pycalphad.io package¶
Submodules¶
pycalphad.io.cs_dat module¶
Support for reading ChemSage DAT files.
- class pycalphad.io.cs_dat.AdditionalCoefficientPair(coefficient: float, exponent: float)[source]¶
Bases:
object
- coefficient: float¶
- exponent: float¶
- class pycalphad.io.cs_dat.Endmember(species_name: str, gibbs_eq_type: str, stoichiometry_pure_elements: List[float], intervals: List[pycalphad.io.cs_dat.IntervalBase])[source]¶
Bases:
object
- expr(indices)[source]¶
Return a Piecewise (in temperature) energy expression for this endmember (i.e. only the data from the energy intervals)
- gibbs_eq_type: str¶
- insert(dbf: Database, phase_name: str, constituent_array: List[List[str]], gibbs_coefficient_idxs: List[int])[source]¶
- intervals: List[IntervalBase]¶
- species(pure_elements) List[Species] [source]¶
Return an unordered list of Species objects detected in this endmember
- species_name: str¶
- stoichiometry_pure_elements: List[float]¶
- class pycalphad.io.cs_dat.EndmemberAqueous(species_name: str, gibbs_eq_type: str, stoichiometry_pure_elements: List[float], intervals: List[pycalphad.io.cs_dat.IntervalBase], charge: float)[source]¶
Bases:
Endmember
- charge: float¶
- class pycalphad.io.cs_dat.EndmemberMagnetic(species_name: str, gibbs_eq_type: str, stoichiometry_pure_elements: List[float], intervals: List[pycalphad.io.cs_dat.IntervalBase], curie_temperature: float, magnetic_moment: float)[source]¶
Bases:
Endmember
- curie_temperature: float¶
- insert(dbf: Database, phase_name: str, pure_elements: List[str], gibbs_coefficient_idxs: List[int])[source]¶
- magnetic_moment: float¶
- class pycalphad.io.cs_dat.EndmemberQKTO(species_name: str, gibbs_eq_type: str, stoichiometry_pure_elements: List[float], intervals: List[pycalphad.io.cs_dat.IntervalBase], stoichiometric_factor: float, chemical_group: int)[source]¶
Bases:
Endmember
- chemical_group: int¶
- insert(dbf: Database, phase_name: str, constituent_array: List[List[str]], gibbs_coefficient_idxs: List[int])[source]¶
- stoichiometric_factor: float¶
- class pycalphad.io.cs_dat.EndmemberRealGas(species_name: str, gibbs_eq_type: str, stoichiometry_pure_elements: List[float], intervals: List[pycalphad.io.cs_dat.IntervalBase], Tc: float, Pc: float, Vc: float, acentric_factor: float, dipole_moment: float)[source]¶
Bases:
Endmember
- Pc: float¶
- Tc: float¶
- Vc: float¶
- acentric_factor: float¶
- dipole_moment: float¶
- class pycalphad.io.cs_dat.ExcessBase(interacting_species_idxs: List[int])[source]¶
Bases:
object
- constituent_array(phase_constituents: List[List[str]]) List[List[str]] [source]¶
Return the constituent array of this interaction using the entire phase sublattice model.
This doesn’t take into account any re-ordering of the phase_constituents or interacting_species_idxs. All mapping on to proper v.Species objects occurs in Database.add_parameter.
