

inline void set_halfedges(pymemb::vector<HE_HalfEdge<PropertyEdges>> &_halfedges)#

set the halfedges loaded in the system

Parameters:: pymemb::vector<HE_HalfEdge<PropertyEdges>>& – _halfedges
Returns:: void

inline void set_vertices(pymemb::vector<HE_Vertex<PropertyVertices>> &_vertices)#

get the vertices loaded in the system

Parameters:: pymemb::vector<HE_Vertex<PropertyVertices>>& – _vertices
Returns:

inline void set_edges(pymemb::vector<HE_Edge<PropertyEdges>> &_edges)#

get the edges loaded in the system

Parameters:: pymemb::vector<HE_Edge<PropertyEdges>>& – _edges
Returns:

inline void set_faces(pymemb::vector<HE_Face<PropertyFaces>> &_faces)#

get the faces loaded in the system

Parameters:: void –
Returns:: pymemb::vector<HE_Face<PropertyFaces>>

inline void set(pymemb::vector<HE_Face<PropertyFaces>> &_faces, pymemb::vector<HE_Vertex<PropertyVertices>> &_vertices, pymemb::vector<HE_Edge<PropertyEdges>> &_edges, pymemb::vector<HE_HalfEdge<PropertyEdges>> &_halfedges)#

Parameters:

_faces – Faces list
_vertices – Vertex list
_edges – Edges list
_halfedges – Half-edge list

inline pymemb::vector<int> get_edge_neighbours_host(int edge_index)#

inline const ComputeMesh &get_compute_mesh(void)#

inline const DumperClass &get_dumper(void)#

inline void init_stresses(void)#

inline pymemb::vector<realTensor> get_stress_vertices(void)#

get the STRESSES in the vertices loaded in the system

Parameters:: void –
Returns:: pymemb::vector<HE_Edge<PropertyEdges>>

inline pymemb::vector<realTensor> get_stress_edges(void)#

get the STRESSES in the edges loaded in the system

Parameters:: void –
Returns:: pymemb::vector<HE_Edge<PropertyEdges>>

inline pymemb::vector<realTensor> get_stress_faces(void)#

get the faces loaded in the system

Parameters:: void –
Returns:: pymemb::vector<HE_Face<PropertyFaces>>

inline pymemb::vector<realTensor> get_stress_virial(void)#

get the faces loaded in the system

Parameters:: void –
Returns:: pymemb::vector<HE_Face<PropertyFaces>>

inline pymemb::vector<realTensor> get_stress_kinetic(void)#

get the faces loaded in the system

Parameters:: void –
Returns:: pymemb::vector<HE_Face<PropertyFaces>>

Public Members

pymemb::vector<HE_Face<PropertyFaces>> faces#: Faces list.

pymemb::vector<HE_Vertex<PropertyVertices>> vertices#: Vertex list.

pymemb::vector<HE_HalfEdge<PropertyEdges>> halfedges#: Half-edge list.

pymemb::vector<HE_Edge<PropertyEdges>> edges#: Edges list.

pymemb::vector<realTensor> stress_group_faces#

pymemb::vector<realTensor> stress_group_vertices#

pymemb::vector<realTensor> stress_group_edges#

pymemb::vector<realTensor> stress_virial_atom#

pymemb::vector<realTensor> stress_kinetic_atom#

int Numvertices#: Number of vertices.

int Numedges#: Number of edges.

int Numfaces#: Number of faces.

int Numhalfedges#: Number of halfedges.

bool close_surface#: Mesh is a close surface.

bool copy_in_host#

ComputeMesh compute_mesh#

DumperClass dumper#