Cp2k 2.0 #2672
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Cp2k 2.0 #2672
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…pdates to the corrections module, which should include some simpler corrections like point charge. Added a WIP update to the thermodynamics module, which is going to include support for predomenance diagrams in the near future
…into CP2K # Conflicts: # pymatgen/command_line/bader_caller.py # pymatgen/io/cp2k/inputs.py # pymatgen/io/cp2k/outputs.py # pymatgen/io/cp2k/sets.py # pymatgen/io/cp2k/tests/test_sets.py # pymatgen/io/cp2k/utils.py
Also removed a print statement.
…into CP2K # Conflicts: # pymatgen/command_line/bader_caller.py # pymatgen/io/cube.py
ordering of the sites, except when you use the get_unique_site_indices
function to get aliases such as {'Mg_1': [...], 'Mg_2': [...], 'O_1': [...]}.
Then, the sites are given by a alias: index dictionary that doesn't preserve
order, and so sites can get jumbled when this happens. It doesn't always happen, so
it was hard to identify. Now, when aliasing is used for the Coord section,
the keywords are created in order of their indices. To further protect against
these sorts of issues for unforseen problems, I'm changing "self.keywords"
to be stored as an OrderedDict once they are provided to the Section. Since
Ordered Dicts inherit from Dicts, this shouldn't change anything.
Lastly, I have applied black formatting to everything to keep consistent.
aliases.get because SupportsLessThan is not part of it, even though it worked in practice. While this new method is less elegant, it still works well enough.
…into CP2K # Conflicts: # pymatgen/command_line/bader_caller.py
…into defects # Conflicts: # pymatgen/analysis/defects/corrections.py # pymatgen/analysis/defects/thermodynamics.py
transformation history of a parent and child task.
the pseudopotential of the atom is turned off, but the basis functions are left behind.
for more information, see https://pre-commit.ci
|
Sorry, currently traveling and not in front of a large enough screen to review such a significant PR. But looks like a lot of great work! 🥇 |
for more information, see https://pre-commit.ci
rename single-letter vars (discouraged by flake8)
…to ValueError complete pymatgen/io/cp2k/utils.py _(pre|post)processor doc strs add type anno
janosh
reviewed
Jan 3, 2023
for more information, see https://pre-commit.ci
required for mypy to analyze functions, found potential dict unpacking error in DftSet subclasses fix typos
lbluque
pushed a commit
to lbluque/pymatgen
that referenced
this pull request
Jan 5, 2023
* Added a property assignment structure for testing. Tests not yet written.
* Modified test file. Removed NLCC_POTENTIALS.yaml, which has no use at the moment.
* Commits to this branch will be updates to defects module. Added WIP updates to the corrections module, which should include some simpler corrections like point charge. Added a WIP update to the thermodynamics module, which is going to include support for predomenance diagrams in the near future
* Defect module WIP
* Try else got tripped unecessarily. Fixed with conditional.
Also removed a print statement.
* Updated import statement.
* Updated import statement.
* Updated import statement.
* Fixed charge transfer, which was not working.
* Slightly better version of last commit
* Plotting updates.
* A very subtle error... Everything in the sets/inputs preserves the
ordering of the sites, except when you use the get_unique_site_indices
function to get aliases such as {'Mg_1': [...], 'Mg_2': [...], 'O_1': [...]}.
Then, the sites are given by a alias: index dictionary that doesn't preserve
order, and so sites can get jumbled when this happens. It doesn't always happen, so
it was hard to identify. Now, when aliasing is used for the Coord section,
the keywords are created in order of their indices. To further protect against
these sorts of issues for unforseen problems, I'm changing "self.keywords"
to be stored as an OrderedDict once they are provided to the Section. Since
Ordered Dicts inherit from Dicts, this shouldn't change anything.
Lastly, I have applied black formatting to everything to keep consistent.
* mypy on github (but not on my machine, oddly) didn't like the use of
aliases.get because SupportsLessThan is not part of it, even though
it worked in practice. While this new method is less elegant, it still
works well enough.
* Reorder import. Couple of formatting corrections from pylint.
* Update plotter.
* Created a polaron class as a child of Substitution.
* Trying out a "RelaxationTransformation" to help stitch together the
transformation history of a parent and child task.
* Tweak as_dict() summary.
* The GhostVacancy is a special vacancy object for CP2K calculations where
the pseudopotential of the atom is turned off, but the basis functions are
left behind.
* added dtype=object to np.array
* Update import statement
* Assembled basis sets, pseudopotential, and DFT+U settings into a single
settings file, which should be cleaner than using separate ones.
* Updated in accordance with new settings.yaml file.
* Update in accordance with new settings.yaml file.
* Update to one of the hubbard values.
* Fixed the getting of hubbard values.
* Updated predominance diagrams
* A temporary measure on my dev branch for avoid Potcar hashing with CP2K calculations
* These files are no longer necessary, as settings.yaml will hold all
this info.
* Update attribute.
* Update attribute
* Update the plot with "combine_charges" to make cleaner figures
* Keywords must have strings for names. Numbers will cause problems.
