#include <ConfigDoF.hh>

Detailed Description

A container class for the different degrees of freedom values a Configuration might have

The values of the discrete site DoF within the supercell ("occupation", Eigen::VectorXi)

Example: Occupation values, accessed via Eigen::VectorXi const &ConfigDoF::occupation(), with integer value corresponding to which Molecule in the the a Site::occupant_dof vector is occupying a particular site:
```
[<- sublattice 0 "occ" values -> | <- sublattice 1 "occ" values -> |
... ]
```

The values of the continuous site DoF within the supercell ("local_dofs", std::map<DoFKey, LocalContinuousConfigDoFValues>)

Example: Displacement values, with prim DoF basis equal to the standard basis (dx, dy, dz), accessed via Eigen::MatrixXd const &ConfigDoF::local_dofs("disp").values():

[<- sublattice 0 dx values -> | <- sublattice 1 dx values -> | ... ]
[<- sublattice 0 dy values -> | <- sublattice 1 dy values -> | ... ]
[<- sublattice 0 dz values -> | <- sublattice 1 dz values -> | ... ]

Example: Displacement values, with non-standard prim DoF basis:

"basis" : [ {
    "coordinate": [c0x, c0y, c0z],
    "occupants": [...],
    "dofs": {
      "disp" : {
        "axis_names" : ["dxy", "dz"],
        "axes" : [[1.0, 1.0, 0.0],
                [0.0, 0.0, 1.0]]}}
  },
  {
    "coordinate": [c1x, c1y, c1z],
    "occupants": [...],
    "dofs": {
      "disp" : {
        "axis_names" : ["d\bar{x}y", "dz"],
        "axes" : [[-1.0, 1.0, 0.0],
                [0.0, 0.0, 1.0]]}}

... }

[<- sublat 0 dxy values -> | <- sublat 1 d\bar{x}y values ->| ... ] [<- sublat 0 dz values -> | <- sublat 1 dz values -> | ... ]

Note that the values matrix has only two rows, this is the maximum site basis dimension.

Example: Displacement values, with varying prim DoF basis:

"basis" : [ {
    "coordinate": [c0x, c0y, c0z],
    "occupants": [...],
    "dofs": {
      "disp" : {}
  },
  {
    "coordinate": [c1x, c1y, c1z],
    "occupants": [...],
    "dofs": {
      "disp" : {
        "axis_names" : ["dxy", "dz"],
        "axes" : [[-1.0, 1.0, 0.0],
                [0.0, 0.0, 1.0]]}}

... }

Note that the values matrix has three rows, this is the maximum site basis dimension, but for sublattices with lower site basis dimension it is padded with fixed zeros.

The values of the continuous global DoF ("global_dofs", std::map<DoFKey, GlobalContinuousConfigDoFValues>).

Example: GLstrain values, with prim DoF basis equal to the standard basis, accessed via Eigen::VectorXd const &ConfigDoF::global_dofs("GLstrain").values():
```
[e_xx, e_yy, e_zz, sqrt(2)*e_yz, sqrt(2)*e_xz, sqrt(2)*e_xy]
```
Note: Continuous DoF values stored in memory in ConfigDoF are coordinates in the prim DoF basis (the "axes" given in "prim.json" which set xtal::SiteDoFSet::basis() or xtal::DoFSet::basis()), but when saved to file (i.e. .casm/config/config_list.json) they are saved as coordinates in the standard DoF basis (with axes meaning as described by AnisoValTraits::standard_var_names()).

Definition at line 117 of file ConfigDoF.hh.

Public Member Functions
template<typename GlobalInfoContainerType , typename LocalInfoContainerType >
	ConfigDoF (Index _N_sublat, Index _N_vol, GlobalInfoContainerType const &global_dof_info, LocalInfoContainerType const &local_dof_info, std::vector< SymGroupRepID > const &occ_symrep_IDs, double _tol)

Index	size () const
	Number of sites in the ConfigDoF. More...

Index	n_vol () const
	Integer volume of ConfigDoF. More...

Index	n_sublat () const
	Number of sublattices in ConfigDoF. More...

double	tol () const
	Tolerance for comparison of continuous DoF values. More...

void	setZero ()
	Set all DoF values to zero. More...

int &	occ (Index i)
	Reference occupation value on site i. More...

const int &	occ (Index i) const
	Const reference to occupation value on site i. More...

void	set_occupation (Eigen::Ref< const Eigen::VectorXi > const &_occupation)
	Set occupation values. More...

