CASM Python packages documentation¶
casm.api¶
casm.api.API() |
Class to provide access to the libccasm C API. |
casm.learn¶
casm.learn.create_halloffame(maxsize[, rel_tol]) |
|||
casm.learn.EqualIndividual([rel_tol]) |
Functor class for checking equivalence of individuals in a HallOfFame. | ||
casm.learn.empty_individual(n_features) |
|||
casm.learn.example_input_Lasso() |
|||
casm.learn.example_input_LassoCV() |
|||
casm.learn.example_input_RFE() |
|||
casm.learn.example_input_GeneticAlgorithm() |
|||
casm.learn.example_input_IndividualBestFirst() |
|||
casm.learn.example_input_PopulationBestFirst() |
|||
casm.learn.example_input_DirectSelection() |
|||
casm.learn.open_input(input_filename) |
Read casm-learn input file into a dict | ||
casm.learn.set_input_defaults(input[, …]) |
Set common input defaults. | ||
casm.learn.FittingData(X, y, cv[, …]) |
FittingData holds feature values, target values, sample weights, etc. | ||
casm.learn.TrainingData(input[, verbose]) |
TrainingData is a data structure used to collect data from the training data file. | ||
casm.learn.print_input_help() |
|||
casm.learn.print_individual(hall, indices[, …]) |
Print selected individuals from hall of fame. | ||
casm.learn.print_population(pop) |
Print all individual in a population. | ||
casm.learn.print_halloffame(hall[, format]) |
Print all individual in hall of fame. | ||
casm.learn.print_eci(eci) |
Print ECI. | ||
casm.learn.to_json(index, indiv) |
Serialize an individual to JSON records. | ||
casm.learn.open_halloffame(halloffame_filename) |
Open hall of fame from .pkl file. | ||
casm.learn.save_halloffame(hall, …[, verbose]) |
Save hall of fame as .pkl file. | ||
casm.learn.checkspecs(input[, verbose]) |
Output data and cv files containing the current problem specs. | ||
casm.learn.checkhull(input, hall[, indices, …]) |
Check for hull properties and add pandas.DataFrame attributes to each individual: | ||
casm.learn.fit_and_select(input[, save, …]) |
|
||
casm.learn.direct_fit(input[, save, …]) |
Fit ECI and add details for a set of individuals specified for feature_selection method ‘DirectSelection’ via the ‘population’ kwarg. |
casm.plotting¶
casm.plotting.ConvexHullPlot([data, …]) |
Attributes: |
casm.plotting.GridPlot(sel[, x, y, type, …]) |
Attributes: |
casm.plotting.Histogram([data, project, …]) |
Attributes: |
casm.plotting.PlottingData() |
|
casm.plotting.RankPlot([data, project, …]) |
Attributes: |
casm.plotting.Scatter([data, project, …]) |
Attributes: |
casm.plotting.TapAction(data) |
Enable execution of a python function when a glyph is ‘tapped’ in a bokeh plot. |
casm.plotting.add_src_data(sel, name, data) |
Add data to Selection’s ColumnDataSource, creating if necessary |
casm.plotting.clex_hull_style(input) |
|
casm.plotting.default_clex_hull_style |
dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.For example: dict(one=1, two=2). |
casm.plotting.default_dft_hull_style |
dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.For example: dict(one=1, two=2). |
casm.plotting.default_figure_kwargs |
dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.For example: dict(one=1, two=2). |
casm.plotting.default_scatter_style |
dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.For example: dict(one=1, two=2). |
casm.plotting.dft_hull_style(input) |
|
casm.plotting.rankplot_style(input) |
|
casm.plotting.rank_select_cutoff_style |
dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.For example: dict(one=1, two=2). |
casm.plotting.scatter_series_style(index, input) |
|
casm.plotting.update_clex_hull_glyphs(sel, style) |
