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Merged
amcadmus merged 1 commit into from
Jun 30, 2020
Merged

convert LabeledSystem to ComputedStructureEntry #104

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21 changes: 21 additions & 0 deletions dpdata/system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -496,6 +496,7 @@ def to_pymatgen_structure(self):
structure=Structure(system.data['cells'][0],species,system.data['coords'][0],coords_are_cartesian=True)
structures.append(structure)
return structures


@register_to_funcs.register_funcs("ase/structure")
def to_ase_structure(self):
Expand Down Expand Up @@ -1329,6 +1330,26 @@ def shuffle(self):
self.data[ii] = self.data[ii][idx]
return idx

def to_pymatgen_ComputedStructureEntry(self):
'''
convert System to Pymagen ComputedStructureEntry obj

'''
try:
from pymatgen.entries.computed_entries import ComputedStructureEntry
except:
raise ImportError('No module ComputedStructureEntry in pymatgen.entries.computed_entries')

entries=[]
for system in self.to_list():
structure=system.to_pymatgen_structure()[0]
energy=system.data['energies'][0]
data={'forces':system.data['forces'][0],
'virials':system.data['virials'][0]}

entry=ComputedStructureEntry(structure,energy,data=data)
entries.append(entry)
return entries

class MultiSystems:
'''A set containing several systems.'''
Expand Down
226 changes: 226 additions & 0 deletions tests/computed_structure_entry.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,226 @@
{
"@module": "pymatgen.entries.computed_entries",
"@class": "ComputedStructureEntry",
"energy": -28.39848822,
"composition": {
"O": 2.0,
"H": 4.0
},
"parameters": {},
"data": {
"forces": {
"@module": "numpy",
"@class": "array",
"dtype": "float64",
"data": [
[
-0.211386,
-1.770018,
0.507873
],
[
-1.47897,
-0.663468,
-0.917499
],
[
-0.178977,
0.946024,
0.351008
],
[
0.38587,
0.822681,
-0.844953
],
[
1.156783,
0.157322,
-0.138993
],
[
0.32185,
0.505766,
1.049144
]
]
},
"virials": {
"@module": "numpy",
"@class": "array",
"dtype": "float64",
"data": [
[
-1.3720085358803906,
-0.2485681009072721,
0.4575213433975083
],
[
-0.2485681009072721,
-1.408552571807875,
-0.2783962730161448
],
[
0.4575213433975083,
-0.2783962730161448,
-1.8782261334719614
]
]
}
},
"entry_id": null,
"correction": 0.0,
"structure": {
"@module": "pymatgen.core.structure",
"@class": "Structure",
"charge": null,
"lattice": {
"matrix": [
[
10.0,
0.0,
0.0
],
[
-0.011409,
10.0,
0.0
],
[
0.1411083,
-0.0595569,
10.0
]
],
"a": 10.0,
"b": 10.000006508261933,
"c": 10.00117286005329,
"alpha": 90.34211999314414,
"beta": 89.19157698565051,
"gamma": 90.06536872648402,
"volume": 1000.0
},
"sites": [
{
"species": [
{
"element": "O",
"occu": 1
}
],
"abc": [
0.4280678471391986,
0.42481761932567,
0.519943
],
"xyz": [
4.3492,
4.217210000000001,
5.19943
],
"label": "O",
"properties": {}
},
{
"species": [
{
"element": "O",
"occu": 1
}
],
"abc": [
0.23060991326548744,
0.62824882136683,
0.113307
],
"xyz": [
2.31492,
6.27574,
1.13307
],
"label": "O",
"properties": {}
},
{
"species": [
{
"element": "H",
"occu": 1
}
],
"abc": [
0.454949233514069,
0.34706581743272,
0.46288799999999997
],
"xyz": [
4.61085,
3.44309,
4.62888
],
"label": "H",
"properties": {}
},
{
"species": [
{
"element": "H",
"occu": 1
}
],
"abc": [
0.39089296133220036,
0.37595081080755,
0.599395
],
"xyz": [
3.98922,
3.72381,
5.99395
],
"label": "H",
"properties": {}
},
{
"species": [
{
"element": "H",
"occu": 1
}
],
"abc": [
0.13515111964029505,
0.62260772656242,
0.144018
],
"xyz": [
1.36473,
6.2175,
1.44018
],
"label": "H",
"properties": {}
},
{
"species": [
{
"element": "H",
"occu": 1
}
],
"abc": [
0.22316222152283632,
0.58830814318196,
0.021684000000000002
],
"xyz": [
2.2279700000000005,
5.8817900000000005,
0.21684000000000003
],
"label": "H",
"properties": {}
}
]
}
}
29 changes: 29 additions & 0 deletions tests/test_to_pymatgen_entry.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
import os
import numpy as np
import unittest
from context import dpdata
from comp_sys import CompSys, IsPBC
from monty.serialization import loadfn
try:
from pymatgen.entries.computed_entries import ComputedStructureEntry
exist_module=True
except:
exist_module=False

@unittest.skipIf(not exist_module,"skip pymatgen")
class TestPymatgen(unittest.TestCase):

def test(self):
ls1= dpdata.LabeledSystem(os.path.join('poscars', 'OUTCAR.ch4.1step'),fmt='OUTCAR')
entry1=ls1.to_pymatgen_ComputedStructureEntry()
self.assertEqual(entry1,[])
ls2= dpdata.LabeledSystem(os.path.join('poscars', 'OUTCAR.h2o.md.10'),fmt='OUTCAR')
entry2=ls2.to_pymatgen_ComputedStructureEntry()
self.assertEqual(len(entry2),10)
last_entry=loadfn("computed_structure_entry.json")
self.assertEqual(last_entry.as_dict(),entry2[-1].as_dict())


if __name__ == '__main__':
unittest.main()