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PR: heat of adsorption for single and multiple components
heat of adsorption for single and multiple components with new XeKr mixture, Bae mix-ligand CO2/methane mixture, and NU2000 p-xylene tests
2 parents c90be10 + b1a377b commit 710c5aa

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Examples/Bae-Mixture/output.txt

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Examples/Bae-Mixture/simulation.input

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
1-
NumberOfInitializationCycles 100000
1+
NumberOfInitializationCycles 300000
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NumberOfEquilibrationCycles 0
3-
NumberOfProductionCycles 100000
3+
NumberOfProductionCycles 1000000
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UseChargesFromCIFFile yes
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Examples/NU2000-pX-LinkerRotations/output.txt

Lines changed: 52 additions & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
1-
/home/z/Desktop/gRASPA_versions/080424-code/gRASPA_fork/src_clean/nvc_main.xChecking if all inputs are defined
2-
True path of exe is /home/z/Desktop/gRASPA_versions/080424-code/gRASPA_fork/src_clean/
1+
/home/z/Desktop/gRASPA_versions/082824-code/gRASPA_fork/src_clean/nvc_main.xChecking if all inputs are defined
2+
True path of exe is /home/z/Desktop/gRASPA_versions/082824-code/gRASPA_fork/src_clean/
33
There are 1 simulations
44
running only one simulation
55
------------------PARSING FORCE FIELD MIXING RULES----------------
@@ -71,6 +71,7 @@ i: 88, ii: 8, jj: 8, Name_i: C_xyl, Name_j: C_xyl, ep: 29.3001479918, sig: 3.550
7171
i: 89, ii: 8, jj: 9, Name_i: C_xyl, Name_j: H_xyl, ep: 19.1351272366, sig: 2.9850000000, shift: -0.0181287134
7272
i: 99, ii: 9, jj: 9, Name_i: H_xyl, Name_j: H_xyl, ep: 12.4966295209, sig: 2.4200000000, shift: -0.0033622375
7373
----- END OF MIXED VDW PARAMETERS -----
74+
THERE ARE 10 PSEUDO ATOMS
7475
-------------PARSING PSEUDO ATOMS FILE-------------
7576
Name: HH, 0.00000, 1.00000, 0.00000, 0.00000
7677
Name: c, 0.00000, 12.00000, 0.00000, 0.00000
@@ -461,8 +462,8 @@ Component: 2, SelfAtomE: 0.00000 (0.00000 kJ/mol)
461462
Component: 0, Intra-Molecular ExclusionE: -32892160.48297 (-39560200.18912 kJ/mol)
462463
Component: 1, Intra-Molecular ExclusionE: -243671.40556 (-293069.51695 kJ/mol)
463464
Component: 2, Intra-Molecular ExclusionE: 0.00000 (0.00000 kJ/mol)
464-
HostEwald took 0.05826 sec
465-
Ewald Summation (total energy) on the CPU took 0.05826 secs
465+
HostEwald took 0.05838 sec
466+
Ewald Summation (total energy) on the CPU took 0.05838 secs
466467
Component 0, Intra Exclusion Energy: 32892160.48297 (39560200.18912 kJ/mol)
467468
Component 0, Atom Self Exclusion Energy: 7123268.40575 (8567327.89803 kJ/mol)
468469
DEBUG: comp: 0, IntraE: 32892160.48297, SelfE: 7123268.40575
@@ -516,7 +517,7 @@ Nblock 127, blocks: 127 0 0, threads needed: 16214 0 0, Nthread: 128
516517
GPU VDW REAL ENERGY:
517518
HHVDW: 5523439918.42259, HHReal: -6257646.54087, HGVDW: 0.00000, HGReal: 0.00000, GGVDW: 0.00000, GGReal: 0.00000, HHEwaldE: 0.00000, HGEwaldE: 0.00000, GGEwaldE: 0.00000, TailE: 0.00000, DNN_E: 0.00000
518519
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
519-
VDW + Real on the GPU took 0.00556 secs
520+
VDW + Real on the GPU took 0.00560 secs
520521
GPU Ewald Summary: NHostAtom: 1856, NGuestAtom: 0
521522
GPU Ewald Summary: Nthread: 128, Host thread: 128, Guest thread: 0
522523
Host NAtomPerThread: 14, Guest NAtomPerThread: 0
@@ -525,7 +526,7 @@ GPU fourier, HHFourier: 7328.67519, GGFourier: 0.00000, HGFourier: 0.00000, TOTF