Eigen::VectorXi const &	occupation () const
	Const reference occupation values. More...

bool	has_occupation () const

std::map< DoFKey, GlobalContinuousConfigDoFValues > const &	global_dofs () const

GlobalContinuousConfigDoFValues const &	global_dof (DoFKey const &_key) const

GlobalContinuousConfigDoFValues &	global_dof (DoFKey const &_key)

bool	has_global_dof (DoFKey const &_key) const

void	set_global_dof (DoFKey const &_key, Eigen::Ref< const Eigen::VectorXd > const &_val)
	Set global continuous DoF values. More...

std::map< DoFKey, LocalContinuousConfigDoFValues > const &	local_dofs () const

LocalContinuousConfigDoFValues const &	local_dof (DoFKey const &_key) const

LocalContinuousConfigDoFValues &	local_dof (DoFKey const &_key)

bool	has_local_dof (DoFKey const &_key) const

void	set_local_dof (DoFKey const &_key, Eigen::Ref< const Eigen::MatrixXd > const &_val)
	Set local continuous DoF values. More...

ConfigDoF &	apply_sym (PermuteIterator const &it)

ConfigDoF &	apply_sym_no_permute (SymOp const &_op)

void	swap (ConfigDoF &RHS)

Private Attributes
LocalDiscreteConfigDoFValues	m_occupation

std::map< std::string, GlobalContinuousConfigDoFValues >	m_global_dofs

std::map< std::string, LocalContinuousConfigDoFValues >	m_local_dofs

double	m_tol

Constructor & Destructor Documentation

◆ ConfigDoF()

template<typename GlobalInfoContainerType , typename LocalInfoContainerType >

CASM::ConfigDoF::ConfigDoF	(	Index	_N_sublat,
		Index	_N_vol,
		GlobalInfoContainerType const &	global_dof_info,
		LocalInfoContainerType const &	local_dof_info,
		std::vector< SymGroupRepID > const &	occ_symrep_IDs,
		double	_tol
	)

Initialize with number of sites, and dimensionality of global and local DoFs GlobalInfoContainerType is an iterable container having value_type std::pair<DoFKey,ContinuousDoFInfo> LocalInfoContainerType is an iterable container having value_type std::pair<DoFKey,std::vector<ContinuousDoFInfo> > OccInfoContainerType is an iterable container having value_type SymGroupRepID

ConfigDoF constructor

Parameters

_N_sublat	Number of sublattices in corresponding prim
_N_vol	Supercell volume, as multiples of the prim volume
global_dof_info	GlobalInfoContainerType is an iterable container of value_type std::pair<DoFKey,ContinuousDoFInfo>.
local_dof_info	LocalInfoContainerType is an iterable container of value_type std::pair<DoFKey,std::vector<ContinuousDoFInfo> > Note: Typically Structure has already been included when a ConfigDoF is constructed, in which case it is best to use `make_configdof` from clex/ConfigDoFTools.hh.

Definition at line 24 of file ConfigDoF_impl.hh.

Member Function Documentation

◆ apply_sym()

ConfigDoF & CASM::ConfigDoF::apply_sym ( PermuteIterator const & it )

Update DoF values using the effect of symmetry, including permutation among sites

The effect is: *this = permute_iterator * (*this)

Definition at line 182 of file ConfigDoF.cc.

◆ apply_sym_no_permute()

ConfigDoF & CASM::ConfigDoF::apply_sym_no_permute ( SymOp const & _op )

Update DoF values using only the effect of symmetry on the value at each site, without permutation among sites

Definition at line 220 of file ConfigDoF.cc.

◆ global_dof() [1/2]

GlobalContinuousConfigDoFValues & CASM::ConfigDoF::global_dof ( DoFKey const & _key )

Definition at line 79 of file ConfigDoF.cc.

◆ global_dof() [2/2]

GlobalContinuousConfigDoFValues const & CASM::ConfigDoF::global_dof ( DoFKey const & _key ) const

Definition at line 69 of file ConfigDoF.cc.

◆ global_dofs()

std::map< DoFKey, GlobalContinuousConfigDoFValues > const & CASM::ConfigDoF::global_dofs ( ) const

Definition at line 65 of file ConfigDoF.cc.

◆ has_global_dof()

bool CASM::ConfigDoF::has_global_dof ( DoFKey const & _key ) const

Definition at line 88 of file ConfigDoF.cc.

◆ has_local_dof()

bool CASM::ConfigDoF::has_local_dof ( DoFKey const & _key ) const

Definition at line 143 of file ConfigDoF.cc.

◆ has_occupation()

bool CASM::ConfigDoF::has_occupation ( ) const

Definition at line 60 of file ConfigDoF.cc.

◆ local_dof() [1/2]

LocalContinuousConfigDoFValues & CASM::ConfigDoF::local_dof ( DoFKey const & _key )

Definition at line 134 of file ConfigDoF.cc.

◆ local_dof() [2/2]

LocalContinuousConfigDoFValues const & CASM::ConfigDoF::local_dof ( DoFKey const & _key ) const

Definition at line 124 of file ConfigDoF.cc.

◆ local_dofs()

std::map< DoFKey, LocalContinuousConfigDoFValues > const & CASM::ConfigDoF::local_dofs ( ) const

Definition at line 119 of file ConfigDoF.cc.