Use the selected and on_hull iterables to update glyph styles based on sel.clex_style. |
casm.plotting.update_dft_hull_glyphs(sel, style) |
Use the selected and on_hull iterables to update glyph styles based on sel.dft_style. |
casm.plotting.update_scatter_glyphs(sel, …) |
|
casm.plotting.view_on_tap(sel, attrname, …) |
Execute ‘casm view’ on tapped configuration |
casm.plotting.PlotTypeCommand |
casm.project¶
casm.project.project_path([dir]) |
Crawl up from dir to find ‘.casm’. |
casm.project.ClexDescription(name, property, …) |
Settings for a cluster expansion |
casm.project.ProjectSettings([path]) |
Settings for a CASM project |
casm.project.DirectoryStructure([path]) |
Standard file and directory locations for a CASM project |
casm.project.Project([path, casm_exe, verbose]) |
The Project class contains information about a CASM project |
casm.project.Prim(proj) |
The Primitive Crystal Structure |
casm.project.Selection([proj, path, all]) |
A Selection object contains information about a CASM project |
casm.project.query(proj, columns[, …]) |
Return a pandas DataFrame object containing the output of a ‘casm query’ command. |
casm.project.write_eci(proj, eci[, …]) |
Write eci.json |
casm.qewrapper¶
casm.qewrapper.QEWrapperError(msg) |
|
casm.qewrapper.Relax([configdir, auto, sort]) |
The Relax class contains functions for setting up, executing, and parsing a Quantum Espresso relaxation. |
casm.qewrapper.qe_input_file_names(dirstruc, …) |
|
casm.qewrapper.read_settings(filename) |
Returns a JSON object reading JSON files containing settings for Quantum Espresso PBS jobs. |
casm.qewrapper.write_settings(settings, filename) |
Write ‘settings’ as json file, ‘filename’ |
casm.quantumespresso¶
casm.quantumespresso.FreezeError() |
Quantum Espresso appears frozen |
casm.quantumespresso.NbandsError() |
Your highest band is occupied at some k-points! Unless you are |
casm.quantumespresso.QuantumEspressoError(msg) |
|
casm.quantumespresso.QuantumEspressoWarning(msg) |
|
casm.quantumespresso.Relax([relaxdir, settings]) |
The Relax class contains functions for setting up, executing, and parsing a Quantum Espresso relaxation. |
casm.quantumespresso.error_check(jobdir, …) |
Check quantum espresso stdout for errors |
casm.quantumespresso.run(infilename, outfilename) |
Run quantum espresso using subprocess. |
casm.quantumespresso.qeio¶
casm.quantumespresso.qeio.QUANTUM_ESPRESSO_INT_LIST |
dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.For example: dict(one=1, two=2). |
casm.quantumespresso.qeio.QUANTUM_ESPRESSO_FLOAT_LIST |
dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.For example: dict(one=1, two=2). |
casm.quantumespresso.qeio.QUANTUM_ESPRESSO_BOOL_LIST |
dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.For example: dict(one=1, two=2). |
casm.quantumespresso.qeio.QUANTUM_ESPRESSO_STR_LIST |
dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.For example: dict(one=1, two=2). |
casm.quantumespresso.qeio.QUANTUM_ESPRESSO_TOTAL_LIST |
dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.For example: dict(one=1, two=2). |
casm.quantumespresso.qeio.ControlError(msg) |
|
casm.quantumespresso.qeio.Control(title, …) |
The Control class contains: |
casm.quantumespresso.qeio.SystemError(msg) |
|
casm.quantumespresso.qeio.System(title, …) |
The Sys class contains: |
casm.quantumespresso.qeio.ElectronsError(msg) |
|
casm.quantumespresso.qeio.Electrons(title, …) |
The Electrons class contains: |
casm.quantumespresso.qeio.IonsError(msg) |
|
casm.quantumespresso.qeio.Ions(title, …) |
The Ions class contains: |
casm.quantumespresso.qeio.CellError(msg) |
|
casm.quantumespresso.qeio.Cell(title, …) |