525526
Framework Component 0 Exclusion: -40015428.88872
526527
Component 1, Nblock: 1, Nthread: 128
527528
Component 1, Exclusion (self + intra) = -1723558.02282
528-
Ewald Summation (total energy) on the GPU took 0.00126 secs
529+
Ewald Summation (total energy) on the GPU took 0.00134 secs
529530
Total GPU Energy:
530531
HHVDW: 5523439918.42259, HHReal: -6257646.54087, HGVDW: 0.00000, HGReal: 0.00000, GGVDW: 0.00000, GGReal: 0.00000, HHEwaldE: -41731658.23635, HGEwaldE: 0.00000, GGEwaldE: 0.00000, TailE: 0.00000, DNN_E: 0.00000
531532
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
@@ -551,8 +552,8 @@ Component: 2, SelfAtomE: 0.00000 (0.00000 kJ/mol)
551552
Component: 0, Intra-Molecular ExclusionE: -32892160.48297 (-39560200.18912 kJ/mol)
552553
Component: 1, Intra-Molecular ExclusionE: -243671.40556 (-293069.51695 kJ/mol)
553554
Component: 2, Intra-Molecular ExclusionE: 0.00000 (0.00000 kJ/mol)
554-
HostEwald took 0.05787 sec
555-
Ewald Summation (total energy) on the CPU took 0.05787 secs
555+
HostEwald took 0.05783 sec
556+
Ewald Summation (total energy) on the CPU took 0.05783 secs
556557
****** CHECKING WaveVectors Stored on CPU vs. GPU ******
557558
Wave Vector 0, CPU: 0.00000 0.00000, GPU: 0.00000 0.00000
558559
Wave Vector 1, CPU: 0.00000 0.00000, GPU: 0.00000 0.00000
@@ -584,7 +585,7 @@ Nblock 127, blocks: 127 0 0, threads needed: 16214 0 0, Nthread: 128
584585
GPU VDW REAL ENERGY:
585586
HHVDW: 5523439918.42259, HHReal: -6257646.54087, HGVDW: 0.00000, HGReal: 0.00000, GGVDW: 0.00000, GGReal: 0.00000, HHEwaldE: 0.00000, HGEwaldE: 0.00000, GGEwaldE: 0.00000, TailE: 0.00000, DNN_E: 0.00000
586587
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
587-
VDW + Real on the GPU took 0.00048 secs
588+
VDW + Real on the GPU took 0.00052 secs
588589
GPU Ewald Summary: NHostAtom: 1856, NGuestAtom: 0
589590
GPU Ewald Summary: Nthread: 128, Host thread: 128, Guest thread: 0
590591
Host NAtomPerThread: 14, Guest NAtomPerThread: 0
@@ -593,7 +594,7 @@ GPU fourier, HHFourier: 7328.67519, GGFourier: 0.00000, HGFourier: 0.00000, TOTF
593594
Framework Component 0 Exclusion: -40015428.88872
594595
Component 1, Nblock: 1, Nthread: 128
595596
Component 1, Exclusion (self + intra) = -1723558.02282
596-
Ewald Summation (total energy) on the GPU took 0.00103 secs
597+
Ewald Summation (total energy) on the GPU took 0.00112 secs
597598
Total GPU Energy:
598599
HHVDW: 5523439918.42259, HHReal: -6257646.54087, HGVDW: 0.00000, HGReal: 0.00000, GGVDW: 0.00000, GGReal: 0.00000, HHEwaldE: -41731658.23635, HGEwaldE: 0.00000, GGEwaldE: 0.00000, TailE: 0.00000, DNN_E: 0.00000
599600
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
@@ -671,13 +672,23 @@ Reinsertion Accepted: 0
671672
=====================IDENTITY SWAP MOVES=====================
672673
=============================================================
673674
================================================================================================
674-
=====================BLOCK AVERAGES (ENERGIES)================
675-
BLOCK [0], Blocksize: 1000, Average: 0.00000, ErrorBar: 0.00000
676-
BLOCK [1], Blocksize: 1000, Average: 0.00000, ErrorBar: 0.00000
677-
BLOCK [2], Blocksize: 1000, Average: 0.00000, ErrorBar: 0.00000
678-
BLOCK [3], Blocksize: 1000, Average: 0.00000, ErrorBar: 0.00000
679-
BLOCK [4], Blocksize: 1000, Average: 0.00000, ErrorBar: 0.00000
680-
Overall: Average: 0.00000, ErrorBar: 0.00000
675+
============= BLOCK AVERAGES (HEAT OF ADSORPTION: kJ/mol) =========
676+
WARNING: Matrix Inversion, Gauss-Jordan: Singular Matrix! Qst for the current component may not get calculated correctly!
