diff --git a/docs/CHANGES.md b/docs/CHANGES.md index d4313f4c186..145de57d5b3 100644 --- a/docs/CHANGES.md +++ b/docs/CHANGES.md @@ -6,6 +6,10 @@ nav_order: 4 # Changelog +## v2024.9.17.1 + +- Emergency release No. 2 to fix yet another regression in chempot diagram. (Thanks @yang-ruoxi for fixing.) + ## v2024.9.17 - Emergency release to fix broken phase diagram plotting due to completely unnecessary refactoring. (Thanks @yang-ruoxi for fixing.) diff --git a/docs/modules.html b/docs/modules.html index 6446d709e47..1a0c5865ee9 100644 --- a/docs/modules.html +++ b/docs/modules.html @@ -1,13 +1,15 @@ - +
-Convert model to a GTH-formatted string.
Bases: MSONable
A keyword argument in CP2K. Within CP2K Sections, which activate features of the CP2K code, the keywords are arguments that control the functionality of that feature. @@ -1615,19 +1617,19 @@
Get a dictionary representation of the Keyword.
Initialize from dictionary.
Initialize from a string.
Keywords must be labeled with strings. If the post-processor finds that the keywords is a number, then None is return (used by @@ -1641,13 +1643,13 @@
String representation of Keyword.
Change the printing of this keyword’s description.
Bases: MSONable
Some keywords can be repeated, which makes accessing them via the normal dictionary methods a little unnatural. This class deals with this by defining a collection @@ -1668,25 +1670,25 @@
Append the keyword list.
Extend the keyword list.
String representation of Keyword.
Silence all keywords in keyword list.
Bases: Section
Specify the information for the different atom types being simulated.
Initialize a KIND section.
@@ -1724,7 +1726,7 @@Bases: Section
Specify a kpoint line to be calculated between special points.
Bases: KpointSet
Bases: Section
Description of the k-points to use for the calculation.
Initialize the section from a Kpoints object (pymatgen.io.vasp.inputs). CP2K does not have an automatic gamma-point constructor, so this is generally used to get the number of divisions from a kpoint static constructor and then @@ -1824,7 +1826,7 @@
Bases: Section
Controls printing of the LDOS (List-Density of states). i.e. projects onto specific atoms.
Initialize the LDOS section.
@@ -1842,7 +1844,7 @@Bases: Section
Controls printing of the molecular orbital eigenvalues.
Initialize the MO_CUBES section.
@@ -1850,14 +1852,14 @@Bases: MOCubes
Initialize the MO_CUBES section.
Bases: Section
Controls the multigrid for numerical integration.
Initialize the MGRID section.
@@ -1881,7 +1883,7 @@Bases: Section
Turns on the Orbital Transformation scheme for diagonalizing the Hamiltonian. Often faster and with guaranteed convergence compared to normal diagonalization, but requires the system @@ -1926,7 +1928,7 @@
Bases: Section
Info about the PBE functional.
Bases: Section
Controls printing of projected density of states onto the different atom KINDS (elemental decomposed DOS).
@@ -1964,12 +1966,12 @@Bases: DataFile
Data file for potentials only.
Initialize from a string representation.
Bases: MSONable
Metadata for this potential.
Total number of electrons
Potential type (e.g. GTH)
Nonlinear core corrected potential
Exchange correlation functional used for creating this potential
Get a CP2K formatted string representation.
Soft matching to see if two potentials match.
Will only match those attributes which are defined for this basis info object (one way checking)
Bases: Section
Controls the quickstep settings (DFT driver).
Initialize the QS Section.
@@ -2088,7 +2090,7 @@Bases: Section
Controls the self consistent field loop.
Initialize the Scf section.
@@ -2122,7 +2124,7 @@Bases: MSONable
Basic input representation of input to CP2K. Activates functionality inside of the CP2K executable.
@@ -2164,13 +2166,13 @@Add another keyword to the current section.
Access a sub-section using a path. Used by the file parser.
Check if section exists within the current using a path. Can be useful for cross-checking whether or not required dependencies have been satisfied, which CP2K does not enforce.
Similar to get for dictionaries. This will attempt to retrieve the section or keyword matching d. Will not raise an error if d does not exist.
Get function, only for subsections.
Get function, only for subsections.
Get string representation of Section.
Mongo style dict modification. Include.
Insert a new section as a subsection of the current one.
Alias for update with strict (no insertions). Used by custodian.
Alias for update. Used by custodian.
Helper function for setting items. Kept separate from the double-underscore function so that “strict” option can be made possible.
strict will only set values for items that already have a key entry (no insertion).
@@ -2274,19 +2276,19 @@Recursively delete all print sections so that only defaults are printed out.
Dict based deletion. Used by custodian.
Update the Section according to a dictionary argument. This is most useful for providing user-override settings to default parameters. As you pass a dictionary the class variables like “description”, “location”, or “repeats” @@ -2320,7 +2322,7 @@
Change the section verbosity recursively by turning on/off the printing of descriptions. Turning off descriptions may reduce the appealing documentation of input files, but also helps de-clutter them.
@@ -2330,7 +2332,7 @@Bases: MSONable
Section list.
