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Fix incompatibility of autotest module with latest pymatgen>2022.7.19 #963

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merged 13 commits into from
Oct 6, 2022
Merged

Fix incompatibility of autotest module with latest pymatgen>2022.7.19 #963

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ec667b5
Fix incompatibility of Interstitial.py and Vacancy.py with pymatgen>2…
ZLI-afk Sep 21, 2022
9f45b4e
add pymatgen-analysis-defect and pybind11 in setup.py.
ZLI-afk Sep 21, 2022
5bb3eb3
revise pymatgen_version in test.yml
ZLI-afk Sep 22, 2022
ff33232
revise pymatgen_version in test.yml
ZLI-afk Sep 22, 2022
371eeb3
revise duplicate import
ZLI-afk Sep 22, 2022
e1c9411
add .readthedocs.yaml
njzjz Sep 26, 2022
cea5985
fix docs path
njzjz Sep 26, 2022
41d2530
Update setup.py
ZLI-afk Sep 27, 2022
00694fb
Update Interstitial.py
ZLI-afk Sep 27, 2022
cdbad26
Update Vacancy.py
ZLI-afk Sep 27, 2022
753862a
Fix SyntaxError in vacancy.py
ZLI-afk Sep 28, 2022
418a846
Update Vacancy.py
ZLI-afk Sep 29, 2022
81d3690
revise inputs of interstitial generator
ZLI-afk Sep 30, 2022
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4 changes: 2 additions & 2 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.7, 3.8]
PYMATGEN_VERSION: [2019.1.13, 2019.7.30]
python-version: [3.8, 3.9]
PYMATGEN_VERSION: [2022.7.19]

steps:
- uses: actions/checkout@v2
Expand Down
24 changes: 24 additions & 0 deletions .readthedocs.yaml
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@@ -0,0 +1,24 @@
# .readthedocs.yaml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Set the version of Python and other tools you might need
build:
os: ubuntu-22.04
tools:
python: "3.10"

# Build documentation in the docs/ directory with Sphinx
sphinx:
configuration: doc/conf.py

# If using Sphinx, optionally build your docs in additional formats such as PDF
formats: all

# Optionally declare the Python requirements required to build your docs
python:
install:
- requirements: doc/requirements.txt
21 changes: 13 additions & 8 deletions dpgen/auto_test/Interstitial.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import json
import os
import re
import numpy as np

from monty.serialization import loadfn, dumpfn
from pymatgen.analysis.defects.generators import InterstitialGenerator
Expand Down Expand Up @@ -147,9 +148,10 @@ def make_confs(self,
os.remove(insert_element_task)

for ii in self.insert_ele:
vds = InterstitialGenerator(ss, ii)
pre_vds = InterstitialGenerator()
vds = pre_vds.generate(ss, {self.insert_ele[0]: [[0, 0.2, 0.5]]})
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for jj in vds:
temp = jj.generate_defect_structure(self.supercell)
temp = jj.get_supercell_structure(sc_mat=np.diag(self.supercell, k=0))
smallest_distance = list(set(temp.distance_matrix.ravel()))[1]
if 'conf_filters' in self.parameter and 'min_dist' in self.parameter['conf_filters']:
min_dist = self.parameter['conf_filters']['min_dist']
Expand Down Expand Up @@ -188,6 +190,9 @@ def make_confs(self,