677+
TIP: Your molecule may have a hard time getting in/out of the system box. Consider making it better by using some moves or NVT moves to relax the system more!
678+
WARNING: Matrix Inversion, Gauss-Jordan: Singular Matrix! Qst for the current component may not get calculated correctly!
679+
TIP: Your molecule may have a hard time getting in/out of the system box. Consider making it better by using some moves or NVT moves to relax the system more!
680+
WARNING: Matrix Inversion, Gauss-Jordan: Singular Matrix! Qst for the current component may not get calculated correctly!
681+
TIP: Your molecule may have a hard time getting in/out of the system box. Consider making it better by using some moves or NVT moves to relax the system more!
682+
WARNING: Matrix Inversion, Gauss-Jordan: Singular Matrix! Qst for the current component may not get calculated correctly!
683+
TIP: Your molecule may have a hard time getting in/out of the system box. Consider making it better by using some moves or NVT moves to relax the system more!
684+
COMPONENT [2] (p-xylene)
685+
BLOCK [0], Blocksize: 1000, Average: -82.49647
686+
BLOCK [1], Blocksize: 1000, Average: -inf
687+
BLOCK [2], Blocksize: 1000, Average: -inf
688+
BLOCK [3], Blocksize: 1000, Average: -inf
689+
BLOCK [4], Blocksize: 1000, Average: -inf
690+
Overall: Average: -inf, ErrorBar: -nan
691+
-----------------------------
681692
==============================================================
682693
=================== BLOCK AVERAGES (LOADING: # MOLECULES)=============
683694
COMPONENT [0] (Al-Bicyclo-AddedH-P1-fix-PBC.cif)
@@ -827,7 +838,7 @@ Printing: Component: 2 [ p-xylene ], NumMol: 3, Molsize: 12
827838
Component 0, Molsize: 448
828839
Component 1, Molsize: 22
829840
Component 2, Molsize: 12
830-
Work took 1.529762 seconds
841+
Work took 1.555274 seconds
831842
======================================
832843
CHECKING FINAL ENERGY FOR SYSTEM [0]
833844
======================================
@@ -851,8 +862,8 @@ Component: 2, SelfAtomE: 9891.85715 (11897.17681 kJ/mol)
851862
Component: 0, Intra-Molecular ExclusionE: -32892160.48297 (-39560200.18912 kJ/mol)
852863
Component: 1, Intra-Molecular ExclusionE: -243671.40556 (-293069.51695 kJ/mol)
853864
Component: 2, Intra-Molecular ExclusionE: 9115.33946 (10963.24013 kJ/mol)
854-
HostEwald took 0.05915 sec
855-
Ewald Summation (total energy) on the CPU took 0.05915 secs
865+
HostEwald took 0.05912 sec
866+
Ewald Summation (total energy) on the CPU took 0.05912 secs
856867
****** CHECKING WaveVectors Stored on CPU vs. GPU ******
857868
Wave Vector 0, CPU: 0.00000 0.00000, GPU: 0.00000 0.00000
858869
Wave Vector 1, CPU: 0.00000 0.00000, GPU: 0.00000 0.00000
