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PR: heat of adsorption for single and multiple components
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heat of adsorption for single and multiple components
with new XeKr mixture, Bae mix-ligand CO2/methane mixture, and NU2000 p-xylene tests
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@Zhaoli2042
Zhaoli2042 authored Aug 29, 2024
2 parents c90be10 + b1a377b commit 710c5aa
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Showing 241 changed files with 265,971 additions and 474 deletions.
1,865 changes: 1,588 additions & 277 deletions Examples/Bae-Mixture/output.txt
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4 changes: 2 additions & 2 deletions Examples/Bae-Mixture/simulation.input
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
NumberOfInitializationCycles 100000
NumberOfInitializationCycles 300000
NumberOfEquilibrationCycles 0
NumberOfProductionCycles 100000
NumberOfProductionCycles 1000000

UseChargesFromCIFFile yes

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93 changes: 52 additions & 41 deletions Examples/NU2000-pX-LinkerRotations/output.txt
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/home/z/Desktop/gRASPA_versions/080424-code/gRASPA_fork/src_clean/nvc_main.xChecking if all inputs are defined
True path of exe is /home/z/Desktop/gRASPA_versions/080424-code/gRASPA_fork/src_clean/
/home/z/Desktop/gRASPA_versions/082824-code/gRASPA_fork/src_clean/nvc_main.xChecking if all inputs are defined
True path of exe is /home/z/Desktop/gRASPA_versions/082824-code/gRASPA_fork/src_clean/
There are 1 simulations
running only one simulation
------------------PARSING FORCE FIELD MIXING RULES----------------
Expand Down Expand Up @@ -71,6 +71,7 @@ i: 88, ii: 8, jj: 8, Name_i: C_xyl, Name_j: C_xyl, ep: 29.3001479918, sig: 3.550
i: 89, ii: 8, jj: 9, Name_i: C_xyl, Name_j: H_xyl, ep: 19.1351272366, sig: 2.9850000000, shift: -0.0181287134
i: 99, ii: 9, jj: 9, Name_i: H_xyl, Name_j: H_xyl, ep: 12.4966295209, sig: 2.4200000000, shift: -0.0033622375
----- END OF MIXED VDW PARAMETERS -----
THERE ARE 10 PSEUDO ATOMS
-------------PARSING PSEUDO ATOMS FILE-------------
Name: HH, 0.00000, 1.00000, 0.00000, 0.00000
Name: c, 0.00000, 12.00000, 0.00000, 0.00000
Expand Down Expand Up @@ -461,8 +462,8 @@ Component: 2, SelfAtomE: 0.00000 (0.00000 kJ/mol)
Component: 0, Intra-Molecular ExclusionE: -32892160.48297 (-39560200.18912 kJ/mol)
Component: 1, Intra-Molecular ExclusionE: -243671.40556 (-293069.51695 kJ/mol)
Component: 2, Intra-Molecular ExclusionE: 0.00000 (0.00000 kJ/mol)
HostEwald took 0.05826 sec
Ewald Summation (total energy) on the CPU took 0.05826 secs
HostEwald took 0.05838 sec
Ewald Summation (total energy) on the CPU took 0.05838 secs
Component 0, Intra Exclusion Energy: 32892160.48297 (39560200.18912 kJ/mol)
Component 0, Atom Self Exclusion Energy: 7123268.40575 (8567327.89803 kJ/mol)
DEBUG: comp: 0, IntraE: 32892160.48297, SelfE: 7123268.40575
Expand Down Expand Up @@ -516,7 +517,7 @@ Nblock 127, blocks: 127 0 0, threads needed: 16214 0 0, Nthread: 128
GPU VDW REAL ENERGY:
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
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
VDW + Real on the GPU took 0.00556 secs
VDW + Real on the GPU took 0.00560 secs
GPU Ewald Summary: NHostAtom: 1856, NGuestAtom: 0
GPU Ewald Summary: Nthread: 128, Host thread: 128, Guest thread: 0
Host NAtomPerThread: 14, Guest NAtomPerThread: 0
Expand All @@ -525,7 +526,7 @@ GPU fourier, HHFourier: 7328.67519, GGFourier: 0.00000, HGFourier: 0.00000, TOTF
Framework Component 0 Exclusion: -40015428.88872
Component 1, Nblock: 1, Nthread: 128
Component 1, Exclusion (self + intra) = -1723558.02282
Ewald Summation (total energy) on the GPU took 0.00126 secs
Ewald Summation (total energy) on the GPU took 0.00134 secs
Total GPU Energy:
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
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
Expand All @@ -551,8 +552,8 @@ Component: 2, SelfAtomE: 0.00000 (0.00000 kJ/mol)
Component: 0, Intra-Molecular ExclusionE: -32892160.48297 (-39560200.18912 kJ/mol)