* Update to the mo_eigenvalues parsing for non-OT compatability. Parsing a raw
text file is incredibly sloppy.
* Update to the file reading. Subsections can have "subsection params",
some of which are used to alias the subsection, but some of which
are variables like "on" or "off". They are problematic from the
point of view of the Section objects. This will fix the issue of cp2k
restart files automatically assigning some of these superfluous
params, but is not a totally robust solution.
* Change to default diagonalization params.
* Update dict band gap.
* Updating mo_eigenvalues parsing, which is getting troublesome mixing
OT and diagonalization FWs now.
* Modifications to the DOS parser so that its more integrated with the
Dos module. Also made the DOS parser the default method for extracting
gaps, vbm, and cbm, which works for either OT or diagonalization.
* Update for aux_basis set. "match" keyword will now use primary basis, which
can be used for defect sites. Starting to get lots of spaghetti code here.
Also fixed indentation error.
* Added aux_basis argument
* Don't assume initial structure was parsed.
* Need hubbard > 0
* Update to diagonalization settings.
* Section Lists
* Reject if sizes don't match
* Testing new plot.
* Possible hash for defects.
* Nevermind.
* Remove warning.
* Update plus_u and xc_functional
* fix
* Update for functional processing. Do not like this as it relies on
having the input file present, but the text in the output file is too
variable to parse reliably.
* Still need to figure out how to get mos automatically. Upped it for
now. Elec temp of 500 maybe have been a little too high.
* Change how output parser gets the functional.
* Use the getattr operation to be case insensitive.
* Update section descriptions.
* So bader can use reference charges with cubes. Will submit patch and merge.
* This function should not default to cm^-3 units. Most/all of pymatgen does things per formula unit / composition object. So that's how this should be as well. The exponential is for an individual atom, and the multiplicity attribute will convert it to a per f.u. basis.
* Dos objects
* Use structure matcher instead of exact equality to deal with empty
site properties.
* fixing cube
* Fix for getting items. Now there is a seperate get function for keyword
and section, so internal methods can be more robust.
* Update to docstring and import.
* Adsorbent class.
* Concentration should be in formula units by default.
* (1) prettier plots
(2) get_doping() added since n/p are reused.
* Docstring.
* Add rotations
* forgot to make msonable
* Kpoints keyword
Scheme keyword was missing. Lead to errors.
* Updates for functionals
Some updates for functionals to make LibXC slightly easier.
* Parse initial structure
For some reason, one example did not show the default blank line. Not sure if it was the new version of cp2k or something else, but make the blank line a conditional now.
* �Parse initial structure
Last commit did not cover edge case. This should work.
* Updates.
Fix readline for both cases of coord table. Modify sets for hybrids. New utility function for truncation radius.
* optFIT basis
Opt fit basis sets should be preferred for C and B. These are not part of standard dist. and should be added to settings as well.
* Convergence criteria
Update the force convergence criteria to roughly match the MPRelaxSet
* Add option for strict updates.
Update now supports optional "strict" keyword to avoid inserting new keywords and sections.
* Update hybrid
Slight tweaks to logic for hybrid sets.
* Update test
Nonsense structure cannot use dummy element. Sets check validity of element inputs now.
* Update functionals
Hybrid was not being registered for PBE0 since only one functional is used.
* Add cutoff radius
Include cutoff radius even if not used in order to suppress warnings.
* Update core defects
Adsorbate is that species that adsorbs onto a surface, adsorbent is surface doing the adsorbing. Also the default defect concentration is back to cm-3. This is not ultimately desirable, but its causing too many problems.
* Updates
* Cutoff radius
Do not override. Just provide a warning. Also make the long range correction default to provide better energies when cutoff is very small.
* Fix cutoff
* Changes and Fixes
Newline in inputs.py
Adjust stride in sets.py
Read energies in outputs.py
* Update args
* Fix
* stress tensor
* Allow positive
* Updates
* New Thermo
* Remove temp
Temporary things were saved during a laptop crash. Now removed.
* SectionList
Modify the file reader with SectionList
* Double loop
* Drop undeveloped corrections and work on 2d correction
* Get section explicit
* Dont check if not running freysoldt
* Rename
Predominance diagram may confuse people. Will use Brouwer diagram instead.
DFT plus U is very finicky in cp2k due to basis sets. It only really works with LOWDIN scheme, which is only available in newer versions of the code, and even then it is prone to instabilities. For these reasons, plus u should not be the default.
* Formatting updates
* Deprecation upcoming
* Formatting
* Formatting
* Formatting
* Defect Complex and Linting
* Typing
* Emergency push
Laptop malfunctioning need to sync
* Update to correction
* Bandstructures
Input objects for band structure and ability to parse the band structure text files generated by cp2k.
* Revisions and Bandstructure support
Some formatting has been updated for new linting. Bandstructure support has been added to inputs and output parsers. Some updates to DOS parsers as well.