◆ n_sublat()

Index CASM::ConfigDoF::n_sublat ( ) const

Number of sublattices in ConfigDoF.

Definition at line 17 of file ConfigDoF.cc.

◆ n_vol()

Index CASM::ConfigDoF::n_vol ( ) const

Integer volume of ConfigDoF.

Definition at line 14 of file ConfigDoF.cc.

◆ occ() [1/2]

int & CASM::ConfigDoF::occ ( Index i )

Reference occupation value on site i.

Definition at line 34 of file ConfigDoF.cc.

◆ occ() [2/2]

const int & CASM::ConfigDoF::occ ( Index i ) const

Const reference to occupation value on site i.

Definition at line 37 of file ConfigDoF.cc.

◆ occupation()

Eigen::VectorXi const & CASM::ConfigDoF::occupation ( ) const

Const reference occupation values.

Definition at line 56 of file ConfigDoF.cc.

◆ set_global_dof()

void CASM::ConfigDoF::set_global_dof	(	DoFKey const &	_key,
		Eigen::Ref< const Eigen::VectorXd > const &	_val
	)

Set global continuous DoF values.

Set global continuous DoF values

Exceptions

std::runtime_error	("Attempting to assign global ConfigDoF values...") if "_key" does not exist in global dofs
std::runtime_error	("Size mismatch in ConfigDoF::set_global_dof...") if input vector size does not match current size

Definition at line 99 of file ConfigDoF.cc.

◆ set_local_dof()

void CASM::ConfigDoF::set_local_dof	(	DoFKey const &	_key,
		Eigen::Ref< const Eigen::MatrixXd > const &	_val
	)

Set local continuous DoF values.

Set local continuous DoF values

Exceptions

std::runtime_error	("Attempting to assign local ConfigDoF values...") if "_key" does not exist in local dofs
std::runtime_error	("Size mismatch in ConfigDoF::set_local_dof...") if input matrix size does not match current matrix size

Definition at line 154 of file ConfigDoF.cc.

◆ set_occupation()

void CASM::ConfigDoF::set_occupation ( Eigen::Ref< const Eigen::VectorXi > const & _occupation )

Set occupation values.

Set occupation values

Exceptions

std::runtime_error ("Size mismatch in ConfigDoF::set_occupation...") if input vector size does not match current size

Definition at line 43 of file ConfigDoF.cc.

◆ setZero()

void CASM::ConfigDoF::setZero ( )

Set all DoF values to zero.

Definition at line 23 of file ConfigDoF.cc.

◆ size()

Index CASM::ConfigDoF::size ( ) const

Number of sites in the ConfigDoF.

Definition at line 11 of file ConfigDoF.cc.

◆ swap()

void CASM::ConfigDoF::swap ( ConfigDoF & RHS )

Definition at line 253 of file ConfigDoF.cc.

◆ tol()

double CASM::ConfigDoF::tol ( ) const

Tolerance for comparison of continuous DoF values.

Definition at line 20 of file ConfigDoF.cc.

Member Data Documentation

◆ m_global_dofs

std::map<std::string, GlobalContinuousConfigDoFValues> CASM::ConfigDoF::m_global_dofs

private

Definition at line 203 of file ConfigDoF.hh.

◆ m_local_dofs

std::map<std::string, LocalContinuousConfigDoFValues> CASM::ConfigDoF::m_local_dofs

private

Definition at line 205 of file ConfigDoF.hh.

◆ m_occupation

LocalDiscreteConfigDoFValues CASM::ConfigDoF::m_occupation

private

Definition at line 201 of file ConfigDoF.hh.

◆ m_tol

double CASM::ConfigDoF::m_tol

mutableprivate

Tolerance used for transformation to canonical form – used also for continuous DoF comparisons, since comparisons are only meaningful to within the tolerance used for finding the canonical form.

Definition at line 210 of file ConfigDoF.hh.

The documentation for this class was generated from the following files:

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clex/ConfigDoF.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clex/ConfigDoF_impl.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/src/casm/clex/ConfigDoF.cc

Detailed Description

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ ConfigDoF()

Member Function Documentation

◆ apply_sym()

◆ apply_sym_no_permute()

◆ global_dof() [1/2]

◆ global_dof() [2/2]

◆ global_dofs()

◆ has_global_dof()

◆ has_local_dof()

◆ has_occupation()

◆ local_dof() [1/2]

◆ local_dof() [2/2]

◆ local_dofs()

◆ n_sublat()

◆ n_vol()

◆ occ() [1/2]

◆ occ() [2/2]

◆ occupation()

◆ set_global_dof()

◆ set_local_dof()

◆ set_occupation()

◆ setZero()

◆ size()

◆ swap()

◆ tol()

Member Data Documentation

◆ m_global_dofs

◆ m_local_dofs

◆ m_occupation

◆ m_tol