if 'bcc_self' in self.parameter and self.parameter['bcc_self']:
super_size = self.supercell[0] * self.supercell[1] * self.supercell[2]
num_atom = super_size * 2
chl = -num_atom - 2
os.chdir(path_to_work)
with open('POSCAR', 'r') as fin:
fin.readline()
Expand All @@ -210,7 +215,7 @@ def make_confs(self,
with open(insert_element_task, 'a+') as fout:
print(self.insert_ele[0], file=fout)
dumpfn(self.supercell, 'supercell.json')
pos_line[-2] = '%.6f' % float(latt_param/4/super_latt_param) + ' ' + '%.6f' % float(latt_param/2/super_latt_param) + ' 0.000000 ' + self.insert_ele[0]
pos_line[chl] = '%.6f' % float(latt_param/4/super_latt_param) + ' ' + '%.6f' % float(latt_param/2/super_latt_param) + ' 0.000000 ' + self.insert_ele[0]
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with open('POSCAR', 'w+') as fout:
for ii in pos_line:
print(ii, file=fout)
Expand All @@ -224,7 +229,7 @@ def make_confs(self,
with open(insert_element_task, 'a+') as fout:
print(self.insert_ele[0], file=fout)
dumpfn(self.supercell, 'supercell.json')
pos_line[-2] = '%.6f' % float(latt_param/2/super_latt_param) + ' ' + '%.6f' % float(latt_param/2/super_latt_param) + ' 0.000000 ' + self.insert_ele[0]
pos_line[chl] = '%.6f' % float(latt_param/2/super_latt_param) + ' ' + '%.6f' % float(latt_param/2/super_latt_param) + ' 0.000000 ' + self.insert_ele[0]
with open('POSCAR', 'w+') as fout:
for ii in pos_line:
print(ii, file=fout)
Expand All @@ -238,7 +243,7 @@ def make_confs(self,
with open(insert_element_task, 'a+') as fout:
print(self.insert_ele[0], file=fout)
dumpfn(self.supercell, 'supercell.json')
pos_line[-2] = '%.6f' % float(latt_param/4/super_latt_param) + ' ' + '%.6f' % float(latt_param/4/super_latt_param) + ' ' + '%.6f' % float(latt_param/4/super_latt_param) + ' ' + self.insert_ele[0]
pos_line[chl] = '%.6f' % float(latt_param/4/super_latt_param) + ' ' + '%.6f' % float(latt_param/4/super_latt_param) + ' ' + '%.6f' % float(latt_param/4/super_latt_param) + ' ' + self.insert_ele[0]
with open('POSCAR', 'w+') as fout:
for ii in pos_line:
print(ii, file=fout)
Expand All @@ -258,7 +263,7 @@ def make_confs(self,
with open(insert_element_task, 'a+') as fout:
print(self.insert_ele[0], file=fout)
dumpfn(self.supercell, 'supercell.json')
pos_line[-2] = '%.6f' % float(latt_param/3/super_latt_param) + ' ' + '%.6f' % float(latt_param/3/super_latt_param) + ' ' + '%.6f' % float(latt_param/3/super_latt_param) + ' ' + self.insert_ele[0]
pos_line[chl] = '%.6f' % float(latt_param/3/super_latt_param) + ' ' + '%.6f' % float(latt_param/3/super_latt_param) + ' ' + '%.6f' % float(latt_param/3/super_latt_param) + ' ' + self.insert_ele[0]
pos_line[replace_label] = '%.6f' % float(latt_param/3*2/super_latt_param) + ' ' + '%.6f' % float(latt_param/3*2/super_latt_param) + ' ' + '%.6f' % float(latt_param/3*2/super_latt_param) + ' ' + self.insert_ele[0]

with open('POSCAR', 'w+') as fout:
Expand All @@ -274,7 +279,7 @@ def make_confs(self,
with open(insert_element_task, 'a+') as fout:
print(self.insert_ele[0], file=fout)
dumpfn(self.supercell, 'supercell.json')
pos_line[-2] = '%.6f' % float((latt_param+2.1/2**0.5)/2/super_latt_param) + ' ' + '%.6f' % float((latt_param-2.1/2**0.5)/2/super_latt_param) + ' ' + '%.6f' % float(latt_param/2/super_latt_param) + ' ' + self.insert_ele[0]
pos_line[chl] = '%.6f' % float((latt_param+2.1/2**0.5)/2/super_latt_param) + ' ' + '%.6f' % float((latt_param-2.1/2**0.5)/2/super_latt_param) + ' ' + '%.6f' % float(latt_param/2/super_latt_param) + ' ' + self.insert_ele[0]
pos_line[replace_label] = '%.6f' % float((latt_param-2.1/2**0.5)/2/super_latt_param) + ' ' + '%.6f' % float((latt_param+2.1/2**0.5)/2/super_latt_param) + ' ' + '%.6f' % float(latt_param/2/super_latt_param) + ' ' + self.insert_ele[0]

