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lammps/lib/atc/CBLattice.h
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CBLattice.h
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#ifndef CBLATTICE_H
#define CBLATTICE_H
#include <set>
#include <vector>
#include <stack>
#include "MatrixLibrary.h"
#include "ATC_TypeDefs.h"
namespace ATC
{
class CbPotential; // forward definition for potentials.
class StressArgs;
/**
* @class AtomCluster
* @brief Base class for a container for a cluster of atoms around an atom at the origin
* (which is not included in the lists).
* Provides routines for outputting the atoms in the cluster to a vtk file,
* and checking for any overlapping atoms (which should not happen).
*/
class AtomCluster
{
friend class CBLattice;
friend DENS_MAT_VEC compute_dynamical_derivative(StressArgs &args);
friend int test_FCB(const StressArgs &args);
public:
//* Returns the number of atoms in the cluster.
INDEX size() const { return cur_bond_len_.size(); }
//* removes all atoms from the cluster
void clear() { cur_bond_len_.clear(), ref_coords_.clear(); }
//* Removes any overlapping atoms (if they exist).
INDEX remove_overlap();
//* Writes the atom positions of the cluster to a dat file.
void write_to_dat(std::string path, bool current_config=true);
//* Writes the atom positions of the cluster to a vtk file.
void write_to_vtk(std::string path, bool current_config=true);
//* Returns an atom coordinate in the reference configuration.
const DENS_VEC &R(INDEX i) const { return ref_coords_[i]; }
//* Returns an atom coordinate in the current configuration.
DENS_VEC r(INDEX i) const { return F_*R(i); }
//* Returns the ith atoms bond length to the central atom.
double bond_length(INDEX i) const { return cur_bond_len_[i]; }
//* Returns a reference to the deformation gradient tensor.
const DENS_MAT& deformation_gradient() const { return F_; }
//* Computes forces on central atom, with atom I displaced by u.
DENS_VEC perturbed_force(const CbPotential *p, int I, DENS_VEC *u) const;
//* Computes the force constant matrix between atoms I and 0.
DENS_MAT force_constants(INDEX I, const CbPotential *p) const;
private:
std::vector<double> cur_bond_len_; //*> Bond lengths (current)
std::vector<DENS_VEC> ref_coords_; //*> Atom coordinates (ref)
DENS_MAT F_; //*> Deformation gradient
};
/**
* @class CBLattice
* @brief Base class that generates a virtual atom clusters given a lattice and
* a deformation gradient.
*/
class CBLattice
{
protected:
double RC2_; //*> cutoff radius^2
std::stack<int> queue0_; //*> cell nghbrs of representative cell
DENS_MAT n_, b_; //*> cols are def base and basis vectors
const MATRIX &N_, &B_; //*> cols are ref base and basis vectors
public:
//* Operator that outputs the lattice and basis to a stream.
friend std::ostream& operator<<(std::ostream& o, const CBLattice& lattice);
CBLattice(const MATRIX &N, const MATRIX &B);
//* generates the virtual atom cluster
void atom_cluster(const MATRIX &F, double cutoff, AtomCluster &v);
protected:
void _FindAtomsInCutoff(AtomCluster &v);
bool _CheckUnitCell(char a, char b, char c, AtomCluster &v);
};
// hash functions: a, b, c must in range [-128, 127]
inline int hash(int a,int b,int c) {return(a+128)|((b+128)<<8)|((c+128)<<16);}
inline void unhash(int r, int &a, int &b, int &c)
{
a = (r&0xFF) - 128;
b = ((r>>8)&0xFF) - 128;
c = ((r>>16)&0xFF) - 128;
}
}
#endif
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