Component: 1, Intra-Molecular ExclusionE: -243671.40556 (-293069.51695 kJ/mol)
Component: 2, Intra-Molecular ExclusionE: 0.00000 (0.00000 kJ/mol)
HostEwald took 0.05787 sec
Ewald Summation (total energy) on the CPU took 0.05787 secs
HostEwald took 0.05783 sec
Ewald Summation (total energy) on the CPU took 0.05783 secs
****** CHECKING WaveVectors Stored on CPU vs. GPU ******
Wave Vector 0, CPU: 0.00000 0.00000, GPU: 0.00000 0.00000
Wave Vector 1, CPU: 0.00000 0.00000, GPU: 0.00000 0.00000
Expand Down Expand Up @@ -584,7 +585,7 @@ Nblock 127, blocks: 127 0 0, threads needed: 16214 0 0, Nthread: 128
GPU VDW REAL ENERGY:
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
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
VDW + Real on the GPU took 0.00048 secs
VDW + Real on the GPU took 0.00052 secs
GPU Ewald Summary: NHostAtom: 1856, NGuestAtom: 0
GPU Ewald Summary: Nthread: 128, Host thread: 128, Guest thread: 0
Host NAtomPerThread: 14, Guest NAtomPerThread: 0
Expand All @@ -593,7 +594,7 @@ GPU fourier, HHFourier: 7328.67519, GGFourier: 0.00000, HGFourier: 0.00000, TOTF
Framework Component 0 Exclusion: -40015428.88872
Component 1, Nblock: 1, Nthread: 128
Component 1, Exclusion (self + intra) = -1723558.02282
Ewald Summation (total energy) on the GPU took 0.00103 secs
Ewald Summation (total energy) on the GPU took 0.00112 secs
Total GPU Energy:
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
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
Expand Down Expand Up @@ -671,13 +672,23 @@ Reinsertion Accepted: 0
=====================IDENTITY SWAP MOVES=====================
=============================================================
================================================================================================
=====================BLOCK AVERAGES (ENERGIES)================
BLOCK [0], Blocksize: 1000, Average: 0.00000, ErrorBar: 0.00000
BLOCK [1], Blocksize: 1000, Average: 0.00000, ErrorBar: 0.00000
BLOCK [2], Blocksize: 1000, Average: 0.00000, ErrorBar: 0.00000
BLOCK [3], Blocksize: 1000, Average: 0.00000, ErrorBar: 0.00000
BLOCK [4], Blocksize: 1000, Average: 0.00000, ErrorBar: 0.00000
Overall: Average: 0.00000, ErrorBar: 0.00000
============= BLOCK AVERAGES (HEAT OF ADSORPTION: kJ/mol) =========
WARNING: Matrix Inversion, Gauss-Jordan: Singular Matrix! Qst for the current component may not get calculated correctly!
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!
WARNING: Matrix Inversion, Gauss-Jordan: Singular Matrix! Qst for the current component may not get calculated correctly!
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!
WARNING: Matrix Inversion, Gauss-Jordan: Singular Matrix! Qst for the current component may not get calculated correctly!
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!
WARNING: Matrix Inversion, Gauss-Jordan: Singular Matrix! Qst for the current component may not get calculated correctly!
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!
COMPONENT [2] (p-xylene)
BLOCK [0], Blocksize: 1000, Average: -82.49647
BLOCK [1], Blocksize: 1000, Average: -inf
BLOCK [2], Blocksize: 1000, Average: -inf
BLOCK [3], Blocksize: 1000, Average: -inf
BLOCK [4], Blocksize: 1000, Average: -inf
Overall: Average: -inf, ErrorBar: -nan
-----------------------------
==============================================================
=================== BLOCK AVERAGES (LOADING: # MOLECULES)=============
COMPONENT [0] (Al-Bicyclo-AddedH-P1-fix-PBC.cif)
Expand Down Expand Up @@ -827,7 +838,7 @@ Printing: Component: 2 [ p-xylene ], NumMol: 3, Molsize: 12
Component 0, Molsize: 448
Component 1, Molsize: 22
Component 2, Molsize: 12
Work took 1.529762 seconds
Work took 1.555274 seconds
======================================
CHECKING FINAL ENERGY FOR SYSTEM [0]
======================================
Expand All @@ -851,8 +862,8 @@ Component: 2, SelfAtomE: 9891.85715 (11897.17681 kJ/mol)
Component: 0, Intra-Molecular ExclusionE: -32892160.48297 (-39560200.18912 kJ/mol)
Component: 1, Intra-Molecular ExclusionE: -243671.40556 (-293069.51695 kJ/mol)