* Kpoints
* Format
* Revert to master
* Last minute fix. Needs to access num_kpts
* Needs to access num_kpts
* Old test and type check
* Some more lint
* Unused import
* Lint
* override_default_params
must not be none
* None->{}
* Add self
* Loops
* remove sigma
* A few changes to tests and test files
* fix assert
* AssertEqual
* Kpoints
* Dict already preserves ordering since py3.7
* use .items()
* EPS_PGF_ORB
* Gamma kpoint
* Basis and Potential
* None
* Dict
* startswith
* get element
* kpts
* Only use trunc if periodic
* Only use trunc if periodic
* ADMM Keywords
* Activate motion
* Delete
* runtype check
* molecules
* processor
* dft set
* multiplicity
* Exchange correction function
* pmg config
* Test set
* Basis and Potentials
* pmg config
* Molecule
* kpts
* Some tests
* Test sets
* Lintings
* Test files and tests
* Lint
* More lint
* Don't use built-in name
* list->List, dict->Dict
* Refactor pydantic to msonable
* Delete settings.yaml
* mypy 0.991 upgrade
* Util types and lint
* Uncomment a line
* Missing arg
* type
* arg
* Dftd3
Might as well add this
* Don't use literal
* Json
A hack so that jsanitized objects still have int keys
* Test for aux
* Tiny fixes
* rename some vars in pymatgen/cli/pmg_config.py to snake case
rename single-letter vars (discouraged by flake8)
* breaking: change CP2K _postprocessor parsing error type from OSError to ValueError
complete pymatgen/io/cp2k/utils.py _(pre|post)processor doc strs
add type anno
* Pre/postprocessor
* add return types in pymatgen/io/cp2k/sets.py
required for mypy to analyze functions, found potential dict unpacking error in DftSet subclasses
fix typos
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
lbluque
pushed a commit
to lbluque/pymatgen
that referenced
this pull request
May 23, 2023
* Added a property assignment structure for testing. Tests not yet written.
* Modified test file. Removed NLCC_POTENTIALS.yaml, which has no use at the moment.
* Commits to this branch will be updates to defects module. Added WIP updates to the corrections module, which should include some simpler corrections like point charge. Added a WIP update to the thermodynamics module, which is going to include support for predomenance diagrams in the near future
* Defect module WIP
* Try else got tripped unecessarily. Fixed with conditional.
Also removed a print statement.
* Updated import statement.
* Updated import statement.
* Updated import statement.
* Fixed charge transfer, which was not working.
* Slightly better version of last commit
* Plotting updates.
* A very subtle error... Everything in the sets/inputs preserves the
ordering of the sites, except when you use the get_unique_site_indices
function to get aliases such as {'Mg_1': [...], 'Mg_2': [...], 'O_1': [...]}.
Then, the sites are given by a alias: index dictionary that doesn't preserve
order, and so sites can get jumbled when this happens. It doesn't always happen, so
it was hard to identify. Now, when aliasing is used for the Coord section,
the keywords are created in order of their indices. To further protect against
these sorts of issues for unforseen problems, I'm changing "self.keywords"
to be stored as an OrderedDict once they are provided to the Section. Since
Ordered Dicts inherit from Dicts, this shouldn't change anything.
Lastly, I have applied black formatting to everything to keep consistent.
* mypy on github (but not on my machine, oddly) didn't like the use of
aliases.get because SupportsLessThan is not part of it, even though
it worked in practice. While this new method is less elegant, it still
works well enough.
* Reorder import. Couple of formatting corrections from pylint.
* Update plotter.
* Created a polaron class as a child of Substitution.
* Trying out a "RelaxationTransformation" to help stitch together the
transformation history of a parent and child task.
* Tweak as_dict() summary.
* The GhostVacancy is a special vacancy object for CP2K calculations where
the pseudopotential of the atom is turned off, but the basis functions are
left behind.
* added dtype=object to np.array
* Update import statement
* Assembled basis sets, pseudopotential, and DFT+U settings into a single
settings file, which should be cleaner than using separate ones.
* Updated in accordance with new settings.yaml file.
* Update in accordance with new settings.yaml file.
* Update to one of the hubbard values.
* Fixed the getting of hubbard values.
* Updated predominance diagrams
* A temporary measure on my dev branch for avoid Potcar hashing with CP2K calculations
* These files are no longer necessary, as settings.yaml will hold all
this info.
* Update attribute.
* Update attribute
* Update the plot with "combine_charges" to make cleaner figures
* Keywords must have strings for names. Numbers will cause problems.
* Update to the mo_eigenvalues parsing for non-OT compatability. Parsing a raw
text file is incredibly sloppy.
* Update to the file reading. Subsections can have "subsection params",
some of which are used to alias the subsection, but some of which
are variables like "on" or "off". They are problematic from the
point of view of the Section objects. This will fix the issue of cp2k
restart files automatically assigning some of these superfluous
params, but is not a totally robust solution.
* Change to default diagonalization params.
* Update dict band gap.
* Updating mo_eigenvalues parsing, which is getting troublesome mixing
OT and diagonalization FWs now.
