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PrimClex
Clex | Project

Detailed Description

PrimClex is the top-level data structure for a CASM project.

Classes

class  CASM::PrimClex
 PrimClex is the top-level data structure for a CASM project. More...
 

Typedefs

typedef ConfigIterator
< Configuration, PrimClex > 		CASM::PrimClex::config_iterator
 
typedef ConfigIterator< const
Configuration, const PrimClex > 		CASM::PrimClex::config_const_iterator
 

Functions

 CASM::PrimClex::PrimClex (const Structure &_prim, const Logging &logging=Logging())
 Initial construction of a PrimClex, from a primitive Structure. More...
 
 CASM::PrimClex::PrimClex (const fs::path &_root, const Logging &logging=Logging())
 
void CASM::PrimClex::refresh (bool read_settings=false, bool read_composition=false, bool read_chem_ref=false, bool read_configs=false, bool clear_clex=false)
 Reload PrimClex data from settings. More...
 
std::string CASM::PrimClex::name () const
 Return project name. More...
 
const DirectoryStructure & CASM::PrimClex::dir () const
 
ProjectSettings & CASM::PrimClex::settings ()
 
const ProjectSettings & CASM::PrimClex::settings () const
 
double CASM::PrimClex::crystallography_tol () const
 
double CASM::PrimClex::lin_alg_tol () const
 
fs::path CASM::PrimClex::get_path () const
 Return casm project directory path. More...
 
fs::path CASM::PrimClex::get_path (const Index &scel_index) const
 Return supercell directory path. More...
 
fs::path CASM::PrimClex::get_path (const Index &scel_index, const Index &config_index) const
 Return configuration directory path. More...
 
fs::path CASM::PrimClex::get_config_list_path () const
 Return config_list.json file path. More...
 
bool CASM::PrimClex::has_composition_axes () const
 check if CompositionConverter object initialized More...
 
const CompositionConverter & CASM::PrimClex::composition_axes () const
 const Access CompositionConverter object More...
 
bool CASM::PrimClex::has_chemical_reference () const
 check if ChemicalReference object initialized More...
 
const ChemicalReference & CASM::PrimClex::chemical_reference () const
 const Access ChemicalReference object More...
 
const Structure & CASM::PrimClex::get_prim () const
 const Access to primitive Structure More...
 
PrimNeighborList & CASM::PrimClex::nlist () const
 Access to the primitive neighbor list. More...
 
bool CASM::PrimClex::vacancy_allowed () const
 returns true if vacancy are an allowed species More...
 
Index CASM::PrimClex::vacancy_index () const
 returns the index of vacancies in composition vectors More...
 
boost::container::stable_vector
< Supercell > & 		CASM::PrimClex::get_supercell_list ()
 Access entire supercell_list. More...
 
const
boost::container::stable_vector
< Supercell > & 		CASM::PrimClex::get_supercell_list () const
 const Access entire supercell_list More...
 
const Supercell & CASM::PrimClex::get_supercell (Index i) const
 const Access supercell by index More...
 
Supercell & CASM::PrimClex::get_supercell (Index i)
 Access supercell by index. More...
 
const Supercell & CASM::PrimClex::get_supercell (std::string scellname) const
 const Access supercell by name More...
 
Supercell & CASM::PrimClex::get_supercell (std::string scellname)
 Access supercell by name. More...
 
Supercell & CASM::PrimClex::get_supercell (const Lattice &lat)
 Access supercell by Lattice, adding if necessary. More...
 
const Configuration & CASM::PrimClex::configuration (const std::string &configname) const
 access configuration by name (of the form "scellname/[NUMBER]", e.g., ("SCEL1_1_1_1_0_0_0/0") More...
 
Configuration & CASM::PrimClex::configuration (const std::string &configname)
 
config_iterator CASM::PrimClex::config_begin ()
 Configuration iterator: begin. More...
 
config_iterator CASM::PrimClex::config_end ()
 Configuration iterator: end. More...
 
config_const_iterator CASM::PrimClex::config_begin () const
 Configuration iterator: begin. More...
 
config_const_iterator CASM::PrimClex::config_end () const
 Configuration iterator: end. More...
 
config_const_iterator CASM::PrimClex::config_cbegin () const
 const Configuration iterator: begin More...
 
config_const_iterator CASM::PrimClex::config_cend () const
 const Configuration iterator: end More...
 
config_iterator CASM::PrimClex::selected_config_begin ()
 Configuration iterator: begin. More...
 
config_iterator CASM::PrimClex::selected_config_end ()
 Configuration iterator: end. More...
 
config_const_iterator CASM::PrimClex::selected_config_cbegin () const
 const Configuration iterator: begin More...
 
config_const_iterator CASM::PrimClex::selected_config_cend () const
 const Configuration iterator: end More...
 