Examples
>>> phase_constituents = [['A'], ['A', 'B'], ['A', 'B', 'C']] >>> ex = ExcessBase([1, 2, 4, 6]) >>> ix_const_arr = ex.constituent_array(phase_constituents) >>> assert ix_const_arr == [['A'], ['A'], ['A', 'C']]
- insert(dbf: Database, phase_name: str, phase_constituents: List[List[str]], excess_coefficient_idxs: List[int])[source]¶
- interacting_species_idxs: List[int]¶
- class pycalphad.io.cs_dat.ExcessQKTO(interacting_species_idxs: List[int], exponents: List[int], coefficients: List[float])[source]¶
Bases:
ExcessBase
- coefficients: List[float]¶
- exponents: List[int]¶
- class pycalphad.io.cs_dat.ExcessRKM(interacting_species_idxs: List[int], parameter_order: int, coefficients: List[float])[source]¶
Bases:
ExcessBase
Examples
>>> assert ExcessRKM([1, 2, 3, 4], 0, [0])._map_const_idxs_to_subl_idxs([2, 3]) == [[0, 1], [0, 1]] >>> assert ExcessRKM([1, 3, 4], 0, [0])._map_const_idxs_to_subl_idxs([2, 3]) == [[0], [0, 1]] >>> assert ExcessRKM([1, 2], 0, [0])._map_const_idxs_to_subl_idxs([4]) == [[0, 1]] >>> assert ExcessRKM([1, 2, 3], 0, [0])._map_const_idxs_to_subl_idxs([3]) == [[0, 1, 2]] >>> assert ExcessRKM([1, 2, 3, 4], 0, [0])._map_const_idxs_to_subl_idxs([1, 1, 2]) == [[0], [0], [0, 1]]
- coefficients: List[float]¶
- insert(dbf: Database, phase_name: str, phase_constituents: List[List[str]], excess_coefficient_idxs: List[int])[source]¶
Requires all Species in dbf.species to be defined.
- parameter_order: int¶
- class pycalphad.io.cs_dat.ExcessRKMMagnetic(interacting_species_idxs: List[int], parameter_order: int, curie_temperature: float, magnetic_moment: float)[source]¶
Bases:
ExcessBase
- curie_temperature: float¶
- insert(dbf: Database, phase_name: str, phase_constituents: List[List[str]], excess_coefficient_idxs: List[int])[source]¶
Requires all Species in dbf.species to be defined.
- magnetic_moment: float¶
- parameter_order: int¶
- class pycalphad.io.cs_dat.Header(list_soln_species_count: List[int], num_stoich_phases: int, pure_elements: List[str], pure_elements_mass: List[float], gibbs_coefficient_idxs: List[int], excess_coefficient_idxs: List[int])[source]¶
Bases:
object
- excess_coefficient_idxs: List[int]¶
- gibbs_coefficient_idxs: List[int]¶
- list_soln_species_count: List[int]¶
- num_stoich_phases: int¶
- pure_elements: List[str]¶
- pure_elements_mass: List[float]¶
- class pycalphad.io.cs_dat.IntervalCP(T_max: float, H298: float, S298: float, CP_coefficients: float, H_trans: float, additional_coeff_pairs: List[pycalphad.io.cs_dat.AdditionalCoefficientPair], PTVm_terms: List[pycalphad.io.cs_dat.PTVmTerms])[source]¶
Bases:
IntervalBase
- CP_coefficients: float¶
- H298: float¶
- H_trans: float¶
- S298: float¶
- additional_coeff_pairs: List[AdditionalCoefficientPair]¶
- class pycalphad.io.cs_dat.IntervalG(T_max: float, coefficients: List[float], additional_coeff_pairs: List[pycalphad.io.cs_dat.AdditionalCoefficientPair], PTVm_terms: List[pycalphad.io.cs_dat.PTVmTerms])[source]¶
Bases:
IntervalBase
- additional_coeff_pairs: List[AdditionalCoefficientPair]¶
- coefficients: List[float]¶
- class pycalphad.io.cs_dat.PhaseBase(phase_name: str, phase_type: str, endmembers: List[pycalphad.io.cs_dat.Endmember])[source]¶
Bases:
object
- insert(dbf: Database, pure_elements: List[str], gibbs_coefficient_idxs: List[int], excess_coefficient_idxs: List[int])[source]¶
Enter this phase and its parameters into the Database.
This method should call:
dbf.add_phase
dbf.structure_entry
dbf.add_phase_constituents
dbf.add_parameter for all parameters
- phase_name: str¶
- phase_type: str¶
- class pycalphad.io.cs_dat.Phase_Aqueous(phase_name: str, phase_type: str, endmembers: List[pycalphad.io.cs_dat.EndmemberAqueous])[source]¶
Bases:
PhaseBase
- endmembers: List[EndmemberAqueous]¶
- class pycalphad.io.cs_dat.Phase_CEF(phase_name: str, phase_type: str, endmembers: List[pycalphad.io.cs_dat.Endmember], subl_ratios: List[float], constituent_array: List[List[str]], endmember_constituent_idxs: List[List[int]], excess_parameters: List[pycalphad.io.cs_dat.ExcessBase], magnetic_afm_factor: float | None, magnetic_structure_factor: float | None)[source]¶
Bases:
PhaseBase
- constituent_array: List[List[str]]¶
- endmember_constituent_idxs: List[List[int]]¶
- excess_parameters: List[ExcessBase]¶
- insert(dbf: Database, pure_elements: List[str], gibbs_coefficient_idxs: List[int], excess_coefficient_idxs: List[int])[source]¶
Enter this phase and its parameters into the Database.
