ATC version 2.0, date: Aug7

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10561 f3b2605a-c512-4ea7-a41b-209d697bcdaa

lib/atc/CBLattice.h

@@ -0,0 +1,98 @@
+#ifndef CBLATTICE_H
+#define CBLATTICE_H
+
+#include <set>
+#include <vector>
+#include <stack>
+#include "MatrixLibrary.h"
+#include "ATC_TypeDefs.h"
+
+using std::vector;
+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