Eigen::MatrixXd CASM::PrimClex::shift_vectors () const
 private: More...
 
void CASM::PrimClex::set_composition_axes (const CompositionConverter &_converter)
 Sets the composition axes. More...
 
void CASM::PrimClex::write_config_list (std::set< std::string > scel_to_delete={})
 
void CASM::PrimClex::generate_supercells (const ScelEnumProps &enum_props)
 Use the given CSPECS. More...
 
void CASM::PrimClex::print_enum_info (std::ostream &stream)
 
void CASM::PrimClex::print_supercells (std::set< std::string > scel_to_delete={}) const
 
void CASM::PrimClex::print_supercells (std::ostream &stream, std::set< std::string > scel_to_delete={}) const
 
void CASM::PrimClex::read_supercells (std::istream &stream)
 
void CASM::PrimClex::print_clex_configurations ()
 
void CASM::PrimClex::read_config_list ()
 
void CASM::PrimClex::read_scel_props (int scel_index, const std::string &JSON_output)
 Fill up props of every configuration for a partucluar supercell. This will be deprecated when props disappears. More...
 
void CASM::PrimClex::read_all_scel_props (const std::string &JSON_output)
 Call read_config_props on every Supercell. More...
 
int CASM::PrimClex::amount_selected () const
 Count over the number of configurations that are selected in all supercells. More...
 
bool CASM::PrimClex::contains_supercell (std::string scellname, Index &index) const
 
bool CASM::PrimClex::contains_supercell (const Supercell &scel) const
 
bool CASM::PrimClex::contains_supercell (const Supercell &scel, Index &index) const
 
Index CASM::PrimClex::add_supercell (const Lattice &superlat)
 
Index CASM::PrimClex::add_canonical_supercell (const Lattice &superlat)
 
Eigen::Matrix3i CASM::PrimClex::calc_transf_mat (const Lattice &superlat) const
 
void CASM::PrimClex::set_global_dof_state (const Configuration &curr_config) const
 Set internal values of each DoFEnvironment. More...
 
void CASM::PrimClex::set_local_dof_state (const Configuration &curr_config, Index l) const
 
bool CASM::PrimClex::has_orbitree (const ClexDescription &key) const
 const Access to global orbitree More...
 
const SiteOrbitree & CASM::PrimClex::orbitree (const ClexDescription &key) const
 
bool CASM::PrimClex::has_clexulator (const ClexDescription &key) const
 
Clexulator CASM::PrimClex::clexulator (const ClexDescription &key) const
 
bool CASM::PrimClex::has_eci (const ClexDescription &key) const
 
const ECIContainer & CASM::PrimClex::eci (const ClexDescription &key) const
 
void CASM::PrimClex::_init ()
 Initialization routines. More...
 
SiteOrbitree CASM::make_orbitree (Structure &prim, const jsonParser &json, double _tol)
 Make orbitree. For now specifically global. More...
 
void CASM::print_clexulator (const Structure &prim, SiteOrbitree &tree, const PrimNeighborList &nlist, std::string class_name, std::ostream &stream, double xtal_tol)
 Print clexulator. More...
 

