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Provide additional functionality to deal with structures in py4vasp #106

Merged
merged 74 commits into from
Sep 1, 2023
Merged

Provide additional functionality to deal with structures in py4vasp #106

merged 74 commits into from
Sep 1, 2023

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martin-schlipf
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sudarshanv01 and others added 30 commits August 1, 2023 14:25
@sudarshanv01
Convert a Series to a frame through the to_frame method in Series
7497775
@sudarshanv01
Implement to_frame for sequence of series
02d54b6
@sudarshanv01
Alter to_frame to allow it to take in multiple y-inputs
c557f72
@sudarshanv01
Refactor to_frame
efca677
@sudarshanv01
Add width to series
9d180c7
@sudarshanv01
assert in to_frame that the dimension of weight and y is the same
18b268d
@sudarshanv01
Allow different length series to to_frame
0bd3f51
@sudarshanv01
Create the to_csv method
cda4814
@sudarshanv01
Implement to_csv method in the Mixin class
be04713
@sudarshanv01
Add to_csv and to_frame to the Mixin class
0b35fe1
@sudarshanv01
Apply black and isort
30b0b13
@sudarshanv01
Added not_core to tests needing pandas
f5a4881
@sudarshanv01
black and isort code formatting
bafcb11
@sudarshanv01
Added more not_core to graph tests
b6db94c
@sudarshanv01
Change resolve to absolute when getting absolute path for mixin tests
ad66601
@sudarshanv01
Added documentation for the and methods
92b51a4
@sudarshanv01
Update developer depedencies with ipykernel
623124a
@sudarshanv01
Merge branch 'vasp-dev:master' into master
bcb6f89
@sudarshanv01
Allow install github actions to run on pull requests
a907827
@sudarshanv01
Merge branch 'master' of github.com:sudarshanv01/py4vasp
0d5838f
@sudarshanv01
Added pip installation of ipykernel into install.yaml
7f8739f
@sudarshanv01
Merge branch 'vasp-dev:master' into master
f4f1515
@sudarshanv01
add pre-commit-config.yaml and pre-commit as a dependency
5c1240d
@sudarshanv01
Merge branch 'master' of github.com:sudarshanv01/py4vasp
9a32998
Implement CONTCAR dataclass in _raw
097cfcb
@sudarshanv01
Merge branch 'vasp-dev:master' into structure-sprint
e36305b
Implement POSCAR input feature
7b1fb13
@martin-schlipf
Implement basic read for CONTCAR file
83cc7ca
Implement getters for comment_line and cells
a80bd14
Implement topology property for parser
c68fa7f
sudarshanv01 and others added 27 commits August 30, 2023 12:05
@sudarshanv01
Implement has_selective_dynamics method
60ba825
@sudarshanv01
Implement selective dynamics parsing
443e9bc
@sudarshanv01
Implement cartesian input -> py4vasp structure in direct coordinates
d438437
@sudarshanv01
Implement lattice velocities
ffc650a
@sudarshanv01
Implement ion velocities
713b66c
@martin-schlipf
Do not set items in dictionary that would be None
95f92d9
@sudarshanv01
Implement has_ion_velocities for to_contcar method
87fbe34
@sudarshanv01
Merge branch 'structure-sprint' of github.com:vasp-dev/py4vasp into s…
d1f5868 
…tructure-sprint
@sudarshanv01
Refactor tests fixture code
d39098b
@sudarshanv01
Refactor tests fixture code
baa3e6c
@sudarshanv01
Refactor the cubic_BN test fixture
5d15c3c
@sudarshanv01
Change to splitlines
312ef88
@martin-schlipf
Implement read for single structure instead of trajectory
0b6b704
@martin-schlipf
Implement reading cartesian positions for single structure
088b61a
@martin-schlipf
Fix number of atoms for single step structure
0b9b2ff
@martin-schlipf
Fix number of steps for single step structure
6edc039
@martin-schlipf
Implement writing of single step Structure
0387521 
Also write scaling factor to POSCAR file
@martin-schlipf
Use the single step structure in CONTCAR class
5fa1240
@martin-schlipf
Implement printing CONTCAR to string
ba2fb09
@martin-schlipf
Update dependencies due to security warning (#107)
3e10851
@martin-schlipf
Fix broken test
232937b
@sudarshanv01
Add some documentation to the Poscar parser
b5c50ff
@martin-schlipf
Implement plot function and check data is read from HDF5
1f981a6
@martin-schlipf
Revert output to one produced by VASP
04c9cf4
@martin-schlipf
Add documentation and fix format
bb1701c
@martin-schlipf
Use capital letters in for CONTCAR in Calculation class
8c90fdf
@martin-schlipf
Skip plot test for py4vasp-core
7f41024
@martin-schlipf martin-schlipf marked this pull request as ready for review September 1, 2023 19:27
@martin-schlipf martin-schlipf merged commit b80bf00 into master Sep 1, 2023
21 checks passed
@martin-schlipf martin-schlipf deleted the structure-sprint branch September 1, 2023 19:50
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2 participants
@martin-schlipf @sudarshanv01