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Symfunc paramgen #15

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@flobuch flobuch commented Jul 10, 2019

Implementation of methods for automated symmetry function parameter generation proposed in the literature.

Florian Buchner added 30 commits April 9, 2019 19:44
WIP: begin implementing symmetry function writer
cae0093
Create classes for symmetry function descriptors.
1311b93
Start work on class SymFuncParamGenerator.
a03c1b2
Begin radial parameter generation.
157a1ca 
Start implementing radial parameter generation method from 2018
'Imbalzano et al' paper
Continue work on radial parameter generation.
1296205 
Add radial parameter generation method from 2018 'Gastegger et al.'
paper.
Began reworking storage of symfunc params.
e0e8c2c 
r_shift, eta, zeta now stored in individual arrays, information on
radial parameter generation settings stored in dictionary.
Implemented method for writing generation settings
f3d0718
Add check for correct input when setting sf type.
3260c36
Make check for correct symfunc type display permitted values in error
cb445cd 
message.
Begin implementation of writing the sf parameters.
2de0465 
Implement method for constructing the necessary element combinations
depending on sf type (done) and begin implementing method for writing sf
parameters in format required for input.nn (WIP, so far only iteration
over element combinations, but not over sf parameters, is implemented).
Merge branch 'master' into symfunc_paramgen
3fb790f
Implement loops over sf parameters during writing.
a627b00
Replace some regular strings with f strings.
6ad3d06
Implement sf type and zeta setters via decorators.
01d895f
Begin systematic in-code documentation.
28a2815
Extend in-code documentation.
1280cec
Make elements and element combinations into properties.
8274717
Remove file SymFuncDescriptors.py.
5615862 
Also rename method create_element_combinations to find_element_combinations.
Remove file write_symfunc.py
d4d4278
Add argument r_upper to radial param generation method.
a3163e3 
Also add checks if values of r_lower, r_upper, r_cutoff are positive and
valid in relation to each other.
Rework and extend in-code documentation.
5655ae6
Make lambdas into class variable.
44bf848
Rename some variables; modify in-code documentation.
3adc365
Allow r_lower=0 for 'gastegger2018', method 'shift'.
a52e249
Clean up output of method write_generation_info().
073c4a4 
Also rename to write_parameter_info().
Add write-to-file option to write_parameter_info().
53d92ea
Add write-to-file option to write_parameter_strings().
208358c
Reorganize folder structure.
b1c0145
Add first basic tests.
8b4c0a5
Set r_cutoff independently of radial parameter generation.
71aa988
Florian Buchner and others added 26 commits May 6, 2019 14:04
Add optional arg to class-state-checking methods.
839323e 
When specified, this makes them print modified error message mentioning
the name of the calling method.
Rename set_radial_params_manually, and check inputs.
60fadc7
Extend tests.
01a78f3
Rework warnings for unused r_lower and r_upper;
93105d6 
Also extend tests.
Cleaner, dedicated test for parameter string writing.
9eb9416
Add dedicated test for settings write method.
928297a
Reword some error messages; extend documentation.
245e3d7
Rename file test_outputs.py to test_misc.py.
e0902f9
First quick build of sphinx documentation.
374986f
Rewrite in-line ifs -> tests report correct coverage.
7d1a7e4
Rewrite various tests using pytest fixtures.
66f2154
Rename main module file to meet PEP-8 conventions.
439e1d9
Begin work on example.
cc1d22f
Continue working on example.
c2c511d
Rework documentation.
7ff5194
Some inter-documentation linking, some rewording.
ddcbea9
Add brief verbal description at beginning of doc.
0ab43d9
Add README.md for docs.
4e853c8
Make small addition to example and fix typo.
cb65687
Delete unused 'stdout-comparison-file.txt' in docs.
62143b7
Mention name of target parameter file 'input.nn'.
2ea8ad2
Bugfix in write_settings_overview.
9b97730 
When printing long arrays, EVERY line of multiline output is now made into comment.
@singraber
PEP8 formatting for sfparamgen.py
59d5258
Very minor refactor of tests for write methods.
c3293b2
Change write method args from paths to file objects.
9171cb3
Adapt example to reflect changed write methods.
6189fa0
@singraber singraber mentioned this pull request Apr 24, 2020
Closed
@singraber singraber added enhancement New feature or request tool Adds a new application to the tools collection labels Sep 5, 2020
hjjvandam added a commit to hjjvandam/DeepDriveMD-pipeline that referenced this pull request Aug 27, 2024
@hjjvandam
N2P2 tool for symmetry function generation
a2faf7e 
This tool stems from the N2P2 project. It is discussed in the pull
request CompPhysVienna/n2p2#15 but not
integrated in the main branch yet. So in the interim I am copying
it so we can use it here. Hopefully it will soon be integrated and
then we can use it from the "official" N2P2 distribution.
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@flobuch @singraber