Skip to content
This repository was archived by the owner on Sep 14, 2022. It is now read-only.

Commit fc32a85

Browse files
prehnerprehner
authored
Add example notebook for a 3D pore calculation (#26)
1 parent 41fdbe3 commit fc32a85

File tree

3 files changed

+680
-0
lines changed

3 files changed

+680
-0
lines changed

‎examples/adsorption_3D.ipynb‎

Lines changed: 364 additions & 0 deletions
Large diffs are not rendered by default.

‎examples/structure_parameters/DREIDING.dat‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -3,3 +3,4 @@
33
H 2.846 7.6489 1.00784
44
N 3.2625 38.9492 14.0067
55
B 3.581 47.8059 10.811
6+
Zn 1.330 109.471 65.38

‎examples/structure_parameters/ZIF-8.cif‎

Lines changed: 315 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,315 @@
1+
data_ZIF-8
2+
3+
_audit_creation_method RASPA-1.0
4+
_audit_creation_date 2011-3-6
5+
_audit_author_name 'David Dubbeldam'
6+
7+
_citation_author_name 'K.S. Park, Z. Ni, A.P. Cote, J.Y. Choi, R.D. Huang, F.J. Uribe-Romo, H.K. Chae, M. O’Keeffe, and O.M. Yaghi'
8+
_citation_title 'Exceptional chemical and thermal stability of zeolitic imidazolate frameworks'
9+
_citation_journal_abbrev 'P. Natl. Acad. Sci. USA'
10+
_citation_journal_volume 103
11+
_citation_journal_number 27
12+
_citation_page_first 10186
13+
_citation_page_last 10191
14+
_citation_year 2006
15+
16+
_cell_length_a 16.991
17+
_cell_length_b 16.991
18+
_cell_length_c 16.991
19+
_cell_angle_alpha 90
20+
_cell_angle_beta 90
21+
_cell_angle_gamma 90
22+
_cell_volume 4905.2
23+
24+
_symmetry_cell_setting cubic
25+
_symmetry_space_group_name_Hall 'P 1'
26+
_symmetry_space_group_name_H-M 'P 1'
27+
_symmetry_Int_Tables_number 1
28+
29+
_symmetry_equiv_pos_as_xyz 'x,y,z'
30+
31+
loop_
32+
_atom_site_label
33+
_atom_site_type_symbol
34+
_atom_site_fract_x
35+
_atom_site_fract_y
36+
_atom_site_fract_z
37+
_atom_site_charge
38+
C1 C 0.37705 0.0079 0.62295 0
39+
C2 C 0.36851 0.89914 0.6875 0
40+
H2 H 0.3777 0.8589 0.7234 0
41+
C3 C 0.4061 0.0855 0.5939 0
42+
N1 N 0.40973 0.96832 0.68278 0
43+
Zn1 Zn 0.5 0 0.75 0
44+
C1 C 0.0079 0.62295 0.37705 0
45+
C2 C 0.89914 0.63149 0.3125 0
46+
H2 H 0.8589 0.6223 0.2766 0
47+
C3 C 0.0855 0.5939 0.4061 0
48+
N1 N 0.96832 0.59027 0.31722 0
49+