The Cell class contains: |
casm.quantumespresso.qeio.AtomicSpeciesError(msg) |
|
casm.quantumespresso.qeio.AtomicSpecies(…) |
The AtomicSpecies class contains: |
casm.quantumespresso.qeio.AtomicPositionsError(msg) |
|
casm.quantumespresso.qeio.AtomicPositions(…) |
The AtomicPositions class contains: |
casm.quantumespresso.qeio.CellParametersError(msg) |
|
casm.quantumespresso.qeio.CellParameters(…) |
The CellParameters class contains: |
casm.quantumespresso.qeio.KPointsError(msg) |
|
casm.quantumespresso.qeio.KPoints(cardstring) |
The KPoints class contains: |
casm.quantumespresso.qeio.QUANTUM_ESPRESSO_NAMELIST_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.quantumespresso.qeio.QUANTUM_ESPRESSO_NAMELIST_OBJ_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.quantumespresso.qeio.QUANTUM_ESPRESSO_CARD_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.quantumespresso.qeio.QUANTUM_ESPRESSO_CARD_OBJ_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.quantumespresso.qeio.QUANTUM_ESPRESSO_BLOCK_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.quantumespresso.qeio.InfileError(msg) |
|
casm.quantumespresso.qeio.Infile(filename[, …]) |
The Infile class contains: |
casm.quantumespresso.qeio.OutfileError(msg) |
|
casm.quantumespresso.qeio.Outfile(filename) |
Parse Outfiles. |
casm.quantumespresso.qeio.PoscarError(msg) |
|
casm.quantumespresso.qeio.Site(cart, position) |
Site in a basis. |
casm.quantumespresso.qeio.Poscar(filename[, …]) |
The Poscar class contains: |
casm.quantumespresso.qeio.DEFAULT_QE_MOVE_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.quantumespresso.qeio.DEFAULT_QE_COPY_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.quantumespresso.qeio.DEFAULT_QE_REMOVE_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.quantumespresso.qeio.QuantumEspressoIOError(msg) |
|
casm.quantumespresso.qeio.job_complete(…) |
Return True if Quantum Espresso job at path ‘jobdir’ is complete |
casm.quantumespresso.qeio.get_infile_tag(…) |
Opens Infile in ‘jobdir’ and returns ‘key’ value. |
casm.quantumespresso.qeio.set_infile_tag(…) |
Opens Infile in ‘jobdir’, sets ‘key’ value, and writes Infile If ‘val’ == None, the tag is removed from the Infile. |
casm.quantumespresso.qeio.ionic_steps(…[, …]) |
Find the number of ionic steps completed in ‘jobdir’ |
casm.quantumespresso.qeio.write_quantum_espresso_input(…) |
Write Quantum Espresso input files in directory ‘dirpath’ |
casm.quantumespresso.qeio.SpeciesError(msg) |
|
casm.quantumespresso.qeio.IndividualSpecies(…) |
The IndividualSpecies class contains: |
casm.quantumespresso.qeio.species_settings(…) |
Returns a dict of IndividualSpecies objects, with keys equal to their names. |
casm.quantumespresso.qeio.write_species_settings(…) |
Write a SPECIES file from a species dict |
casm.quantumespresso.qeio.QErunError(msg) |
|
casm.quantumespresso.qeio.QErun(outfilename) |
An object containing values read from outfile |
casm.questwrapper¶
casm.questwrapper.Relax([configdir, auto, sort]) |
The Relax class contains functions for setting up, executing, and parsing a SeqQuest relaxation. |
casm.questwrapper.QuestWrapperError |
Errors related to QuestWrapper |
casm.questwrapper.read_settings(filename) |
Returns a JSON object reading JSON files containing settings for seqquest cluster jobs. |
casm.questwrapper.write_settings(settings, …) |
Write ‘settings’ as json file, ‘filename’ |
casm.questwrapper.quest_input_file_names(…) |
Collect casm.questwrapper input files from the CASM project hierarchy |
casm.seqquest¶
casm.seqquest.RelaxError |
Relax-specific errors |