This method should call:
dbf.add_phase
dbf.structure_entry
dbf.add_phase_constituents
dbf.add_parameter for all parameters
- magnetic_afm_factor: float | None¶
- magnetic_structure_factor: float | None¶
- subl_ratios: List[float]¶
- class pycalphad.io.cs_dat.Phase_RealGas(phase_name: str, phase_type: str, endmembers: List[pycalphad.io.cs_dat.EndmemberRealGas])[source]¶
Bases:
PhaseBase
- endmembers: List[EndmemberRealGas]¶
- class pycalphad.io.cs_dat.Phase_SUBQ(phase_name: str, phase_type: str, endmembers: List[pycalphad.io.cs_dat.Endmember], num_pairs: int, num_quadruplets: int, num_subl_1_const: int, num_subl_2_const: int, subl_1_const: List[str], subl_2_const: List[str], subl_1_charges: List[float], subl_1_chemical_groups: List[int], subl_2_charges: List[float], subl_2_chemical_groups: List[int], subl_const_idx_pairs: List[Tuple[int, int]], quadruplets: List[pycalphad.io.cs_dat.SUBQQuadrupletCoordinations], excess_parameters: List[pycalphad.io.cs_dat.SUBQExcessQuadruplet], chemical_group_overrides: List[str])[source]¶
Bases:
PhaseBase
- chemical_group_overrides: List[str]¶
- excess_parameters: List[SUBQExcessQuadruplet]¶
- insert(dbf: Database, pure_elements: List[str], gibbs_coefficient_idxs: List[int], excess_coefficient_idxs: List[int])[source]¶
Enter this phase and its parameters into the Database.
This method should call:
dbf.add_phase
dbf.structure_entry
dbf.add_phase_constituents
dbf.add_parameter for all parameters
- num_pairs: int¶
- num_quadruplets: int¶
- num_subl_1_const: int¶
- num_subl_2_const: int¶
- quadruplets: List[SUBQQuadrupletCoordinations]¶
- subl_1_charges: List[float]¶
- subl_1_chemical_groups: List[int]¶
- subl_1_const: List[str]¶
- subl_2_charges: List[float]¶
- subl_2_chemical_groups: List[int]¶
- subl_2_const: List[str]¶
- subl_const_idx_pairs: List[Tuple[int, int]]¶
- class pycalphad.io.cs_dat.Phase_Stoichiometric(phase_name: str, phase_type: str, endmembers: List[pycalphad.io.cs_dat.Endmember], magnetic_afm_factor: float | None, magnetic_structure_factor: float | None)[source]¶
Bases:
PhaseBase
- insert(dbf: Database, pure_elements: List[str], gibbs_coefficient_idxs: List[int], excess_coefficient_idxs: List[int])[source]¶
Enter this phase and its parameters into the Database.
