struct gpr::AtomsConfiguration

Overview

Stores configurations of all atoms in the system. More…

#include <Structures.h>
 
struct AtomsConfiguration {
    // fields
 
    Coord positions;
    FieldMatrixU8 is_frozen;
    FieldMatrixIdx id;
    FieldMatrixi atomicNrs;
    FieldMatrixIdx type;
    AtomsPositionAndType atoms_froz_active;
    AtomsPositionAndType atoms_froz_inactive;
    AtomsPositionAndType atoms_mov;
    FieldMatrixi pairtype;
    Index_t n_pt;
 
    // methods
 
    void assignFromField(const FieldMatrixd& field);
    void clear();
    void clearDistribution();
    void copy(const AtomsConfiguration& other);
    Index_t countMovingAtoms();
};

Detailed Documentation

Stores configurations of all atoms in the system.

Fields

Coord positions

Positions of all atoms in the system.

FieldMatrixU8 is_frozen

Indicates whether atom is frozen or not.

ID of each atom (we do not use it)

FieldMatrixi atomicNrs

Atomic Number of each atom.

Type of each atom.

AtomsPositionAndType atoms_froz_active

Info on active frozen atoms.

AtomsPositionAndType atoms_froz_inactive

Info on inactive frozen atoms.

Info on moving atoms.

FieldMatrixi pairtype

Pairtype indices for pairs of atomtypes (n_at x n_at). Active pairtypes are indexed as 0,1,2,…,n_pt-1. Inactive pairtypes are given index -1.

Index_t n_pt

Number of active pairtypes.

Methods

void assignFromField(const FieldMatrixd& field)

Extract data from a 5-column field.