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CBLattice.h
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Thu, Aug 15, 06:26
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Sat, Aug 17, 06:26 (1 d, 23 h)
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rLAMMPS lammps
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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