This method should call:
dbf.add_phase
dbf.structure_entry
dbf.add_phase_constituents
dbf.add_parameter for all parameters
- magnetic_afm_factor: float | None¶
- magnetic_structure_factor: float | None¶
- class pycalphad.io.cs_dat.SUBQExcessQuadruplet(mixing_type: int, mixing_code: str, mixing_const: List[int], mixing_exponents: List[int], metadata: List[float], additional_cation_mixing_const: int, additional_anion_mixing_const: int, excess_coeffs: List[float])[source]¶
Bases:
object
- additional_anion_mixing_const: int¶
- additional_cation_mixing_const: int¶
- excess_coeffs: List[float]¶
- insert(dbf: Database, phase_name: str, As: List[str], Xs: List[str], excess_coeff_indices: List[int])[source]¶
- metadata: List[float]¶
- mixing_code: str¶
- mixing_const: List[int]¶
- mixing_exponents: List[int]¶
- mixing_type: int¶
- class pycalphad.io.cs_dat.SUBQPair(species_name: str, gibbs_eq_type: str, stoichiometry_pure_elements: List[float], intervals: List[pycalphad.io.cs_dat.IntervalBase], stoichiometry_quadruplet: List[float], zeta: float)[source]¶
Bases:
Endmember
- insert(dbf: Database, phase_name: str, constituent_array: List[str], gibbs_coefficient_idxs: List[int])[source]¶
- stoichiometry_quadruplet: List[float]¶
- zeta: float¶
- class pycalphad.io.cs_dat.SUBQQuadrupletCoordinations(quadruplet_idxs: List[int], quadruplet_coordinations: List[float])[source]¶
Bases:
object
- insert(dbf: Database, phase_name: str, As: List[str], Xs: List[str])[source]¶
Add a Z_i_AB:XY parameter for each species defined in the quadruplet
- quadruplet_coordinations: List[float]¶
- quadruplet_idxs: List[int]¶
- exception pycalphad.io.cs_dat.TokenParserError[source]¶
Bases:
Exception
Exception raised when the TokenParser hits a parsing error.
- pycalphad.io.cs_dat.parse_PTVm_terms(toks: TokenParser) PTVmTerms [source]¶
- pycalphad.io.cs_dat.parse_additional_terms(toks: TokenParser) List[AdditionalCoefficientPair] [source]¶
- pycalphad.io.cs_dat.parse_endmember(toks: TokenParser, num_pure_elements, num_gibbs_coeffs, is_stoichiometric=False)[source]¶
- pycalphad.io.cs_dat.parse_endmember_aqueous(toks: TokenParser, num_pure_elements: int, num_gibbs_coeffs: int)[source]¶
- pycalphad.io.cs_dat.parse_endmember_qkto(toks: TokenParser, num_pure_elements: int, num_gibbs_coeffs: int)[source]¶
- pycalphad.io.cs_dat.parse_endmember_subq(toks: TokenParser, num_pure_elements, num_gibbs_coeffs, zeta=None)[source]¶
- pycalphad.io.cs_dat.parse_header(toks: TokenParser) Header [source]¶
- pycalphad.io.cs_dat.parse_interval_Gibbs(toks: TokenParser, num_gibbs_coeffs, has_additional_terms, has_PTVm_terms) IntervalG [source]¶
- pycalphad.io.cs_dat.parse_interval_heat_capacity(toks: TokenParser, num_gibbs_coeffs, H298, S298, has_H_trans, has_additional_terms, has_PTVm_terms) IntervalCP [source]¶
- pycalphad.io.cs_dat.parse_phase(toks, num_pure_elements, num_gibbs_coeffs, num_excess_coeffs, num_const)[source]¶
Dispatches to the correct parser depending on the phase type
- pycalphad.io.cs_dat.parse_phase_aqueous(toks, phase_name, phase_type, num_pure_elements, num_gibbs_coeffs, num_const)[source]¶
- pycalphad.io.cs_dat.parse_phase_cef(toks, phase_name, phase_type, num_pure_elements, num_gibbs_coeffs, num_excess_coeffs, num_const)[source]¶
- pycalphad.io.cs_dat.parse_phase_real_gas(toks, phase_name, phase_type, num_pure_elements, num_gibbs_coeffs, num_const)[source]¶
- pycalphad.io.cs_dat.parse_phase_subq(toks, phase_name, phase_type, num_pure_elements, num_gibbs_coeffs, num_excess_coeffs)[source]¶
- pycalphad.io.cs_dat.read_cs_dat(dbf: Database, fd)[source]¶
Parse a ChemSage DAT file into a pycalphad Database object.
- Parameters:
dbf (Database) – A pycalphad Database.
fd (file-like) – File descriptor.
pycalphad.io.database module¶
The database module provides support for reading and writing data types associated with structured thermodynamic/kinetic data.
- class pycalphad.io.database.Database(*args)[source]¶
Bases:
object
Structured thermodynamic and/or kinetic data.
- elements¶
Set of elements in database.