* Modifications to the DOS parser so that its more integrated with the
Dos module. Also made the DOS parser the default method for extracting
gaps, vbm, and cbm, which works for either OT or diagonalization.
* Update for aux_basis set. "match" keyword will now use primary basis, which
can be used for defect sites. Starting to get lots of spaghetti code here.
Also fixed indentation error.
* Added aux_basis argument
* Don't assume initial structure was parsed.
* Need hubbard > 0
* Update to diagonalization settings.
* Section Lists
* Reject if sizes don't match
* Testing new plot.
* Possible hash for defects.
* Nevermind.
* Remove warning.
* Update plus_u and xc_functional
* fix
* Update for functional processing. Do not like this as it relies on
having the input file present, but the text in the output file is too
variable to parse reliably.
* Still need to figure out how to get mos automatically. Upped it for
now. Elec temp of 500 maybe have been a little too high.
* Change how output parser gets the functional.
* Use the getattr operation to be case insensitive.
* Update section descriptions.
* So bader can use reference charges with cubes. Will submit patch and merge.
* This function should not default to cm^-3 units. Most/all of pymatgen does things per formula unit / composition object. So that's how this should be as well. The exponential is for an individual atom, and the multiplicity attribute will convert it to a per f.u. basis.
* Dos objects
* Use structure matcher instead of exact equality to deal with empty
site properties.
* fixing cube
* Fix for getting items. Now there is a seperate get function for keyword
and section, so internal methods can be more robust.
* Update to docstring and import.
* Adsorbent class.
* Concentration should be in formula units by default.
* (1) prettier plots
(2) get_doping() added since n/p are reused.
* Docstring.
* Add rotations
* forgot to make msonable
* Kpoints keyword
Scheme keyword was missing. Lead to errors.
* Updates for functionals
Some updates for functionals to make LibXC slightly easier.
* Parse initial structure
For some reason, one example did not show the default blank line. Not sure if it was the new version of cp2k or something else, but make the blank line a conditional now.
* �Parse initial structure
Last commit did not cover edge case. This should work.
* Updates.
Fix readline for both cases of coord table. Modify sets for hybrids. New utility function for truncation radius.
* optFIT basis
Opt fit basis sets should be preferred for C and B. These are not part of standard dist. and should be added to settings as well.
* Convergence criteria
Update the force convergence criteria to roughly match the MPRelaxSet
* Add option for strict updates.
Update now supports optional "strict" keyword to avoid inserting new keywords and sections.
* Update hybrid
Slight tweaks to logic for hybrid sets.
* Update test
Nonsense structure cannot use dummy element. Sets check validity of element inputs now.
* Update functionals
Hybrid was not being registered for PBE0 since only one functional is used.
* Add cutoff radius
Include cutoff radius even if not used in order to suppress warnings.
* Update core defects
Adsorbate is that species that adsorbs onto a surface, adsorbent is surface doing the adsorbing. Also the default defect concentration is back to cm-3. This is not ultimately desirable, but its causing too many problems.
* Updates
* Cutoff radius
Do not override. Just provide a warning. Also make the long range correction default to provide better energies when cutoff is very small.
* Fix cutoff
* Changes and Fixes
Newline in inputs.py
Adjust stride in sets.py
Read energies in outputs.py
* Update args
* Fix
* stress tensor
* Allow positive
* Updates
* New Thermo
* Remove temp
Temporary things were saved during a laptop crash. Now removed.
* SectionList
Modify the file reader with SectionList
* Double loop
* Drop undeveloped corrections and work on 2d correction
* Get section explicit
* Dont check if not running freysoldt
* Rename
Predominance diagram may confuse people. Will use Brouwer diagram instead.
DFT plus U is very finicky in cp2k due to basis sets. It only really works with LOWDIN scheme, which is only available in newer versions of the code, and even then it is prone to instabilities. For these reasons, plus u should not be the default.
* Formatting updates
* Deprecation upcoming
* Formatting
* Formatting
* Formatting
* Defect Complex and Linting
* Typing
* Emergency push
Laptop malfunctioning need to sync
* Update to correction
* Bandstructures
Input objects for band structure and ability to parse the band structure text files generated by cp2k.
* Revisions and Bandstructure support
Some formatting has been updated for new linting. Bandstructure support has been added to inputs and output parsers. Some updates to DOS parsers as well.