@@ -895,7 +906,7 @@ Component 1, Nblock: 1, Nthread: 128
895906
Component 1, Exclusion (self + intra) = -1723558.02282
896907
Component 2, Nblock: 1, Nthread: 128
897908
Component 2, Exclusion (self + intra) = -776.51769
898-
Ewald Summation (total energy) on the GPU took 0.00109 secs
909+
Ewald Summation (total energy) on the GPU took 0.00112 secs
899910
Total GPU Energy:
900911
HHVDW: 5523450487.06017, HHReal: -6257686.00080, HGVDW: -22522.69448, HGReal: 173.17031, GGVDW: 20.02303, GGReal: 59.87284, HHEwaldE: -41731646.37098, HGEwaldE: -575.66969, GGEwaldE: -16.86955, TailE: 0.00000, DNN_E: 0.00000
901912
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
@@ -1041,33 +1052,33 @@ Total Energy: 0.00009 (0.00011 [K])
10411052
======================== PRODUCTION PHASE AVERAGE ENERGIES (Simulation 0) =========================
10421053
*** PRODUCTION PHASE AVERAGE ENERGY ***
10431054
========================================================================
1044-
VDW [Host-Host]: 11597.70969 (13948.84709 [K])
1045-
VDW [Host-Guest]: -21925.03318 (-26369.76985 [K])
1046-
VDW [Guest-Guest]: -48.11072 (-57.86393 [K])
1047-
Real Coulomb [Host-Host]: -42.84603 (-51.53196 [K])
1048-
Real Coulomb [Host-Guest]: 159.53179 (191.87275 [K])
1049-
Real Coulomb [Guest-Guest]: 23.53715 (28.30870 [K])
1050-
Ewald [Host-Host]: 12.62644 (15.18613 [K])
1051-
Ewald [Host-Guest]: -532.30799 (-640.21974 [K])
1052-
Ewald [Guest-Guest]: 12.62644 (15.18613 [K])
1055+
VDW [Host-Host]: 12263.74250 (14749.90093 [K])
1056+
VDW [Host-Guest]: -23404.97246 (-28149.72877 [K])
1057+
VDW [Guest-Guest]: -46.88289 (-56.38719 [K])
1058+
Real Coulomb [Host-Host]: -45.52184 (-54.75022 [K])
1059+
Real Coulomb [Host-Guest]: 171.36276 (206.10216 [K])
1060+
Real Coulomb [Guest-Guest]: 27.20859 (32.72443 [K])
1061+
Ewald [Host-Host]: 13.36065 (16.06918 [K])
1062+
Ewald [Host-Guest]: -567.56469 (-682.62383 [K])
1063+
Ewald [Guest-Guest]: 13.36065 (16.06918 [K])
10531064
DNN Energy: 0.00000 (0.00000 [K])
10541065
Tail Correction Energy: 0.00000 (0.00000 [K])
1055-
Total Energy: -10742.26640 (-12919.98467 [K])
1066+
Total Energy: -11575.90672 (-13922.62412 [K])
10561067
========================================================================
10571068
*** PRODUCTION PHASE AVERAGE ENERGY ERRORBAR ***
10581069
========================================================================
1059-
VDW [Host-Host]: 4055.57520 (4877.73879 [K])
1060-
VDW [Host-Guest]: 5580.27053 (6711.52688 [K])
1061-
VDW [Guest-Guest]: 62.98280 (75.75094 [K])
1062-
Real Coulomb [Host-Host]: 16.73334 (20.12559 [K])
1063-
Real Coulomb [Host-Guest]: 31.82580 (38.27767 [K])
1064-
Real Coulomb [Guest-Guest]: 29.61152 (35.61450 [K])
