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change: start materials.basis.coordinates.id enumeration from 0 instead of 1 #142

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merged 5 commits into from
Feb 21, 2024
Merged

change: start materials.basis.coordinates.id enumeration from 0 instead of 1 #142

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07dc368
update: start arrays in basis from 0
VsevolodX Feb 20, 2024
4aeb0ab
chore: id 1,2 -> id 0,1
VsevolodX Feb 21, 2024
e015cea
fix: patch only one os function, not the whole module
VsevolodX Feb 21, 2024
249ef89
chore: change the id logic to start from 0 instead of 1 in test fixtures
VsevolodX Feb 21, 2024
e33900d
chore: change the indexing from + 1 to normal
VsevolodX Feb 21, 2024
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16 changes: 8 additions & 8 deletions express/parsers/apps/espresso/formats/txt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -333,8 +333,8 @@ def initial_basis(self, text):
Example:
{
'units': 'angstrom',
'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [2.1095228, 1.49165, 3.6538]}]
'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [2.1095228, 1.49165, 3.6538]}]
}
"""
alat = self._get_alat(text)
Expand Down Expand Up @@ -436,14 +436,14 @@ def _basis_convergence(self, text):
[
{
'units': 'crystal',
'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
},
...
{
'units': 'crystal',
'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
}
]
"""
Expand All @@ -462,8 +462,8 @@ def _extract_basis_from_bfgs_blocks(self, text):
Example:
{
'units': 'crystal',
'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
}
"""
basis = {"units": "crystal", "elements": [], "coordinates": []}
Expand Down
4 changes: 2 additions & 2 deletions express/parsers/apps/espresso/formats/xml/xml_base.py
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Expand Up @@ -139,8 +139,8 @@ def final_basis(self):
Example:
{
'units': 'angstrom',
'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
}
"""
pass
4 changes: 2 additions & 2 deletions express/parsers/apps/espresso/formats/xml/xml_pre64.py
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Original file line number Diff line number Diff line change
Expand Up @@ -165,8 +165,8 @@ def final_basis(self):
Example:
{
'units': 'angstrom',
'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
}
"""
elements, coordinates = [], []
Expand Down
8 changes: 4 additions & 4 deletions express/parsers/apps/vasp/formats/txt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,14 +111,14 @@ def _basis_convergence(self, text, atom_names):
[
{
'units': 'crystal',
'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
},
...
{
'units': 'crystal',
'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.0, 0.0, 0.0]}]
'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.0, 0.0, 0.0]}]
}
]
"""
Expand Down
4 changes: 2 additions & 2 deletions express/parsers/apps/vasp/formats/xml.py
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Expand Up @@ -292,8 +292,8 @@ def final_basis(self):
Example:
{
'units': 'angstrom',
'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [1.11, 0.78, 1.93]}]
'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [1.11, 0.78, 1.93]}]
}
"""
lattice = self.final_lattice_vectors()
Expand Down
8 changes: 4 additions & 4 deletions express/parsers/mixins/ionic.py
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Expand Up @@ -42,8 +42,8 @@ def initial_basis(self):
Example:
{
'units': 'crystal',
'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.25, 0.25, 0.25]}]
'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.25, 0.25, 0.25]}]
}
"""
pass
Expand Down Expand Up @@ -81,8 +81,8 @@ def final_basis(self):
Example:
{
'units': 'crystal',
'elements': [{'id': 1, 'value': 'Si'}, {'id': 2, 'value': 'Si'}],
'coordinates': [{'id': 1, 'value': [0.0, 0.0, 0.0]}, {'id': 2, 'value': [0.25, 0.25, 0.25]}]
'elements': [{'id': 0, 'value': 'Si'}, {'id': 1, 'value': 'Si'}],
'coordinates': [{'id': 0, 'value': [0.0, 0.0, 0.0]}, {'id': 1, 'value': [0.25, 0.25, 0.25]}]
}
"""
pass
Expand Down
4 changes: 2 additions & 2 deletions express/parsers/structure.py
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Expand Up @@ -158,8 +158,8 @@ def basis(self):
"""
return {
"units": "crystal",
"elements": [{"id": i + 1, "value": v.species_string} for i, v in enumerate(self.structure.sites)],
"coordinates": [{"id": i + 1, "value": v.frac_coords.tolist()} for i, v in enumerate(self.structure.sites)],
"elements": [{"id": i, "value": v.species_string} for i, v in enumerate(self.structure.sites)],
"coordinates": [{"id": i, "value": v.frac_coords.tolist()} for i, v in enumerate(self.structure.sites)],
}

