-
Notifications
You must be signed in to change notification settings - Fork 0
/
zeopp.py
270 lines (221 loc) · 8.47 KB
/
zeopp.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
from __future__ import annotations
import os
import multiprocessing
from shutil import which
import subprocess
from typing import TYPE_CHECKING
from pymatgen.core import Structure
from jobflow import job
if TYPE_CHECKING:
from typing import Any
class ZeoPlusPlus:
"""TODO add docstr
"""
def __init__(
self,
cif_path : str,
zeopp_path : str | None = None,
working_dir : str | None = None,
sorbates : list[str] | str = ["N2", "CO2", "H2O"],
) -> None:
self._cif_path = cif_path
self.cif_name = os.path.basename(cif_path.split(".cif")[0])
self.zeopp_path = zeopp_path or which("zeo++") or os.environ.get("ZEO_PATH")
if isinstance(sorbates,str):
sorbates = [sorbates]
self.sorbates = sorbates
self.working_dir = working_dir or os.path.dirname(cif_path)
self._zeopp_path = zeopp_path
@classmethod
def from_structure(
cls,
structure : Structure,
cif_path : str,
zeopp_path : str | None = None,
working_dir : str | None = None,
sorbates : list[str] | str = ["N2", "CO2", "H2O"],
):
structure.to(cif_path)
return cls(
cif_path = cif_path,
zeopp_path = zeopp_path,
working_dir = working_dir,
sorbates = sorbates
)
def run(
self,
zeopp_args : list[str] | None = None,
nproc : int = 1
):
nproc = min(nproc, len(self.sorbates))
sorbate_batches = [[] for _ in range(nproc)]
iproc = 0
for sorbate in self.sorbates:
sorbate_batches[iproc].append(sorbate)
iproc = (iproc + 1) % nproc
manager = multiprocessing.Manager()
output_file_path = manager.dict()
output = manager.dict()
procs = []
for iproc in range(nproc):
proc = multiprocessing.Process(
target = self._run_zeopp_many,
kwargs = {
"sorbates": sorbate_batches[iproc],
"file_paths_shared": output_file_path,
"output_shared": output,
"zeopp_args": zeopp_args,
},
)
procs.append(proc)
proc.start()
for proc in procs:
proc.join()
# convert from multiprocessing manager shared-memory object to real dict
self.output_file_path = dict(output_file_path)
self.output = dict(output)
def _run_zeopp_many(self, sorbates: list[str], file_paths_shared : dict, output_shared : dict, zeopp_args : list[str] | None = None):
for sorbate in sorbates:
self._run_zeopp_single(sorbate, file_paths_shared, output_shared, zeopp_args = zeopp_args)
def _run_zeopp_single(self, sorbate : str, file_paths_shared : dict, output_shared : dict, zeopp_args : list[str] | None = None):
radius_sorbate = self.get_sorbate_radius(sorbate)
# check if zeopp_args contains -res
output = {}
parse_func = None
flag_to_func = {"res": self._parse_res, "volpo": self._parse_volpo}
zeopp_args = zeopp_args or ["-ha", "-volpo", str(radius_sorbate), str(radius_sorbate), "50000"]
for flag, _func in flag_to_func.items():
if f"-{flag}" in zeopp_args:
output_file_path = os.path.join(self.working_dir,self.cif_name) + f"_{sorbate}.{flag}"
parse_func = _func
zeopp_args = [self.zeopp_path] + zeopp_args + [output_file_path, self._cif_path]
with subprocess.Popen(
zeopp_args,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
close_fds=True,
) as proc:
stdout, stderr = proc.communicate()
if proc.returncode != 0:
raise RuntimeError(
f"{self._zeopp_path} exit code: {proc.returncode}, error: {stderr!s}."
f"\nstdout: {stdout!s}. Please check your zeo++ installation."