Initialize a SectionList object using a sequence of sections.
@@ -2341,32 +2343,32 @@Append the section list.
Extend the section list.
Get for section list. If index is specified, return the section at that index. Otherwise, return a get on the last section.
Return string representation of section list.
Silence all sections in section list.
Bases: Section
Control electron smearing.
Basic object representing a CP2K Section. Sections activate different parts of the @@ -2417,7 +2419,7 @@
Bases: Section
Controls the definition of the system to be simulated.
Initialize the subsys section.
@@ -2425,7 +2427,7 @@Bases: Section
Controls printing of the hartree potential as a cube file.
Basic object representing a CP2K Section. Sections activate different parts of the @@ -2468,7 +2470,7 @@
Bases: VHartreeCube
Basic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate @@ -2510,7 +2512,7 @@
Bases: Section
Info about which XC functional to use.
Basic object representing a CP2K Section. Sections activate different parts of the @@ -2553,7 +2555,7 @@
Bases: XCFunctional
Basic object representing a CP2K Section. Sections activate different parts of the calculation. For example, FORCE_EVAL section will activate CP2K’s ability to calculate @@ -2600,7 +2602,7 @@
Bases: object
Parse output file from CP2K. The CP2K output file is very flexible in the way that it is returned. This class will automatically parse parameters that should always be present, @@ -2619,93 +2621,93 @@
Return dictionary representation of the output.
Band structure object if it has been parsed.
The calculation type (what io.vasp.outputs calls run_type).
Charge from the input file.
Complete dos object if it has been parsed.
Did the calculation complete.
Check whether or not the SCF and geometry optimization cycles converged.
The CP2K version used in the calculation.
True if hubbard +U correction was used.
Was a band gap found? i.e. is it a metal.
True if the CP2K output was generated for a molecule (i.e. no periodicity in the cell).
The spin multiplicity from input file.
How many warnings showed up during the run.
Parse info on what atomic kinds are present and what basis/pseudopotential is describing each of them.
Parse a CP2K bandstructure file.
Parse the lattice parameters (initial) from the output file.
Parse the magnetic susceptibility tensor.
Parse the CP2K general parameters from CP2K output file into a dictionary.
Parse the DFT parameters (as well as functional, HF, vdW params).
Parse the dos files produced by CP2K calculation. CP2K produces different files based on the input file rather than assimilating them all into one file.
One file type is the overall DOS file, which is used for k-point calculations. For @@ -2770,7 +2772,7 @@
Get the total energy from a CP2K calculation. Presently, the energy reported in the trajectory (pos.xyz) file takes precedence over the energy reported in the main output file. This is because the trajectory file keeps track of energies in between restarts, @@ -2780,69 +2782,69 @@
Identify files present in the directory with the CP2K output file. Looks for trajectories, dos, and cubes.
Get the forces from the forces file, or from the main output file.
Parse the GLOBAL section parameters from CP2K output file into a dictionary.
Parse a file containing g tensor.
Parse the Hirshfeld population analysis for each step.
Find the HOMO - LUMO gap in [eV]. Returns the last value. For gaps/eigenvalues decomposed by spin up/spin down channel and over many ionic steps, see parse_mo_eigenvalues().
Parse a file containing hyperfine coupling tensors for each atomic site.
Parse the initial structure from the main CP2K output file.
Load in the input set from the input file (if it can be found).
Parse the ionic step info. If already parsed, this will just assimilate.
Parse the MO eigenvalues from the CP2K output file. Will get the eigenvalues (and band gap) at each ionic step (if more than one exist).
Everything is decomposed by spin channel. If calculation was performed without spin @@ -2852,68 +2854,68 @@
Parse the mulliken population analysis info for each step.
Parse NMR calculation.
Parse the geometry optimization information.
Retrieve the overlap condition number.
Parse the DFT+U params.
Parse the DFT parameters (as well as functional, HF, vdW params).
Parse raman calculation.
Parse the SCF cycles (not usually important).
Retrieve the most import SCF parameters: the max number of scf cycles (max_scf), the convergence cutoff for scf (eps_scf),.
Get the stresses from stress file, or from the main output file.
Parse the structures from a CP2K calculation. Static calculations simply use the initial structure. For calculations with ionic motion, the function will look for the appropriate trajectory and lattice files based on naming convention. If no file is given, and no file @@ -2924,31 +2926,31 @@
Parse TDDFPT calculation.
Parse the timing info (how long did the run take).
Parse total numbers (not usually important).
What project name was used for this calculation.
Sanity checks that the program ran successfully. Looks at the bottom of the CP2K output file for the “PROGRAM ENDED” line, which is printed when successfully ran. Also grabs the number of warnings issued.
@@ -2956,7 +2958,7 @@Originally from pymatgen.io.vasp.outputs.Outcar.
General pattern reading. Uses monty’s regrep method. Takes the same arguments.
@@ -2987,7 +2989,7 @@This function originated in pymatgen.io.vasp.outputs.Outcar.
Parse table-like data. A table composes of three parts: header, main body, footer. All the data matches “row pattern” in the main body @@ -3032,13 +3034,13 @@
What type of run (Energy, MD, etc.) was performed.