1065-
Ewald [Host-Host]: 4.30874 (5.18223 [K])
1066-
Ewald [Host-Guest]: 135.59088 (163.07844 [K])
1067-
Ewald [Guest-Guest]: 4.30874 (5.18223 [K])
1070+
VDW [Host-Host]: 1620.28603 (1948.75736 [K])
1071+
VDW [Host-Guest]: 2362.08648 (2840.93877 [K])
1072+
VDW [Guest-Guest]: 67.82257 (81.57185 [K])
1073+
Real Coulomb [Host-Host]: 10.69773 (12.86642 [K])
1074+
Real Coulomb [Host-Guest]: 36.50286 (43.90288 [K])
1075+
Real Coulomb [Guest-Guest]: 40.25629 (48.41722 [K])
1076+
Ewald [Host-Host]: 1.71686 (2.06491 [K])
1077+
Ewald [Host-Guest]: 22.01905 (26.48285 [K])
1078+
Ewald [Guest-Guest]: 1.71686 (2.06491 [K])
10681079
DNN Energy: 0.00000 (0.00000 [K])
10691080
Tail Correction Energy: 0.00000 (0.00000 [K])
1070-
Total Energy: 9921.20756 (11932.47727 [K])
1081+
Total Energy: 4163.10474 (5007.06717 [K])
10711082
========================================================================
10721083
================================================================================
10731084
DNN Rejection Summary:

Examples/XeKr-Mixture/25.cif

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data_POSCAR
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_audit_creation_date 2014-09-24
3+
_audit_creation_method 'ToBaCCo'
4+
_symmetry_space_group_name_H-M 'P1'
5+
_symmetry_Int_Tables_number 1
6+
_symmetry_cell_setting triclinic
7+
loop_
8+
_symmetry_equiv_pos_as_xyz
9+
x,y,z
10+
_cell_length_a 20.9550
11+
_cell_length_b 21.0407
12+
_cell_length_c 23.4288
13+
_cell_angle_alpha 89.997100
14+
_cell_angle_beta 90.243100
15+
_cell_angle_gamma 120.145800
16+
loop_
17+
_atom_site_label
18+
_atom_site_type_symbol
19+
_atom_site_fract_x
20+
_atom_site_fract_y
21+
_atom_site_fract_z
22+
O1 O 0.34875 0.55534 0.29757
23+
O2 O 0.22735 0.55814 0.31441
24+
C3 C 0.19442 0.59326 0.32520
25+
O4 O 0.20430 0.64918 0.29726
26+
O5 O 0.32888 0.77039 0.31468
27+
C6 C 0.39726 0.80342 0.32571
28+
O7 O 0.44349 0.79352 0.29797
29+
O8 O 0.44038 0.66961 0.31505
30+
C9 C 0.40505 0.60151 0.32570
31+
O10 O 0.32873 0.55839 0.18384
32+
O11 O 0.20412 0.55488 0.20066
33+
C12 C 0.19401 0.60077 0.17264
34+
O13 O 0.22708 0.66886 0.18359
35+
O14 O 0.34853 0.79315 0.20104
36+
C15 C 0.40485 0.80335 0.17334
37+
O16 O 0.44025 0.77067 0.18427
38+
O17 O 0.44338 0.64986 0.20136
39+
C18 C 0.39710 0.59374 0.17328
40+
Cr19 Cr 0.27929 0.56079 0.24913
41+
Cr20 Cr 0.27925 0.71835 0.24915
42+
Cr21 Cr 0.43775 0.71885 0.24965
43+
O22 O 0.33211 0.66601 0.24931
44+
O23 O 0.55891 0.33002 0.68481
45+
O24 O 0.55579 0.20610 0.70187
46+
C25 C 0.60200 0.19620 0.67412
47+
O26 O 0.67039 0.22922 0.68515
48+
O27 O 0.79498 0.35041 0.70254
49+
C28 C 0.80489 0.40636 0.67463
50+
O29 O 0.77200 0.44151 0.68545
51+