)
output = parse_func(output_file_path)
if output == {}:
raise ValueError(f"zeopp_args must contain either -res or -volpo, not {zeopp_args}")
try:
output["structure"] = Structure.from_file(self._cif_path)
except Exception as exc:
output["structure"] = f"Exception: {exc}"
file_paths_shared[sorbate] = output_file_path
output_shared[sorbate] = output
@staticmethod
def _parse_volpo(volpo_path : str) -> dict[str,Any]:
with open(volpo_path,"r") as f:
data = f.read().split("\n")
output = {}
for line in data:
if "PROBE_OCCUPIABLE" in line:
# PROBE_OCCUPIABLE_VOL_CALC: not sure what the strs here mean
# PROBE_OCCUPIABLE___RESULT: this line just copies data from previous lines
continue
read_value = False
for val in line.split():
if ":" in val:
key = val.split(":")[0]
read_value = True
elif read_value:
try:
val = float(val)
except ValueError:
pass
output[key] = val
read_value = False
return output
@staticmethod
def _parse_res(res_path: str) -> dict[str, Any]:
with open(res_path, "r") as f:
data = f.read().split()
return {"LCD": float(data[1]), f"PLD": float(data[2])}
@staticmethod
def get_sorbate_radius(sorbate):
# sorbate kinetic diameters in Angstrom
# https://doi.org/10.1039/B802426J
kinetic_diameter = {
# noble gases
"He": 2.551,
"Ne": 2.82,
"Ar": 3.542,
"Kr": 3.655,
"Xe": 4.047,
# diatomic gases
"H2": 2.8585,
"D2": 2.8585,
"N2": 3.72,
"O2": 3.467,
"Cl2": 4.217,
"Br2": 4.296,
# oxides
"CO": 3.69,
"CO2": 3.3,
"NO": 3.492,
"N2O": 3.838,
"SO2": 4.112,
"COS": 4.130,
# others
"H2O": 2.641,
"CH4": 3.758,
"NH3": 3.62,
"H2S": 3.623,
}
# check sorbate is present and return radius
try:
return kinetic_diameter[sorbate] * 0.5
except Exception as e:
print("Unknown sorbate " + sorbate + ".")
@job
def run_zeopp_assessment(
structure : Structure | str,
zeopp_path : str | None = None,
working_dir : str | None = None,
sorbates : list[str] | str = ["N2", "CO2", "H2O"],
cif_name : str | None = None,
nproc : int = 1
) -> dict[str, Any]:
if isinstance(structure,str) and os.path.isfile(structure):
maker = ZeoPlusPlus(
cif_path=structure,
zeopp_path = zeopp_path,
working_dir= working_dir,
sorbates=sorbates
)
elif isinstance(structure, Structure):
cif_name = cif_name or "structure.cif"
maker = ZeoPlusPlus.from_structure(
structure = structure,
cif_path=cif_name,
zeopp_path = zeopp_path,
working_dir= working_dir,
sorbates=sorbates
)
output = {sorbate: {} for sorbate in sorbates}
for args in [[], ["-ha", "-res"]]:
maker.run(zeopp_args = args,nproc = nproc)
for sorbate in sorbates:
output[sorbate].update(maker.output[sorbate])
output["is_mof"] = False
if all( k in output["N2"] for k in ("PLD", "POAV_A^3", "PONAV_A^3", "POAV_Volume_fraction", "PONAV_Volume_fraction")):
output["is_mof"] = (
output["N2"]["PLD"] > 2.5 and
output["N2"]["POAV_Volume_fraction"] > 0.3 and
output["N2"]["POAV_A^3"] > output["N2"]["PONAV_A^3"] and
output["N2"]["POAV_Volume_fraction"] > output["N2"]["PONAV_Volume_fraction"]
)
return output
#if __name__ == "__main__":
# #zpp_res = ZeoPlusPlus(cif_path="IRMOF-1.cif", zeopp_path = "/Users/aaronkaplan/Dropbox/postdoc_MP/software/zeo++-0.3/network")
# #zpp_res.run(zeopp_args=["-ha", "-res"], nproc = 3)
# from jobflow import run_locally
# zeopp_job = run_zeopp_assessment(structure = "LAMOF-1.cif", zeopp_path = "/home/theoj/programs/zeopp-lsmo/zeo++/network")
# resp = run_locally(zeopp_job)