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amcadmusamcadmus
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Merge pull request #104 from haidi-ustc/devel
convert LabeledSystem to ComputedStructureEntry
2 parents 20f810b + 4a0d7ee commit 3bbd2f8

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3 files changed

+276
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lines changed

‎dpdata/system.py

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Original file line numberDiff line numberDiff line change
@@ -496,6 +496,7 @@ def to_pymatgen_structure(self):
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structure=Structure(system.data['cells'][0],species,system.data['coords'][0],coords_are_cartesian=True)
497497
structures.append(structure)
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return structures
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500501
@register_to_funcs.register_funcs("ase/structure")
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def to_ase_structure(self):
@@ -1329,6 +1330,26 @@ def shuffle(self):
13291330
self.data[ii] = self.data[ii][idx]
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return idx
13311332

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def to_pymatgen_ComputedStructureEntry(self):
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'''
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convert System to Pymagen ComputedStructureEntry obj
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1337+
'''
1338+
try:
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from pymatgen.entries.computed_entries import ComputedStructureEntry
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except:
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raise ImportError('No module ComputedStructureEntry in pymatgen.entries.computed_entries')
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entries=[]
1344+
for system in self.to_list():
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structure=system.to_pymatgen_structure()[0]
1346+
energy=system.data['energies'][0]
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data={'forces':system.data['forces'][0],
1348+
'virials':system.data['virials'][0]}
1349+
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entry=ComputedStructureEntry(structure,energy,data=data)
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entries.append(entry)
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return entries
13321353

13331354
class MultiSystems:
13341355
'''A set containing several systems.'''

‎tests/computed_structure_entry.json

Lines changed: 226 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,226 @@
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{
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"@module": "pymatgen.entries.computed_entries",
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"@class": "ComputedStructureEntry",
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"energy": -28.39848822,
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"composition": {
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"O": 2.0,
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"H": 4.0
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},
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"parameters": {},
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"data": {
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"forces": {
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"@module": "numpy",
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"@class": "array",
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"dtype": "float64",
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"data": [
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[
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-0.211386,
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-1.770018,
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0.507873
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],
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[
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-1.47897,
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-0.663468,
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-0.917499
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],
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[
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-0.178977,
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0.946024,
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0.351008
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],
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[
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0.38587,
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0.822681,
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-0.844953
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],
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[
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1.156783,
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0.157322,
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-0.138993
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],
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[
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0.32185,
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0.505766,
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1.049144
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]
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]
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},
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"virials": {
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"@module": "numpy",
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"@class": "array",
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"dtype": "float64",
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"data": [
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[
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-1.3720085358803906,
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-0.2485681009072721,
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0.4575213433975083
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],
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[
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-0.2485681009072721,
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-1.408552571807875,
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-0.2783962730161448
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],
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[
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0.4575213433975083,
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-0.2783962730161448,
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-1.8782261334719614
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]
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]
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}
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},
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"entry_id": null,
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"correction": 0.0,
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"structure": {
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"@module": "pymatgen.core.structure",
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"@class": "Structure",
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"charge": null,
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"lattice": {
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"matrix": [
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[
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10.0,
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0.0,
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0.0
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],
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[
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-0.011409,
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10.0,
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0.0
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],
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[
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0.1411083,
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-0.0595569,
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10.0
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]
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],
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"a": 10.0,
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"b": 10.000006508261933,
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"c": 10.00117286005329,
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"alpha": 90.34211999314414,
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"beta": 89.19157698565051,
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"gamma": 90.06536872648402,
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"volume": 1000.0
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},
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"sites": [
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{
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"species": [
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{
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"element": "O",
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"occu": 1
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}
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],
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"abc": [
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0.4280678471391986,
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0.42481761932567,
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0.519943
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],
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"xyz": [
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4.3492,
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4.217210000000001,
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5.19943
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],
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"label": "O",
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"properties": {}
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},
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{
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"species": [
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{
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"element": "O",
128+
"occu": 1
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}
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],
131+
"abc": [
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0.23060991326548744,
133+
0.62824882136683,
134+
0.113307
135+
],
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"xyz": [
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2.31492,
138+
6.27574,
139+
1.13307
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],
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"label": "O",
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"properties": {}
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},
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{
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"species": [
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{
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"element": "H",
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"occu": 1
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}
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],
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"abc": [
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0.454949233514069,
153+
0.34706581743272,
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0.46288799999999997
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],
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"xyz": [
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4.61085,
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3.44309,
159+
4.62888
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],
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"label": "H",
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"properties": {}
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},
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{
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"species": [
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{
167+
"element": "H",
168+
"occu": 1
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}
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],
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"abc": [
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0.39089296133220036,
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0.37595081080755,
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0.599395
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],
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"xyz": [
177+
3.98922,
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3.72381,
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5.99395
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],
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"label": "H",
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"properties": {}
183+
},
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{
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"species": [
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{
187+
"element": "H",
188+
"occu": 1
189+
}
190+
],
191+
"abc": [
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0.13515111964029505,
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0.62260772656242,
194+
0.144018
195+
],
196+
"xyz": [
197+
1.36473,
198+
6.2175,
199+
1.44018
200+
],
201+
"label": "H",
202+
"properties": {}
203+
},
204+
{
205+
"species": [
206+
{
207+
"element": "H",
208+
"occu": 1
209+
}
210+
],
211+
"abc": [
212+
0.22316222152283632,
213+
0.58830814318196,
214+
0.021684000000000002
215+
],
216+
"xyz": [
217+
2.2279700000000005,
218+
5.8817900000000005,
219+
0.21684000000000003
220+
],
221+
"label": "H",
222+
"properties": {}
223+
}
224+
]
225+
}
226+
}

‎tests/test_to_pymatgen_entry.py

Lines changed: 29 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,29 @@
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import os
2+
import numpy as np
3+
import unittest
4+
from context import dpdata
5+
from comp_sys import CompSys, IsPBC
6+
from monty.serialization import loadfn
7+
try:
8+
from pymatgen.entries.computed_entries import ComputedStructureEntry
9+
exist_module=True
10+
except:
11+
exist_module=False
12+
13+
@unittest.skipIf(not exist_module,"skip pymatgen")
14+
class TestPymatgen(unittest.TestCase):
15+
16+
def test(self):
17+
ls1= dpdata.LabeledSystem(os.path.join('poscars', 'OUTCAR.ch4.1step'),fmt='OUTCAR')
18+
entry1=ls1.to_pymatgen_ComputedStructureEntry()
19+
self.assertEqual(entry1,[])
20+
ls2= dpdata.LabeledSystem(os.path.join('poscars', 'OUTCAR.h2o.md.10'),fmt='OUTCAR')
21+
entry2=ls2.to_pymatgen_ComputedStructureEntry()
22+
self.assertEqual(len(entry2),10)
23+
last_entry=loadfn("computed_structure_entry.json")
24+
self.assertEqual(last_entry.as_dict(),entry2[-1].as_dict())
25+
26+
27+
if __name__ == '__main__':
28+
unittest.main()
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