Was the calculation spin polarized.
Parse a dos file. This format is different from the pdos files.
Parse energy file for calculations with multiple ionic steps.
Parse a single DOS file created by CP2K. Must contain one PDOS snapshot. i.e. you cannot use this cannot deal with multiple concatenated dos files.
Bases: DftSet
Quick Constructor for cell optimization relaxation.
Bases: Exception
CP2K validation exception. Not exhausted. May raise validation errors for features which actually do work if using a newer version of CP2K.
Bases: Cp2kInput
Base for an input set using the Quickstep module (i.e. a DFT calculation). The DFT section is pretty vast in CP2K, so this set hopes to make the DFT setup fairly simple. The provided @@ -3282,19 +3284,19 @@
Calculate g-tensor. Requires localize. Suggested with GAPW.
Modify the set to use fast SCF minimization.
Basic set for activating hybrid DFT calculation using Auxiliary Density Matrix Method.
Note 1: When running ADMM with CP2K, memory is very important. If the memory requirements exceed what is available (see max_memory), then CP2K will have to calculate the 4-electron @@ -3362,13 +3364,13 @@
Print the hyperfine coupling constants.
Activate calculation of the maximally localized wannier functions.
Turns on the motion section for GEO_OPT, CELL_OPT, etc. calculations. Will turn on the printing subsections and also bind any constraints to their respective atoms.
@@ -3392,44 +3394,44 @@Calculate nmr shifts. Requires localize. Suggested with GAPW.
Activates a calculation with non-periodic calculations by turning of PBC and changing the poisson solver. Still requires a CELL to put the atoms.
Calculate polarizations (including raman).
Modify the set to use more robust SCF minimization technique.
Calculate spin-spin coupling tensor. Requires localize.
Activate TDDFPT for calculating excited states. Only works with GPW. Supports hfx.
Activate van der Waals dispersion corrections.
Method to modify the set to use very strict SCF minimization scheme.
Create the structure for the input.
Get a dictionary of basis and potential info for constructing the input file.
data in basis_and_potential argument can be specified in several ways:
@@ -3515,20 +3517,20 @@Submodules
- -static get_cutoff_from_basis(basis_sets, rel_cutoff) float [source]
+static get_cutoff_from_basis(basis_sets, rel_cutoff) float [source]Given a basis and a relative cutoff. Determine the ideal cutoff variable.
Get XC functionals. If simplified names are provided in kwargs, they will be expanded into their corresponding X and C names.
Modify all DFT print iterations at once. Common use is to set iters to the max number of iterations + 1 and then set add_last to numeric. This would have the effect of printing only the first and last iteration, which might be useful for @@ -3549,7 +3551,7 @@
Attaches a non-scf band structure calc the end of an SCF loop.
This requires a kpoint calculation, which is not always default in CP2K.
Activate printing of the overall DOS file.
Note: As of 2022.1, ndigits needs to be set to a sufficient value to ensure data is not lost. Note: As of 2022.1, can only be used with a k-point calculation.
@@ -3569,25 +3571,25 @@Controls the printing of cube files with electronic density and, for UKS, the spin density.
Print out the forces and stress during calculation.
Activate or deactivate printing of Hirshfeld charges.
Activate the printing of LDOS files, printing one for each atom kind by default.
Print molecular orbitals when running non-OT diagonalization.
Activate printing of molecular orbitals.
Activate or deactivate printing of Mulliken charges.
Activate creation of the PDOS file.
total density (electrons+ions). It is valid only for QS with GPW formalism.
Set the overall charge of the simulation cell.
Implements a few checks for a valid input set.
Write the basis sets to a file.
Write the potentials to a file.
Bases: DftSet
Quick Constructor for hybrid cell optimization relaxation.
Bases: DftSet
Quick Constructor for hybrid geometry relaxation.
Bases: DftSet
Quick Constructor for static calculations.
Bases: DftSet
Quick Constructor for geometry relaxation.
Bases: DftSet
Quick Constructor for static calculations.
Chunk the string from a CP2K basis or potential file.
Get the truncated Coulomb cutoff for a given structure.
Get unique site indices for a structure according to site properties. Whatever site-property has the most unique values is used for indexing.
For example, if you have magnetic CoO with half Co atoms having a positive moment, and the @@ -4091,7 +4093,7 @@
Sort text by numbers coming after an underscore with natural number convention, Ex: [file_1, file_12, file_2] becomes [file_1, file_2, file_12].
@@ -4099,7 +4101,7 @@Helper function to post process the results of the pattern matching functions in Cp2kOutput and turn them to Python types.
CP2K contains internal preprocessor flags that are evaluated before execution. This helper function recognizes those preprocessor flags and replaces them with an equivalent CP2K input (this way everything is contained neatly in the CP2K input structure, even if the user preferred diff --git a/docs/pymatgen.io.exciting.html b/docs/pymatgen.io.exciting.html index 3218aff10b7..5541d855215 100644 --- a/docs/pymatgen.io.exciting.html +++ b/docs/pymatgen.io.exciting.html @@ -1,13 +1,15 @@ - +
-