* Kpoints
* Format
* Revert to master
* Last minute fix. Needs to access num_kpts
* Needs to access num_kpts
* Old test and type check
* Some more lint
* Unused import
* Lint
* override_default_params
must not be none
* None->{}
* Add self
* Loops
* remove sigma
* A few changes to tests and test files
* fix assert
* AssertEqual
* Kpoints
* Dict already preserves ordering since py3.7
* use .items()
* EPS_PGF_ORB
* Gamma kpoint
* Basis and Potential
* None
* Dict
* startswith
* get element
* kpts
* Only use trunc if periodic
* Only use trunc if periodic
* ADMM Keywords
* Activate motion
* Delete
* runtype check
* molecules
* processor
* dft set
* multiplicity
* Exchange correction function
* pmg config
* Test set
* Basis and Potentials
* pmg config
* Molecule
* kpts
* Some tests
* Test sets
* Lintings
* Test files and tests
* Lint
* More lint
* Don't use built-in name
* list->List, dict->Dict
* Refactor pydantic to msonable
* Delete settings.yaml
* mypy 0.991 upgrade
* Util types and lint
* Uncomment a line
* Missing arg
* type
* arg
* Dftd3
Might as well add this
* Don't use literal
* Json
A hack so that jsanitized objects still have int keys
* Test for aux
* Tiny fixes
* rename some vars in pymatgen/cli/pmg_config.py to snake case
rename single-letter vars (discouraged by flake8)
* breaking: change CP2K _postprocessor parsing error type from OSError to ValueError
complete pymatgen/io/cp2k/utils.py _(pre|post)processor doc strs
add type anno
* Pre/postprocessor
* add return types in pymatgen/io/cp2k/sets.py
required for mypy to analyze functions, found potential dict unpacking error in DftSet subclasses
fix typos
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
lbluque
pushed a commit
to lbluque/pymatgen
that referenced
this pull request
May 25, 2023
* Added a property assignment structure for testing. Tests not yet written.
* Modified test file. Removed NLCC_POTENTIALS.yaml, which has no use at the moment.
* Commits to this branch will be updates to defects module. Added WIP updates to the corrections module, which should include some simpler corrections like point charge. Added a WIP update to the thermodynamics module, which is going to include support for predomenance diagrams in the near future
* Defect module WIP
* Try else got tripped unecessarily. Fixed with conditional.
Also removed a print statement.
* Updated import statement.
* Updated import statement.
* Updated import statement.
* Fixed charge transfer, which was not working.
* Slightly better version of last commit
* Plotting updates.
* A very subtle error... Everything in the sets/inputs preserves the
ordering of the sites, except when you use the get_unique_site_indices
function to get aliases such as {'Mg_1': [...], 'Mg_2': [...], 'O_1': [...]}.
Then, the sites are given by a alias: index dictionary that doesn't preserve
order, and so sites can get jumbled when this happens. It doesn't always happen, so
it was hard to identify. Now, when aliasing is used for the Coord section,
the keywords are created in order of their indices. To further protect against
these sorts of issues for unforseen problems, I'm changing "self.keywords"
to be stored as an OrderedDict once they are provided to the Section. Since
Ordered Dicts inherit from Dicts, this shouldn't change anything.
Lastly, I have applied black formatting to everything to keep consistent.
* mypy on github (but not on my machine, oddly) didn't like the use of
aliases.get because SupportsLessThan is not part of it, even though
it worked in practice. While this new method is less elegant, it still
works well enough.
* Reorder import. Couple of formatting corrections from pylint.
* Update plotter.
* Created a polaron class as a child of Substitution.
* Trying out a "RelaxationTransformation" to help stitch together the
transformation history of a parent and child task.
* Tweak as_dict() summary.
* The GhostVacancy is a special vacancy object for CP2K calculations where
the pseudopotential of the atom is turned off, but the basis functions are
left behind.
* added dtype=object to np.array
* Update import statement
* Assembled basis sets, pseudopotential, and DFT+U settings into a single
settings file, which should be cleaner than using separate ones.
* Updated in accordance with new settings.yaml file.
* Update in accordance with new settings.yaml file.
* Update to one of the hubbard values.
* Fixed the getting of hubbard values.
* Updated predominance diagrams
* A temporary measure on my dev branch for avoid Potcar hashing with CP2K calculations
* These files are no longer necessary, as settings.yaml will hold all
this info.
* Update attribute.
* Update attribute
* Update the plot with "combine_charges" to make cleaner figures
* Keywords must have strings for names. Numbers will cause problems.
* Update to the mo_eigenvalues parsing for non-OT compatability. Parsing a raw
text file is incredibly sloppy.
* Update to the file reading. Subsections can have "subsection params",
some of which are used to alias the subsection, but some of which
are variables like "on" or "off". They are problematic from the
point of view of the Section objects. This will fix the issue of cp2k
restart files automatically assigning some of these superfluous
params, but is not a totally robust solution.
* Change to default diagonalization params.
* Update dict band gap.
* Updating mo_eigenvalues parsing, which is getting troublesome mixing
OT and diagonalization FWs now.
* Modifications to the DOS parser so that its more integrated with the
Dos module. Also made the DOS parser the default method for extracting
gaps, vbm, and cbm, which works for either OT or diagonalization.
* Update for aux_basis set. "match" keyword will now use primary basis, which
can be used for defect sites. Starting to get lots of spaghetti code here.
Also fixed indentation error.
* Added aux_basis argument
* Don't assume initial structure was parsed.
* Need hubbard > 0
* Update to diagonalization settings.
* Section Lists
* Reject if sizes don't match
* Testing new plot.
* Possible hash for defects.
* Nevermind.
* Remove warning.