- Type:
set
- species¶
Set of species in database.
- Type:
set
- phases¶
Phase objects indexed by their system-local name.
- Type:
dict
- symbols¶
SymEngine objects indexed by their name (FUNCTIONs in Thermo-Calc).
- Type:
dict
- references¶
Reference objects indexed by their system-local identifier.
- Type:
dict
Examples
>>> mydb = Database(open('crfeni_mie.tdb')) >>> mydb = Database('crfeni_mie.tdb') >>> f = StringIO(u'$a complete TDB file as a string\n') >>> mydb = Database(f)
- add_parameter(param_type, phase_name, constituent_array, param_order, param, ref=None, diffusing_species=None, force_insert=True, **kwargs)[source]¶
Add a parameter.
- Parameters:
param_type (str) – Type name of the parameter, e.g., G, L, BMAGN.
phase_name (str) – Name of the phase.
constituent_array (list) – Configuration of the sublattices (elements and/or species).
param_order (int) – Polynomial order of the parameter.
param (object) – Abstract representation of the parameter, e.g., in SymEngine format.
ref (str, optional) – Reference for the parameter.
diffusing_species (str, optional) – (If kinetic parameter) Diffusing species for this parameter.
force_insert (bool, optional) – If True, inserts into the database immediately. False is a delayed insert (for performance).
kwargs (Any) – Additional metadata to insert into the parameter dictionary
Examples
None yet.
- add_phase(phase_name, model_hints, sublattices)[source]¶
Add a phase.
- Parameters:
phase_name (string) – System-local name of the phase.
model_hints (dict) – Structured “hints” for a Model trying to read this phase. Hints for major constituents and typedefs (Thermo-Calc) go here.
sublattices (list) – Site ratios of sublattices.
Examples
None yet.
- add_phase_constituents(phase_name, constituents)[source]¶
Add a phase.
- Parameters:
phase_name (string) – System-local name of the phase.
constituents (list) – Possible phase constituents (elements and/or species).
Examples
None yet.
- add_structure_entry(local_name, global_name)[source]¶
Define a relation between the system-local name of a phase and a “global” identifier. This is used to link crystallographically similar phases known by different colloquial names.
- Parameters:
local_name (string) – System-local name of the phase.
global_name (object) – Abstract representation of symbol, e.g., in SymEngine format.
Examples
None yet.
- static from_file(fname, fmt=None)[source]¶
Create a Database from a file.
- Parameters:
fname (str or file-like) – File name/descriptor to read.
fmt (str, optional) – File format. If not specified, an attempt at auto-detection is made.
- Returns:
dbf – Database from file.
- Return type:
Examples
None yet.
- classmethod from_string(data, **kwargs)[source]¶
Returns Database from a string in the specified format. This function is a wrapper for calling from_file with StringIO.
- Parameters:
data (str) – Raw database string in the specified format.
kwargs (optional) – See keyword arguments for from_file.
- Returns:
dbf
- Return type:
- process_parameter_queue()[source]¶
Process the queue of parameters so they are added to the TinyDB in one transaction. This avoids repeated (expensive) calls to insert().
- static register_format(fmt, read=None, write=None)[source]¶
Add support for reading and/or writing the specified format.
- Parameters:
fmt (str) – Format.
read (callable, optional) – Read function with arguments (Database, file_descriptor)
write (callable, optional) – Write function with arguments (Database, file_descriptor)
Examples
None yet.
- search(query)[source]¶
Search for parameters matching the specified query.
- Parameters:
query (object) – Structured database query in TinyDB format.
Examples
>>>> from tinydb import where >>>> db = Database() >>>> eid = db.add_parameter(…) #TODO >>>> db.search(where(‘eid’) == eid)
- to_file(fname, fmt=None, if_exists='raise', **write_kwargs)[source]¶
Write the Database to a file.
- Parameters:
fname (str or file-like) – File name/descriptor to write.
fmt (str, optional) – File format. If not specified, an attempt at auto-detection is made.
if_exists (string, optional ['raise', 'rename', 'overwrite']) – Strategy if ‘fname’ already exists. The ‘raise’ option (default) will raise a FileExistsError. The ‘rename’ option will append the date/time to the filename. The ‘overwrite’ option will overwrite the file. This argument is ignored if ‘fname’ is file-like.
write_kwargs (optional) – Keyword arguments to pass to write function.