def space_group_symbol(self):
Expand Down
2 changes: 1 addition & 1 deletion express/properties/utils.py
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Expand Up @@ -26,4 +26,4 @@ def to_array_with_ids(array):
Returns:
list
"""
return [{"id": index + 1, "value": value} for index, value in enumerate(array)]
return [{"id": index, "value": value} for index, value in enumerate(array)]
2 changes: 1 addition & 1 deletion tests/fixtures/data.py
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2 changes: 1 addition & 1 deletion tests/fixtures/espresso/v5_4/references.py
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8 changes: 4 additions & 4 deletions tests/fixtures/nwchem/references.py
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Expand Up @@ -14,10 +14,10 @@

BASIS = {
"units": "angstrom",
"elements": [{"id": 1, "value": "O"}, {"id": 2, "value": "H"}, {"id": 3, "value": "H"}],
"elements": [{"id": 0, "value": "O"}, {"id": 1, "value": "H"}, {"id": 2, "value": "H"}],
"coordinates": [
{"id": 1, "value": [0.00000000, 0.00000000, 0.22143053]},
{"id": 2, "value": [0.00000000, 1.43042809, -0.88572213]},
{"id": 3, "value": [0.00000000, -1.43042809, -0.88572213]},
{"id": 0, "value": [0.00000000, 0.00000000, 0.22143053]},
{"id": 1, "value": [0.00000000, 1.43042809, -0.88572213]},
{"id": 2, "value": [0.00000000, -1.43042809, -0.88572213]},
],
}
2 changes: 1 addition & 1 deletion tests/unit/properties/non_scalar/test_atomic_forces.py
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Expand Up @@ -5,7 +5,7 @@
ATOMIC_FORCES = {
"units": "eV/angstrom",
"name": "atomic_forces",
"values": [{"id": 1, "value": [-3.9e-07, -2.4e-07, 0.0]}, {"id": 2, "value": [3.9e-07, 2.4e-07, 0.0]}],
"values": [{"id": 0, "value": [-3.9e-07, -2.4e-07, 0.0]}, {"id": 1, "value": [3.9e-07, 2.4e-07, 0.0]}],
}


Expand Down
2 changes: 1 addition & 1 deletion tests/unit/properties/non_scalar/test_magnetic_moments.py
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Expand Up @@ -5,7 +5,7 @@
MAGNETIC_MOMENTS = {
"units": "uB",
"name": "magnetic_moments",
"values": [{"id": 1, "value": [0, 0, 1.235]}, {"id": 2, "value": [0, 0, -1.235]}],
"values": [{"id": 0, "value": [0, 0, 1.235]}, {"id": 1, "value": [0, 0, -1.235]}],
}


Expand Down
6 changes: 3 additions & 3 deletions tests/unit/properties/non_scalar/test_workflow.py
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Expand Up @@ -13,9 +13,9 @@ def setUp(self):
def tearDown(self):
super().setUp()

@mock.patch("express.properties.workflow.os")
def test_pyml_workflow(self, mock_os):
mock_os.listdir.return_value = MOCK_BASENAMES
@mock.patch("express.properties.workflow.os.listdir")
def test_pyml_workflow(self, mock_os_listdir):
mock_os_listdir.return_value = MOCK_BASENAMES

name = NAME
parser = PARSER
Expand Down
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