Variables

fs::path CASM::PrimClex::root
 
DirectoryStructure CASM::PrimClex::m_dir
 
ProjectSettings CASM::PrimClex::m_settings
 
Structure CASM::PrimClex::prim
 
bool CASM::PrimClex::m_vacancy_allowed
 
Index CASM::PrimClex::m_vacancy_index
 
DoFManager CASM::PrimClex::m_dof_manager
 
boost::container::stable_vector
< Supercell > 		CASM::PrimClex::supercell_list
 Contains all the supercells that were involved in the enumeration. More...
 
bool CASM::PrimClex::m_has_composition_axes = false
 
CompositionConverter CASM::PrimClex::m_comp_converter
 
notstd::cloneable_ptr
< ChemicalReference > 		CASM::PrimClex::m_chem_ref
 
notstd::cloneable_ptr
< PrimNeighborList > 		CASM::PrimClex::m_nlist
 
std::map< ClexDescription,
SiteOrbitree > 		CASM::PrimClex::m_orbitree
 
std::map< ClexDescription,
Clexulator > 		CASM::PrimClex::m_clexulator
 
std::map< ClexDescription,
ECIContainer > 		CASM::PrimClex::m_eci
 

Typedef Documentation

typedef ConfigIterator<const Configuration, const PrimClex> CASM::PrimClex::config_const_iterator

Definition at line 86 of file PrimClex.hh.

typedef ConfigIterator<Configuration, PrimClex> CASM::PrimClex::config_iterator

Definition at line 85 of file PrimClex.hh.

Function Documentation

void CASM::PrimClex::_init ( )
private

Initialization routines.

Initialization routines

  • If !root.empty(), read all saved data to generate all Supercells and Configurations, etc.

Definition at line 49 of file PrimClex.cc.

Index CASM::PrimClex::add_canonical_supercell ( const Lattice &  superlat)

add a supercell if it doesn't already exist return the index of the supercell in supercell_list

TODO: Check to see if superlat is linear combination of previously enumerated Supercell. You'll have to transform the coordinates if you're trying to import something with a supercell that already exists. Should return operations involved. If supercell doesn't exist add it as it is without transforming

Definition at line 511 of file PrimClex.cc.

Index CASM::PrimClex::add_supercell ( const Lattice &  superlat)

add a supercell if it doesn't already exist return the index of the supercell in supercell_list

Unlike the initial version above this, this routine will use an Array of SymOps (probably the point group of the lattice) to determine whether the provided superlat is equivalent to a Supercell in the PrimClex list. It will then populate the transformation matrix that maps the passed lattice onto the one on the list (i.e. the one on on the list is treated as 'primitive'). If it doesn't map, then the matrix gets flattened to zeros.

This routine should replace the original one once it converges to something people can agree on.

Definition at line 550 of file PrimClex.cc.

int CASM::PrimClex::amount_selected ( ) const

Count over the number of configurations that are selected in all supercells.

Definition at line 700 of file PrimClex.cc.

Eigen::Matrix3i CASM::PrimClex::calc_transf_mat ( const Lattice &  superlat) const

Definition at line 731 of file PrimClex.cc.

const ChemicalReference & CASM::PrimClex::chemical_reference ( ) const

const Access ChemicalReference object

Definition at line 251 of file PrimClex.cc.

Clexulator CASM::PrimClex::clexulator ( const ClexDescription &  key) const

Definition at line 1030 of file PrimClex.cc.

const CompositionConverter & CASM::PrimClex::composition_axes ( ) const

const Access CompositionConverter object

Definition at line 237 of file PrimClex.cc.

PrimClex::config_iterator CASM::PrimClex::config_begin ( )

Configuration iterator: begin.

Definition at line 371 of file PrimClex.cc.

PrimClex::config_const_iterator CASM::PrimClex::config_begin ( ) const

Configuration iterator: begin.

const Configuration iterator: begin

Definition at line 385 of file PrimClex.cc.

PrimClex::config_const_iterator CASM::PrimClex::config_cbegin ( ) const

const Configuration iterator: begin

Definition at line 399 of file PrimClex.cc.

PrimClex::config_const_iterator CASM::PrimClex::config_cend ( ) const

const Configuration iterator: end

Definition at line 407 of file PrimClex.cc.

PrimClex::config_iterator CASM::PrimClex::config_end ( )

Configuration iterator: end.

Definition at line 379 of file PrimClex.cc.

PrimClex::config_const_iterator CASM::PrimClex::config_end ( ) const

Configuration iterator: end.

const Configuration iterator: end

Definition at line 393 of file PrimClex.cc.

const Configuration & CASM::PrimClex::configuration ( const std::string &  configname) const

access configuration by name (of the form "scellname/[NUMBER]", e.g., ("SCEL1_1_1_1_0_0_0/0")

Definition at line 347 of file PrimClex.cc.

