pymatgen update, adsorption vector, dockerfile update #92
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added 4 commits
April 1, 2020 08:10
ktran9891
approved these changes
Apr 2, 2020
| return vector | ||
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| def _ang_between_vectors(v1, v2): | ||
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No need or extra lines between function definition & docstring
| @@ -251,6 +252,172 @@ def find_adsorption_sites(atoms): | |||
| sites = sites_dict['all'] | |||
| return sites | |||
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We try to keep two lines between functions
| vector[2] = -1.0 | ||
| vector /= -np.linalg.norm(vector) | ||
| return vector | ||
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2 lines between functions
| vector = np.array([0., 0., 1.]) | ||
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| del slab_atoms[[U_index]] | ||
| return vector | ||
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2 lines between functions
| if elem not in cn_dict.keys(): | ||
| cn_dict[elem] = [] | ||
| cn = v.get_cn(sym_struct, idx, use_weights=True) | ||
| cn = float('%.5f' %(round(cn, 5))) |
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flake8 flag E225: missing whitespace around operator (add space after %)
| the surface atoms | ||
| ''' | ||
| struct = AseAtomsAdaptor.get_structure(atoms) | ||
| v = VoronoiNN() |
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Single-letter object names are not a good practice. Expand it out to be more descriptive.
| # for atoms in each structure. | ||
| # for example, Pt[1,1,1] would have cn=3 and cn=12 | ||
| # depends on the Pt atom. | ||
| v = VoronoiNN() |
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Single-letter object names are not a good practice. Expand it out to be more descriptive.
| @@ -42,6 +47,7 @@ | |||
| from ..gasdb import get_mongo_collection | |||
| from ..mongo import make_atoms_from_doc | |||
| from ..tasks.atoms_generators import GenerateBulk | |||
| from ..tasks.calculation_finders import FindBulk | |||
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| expected_heights = [6.272210880031006, 6.176446311678471, 4.984647756561888, | ||
| 5.121238738402999, 4.984647756561888, 6.176446311678471, | ||
| 6.272210880031005, 6.147996384691849, 4.839115752287323, | ||
| 4.839115752287323, 6.147996384691849, 6.176446311678471, | ||
| 3.275555302966866, 4.839115752287323, 4.984647756561887, | ||
| 3.4354313844223103, 5.021787742477727, 5.121238738402999, | ||
| 3.275555302966866, 4.839115752287322, 6.14799638469185] | ||
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| 2.8129223518338944, | ||
| 20.895846464363103), | ||
| adsorption_site=(1.40646118, | ||
| 1.40646118, |
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Dockerfile has been updated, which contains a newer version of miniconda (with python 3.6) and several packages updates, the biggest one being pymatgen (2019.12.3 version).
Pymatgen update provides better adsorption sites to our catalog. It also has the new "fast porbaix" algorithm, which makes bulk stability screening faster and can/should be incorporated into GASpy screening in the future.
The addition of the adsorption vector pieces allows us to place adsorbates better. Instead of placing adsorbates normal to the entire slab (default is [0,0,1]), it will figure out the local plane and place adsorbates normal to it.