* Update plus_u and xc_functional
* fix
* Update for functional processing. Do not like this as it relies on
having the input file present, but the text in the output file is too
variable to parse reliably.
* Still need to figure out how to get mos automatically. Upped it for
now. Elec temp of 500 maybe have been a little too high.
* Change how output parser gets the functional.
* Use the getattr operation to be case insensitive.
* Update section descriptions.
* So bader can use reference charges with cubes. Will submit patch and merge.
* This function should not default to cm^-3 units. Most/all of pymatgen does things per formula unit / composition object. So that's how this should be as well. The exponential is for an individual atom, and the multiplicity attribute will convert it to a per f.u. basis.
* Dos objects
* Use structure matcher instead of exact equality to deal with empty
site properties.
* fixing cube
* Fix for getting items. Now there is a seperate get function for keyword
and section, so internal methods can be more robust.
* Update to docstring and import.
* Adsorbent class.
* Concentration should be in formula units by default.
* (1) prettier plots
(2) get_doping() added since n/p are reused.
* Docstring.
* Add rotations
* forgot to make msonable
* Kpoints keyword
Scheme keyword was missing. Lead to errors.
* Updates for functionals
Some updates for functionals to make LibXC slightly easier.
* Parse initial structure
For some reason, one example did not show the default blank line. Not sure if it was the new version of cp2k or something else, but make the blank line a conditional now.
* �Parse initial structure
Last commit did not cover edge case. This should work.
* Updates.
Fix readline for both cases of coord table. Modify sets for hybrids. New utility function for truncation radius.
* optFIT basis
Opt fit basis sets should be preferred for C and B. These are not part of standard dist. and should be added to settings as well.
* Convergence criteria
Update the force convergence criteria to roughly match the MPRelaxSet
* Add option for strict updates.
Update now supports optional "strict" keyword to avoid inserting new keywords and sections.
* Update hybrid
Slight tweaks to logic for hybrid sets.
* Update test
Nonsense structure cannot use dummy element. Sets check validity of element inputs now.
* Update functionals
Hybrid was not being registered for PBE0 since only one functional is used.
* Add cutoff radius
Include cutoff radius even if not used in order to suppress warnings.
* Update core defects
Adsorbate is that species that adsorbs onto a surface, adsorbent is surface doing the adsorbing. Also the default defect concentration is back to cm-3. This is not ultimately desirable, but its causing too many problems.
* Updates
* Cutoff radius
Do not override. Just provide a warning. Also make the long range correction default to provide better energies when cutoff is very small.
* Fix cutoff
* Changes and Fixes
Newline in inputs.py
Adjust stride in sets.py
Read energies in outputs.py
* Update args
* Fix
* stress tensor
* Allow positive
* Updates
* New Thermo
* Remove temp
Temporary things were saved during a laptop crash. Now removed.
* SectionList
Modify the file reader with SectionList
* Double loop
* Drop undeveloped corrections and work on 2d correction
* Get section explicit
* Dont check if not running freysoldt
* Rename
Predominance diagram may confuse people. Will use Brouwer diagram instead.
DFT plus U is very finicky in cp2k due to basis sets. It only really works with LOWDIN scheme, which is only available in newer versions of the code, and even then it is prone to instabilities. For these reasons, plus u should not be the default.
* Formatting updates
* Deprecation upcoming
* Formatting
* Formatting
* Formatting
* Defect Complex and Linting
* Typing
* Emergency push
Laptop malfunctioning need to sync
* Update to correction
* Bandstructures
Input objects for band structure and ability to parse the band structure text files generated by cp2k.
* Revisions and Bandstructure support
Some formatting has been updated for new linting. Bandstructure support has been added to inputs and output parsers. Some updates to DOS parsers as well.
* Kpoints
* Format
* Revert to master
* Last minute fix. Needs to access num_kpts
* Needs to access num_kpts
* Old test and type check
* Some more lint
* Unused import
* Lint
* override_default_params
must not be none
* None->{}
* Add self
* Loops
* remove sigma
* A few changes to tests and test files
* fix assert
* AssertEqual
* Kpoints
* Dict already preserves ordering since py3.7
* use .items()
* EPS_PGF_ORB
* Gamma kpoint
* Basis and Potential
* None
* Dict
* startswith
* get element
* kpts
* Only use trunc if periodic
* Only use trunc if periodic
* ADMM Keywords
* Activate motion
* Delete
* runtype check
* molecules
* processor
* dft set
* multiplicity
* Exchange correction function
* pmg config
* Test set
* Basis and Potentials
* pmg config
* Molecule
* kpts
* Some tests
* Test sets
* Lintings
* Test files and tests
* Lint
* More lint
* Don't use built-in name
* list->List, dict->Dict
* Refactor pydantic to msonable
* Delete settings.yaml
* mypy 0.991 upgrade
* Util types and lint
* Uncomment a line
* Missing arg
* type
* arg
* Dftd3
Might as well add this
* Don't use literal
* Json
A hack so that jsanitized objects still have int keys
* Test for aux
* Tiny fixes
* rename some vars in pymatgen/cli/pmg_config.py to snake case
rename single-letter vars (discouraged by flake8)
* breaking: change CP2K _postprocessor parsing error type from OSError to ValueError
complete pymatgen/io/cp2k/utils.py _(pre|post)processor doc strs
add type anno
* Pre/postprocessor
* add return types in pymatgen/io/cp2k/sets.py
required for mypy to analyze functions, found potential dict unpacking error in DftSet subclasses
fix typos
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
janosh
added a commit
that referenced
this pull request
May 26, 2023
* Added a property assignment structure for testing. Tests not yet written.