casm.seqquest.Relax([relaxdir, settings]) |
The Relax class contains functions for setting up, executing, and parsing a seqquest calc. |
casm.seqquest.SeqQuestError |
Class for SeqQuest errors |
casm.seqquest.SeqQuestWarning |
Class for SeqQuest warnings |
casm.seqquest.continue_job(jobdir, contdir, …) |
Use the files in seqquest job directory ‘jobdir’, to setup a seqquest job in directory |
casm.seqquest.complete_job(jobdir, settings) |
Remove files from a quest job directory |
casm.seqquest.run([jobdir, stdout, stderr, …]) |
Run seqquest using subprocess. |
casm.seqquest.seqquest_io¶
casm.seqquest.seqquest_io.Cell([POS, …]) |
Container class for cell data |
casm.seqquest.seqquest_io.Geom([POS, …]) |
Container class for geometry data |
casm.seqquest.seqquest_io.Site(position[, …]) |
Site in a basis. |
casm.seqquest.seqquest_io.LcaoIN([filename, …]) |
Container object for reading, parsing, and writing lcao.in files |
casm.seqquest.seqquest_io.LcaoOUT([filename]) |
Container object for reading and parsing lcao.out files |
casm.seqquest.seqquest_io.DEFAULT_QUEST_MOVE_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.seqquest.seqquest_io.DEFAULT_QUEST_COPY_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.seqquest.seqquest_io.DEFAULT_QUEST_REMOVE_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.seqquest.seqquest_io.QUEST_INPUT_FILE_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.seqquest.seqquest_io.SeqquestIO(…[, …]) |
Generate a set of SeqQuest input files from settings files |
casm.seqquest.seqquest_io.get_lcao_tag(keys) |
Opens lcao.in in ‘jobdir’ and returns ‘key’ value |
casm.seqquest.seqquest_io.job_complete([jobdir]) |
return True if the seqquest job at path ‘jobdir’ is complete |
casm.seqquest.seqquest_io.species_settings(…) |
Returns a dict of IndividualSpecies objects, with keys equal to their names. |
casm.vasp¶
casm.vasp.io |
Tools for VASP input and output |
casm.vasp.VaspError |
VASP related errors |
casm.vasp.VaspWarning(msg) |
VASP related warnings |
casm.vasp.continue_job(jobdir, contdir, settings) |
Use the files in vasp job directory ‘jobdir’, to setup a vasp job in directory ‘contdir’. |
casm.vasp.IbzkptError |
VERY BAD NEWS! internal error in subroutine IBZKPT |
casm.vasp.FEXCFError |
ERROR FEXCF: supplied exchange-correlation table |
casm.vasp.SubSpaceMatrixError |
WARNING: Sub-Space-Matrix is not hermitian |
casm.vasp.InisymError |
VASP can’t figure out the (magnetic) symmetry |
casm.vasp.SgrconError |
VASP is having yet another symmetry problem |
casm.vasp.WavecarError |
A bad WAVECAR is causing the job to crash/abort |
casm.vasp.NbandsError |
Your highest band is occupied at some k-points! Unless you are |
casm.vasp.NoConvergeError |
An ionic step was performed without a fully-converged density |
casm.vasp.FreezeError |
VASP appears frozen |
casm.vasp.error_check(jobdir, stdoutfile, …) |
Check vasp stdout for errors |
casm.vasp.crash_check(jobdir, stdoutfile, …) |
Check vasp stdout for evidence of a crash |
casm.vasp.complete_job(jobdir, settings) |
Remove files from a vasp job directory |
casm.vasp.run([jobdir, stdout, stderr, …]) |
Run vasp using subprocess. |
casm.vasp.Relax([relaxdir, settings]) |
The Relax class contains functions for setting up, executing, and parsing a VASP relaxation. |
casm.vasp.Converge([propdir, settings, prop]) |
The Converge class contains functions for setting up, executing, and parsing a VASP convergence. |
casm.vasp.io¶
casm.vasp.io.VASP_INPUT_FILE_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.DEFAULT_VASP_MOVE_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.DEFAULT_VASP_COPY_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.DEFAULT_VASP_REMOVE_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.VaspIOError(msg) |