Zn1 Zn 0 0.5 0.25 0
50+
C1 C 0.62295 0.9921 0.62295 0
51+
C2 C 0.63149 0.10086 0.6875 0
52+
H2 H 0.6223 0.1411 0.7234 0
53+
C3 C 0.5939 0.9145 0.5939 0
54+
H3A H 0.5413 0.9202 0.5743 0
55+
H3B H 0.5942 0.8772 0.6364 0
56+
H3C H 0.6276 0.8961 0.5525 0
57+
N1 N 0.59027 0.03168 0.68278 0
58+
C1 C 0.9921 0.37705 0.37705 0
59+
C2 C 0.10086 0.36851 0.3125 0
60+
H2 H 0.1411 0.3777 0.2766 0
61+
C3 C 0.9145 0.4061 0.4061 0
62+
H3A H 0.9202 0.4587 0.4257 0
63+
H3B H 0.8772 0.4058 0.3636 0
64+
H3C H 0.8961 0.3724 0.4475 0
65+
N1 N 0.03168 0.40973 0.31722 0
66+
C1 C 0.37705 0.9921 0.37705 0
67+
C2 C 0.36851 0.10086 0.3125 0
68+
H2 H 0.3777 0.1411 0.2766 0
69+
C3 C 0.4061 0.9145 0.4061 0
70+
N1 N 0.40973 0.03168 0.31722 0
71+
Zn1 Zn 0.5 0 0.25 0
72+
C1 C 0.9921 0.62295 0.62295 0
73+
C2 C 0.10086 0.63149 0.6875 0
74+
H2 H 0.1411 0.6223 0.7234 0
75+
C3 C 0.9145 0.5939 0.5939 0
76+
N1 N 0.03168 0.59027 0.68278 0
77+
Zn1 Zn 0 0.5 0.75 0
78+
C1 C 0.62295 0.0079 0.37705 0
79+
C2 C 0.63149 0.89914 0.3125 0
80+
H2 H 0.6223 0.8589 0.2766 0
81+
C3 C 0.5939 0.0855 0.4061 0
82+
H3A H 0.5413 0.0798 0.4257 0
83+
H3B H 0.5942 0.1228 0.3636 0
84+
H3C H 0.6276 0.1039 0.4475 0
85+
N1 N 0.59027 0.96832 0.31722 0
86+
C1 C 0.0079 0.37705 0.62295 0
87+
C2 C 0.89914 0.36851 0.6875 0
88+
H2 H 0.8589 0.3777 0.7234 0
89+
C3 C 0.0855 0.4061 0.5939 0
90+
H3A H 0.0798 0.4587 0.5743 0
91+
H3B H 0.1228 0.4058 0.6364 0
92+
H3C H 0.1039 0.3724 0.5525 0
93+
N1 N 0.96832 0.40973 0.68278 0
94+
C1 C 0.62295 0.37705 0.0079 0
95+
C2 C 0.6875 0.36851 0.89914 0
96+
H2 H 0.7234 0.3777 0.8589 0
97+
C3 C 0.5939 0.4061 0.0855 0
98+
N1 N 0.68278 0.40973 0.96832 0
99+
Zn1 Zn 0.75 0.5 0 0
100+
C1 C 0.37705 0.37705 0.9921 0
101+
C2 C 0.36851 0.3125 0.10086 0
102+
H2 H 0.3777 0.2766 0.1411 0
103+
C3 C 0.4061 0.4061 0.9145 0
104+
H3A H 0.4587 0.4257 0.9202 0
105+
H3B H 0.4058 0.3636 0.8772 0
106+
H3C H 0.3724 0.4475 0.8961 0
107+
N1 N 0.40973 0.31722 0.03168 0
108+
Zn1 Zn 0.5 0.25 0 0
109+
C1 C 0.37705 0.62295 0.0079 0
110+
C2 C 0.3125 0.63149 0.89914 0
111+
H2 H 0.2766 0.6223 0.8589 0
112+
C3 C 0.4061 0.5939 0.0855 0
113+
N1 N 0.31722 0.59027 0.96832 0
114+
Zn1 Zn 0.25 0.5 0 0
115+
C1 C 0.62295 0.62295 0.9921 0
116+
C2 C 0.63149 0.6875 0.10086 0
117+
H2 H 0.6223 0.7234 0.1411 0