* Modified test file. Removed NLCC_POTENTIALS.yaml, which has no use at the moment.
* Commits to this branch will be updates to defects module. Added WIP updates to the corrections module, which should include some simpler corrections like point charge. Added a WIP update to the thermodynamics module, which is going to include support for predomenance diagrams in the near future
* Defect module WIP
* Try else got tripped unecessarily. Fixed with conditional.
Also removed a print statement.
* Updated import statement.
* Updated import statement.
* Updated import statement.
* Fixed charge transfer, which was not working.
* Slightly better version of last commit
* Plotting updates.
* A very subtle error... Everything in the sets/inputs preserves the
ordering of the sites, except when you use the get_unique_site_indices
function to get aliases such as {'Mg_1': [...], 'Mg_2': [...], 'O_1': [...]}.
Then, the sites are given by a alias: index dictionary that doesn't preserve
order, and so sites can get jumbled when this happens. It doesn't always happen, so
it was hard to identify. Now, when aliasing is used for the Coord section,
the keywords are created in order of their indices. To further protect against
these sorts of issues for unforseen problems, I'm changing "self.keywords"
to be stored as an OrderedDict once they are provided to the Section. Since
Ordered Dicts inherit from Dicts, this shouldn't change anything.
Lastly, I have applied black formatting to everything to keep consistent.
* mypy on github (but not on my machine, oddly) didn't like the use of
aliases.get because SupportsLessThan is not part of it, even though
it worked in practice. While this new method is less elegant, it still
works well enough.
* Reorder import. Couple of formatting corrections from pylint.
* Update plotter.
* Created a polaron class as a child of Substitution.
* Trying out a "RelaxationTransformation" to help stitch together the
transformation history of a parent and child task.
* Tweak as_dict() summary.
* The GhostVacancy is a special vacancy object for CP2K calculations where
the pseudopotential of the atom is turned off, but the basis functions are
left behind.
* added dtype=object to np.array
* Update import statement
* Assembled basis sets, pseudopotential, and DFT+U settings into a single
settings file, which should be cleaner than using separate ones.
* Updated in accordance with new settings.yaml file.
* Update in accordance with new settings.yaml file.
* Update to one of the hubbard values.
* Fixed the getting of hubbard values.
* Updated predominance diagrams
* A temporary measure on my dev branch for avoid Potcar hashing with CP2K calculations
* These files are no longer necessary, as settings.yaml will hold all
this info.
* Update attribute.
* Update attribute
* Update the plot with "combine_charges" to make cleaner figures
* Keywords must have strings for names. Numbers will cause problems.
* Update to the mo_eigenvalues parsing for non-OT compatability. Parsing a raw
text file is incredibly sloppy.
* Update to the file reading. Subsections can have "subsection params",
some of which are used to alias the subsection, but some of which
are variables like "on" or "off". They are problematic from the
point of view of the Section objects. This will fix the issue of cp2k
restart files automatically assigning some of these superfluous
params, but is not a totally robust solution.
* Change to default diagonalization params.
* Update dict band gap.
* Updating mo_eigenvalues parsing, which is getting troublesome mixing
OT and diagonalization FWs now.
* Modifications to the DOS parser so that its more integrated with the
Dos module. Also made the DOS parser the default method for extracting
gaps, vbm, and cbm, which works for either OT or diagonalization.
* Update for aux_basis set. "match" keyword will now use primary basis, which
can be used for defect sites. Starting to get lots of spaghetti code here.
Also fixed indentation error.
* Added aux_basis argument
* Don't assume initial structure was parsed.
* Need hubbard > 0
* Update to diagonalization settings.
* Section Lists
* Reject if sizes don't match
* Testing new plot.
* Possible hash for defects.
* Nevermind.
* Remove warning.
* Update plus_u and xc_functional
* fix
* Update for functional processing. Do not like this as it relies on
having the input file present, but the text in the output file is too
variable to parse reliably.
* Still need to figure out how to get mos automatically. Upped it for
now. Elec temp of 500 maybe have been a little too high.
* Change how output parser gets the functional.
* Use the getattr operation to be case insensitive.
* Update section descriptions.
* So bader can use reference charges with cubes. Will submit patch and merge.
* This function should not default to cm^-3 units. Most/all of pymatgen does things per formula unit / composition object. So that's how this should be as well. The exponential is for an individual atom, and the multiplicity attribute will convert it to a per f.u. basis.
* Dos objects
* Use structure matcher instead of exact equality to deal with empty
site properties.