|
casm.vasp.io.job_complete([jobdir]) |
Return True if vasp job at path ‘jobdir’ is complete |
casm.vasp.io.get_incar_tag(key[, jobdir]) |
Opens INCAR in ‘jobdir’ and returns ‘key’ value. |
casm.vasp.io.set_incar_tag(tag_dict[, …]) |
Opens INCAR in ‘jobdir’, sets ‘key’ value, and writes INCAR If ‘val’ is None, the tag is removed from the INCAR. |
casm.vasp.io.ionic_steps([jobdir]) |
Find the number of ionic steps completed in ‘jobdir’ |
casm.vasp.io.write_potcar(filename, poscar, …) |
Write an appropriate POTCAR |
casm.vasp.io.write_stopcar([mode, jobdir]) |
Write STOPCAR file with two modes: mode = ‘e’ for ‘VASP stops at the next electronic step’ mode = ‘i’ for ‘VASP stops at the next ionic step’ |
casm.vasp.io.write_vasp_input(dirpath, …) |
Write VASP input files in directory ‘dirpath’ |
casm.vasp.io.VASP_TAG_INT_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.VASP_TAG_FLOAT_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.VASP_TAG_BOOL_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.VASP_TAG_SITEF_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.VASP_TAG_SPECF_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.VASP_TAG_SPECI_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.VASP_TAG_STRING_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.VASP_TAG_LIST |
list() -> new empty list list(iterable) -> new list initialized from iterable’s items |
casm.vasp.io.IncarError(msg) |
|
casm.vasp.io.Incar(filename[, species, …]) |
The INCAR class contains: |
casm.vasp.io.KpointsError(msg) |
|
casm.vasp.io.Kpoints(filename) |
The Kpoints class contains: |
casm.vasp.io.OutcarError(msg) |
|
casm.vasp.io.Outcar(filename) |
Parse OUTCAR files. |
casm.vasp.io.OszicarError(msg) |
|
casm.vasp.io.Oszicar(filename) |
Parse OSZICAR files. |
casm.vasp.io.Site(cart, position[, SD_FLAG, …]) |
Site in a basis. |
casm.vasp.io.PoscarError(msg) |
|
casm.vasp.io.Poscar(filename[, species, …]) |
The Poscar class contains: |
casm.vasp.io.SpeciesError(msg) |
|
casm.vasp.io.SpeciesDict |
SpeciesDict subclasses dict so it can hold additional metadata without disrupting routines that |
casm.vasp.io.IndividualSpecies(values, tags, …) |
The IndividualSpecies class contains: |
casm.vasp.io.species_settings(filename) |
Returns a SpeciesDict of IndividualSpecies objects, with keys equal to their names. |
casm.vasp.io.write_species_settings(species, …) |
Write a SPECIES file from a species dict |
casm.vasp.io.VaspIO(incarfile, …[, sort]) |
Generate a set of VASP input files from settings files |
casm.vasp.io.VasprunError(msg) |
|
casm.vasp.io.Vasprun(filename[, DOS, Band]) |
An object containing values read from vasprun.xml |
casm.vaspwrapper¶
casm.vaspwrapper.Relax([configdir, auto, sort]) |
The Relax class contains functions for setting up, executing, and parsing a VASP relaxation. |
casm.vaspwrapper.Converge([configdir, auto, …]) |
The Converge class contains functions for setting up, executing, and parsing a VASP convergence test. |
casm.vaspwrapper.VaspWrapperError(msg) |
|
casm.vaspwrapper.read_settings(filename) |
Returns a JSON object reading JSON files containing settings for VASP PBS jobs. |
casm.vaspwrapper.write_settings(settings, …) |
Write ‘settings’ as json file, ‘filename’ |
casm.vaspwrapper.vasp_input_file_names(dir, …) |
Collect casm.vaspwrapper input files from the CASM project hierarchy |
casm.wrapper¶
casm.wrapper.jobname(configname) |
Return a name for a submitted job for configuration with ‘configname’ |