118+
C3 C 0.5939 0.5939 0.9145 0
119+
H3A H 0.5413 0.5743 0.9202 0
120+
H3B H 0.5942 0.6364 0.8772 0
121+
H3C H 0.6276 0.5525 0.8961 0
122+
N1 N 0.59027 0.68278 0.03168 0
123+
Zn1 Zn 0.5 0.75 0 0
124+
C2 C 0.6875 0.63149 0.10086 0
125+
H2 H 0.7234 0.6223 0.1411 0
126+
N1 N 0.68278 0.59027 0.03168 0
127+
C2 C 0.63149 0.3125 0.89914 0
128+
H2 H 0.6223 0.2766 0.8589 0
129+
H3A H 0.5413 0.4257 0.0798 0
130+
H3B H 0.5942 0.3636 0.1228 0
131+
H3C H 0.6276 0.4475 0.1039 0
132+
N1 N 0.59027 0.31722 0.96832 0
133+
C2 C 0.3125 0.36851 0.10086 0
134+
H2 H 0.2766 0.3777 0.1411 0
135+
N1 N 0.31722 0.40973 0.03168 0
136+
C2 C 0.36851 0.6875 0.89914 0
137+
H2 H 0.3777 0.7234 0.8589 0
138+
H3A H 0.4587 0.5743 0.0798 0
139+
H3B H 0.4058 0.6364 0.1228 0
140+
H3C H 0.3724 0.5525 0.1039 0
141+
N1 N 0.40973 0.68278 0.96832 0
142+
C2 C 0.89914 0.6875 0.36851 0
143+
H2 H 0.8589 0.7234 0.3777 0
144+
H3A H 0.0798 0.5743 0.4587 0
145+
H3B H 0.1228 0.6364 0.4058 0
146+
H3C H 0.1039 0.5525 0.3724 0
147+
N1 N 0.96832 0.68278 0.40973 0
148+
Zn1 Zn 0 0.75 0.5 0
149+
C2 C 0.89914 0.3125 0.63149 0
150+
H2 H 0.8589 0.2766 0.6223 0
151+
N1 N 0.96832 0.31722 0.59027 0
152+
Zn1 Zn 0 0.25 0.5 0
153+
C2 C 0.3125 0.10086 0.36851 0
154+
H2 H 0.2766 0.1411 0.3777 0
155+
H3A H 0.4257 0.9202 0.4587 0
156+
H3B H 0.3636 0.8772 0.4058 0
157+
H3C H 0.4475 0.8961 0.3724 0
158+
N1 N 0.31722 0.03168 0.40973 0
159+
Zn1 Zn 0.25 0 0.5 0
160+
C2 C 0.10086 0.6875 0.63149 0
161+
H2 H 0.1411 0.7234 0.6223 0
162+
H3A H 0.9202 0.5743 0.5413 0
163+
H3B H 0.8772 0.6364 0.5942 0
164+
H3C H 0.8961 0.5525 0.6276 0
165+
N1 N 0.03168 0.68278 0.59027 0
166+
C2 C 0.6875 0.89914 0.36851 0
167+
H2 H 0.7234 0.8589 0.3777 0
168+
N1 N 0.68278 0.96832 0.40973 0
169+
Zn1 Zn 0.75 0 0.5 0
170+
C2 C 0.10086 0.3125 0.36851 0
171+
H2 H 0.1411 0.2766 0.3777 0
172+
N1 N 0.03168 0.31722 0.40973 0
173+
C2 C 0.3125 0.89914 0.63149 0
174+
H2 H 0.2766 0.8589 0.6223 0
175+
H3A H 0.4257 0.0798 0.5413 0
176+
H3B H 0.3636 0.1228 0.5942 0
177+
H3C H 0.4475 0.1039 0.6276 0
178+
N1 N 0.31722 0.96832 0.59027 0
179+
C2 C 0.6875 0.10086 0.63149 0
180+
H2 H 0.7234 0.1411 0.6223 0
181+
N1 N 0.68278 0.03168 0.59027 0
182+
C1 C 0.87705 0.5079 0.12295 0
183+
C2 C 0.86851 0.39914 0.1875 0
184+