Configuration & CASM::PrimClex::configuration ( const std::string &  configname)

Definition at line 365 of file PrimClex.cc.

bool CASM::PrimClex::contains_supercell ( std::string  scellname,
Index &  index 
) const

Definition at line 709 of file PrimClex.cc.

bool CASM::PrimClex::contains_supercell ( const Supercell &  scel) const

Definition at line 721 of file PrimClex.cc.

bool CASM::PrimClex::contains_supercell ( const Supercell &  scel,
Index &  index 
) const

Definition at line 726 of file PrimClex.cc.

double CASM::PrimClex::crystallography_tol ( ) const
inline

Definition at line 124 of file PrimClex.hh.

const DirectoryStructure& CASM::PrimClex::dir ( ) const
inline

Definition at line 112 of file PrimClex.hh.

const ECIContainer & CASM::PrimClex::eci ( const ClexDescription &  key) const

Definition at line 1076 of file PrimClex.cc.

void CASM::PrimClex::generate_supercells ( const ScelEnumProps &  enum_props)

Use the given CSPECS.

Generate supercells of a certain volume and shape and store them in the array of supercells.

Generate supercells of a certain volume and shape and store them in the array of supercells

Parameters
enum_propsAn ScelEnumProps instance, see constructor for details

Definition at line 492 of file PrimClex.cc.

fs::path CASM::PrimClex::get_config_list_path ( ) const

Return config_list.json file path.

Definition at line 220 of file PrimClex.cc.

fs::path CASM::PrimClex::get_path ( ) const

Return casm project directory path.

Definition at line 202 of file PrimClex.cc.

fs::path CASM::PrimClex::get_path ( const Index &  scel_index) const

Return supercell directory path.

Definition at line 208 of file PrimClex.cc.

fs::path CASM::PrimClex::get_path ( const Index &  scel_index,
const Index &  config_index 
) const

Return configuration directory path.

Definition at line 214 of file PrimClex.cc.

const Structure & CASM::PrimClex::get_prim ( ) const

const Access to primitive Structure

Definition at line 260 of file PrimClex.cc.

const Supercell & CASM::PrimClex::get_supercell ( Index  i) const

const Access supercell by index

Definition at line 311 of file PrimClex.cc.

Supercell & CASM::PrimClex::get_supercell ( Index  i)

Access supercell by index.

Definition at line 317 of file PrimClex.cc.

const Supercell & CASM::PrimClex::get_supercell ( std::string  scellname) const

const Access supercell by name

Definition at line 323 of file PrimClex.cc.

Supercell & CASM::PrimClex::get_supercell ( std::string  scellname)

Access supercell by name.

Definition at line 335 of file PrimClex.cc.

Supercell & CASM::PrimClex::get_supercell ( const Lattice &  lat)

Access supercell by Lattice, adding if necessary.

Definition at line 341 of file PrimClex.cc.

boost::container::stable_vector< Supercell > & CASM::PrimClex::get_supercell_list ( )

Access entire supercell_list.

const Access entire supercell_list

Definition at line 299 of file PrimClex.cc.

const boost::container::stable_vector< Supercell > & CASM::PrimClex::get_supercell_list ( ) const

const Access entire supercell_list

Definition at line 305 of file PrimClex.cc.

bool CASM::PrimClex::has_chemical_reference ( ) const

check if ChemicalReference object initialized

Definition at line 245 of file PrimClex.cc.

bool CASM::PrimClex::has_clexulator ( const ClexDescription &  key) const

Definition at line 1018 of file PrimClex.cc.

bool CASM::PrimClex::has_composition_axes ( ) const

check if CompositionConverter object initialized

const Access CompositionConverter object

Definition at line 231 of file PrimClex.cc.

bool CASM::PrimClex::has_eci ( const ClexDescription &  key) const

Definition at line 1065 of file PrimClex.cc.