O30 O 0.65057 0.44428 0.70223
52+
C31 C 0.59425 0.39812 0.67413
53+
O32 O 0.55591 0.34974 0.79850
54+
O33 O 0.55904 0.22893 0.81557
55+
C34 C 0.59445 0.19625 0.82649
56+
O35 O 0.65078 0.20646 0.79879
57+
O36 O 0.77228 0.33074 0.81621
58+
C37 C 0.80525 0.39883 0.82715
59+
O38 O 0.79515 0.44478 0.79922
60+
O39 O 0.67054 0.44127 0.81597
61+
C40 C 0.60218 0.40589 0.82655
62+
Cr41 Cr 0.56154 0.28077 0.75020
63+
Cr42 Cr 0.72004 0.28126 0.75067
64+
Cr43 Cr 0.72001 0.43885 0.75071
65+
O44 O 0.66720 0.33362 0.75054
66+
C45 C 0.46795 0.04163 0.49763
67+
C46 C 0.51613 0.03611 0.45008
68+
C47 C 0.47470 -0.04775 0.45756
69+
C48 C 0.42609 -0.04306 0.50437
70+
C49 C 0.52455 0.04736 0.54227
71+
C50 C 0.48312 -0.03649 0.54975
72+
C51 C 0.57315 0.04267 0.49545
73+
C52 C 0.53130 -0.04201 0.50220
74+
C53 C 0.44697 -0.10076 0.41042
75+
C54 C 0.42423 -0.14445 0.37170
76+
C55 C 0.55228 0.10038 0.58941
77+
C56 C 0.57503 0.14407 0.62813
78+
H57 H 0.44222 0.07661 0.49628
79+
H58 H 0.52938 0.06538 0.40858
80+
H59 H 0.36532 -0.07890 0.50751
81+
H60 H 0.46986 -0.06576 0.59125
82+
H61 H 0.63393 0.07852 0.49232
83+
H62 H 0.55703 -0.07699 0.50355
84+
C63 C 1.03692 0.51838 0.54961
85+
C64 C 1.04118 0.46785 0.50352
86+
C65 C 1.04669 0.52223 0.45736
87+
C66 C 1.04325 0.57315 0.50272
88+
C67 C 0.95261 0.47740 0.54247
89+
C68 C 0.95812 0.53178 0.49631
90+
C69 C 0.95605 0.42648 0.49711
91+
C70 C 0.96238 0.48125 0.45022
92+
C71 C 1.09918 0.54731 0.41003
93+
C72 C 1.14254 0.56814 0.37120
94+
C73 C 0.90012 0.45232 0.58980
95+
C74 C 0.85677 0.43149 0.62863
96+
H75 H 1.06699 0.53338 0.59101
97+
H76 H 1.07591 0.44184 0.50595
98+
H77 H 1.07969 0.63375 0.50449
99+
H78 H 0.92339 0.55780 0.49387
100+
H79 H 0.91961 0.36588 0.49534
101+
H80 H 0.93231 0.46625 0.40882
102+
C81 C 0.48179 0.51824 0.54976
103+
C82 C 0.53223 0.57328 0.50375
104+
C83 C 0.47693 0.52461 0.45756
105+
C84 C 0.42610 0.46999 0.50283
106+
C85 C 0.52237 0.47499 0.54226
107+
C86 C 0.46707 0.42632 0.49607
108+
C87 C 0.57320 0.52961 0.49699
109+
C88 C 0.51751 0.48136 0.45006
110+
C89 C 0.45153 0.55219 0.41041
111+
C90 C 0.43045 0.57478 0.37169
112+
C91 C 0.54777 0.44741 0.58941
113+
C92 C 0.56886 0.42483 0.62814
114+
H93 H 0.46737 0.53308 0.59127
115+
H94 H 0.55874 0.63402 0.50637
116+
H95 H 0.36532 0.44578 0.50470
117+
H96 H 0.44056 0.36558 0.49344
118+
H97 H 0.63398 0.55382 0.49511
119+
H98 H 0.53193 0.46652 0.40854
120+
C99 C 0.48308 -0.03641 0.94991
121+
C100 C 0.53323 -0.04021 0.99696
122+
C101 C 0.47682 -0.04779 1.04206
123+
C102 C 0.42628 -0.04481 0.99574
124+
C103 C 0.52248 0.04738 0.95776
125+
C104 C 0.46607 0.03981 1.00286
126+
C105 C 0.57302 0.04440 1.00408
127+
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