H2 H 0.8777 0.3589 0.2234 0
185+
C3 C 0.9061 0.5855 0.0939 0
186+
H3A H 0.9587 0.5798 0.0743 0
187+
H3B H 0.9058 0.6228 0.1364 0
188+
H3C H 0.8724 0.6039 0.0525 0
189+
N1 N 0.90973 0.46832 0.18278 0
190+
C1 C 0.5079 0.12295 0.87705 0
191+
C2 C 0.39914 0.13149 0.8125 0
192+
H2 H 0.3589 0.1223 0.7766 0
193+
C3 C 0.5855 0.0939 0.9061 0
194+
N1 N 0.46832 0.09027 0.81722 0
195+
C1 C 0.12295 0.4921 0.12295 0
196+
C2 C 0.13149 0.60086 0.1875 0
197+
H2 H 0.1223 0.6411 0.2234 0
198+
C3 C 0.0939 0.4145 0.0939 0
199+
H3A H 0.0413 0.4202 0.0743 0
200+
H3B H 0.0942 0.3772 0.1364 0
201+
H3C H 0.1276 0.3961 0.0525 0
202+
N1 N 0.09027 0.53168 0.18278 0
203+
C1 C 0.4921 0.87705 0.87705 0
204+
C2 C 0.60086 0.86851 0.8125 0
205+
H2 H 0.6411 0.8777 0.7766 0
206+
C3 C 0.4145 0.9061 0.9061 0
207+
H3A H 0.4202 0.9587 0.9257 0
208+
H3B H 0.3772 0.9058 0.8636 0
209+
H3C H 0.3961 0.8724 0.9475 0
210+
N1 N 0.53168 0.90973 0.81722 0
211+
C1 C 0.87705 0.4921 0.87705 0
212+
C2 C 0.86851 0.60086 0.8125 0
213+
H2 H 0.8777 0.6411 0.7766 0
214+
C3 C 0.9061 0.4145 0.9061 0
215+
H3A H 0.9587 0.4202 0.9257 0
216+
H3B H 0.9058 0.3772 0.8636 0
217+
H3C H 0.8724 0.3961 0.9475 0
218+
N1 N 0.90973 0.53168 0.81722 0
219+
C1 C 0.4921 0.12295 0.12295 0
220+
C2 C 0.60086 0.13149 0.1875 0
221+
H2 H 0.6411 0.1223 0.2234 0
222+
C3 C 0.4145 0.0939 0.0939 0
223+
N1 N 0.53168 0.09027 0.18278 0
224+
C1 C 0.12295 0.5079 0.87705 0
225+
C2 C 0.13149 0.39914 0.8125 0
226+
H2 H 0.1223 0.3589 0.7766 0
227+
C3 C 0.0939 0.5855 0.9061 0
228+
N1 N 0.09027 0.46832 0.81722 0
229+
C1 C 0.5079 0.87705 0.12295 0
230+
C2 C 0.39914 0.86851 0.1875 0
231+
H2 H 0.3589 0.8777 0.2234 0
232+
C3 C 0.5855 0.9061 0.0939 0
233+
N1 N 0.46832 0.90973 0.18278 0
234+
C1 C 0.12295 0.87705 0.5079 0
235+
C2 C 0.1875 0.86851 0.39914 0
236+
H2 H 0.2234 0.8777 0.3589 0
237+
C3 C 0.0939 0.9061 0.5855 0
238+
N1 N 0.18278 0.90973 0.46832 0
239+
C1 C 0.87705 0.87705 0.4921 0
240+
C2 C 0.86851 0.8125 0.60086 0
241+
H2 H 0.8777 0.7766 0.6411 0
242+
C3 C 0.9061 0.9061 0.4145 0
243+
H3A H 0.9587 0.9257 0.4202 0
244+
H3B H 0.9058 0.8636 0.3772 0
245+
H3C H 0.8724 0.9475 0.3961 0
246+
N1 N 0.90973 0.81722 0.53168 0
247+
C1 C 0.87705 0.12295 0.5079 0
248+
C2 C 0.8125 0.13149 0.39914 0
249+
H2 H 0.7766 0.1223 0.3589 0