bool CASM::PrimClex::has_orbitree ( const ClexDescription &  key) const

const Access to global orbitree

Delete 'properties.ref_state.X.json' files, Then call 'clear_reference_properties' Sets the root reference state to be the calculated properties of the chosen config Calls 'clear_reference_properties' Check that it is valid to use 'config' as reference state 'refid', returns bool and if false, sets 'reason_invalid' Currently checks: 1) that the necessary properties have been calculated, 2) that the same Configuration is not being used twice Needs to check that reference states span composition space find calculated configurations closest to [0, 0, 0, ...], [1, 0, 0, ...], [0, 1, 0, ...], [0, 0, 1, ...], ... and set them as the root reference states, also calls regenerate_references Clears reference states and properties whether or not it succeeds Clear 'reference' and 'delta' properties from all Configurations Re-write all Configurations, updating: param_composition.json properties.calc.json properties.ref.json properties.delta.json

Definition at line 983 of file PrimClex.cc.

double CASM::PrimClex::lin_alg_tol ( ) const
inline

Definition at line 128 of file PrimClex.hh.

SiteOrbitree CASM::make_orbitree ( Structure &  prim,
const jsonParser &  json,
double  _tol 
)

Make orbitree. For now specifically global.

Parameters
primPrimitive Structure. non-const due to Structure::set_site_internals.
jsonbspecs.json file

Definition at line 1097 of file PrimClex.cc.

std::string CASM::PrimClex::name ( ) const

Return project name.

Definition at line 194 of file PrimClex.cc.

PrimNeighborList & CASM::PrimClex::nlist ( ) const

Access to the primitive neighbor list.

Definition at line 266 of file PrimClex.cc.

const SiteOrbitree & CASM::PrimClex::orbitree ( const ClexDescription &  key) const

Definition at line 996 of file PrimClex.cc.

CASM::PrimClex::PrimClex ( const Structure &  _prim,
const Logging &  logging = Logging() 
)

Initial construction of a PrimClex, from a primitive Structure.

Definition at line 21 of file PrimClex.cc.

CASM::PrimClex::PrimClex ( const fs::path &  _root,
const Logging &  logging = Logging() 
)

Construct PrimClex from existing CASM project directory

  • read PrimClex and directory structure to generate all its Supercells and Configurations, etc.

Definition at line 36 of file PrimClex.cc.

void CASM::PrimClex::print_clex_configurations ( )
void CASM::print_clexulator ( const Structure &  prim,
SiteOrbitree &  tree,
const PrimNeighborList &  nlist,
std::string  class_name,
std::ostream &  stream,
double  xtal_tol 
)

Print clexulator.

Definition at line 1219 of file PrimClex.cc.

void CASM::PrimClex::print_enum_info ( std::ostream &  stream)
void CASM::PrimClex::print_supercells ( std::set< std::string >  scel_to_delete = {}) const

Definition at line 557 of file PrimClex.cc.

void CASM::PrimClex::print_supercells ( std::ostream &  stream,
std::set< std::string >  scel_to_delete = {} 
) const

Definition at line 593 of file PrimClex.cc.

void CASM::PrimClex::read_all_scel_props ( const std::string &  JSON_output)

Call read_config_props on every Supercell.

void CASM::PrimClex::read_config_list ( )

Read the config_list file at 'file_name' and adds config to supercell, assuming it is already canonical. If 'print_dirs', call Supercell::print_clex_configuration() for each config to be made.

Definition at line 680 of file PrimClex.cc.

void CASM::PrimClex::read_scel_props ( int  scel_index,
const std::string &  JSON_output 
)

Fill up props of every configuration for a partucluar supercell. This will be deprecated when props disappears.

void CASM::PrimClex::read_supercells ( std::istream &  stream)

Definition at line 605 of file PrimClex.cc.

void CASM::PrimClex::refresh ( bool  read_settings = false,
bool  read_composition = false,
bool  read_chem_ref = false,
bool  read_configs = false,
bool  clear_clex = false 
)

Reload PrimClex data from settings.

Parameters
read_settingsRead project_settings.json and plugins
read_compositionRead composition_axes.json
read_chem_refRead chemical_reference.json
read_configsRead SCEL and config_list.json
clear_clexClear stored orbitrees, clexulators, and eci
  • This does not check if what you request will cause problems.
  • ToDo: refactor into separate functions

Definition at line 90 of file PrimClex.cc.

PrimClex::config_iterator CASM::PrimClex::selected_config_begin ( )

Configuration iterator: begin.

Definition at line 413 of file PrimClex.cc.

PrimClex::config_const_iterator CASM::PrimClex::selected_config_cbegin ( ) const

const Configuration iterator: begin

Definition at line 430 of file PrimClex.cc.