Examples
None yet.
- exception pycalphad.io.database.DatabaseExportError[source]¶
Bases:
Exception
Raised when a database cannot be written.
- class pycalphad.io.database.DatabaseFormat(read, write)¶
Bases:
tuple
- read¶
Alias for field number 0
- write¶
Alias for field number 1
- class pycalphad.io.database.Phase[source]¶
Bases:
object
Phase in the database.
- name¶
System-local name of the phase.
- Type:
string
- constituents¶
Possible sublattice constituents (elements and/or species).
- Type:
tuple of frozenset
- sublattices¶
Site ratios of sublattices.
- Type:
list
- model_hints¶
Structured “hints” for a Model trying to read this phase. Hints for major constituents and typedefs (Thermo-Calc) go here.
- Type:
dict
pycalphad.io.grammar module¶
“Common pyparsing grammar patterns.
pycalphad.io.tdb module¶
The tdb module provides support for reading and writing databases in Thermo-Calc TDB format.
- class pycalphad.io.tdb.TCCommand(matchString, identChars=None)[source]¶
Bases:
CaselessKeyword
Parser element for dealing with Thermo-Calc command abbreviations.
- class pycalphad.io.tdb.TCPrinter(if_incompatible='warn')[source]¶
Bases:
object
Prints Thermo-Calc style function expressions.
- pycalphad.io.tdb.get_supported_variables()[source]¶
When loading databases, these symbols should be replaced by their IndependentPotential counterparts
- pycalphad.io.tdb.read_tdb(dbf, fd)[source]¶
Parse a TDB file into a pycalphad Database object.
- Parameters:
dbf (Database) – A pycalphad Database.
fd (file-like) – File descriptor.
- pycalphad.io.tdb.reflow_text(text, linewidth=80)[source]¶
Add line breaks to ensure text doesn’t exceed a certain line width.
- Parameters:
text (str)
linewidth (int, optional)
- Returns:
reflowed_text
- Return type:
str
- pycalphad.io.tdb.write_tdb(dbf, fd, groupby='subsystem', if_incompatible='warn')[source]¶
Write a TDB file from a pycalphad Database object.
The goal is to produce TDBs that conform to the most restrictive subset of database specifications. Some of these can be adjusted for automatically, such as the Thermo-Calc line length limit of 78. Others require changing the database in non-trivial ways, such as the maximum length of function names (8). The default is to warn the user when attempting to write an incompatible database and the user must choose whether to warn and write the file anyway or to fix the incompatibility.
Currently the supported compatibility fixes are: - Line length <= 78 characters (Thermo-Calc) - Function names <= 8 characters (Thermo-Calc)
The current unsupported fixes include: - Keyword length <= 2000 characters (Thermo-Calc) - Element names <= 2 characters (Thermo-Calc) - Phase names <= 24 characters (Thermo-Calc)
Other TDB compatibility issues required by Thermo-Calc or other software should be reported to the issue tracker.
- Parameters:
dbf (Database) – A pycalphad Database.
fd (file-like) – File descriptor.
groupby (['subsystem', 'phase'], optional) – Desired grouping of parameters in the file.
if_incompatible (string, optional ['raise', 'warn', 'fix']) – Strategy if the database does not conform to the most restrictive database specification. The ‘warn’ option (default) will write out the incompatible database with a warning. The ‘raise’ option will raise a DatabaseExportError. The ‘ignore’ option will write out the incompatible database silently. The ‘fix’ option will rectify the incompatibilities e.g. through name mangling.
pycalphad.io.tdb_keywords module¶
This module defines valid Thermo-Calc TDB keywords and handles abbreviations. Note that not all of these keywords are fully supported yet.
- pycalphad.io.tdb_keywords.expand_keyword(possible, candidate)[source]¶
Expand an abbreviated keyword based on the provided list.
- Parameters:
possible (list of str) – Possible keywords for ‘candidate’ to be matched against.
candidate (str) – Abbreviated keyword to expand.
- Return type:
list of str of matching expanded keywords
Examples
None yet.