250+
C3 C 0.9061 0.0939 0.5855 0
251+
N1 N 0.81722 0.09027 0.46832 0
252+
C1 C 0.12295 0.12295 0.4921 0
253+
C2 C 0.13149 0.1875 0.60086 0
254+
H2 H 0.1223 0.2234 0.6411 0
255+
C3 C 0.0939 0.0939 0.4145 0
256+
H3A H 0.0413 0.0743 0.4202 0
257+
H3B H 0.0942 0.1364 0.3772 0
258+
H3C H 0.1276 0.0525 0.3961 0
259+
N1 N 0.09027 0.18278 0.53168 0
260+
C2 C 0.1875 0.13149 0.60086 0
261+
H2 H 0.2234 0.1223 0.6411 0
262+
N1 N 0.18278 0.09027 0.53168 0
263+
C2 C 0.13149 0.8125 0.39914 0
264+
H2 H 0.1223 0.7766 0.3589 0
265+
H3A H 0.0413 0.9257 0.5798 0
266+
H3B H 0.0942 0.8636 0.6228 0
267+
H3C H 0.1276 0.9475 0.6039 0
268+
N1 N 0.09027 0.81722 0.46832 0
269+
C2 C 0.8125 0.86851 0.60086 0
270+
H2 H 0.7766 0.8777 0.6411 0
271+
N1 N 0.81722 0.90973 0.53168 0
272+
C2 C 0.86851 0.1875 0.39914 0
273+
H2 H 0.8777 0.2234 0.3589 0
274+
H3A H 0.9587 0.0743 0.5798 0
275+
H3B H 0.9058 0.1364 0.6228 0
276+
H3C H 0.8724 0.0525 0.6039 0
277+
N1 N 0.90973 0.18278 0.46832 0
278+
C2 C 0.39914 0.1875 0.86851 0
279+
H2 H 0.3589 0.2234 0.8777 0
280+
H3A H 0.5798 0.0743 0.9587 0
281+
H3B H 0.6228 0.1364 0.9058 0
282+
H3C H 0.6039 0.0525 0.8724 0
283+
N1 N 0.46832 0.18278 0.90973 0
284+
C2 C 0.39914 0.8125 0.13149 0
285+
H2 H 0.3589 0.7766 0.1223 0
286+
H3A H 0.5798 0.9257 0.0413 0
287+
H3B H 0.6228 0.8636 0.0942 0
288+
H3C H 0.6039 0.9475 0.1276 0
289+
N1 N 0.46832 0.81722 0.09027 0
290+
C2 C 0.8125 0.60086 0.86851 0
291+
H2 H 0.7766 0.6411 0.8777 0
292+
N1 N 0.81722 0.53168 0.90973 0
293+
C2 C 0.60086 0.1875 0.13149 0
294+
H2 H 0.6411 0.2234 0.1223 0
295+
H3A H 0.4202 0.0743 0.0413 0
296+
H3B H 0.3772 0.1364 0.0942 0
297+
H3C H 0.3961 0.0525 0.1276 0
298+
N1 N 0.53168 0.18278 0.09027 0
299+
C2 C 0.1875 0.39914 0.86851 0
300+
H2 H 0.2234 0.3589 0.8777 0
301+
H3A H 0.0743 0.5798 0.9587 0
302+
H3B H 0.1364 0.6228 0.9058 0
303+
H3C H 0.0525 0.6039 0.8724 0
304+
N1 N 0.18278 0.46832 0.90973 0
305+
C2 C 0.60086 0.8125 0.86851 0
306+
H2 H 0.6411 0.7766 0.8777 0
307+
N1 N 0.53168 0.81722 0.90973 0
308+
C2 C 0.8125 0.39914 0.13149 0
309+
H2 H 0.7766 0.3589 0.1223 0
310+
N1 N 0.81722 0.46832 0.09027 0
311+
C2 C 0.1875 0.60086 0.13149 0
312+
H2 H 0.2234 0.6411 0.1223 0
313+
N1 N 0.18278 0.53168 0.09027 0
314+
315+

0 commit comments

Comments
 (0)