with open('POSCAR', 'w+') as fout:
Expand All @@ -290,7 +295,7 @@ def make_confs(self,
with open(insert_element_task, 'a+') as fout:
print(self.insert_ele[0], file=fout)
dumpfn(self.supercell, 'supercell.json')
pos_line[-2] = '%.6f' % float(latt_param/2/super_latt_param) + ' ' + '%.6f' % float(latt_param/2/super_latt_param) + ' ' + '%.6f' % float((latt_param-2.1)/2/super_latt_param) + ' ' + self.insert_ele[0]
pos_line[chl] = '%.6f' % float(latt_param/2/super_latt_param) + ' ' + '%.6f' % float(latt_param/2/super_latt_param) + ' ' + '%.6f' % float((latt_param-2.1)/2/super_latt_param) + ' ' + self.insert_ele[0]
pos_line[replace_label] = '%.6f' % float(latt_param/2/super_latt_param) + ' ' + '%.6f' % float(latt_param/2/super_latt_param) + ' ' + '%.6f' % float((latt_param+2.1)/2/super_latt_param) + ' ' + self.insert_ele[0]

with open('POSCAR', 'w+') as fout:
Expand Down
6 changes: 4 additions & 2 deletions dpgen/auto_test/Vacancy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import json
import os
import re
import numpy as np

from monty.serialization import loadfn, dumpfn
from pymatgen.analysis.defects.generators import VacancyGenerator
Expand Down Expand Up @@ -134,10 +135,11 @@ def make_confs(self,
else:
ss = Structure.from_file(equi_contcar)

vds = VacancyGenerator(ss)
pre_vds = VacancyGenerator()
vds = pre_vds.generate(ss)
dss = []
for jj in vds:
dss.append(jj.generate_defect_structure(self.supercell))
dss.append(jj.get_supercell_structure(sc_mat=np.diag(self.supercell, k=0))

print('gen vacancy with supercell ' + str(self.supercell))
os.chdir(path_to_work)
Expand Down
3 changes: 2 additions & 1 deletion setup.py
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Expand Up @@ -20,7 +20,7 @@
install_requires=[
'numpy>=1.14.3',
'dpdata>=0.2.6',
'pymatgen>=2019.1.13',
'pymatgen>=2022.7.19',
'ase',
'monty>2.0.0',
'paramiko',
Expand All @@ -29,6 +29,7 @@
'dpdispatcher>=0.3.11',
'netCDF4',
'dargs>=0.2.9',
'pymatgen-analysis-defects'
]

setuptools.setup(
Expand Down
8 changes: 4 additions & 4 deletions tests/auto_test/test_interstitial.py
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Expand Up @@ -85,16 +85,16 @@ def test_make_confs_bcc(self):
st_file = os.path.join(ii, 'POSCAR')
self.assertTrue(os.path.isfile(st_file))
st0 = Structure.from_file(st_file)
inter_site = st0[-1]
inter = pmg_Interstitial(ref_st, inter_site, charge=0.0)
st1 = inter.generate_defect_structure(self.prop_param[0]['supercell'])
inter_site = st0[0]
inter = pmg_Interstitial(ref_st, inter_site)
st1 = inter.get_supercell_structure(sc_mat=np.eye(3)*self.prop_param[0]['supercell'])
self.assertEqual(st0, st1)

for ii in dfm_dirs[4:]:
st_file = os.path.join(ii, 'POSCAR')
self.assertTrue(os.path.isfile(st_file))
st0 = Structure.from_file(st_file)
inter_site1 = st0.pop(-1)
inter_site1 = st0.pop(0)
inter_site2 = st0.pop(-1)
center = (inter_site1.coords + inter_site2.coords) / 2
self.assertTrue((center[0] - center[1]) < 1e-4)
Expand Down
4 changes: 2 additions & 2 deletions tests/auto_test/test_vacancy.py
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Expand Up @@ -85,6 +85,6 @@ def test_make_confs_0(self):
self.assertTrue(os.path.isfile(st_file))
st0 = Structure.from_file(st_file)
vac_site = equiv_site_seq.pop(0)
vac = pmg_Vacancy(ref_st, vac_site[0], charge=0.0)
st1 = vac.generate_defect_structure(self.prop_param[0]['supercell'])
vac = pmg_Vacancy(ref_st, vac_site[0])
st1 = vac.get_supercell_structure(sc_mat=np.eye(3)*self.prop_param[0]['supercell'])
self.assertEqual(st0, st1)