PrimClex::config_const_iterator CASM::PrimClex::selected_config_cend ( ) const

const Configuration iterator: end

Definition at line 438 of file PrimClex.cc.

PrimClex::config_iterator CASM::PrimClex::selected_config_end ( )

Configuration iterator: end.

Definition at line 424 of file PrimClex.cc.

void CASM::PrimClex::set_composition_axes ( const CompositionConverter &  _converter)

Sets the composition axes.

Sets the composition axes, updates all configuration references, and writes the updated configuration info

Also:

  • updates all configuration references,
  • writes the updated configuration info
  • does not update composition_axes file

Definition at line 749 of file PrimClex.cc.

void CASM::PrimClex::set_global_dof_state ( const Configuration &  curr_config) const
inline

Set internal values of each DoFEnvironment.

Definition at line 293 of file PrimClex.hh.

void CASM::PrimClex::set_local_dof_state ( const Configuration &  curr_config,
Index  l 
) const
inline

Definition at line 297 of file PrimClex.hh.

ProjectSettings& CASM::PrimClex::settings ( )
inline

Definition at line 116 of file PrimClex.hh.

const ProjectSettings& CASM::PrimClex::settings ( ) const
inline

Definition at line 120 of file PrimClex.hh.

Eigen::MatrixXd CASM::PrimClex::shift_vectors ( ) const

private:

Definition at line 973 of file PrimClex.cc.

bool CASM::PrimClex::vacancy_allowed ( ) const

returns true if vacancy are an allowed species

Definition at line 284 of file PrimClex.cc.

Index CASM::PrimClex::vacancy_index ( ) const

returns the index of vacancies in composition vectors

Definition at line 290 of file PrimClex.cc.

void CASM::PrimClex::write_config_list ( std::set< std::string >  scel_to_delete = {})

Call Configuration::write on every configuration to update files

  • call update to also read all files

Re-write config_list.json, excluding specified scel

Definition at line 450 of file PrimClex.cc.

Variable Documentation

notstd::cloneable_ptr<ChemicalReference> CASM::PrimClex::m_chem_ref
private

ChemicalReference specifies a reference for formation energies, chemical potentials, etc.

Definition at line 76 of file PrimClex.hh.

std::map<ClexDescription, Clexulator> CASM::PrimClex::m_clexulator
mutableprivate

Definition at line 345 of file PrimClex.hh.

CompositionConverter CASM::PrimClex::m_comp_converter
private

Definition at line 72 of file PrimClex.hh.

DirectoryStructure CASM::PrimClex::m_dir
private

Definition at line 56 of file PrimClex.hh.

DoFManager CASM::PrimClex::m_dof_manager
mutableprivate

Definition at line 63 of file PrimClex.hh.

std::map<ClexDescription, ECIContainer> CASM::PrimClex::m_eci
mutableprivate

Definition at line 346 of file PrimClex.hh.

bool CASM::PrimClex::m_has_composition_axes = false
private

CompositionConverter specifies parameteric composition axes and converts between parametric composition and mol composition

Definition at line 71 of file PrimClex.hh.

notstd::cloneable_ptr<PrimNeighborList> CASM::PrimClex::m_nlist
mutableprivate

Stores the neighboring UnitCell and which sublattices to include in neighbor lists

  • mutable for lazy construction

Definition at line 80 of file PrimClex.hh.

std::map<ClexDescription, SiteOrbitree> CASM::PrimClex::m_orbitree
mutableprivate

Definition at line 344 of file PrimClex.hh.

ProjectSettings CASM::PrimClex::m_settings
private

Definition at line 57 of file PrimClex.hh.

bool CASM::PrimClex::m_vacancy_allowed
private

Definition at line 60 of file PrimClex.hh.

Index CASM::PrimClex::m_vacancy_index
private

Definition at line 61 of file PrimClex.hh.

Structure CASM::PrimClex::prim
private

Definition at line 59 of file PrimClex.hh.

fs::path CASM::PrimClex::root
private

Definition at line 54 of file PrimClex.hh.

boost::container::stable_vector< Supercell > CASM::PrimClex::supercell_list
private

Contains all the supercells that were involved in the enumeration.

Definition at line 66 of file PrimClex.hh.