* fixing cube
* Fix for getting items. Now there is a seperate get function for keyword
and section, so internal methods can be more robust.
* Update to docstring and import.
* Adsorbent class.
* Concentration should be in formula units by default.
* (1) prettier plots
(2) get_doping() added since n/p are reused.
* Docstring.
* Add rotations
* forgot to make msonable
* Kpoints keyword
Scheme keyword was missing. Lead to errors.
* Updates for functionals
Some updates for functionals to make LibXC slightly easier.
* Parse initial structure
For some reason, one example did not show the default blank line. Not sure if it was the new version of cp2k or something else, but make the blank line a conditional now.
* �Parse initial structure
Last commit did not cover edge case. This should work.
* Updates.
Fix readline for both cases of coord table. Modify sets for hybrids. New utility function for truncation radius.
* optFIT basis
Opt fit basis sets should be preferred for C and B. These are not part of standard dist. and should be added to settings as well.
* Convergence criteria
Update the force convergence criteria to roughly match the MPRelaxSet
* Add option for strict updates.
Update now supports optional "strict" keyword to avoid inserting new keywords and sections.
* Update hybrid
Slight tweaks to logic for hybrid sets.
* Update test
Nonsense structure cannot use dummy element. Sets check validity of element inputs now.
* Update functionals
Hybrid was not being registered for PBE0 since only one functional is used.
* Add cutoff radius
Include cutoff radius even if not used in order to suppress warnings.
* Update core defects
Adsorbate is that species that adsorbs onto a surface, adsorbent is surface doing the adsorbing. Also the default defect concentration is back to cm-3. This is not ultimately desirable, but its causing too many problems.
* Updates
* Cutoff radius
Do not override. Just provide a warning. Also make the long range correction default to provide better energies when cutoff is very small.
* Fix cutoff
* Changes and Fixes
Newline in inputs.py
Adjust stride in sets.py
Read energies in outputs.py
* Update args
* Fix
* stress tensor
* Allow positive
* Updates
* New Thermo
* Remove temp
Temporary things were saved during a laptop crash. Now removed.
* SectionList
Modify the file reader with SectionList
* Double loop
* Drop undeveloped corrections and work on 2d correction
* Get section explicit
* Dont check if not running freysoldt
* Rename
Predominance diagram may confuse people. Will use Brouwer diagram instead.
DFT plus U is very finicky in cp2k due to basis sets. It only really works with LOWDIN scheme, which is only available in newer versions of the code, and even then it is prone to instabilities. For these reasons, plus u should not be the default.
* Formatting updates
* Deprecation upcoming
* Formatting
* Formatting
* Formatting
* Defect Complex and Linting
* Typing
* Emergency push
Laptop malfunctioning need to sync
* Update to correction
* Bandstructures
Input objects for band structure and ability to parse the band structure text files generated by cp2k.
* Revisions and Bandstructure support
Some formatting has been updated for new linting. Bandstructure support has been added to inputs and output parsers. Some updates to DOS parsers as well.
* Kpoints
* Format
* Revert to master
* Last minute fix. Needs to access num_kpts
* Needs to access num_kpts
* Old test and type check
* Some more lint
* Unused import
* Lint
* override_default_params
must not be none
* None->{}
* Add self
* Loops
* remove sigma
* A few changes to tests and test files
* fix assert
* AssertEqual
* Kpoints
* Dict already preserves ordering since py3.7
* use .items()
* EPS_PGF_ORB
* Gamma kpoint
* Basis and Potential
* None
* Dict
* startswith
* get element
* kpts
* Only use trunc if periodic
* Only use trunc if periodic
* ADMM Keywords
* Activate motion
* Delete
* runtype check
* molecules
* processor
* dft set
* multiplicity
* Exchange correction function
* pmg config
* Test set
* Basis and Potentials
* pmg config
* Molecule
* kpts
* Some tests
* Test sets
* Lintings
* Test files and tests
* Lint
* More lint
* Don't use built-in name
* list->List, dict->Dict
* Refactor pydantic to msonable
* Delete settings.yaml
* mypy 0.991 upgrade
* Util types and lint
* Uncomment a line
* Missing arg
* type
* arg
* Dftd3
Might as well add this
* Don't use literal
* Json
A hack so that jsanitized objects still have int keys
* Test for aux
* Tiny fixes
* rename some vars in pymatgen/cli/pmg_config.py to snake case
rename single-letter vars (discouraged by flake8)
* breaking: change CP2K _postprocessor parsing error type from OSError to ValueError
complete pymatgen/io/cp2k/utils.py _(pre|post)processor doc strs
add type anno
* Pre/postprocessor
* add return types in pymatgen/io/cp2k/sets.py
required for mypy to analyze functions, found potential dict unpacking error in DftSet subclasses
fix typos
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
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Summary
PR for major updates to CP2K functionality in pmg, plus a minor edit to
compatibility.py. PR has been geared towards simplifying certain features, while making others more compatible with the newatomate2package, which will use this version.inputs.pysets.pyoutputs.py:utils.pyinputs.pypmg_config.py