Component: 2, Intra-Molecular ExclusionE: 9115.33946 (10963.24013 kJ/mol)
HostEwald took 0.05915 sec
Ewald Summation (total energy) on the CPU took 0.05915 secs
HostEwald took 0.05912 sec
Ewald Summation (total energy) on the CPU took 0.05912 secs
****** CHECKING WaveVectors Stored on CPU vs. GPU ******
Wave Vector 0, CPU: 0.00000 0.00000, GPU: 0.00000 0.00000
Wave Vector 1, CPU: 0.00000 0.00000, GPU: 0.00000 0.00000
Expand Down Expand Up @@ -895,7 +906,7 @@ Component 1, Nblock: 1, Nthread: 128
Component 1, Exclusion (self + intra) = -1723558.02282
Component 2, Nblock: 1, Nthread: 128
Component 2, Exclusion (self + intra) = -776.51769
Ewald Summation (total energy) on the GPU took 0.00109 secs
Ewald Summation (total energy) on the GPU took 0.00112 secs
Total GPU Energy:
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
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
Expand Down Expand Up @@ -1041,33 +1052,33 @@ Total Energy: 0.00009 (0.00011 [K])
======================== PRODUCTION PHASE AVERAGE ENERGIES (Simulation 0) =========================
*** PRODUCTION PHASE AVERAGE ENERGY ***
========================================================================
VDW [Host-Host]: 11597.70969 (13948.84709 [K])
VDW [Host-Guest]: -21925.03318 (-26369.76985 [K])
VDW [Guest-Guest]: -48.11072 (-57.86393 [K])
Real Coulomb [Host-Host]: -42.84603 (-51.53196 [K])
Real Coulomb [Host-Guest]: 159.53179 (191.87275 [K])
Real Coulomb [Guest-Guest]: 23.53715 (28.30870 [K])
Ewald [Host-Host]: 12.62644 (15.18613 [K])
Ewald [Host-Guest]: -532.30799 (-640.21974 [K])
Ewald [Guest-Guest]: 12.62644 (15.18613 [K])
VDW [Host-Host]: 12263.74250 (14749.90093 [K])
VDW [Host-Guest]: -23404.97246 (-28149.72877 [K])
VDW [Guest-Guest]: -46.88289 (-56.38719 [K])
Real Coulomb [Host-Host]: -45.52184 (-54.75022 [K])
Real Coulomb [Host-Guest]: 171.36276 (206.10216 [K])
Real Coulomb [Guest-Guest]: 27.20859 (32.72443 [K])
Ewald [Host-Host]: 13.36065 (16.06918 [K])
Ewald [Host-Guest]: -567.56469 (-682.62383 [K])
Ewald [Guest-Guest]: 13.36065 (16.06918 [K])
DNN Energy: 0.00000 (0.00000 [K])
Tail Correction Energy: 0.00000 (0.00000 [K])
Total Energy: -10742.26640 (-12919.98467 [K])
Total Energy: -11575.90672 (-13922.62412 [K])
========================================================================
*** PRODUCTION PHASE AVERAGE ENERGY ERRORBAR ***
========================================================================
VDW [Host-Host]: 4055.57520 (4877.73879 [K])
VDW [Host-Guest]: 5580.27053 (6711.52688 [K])
VDW [Guest-Guest]: 62.98280 (75.75094 [K])
Real Coulomb [Host-Host]: 16.73334 (20.12559 [K])
Real Coulomb [Host-Guest]: 31.82580 (38.27767 [K])
Real Coulomb [Guest-Guest]: 29.61152 (35.61450 [K])
Ewald [Host-Host]: 4.30874 (5.18223 [K])
Ewald [Host-Guest]: 135.59088 (163.07844 [K])
Ewald [Guest-Guest]: 4.30874 (5.18223 [K])
VDW [Host-Host]: 1620.28603 (1948.75736 [K])
VDW [Host-Guest]: 2362.08648 (2840.93877 [K])
VDW [Guest-Guest]: 67.82257 (81.57185 [K])
Real Coulomb [Host-Host]: 10.69773 (12.86642 [K])
Real Coulomb [Host-Guest]: 36.50286 (43.90288 [K])
Real Coulomb [Guest-Guest]: 40.25629 (48.41722 [K])
Ewald [Host-Host]: 1.71686 (2.06491 [K])
Ewald [Host-Guest]: 22.01905 (26.48285 [K])
Ewald [Guest-Guest]: 1.71686 (2.06491 [K])
DNN Energy: 0.00000 (0.00000 [K])
Tail Correction Energy: 0.00000 (0.00000 [K])
Total Energy: 9921.20756 (11932.47727 [K])
Total Energy: 4163.10474 (5007.06717 [K])
========================================================================
================================================================================
DNN Rejection Summary:
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174 changes: 174 additions & 0 deletions Examples/XeKr-Mixture/25.cif
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Original file line number Diff line number Diff line change
@@ -0,0 +1,174 @@
data_POSCAR
_audit_creation_date 2014-09-24
_audit_creation_method 'ToBaCCo'
_symmetry_space_group_name_H-M 'P1'
_symmetry_Int_Tables_number 1
_symmetry_cell_setting triclinic
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
_cell_length_a 20.9550
_cell_length_b 21.0407
_cell_length_c 23.4288
_cell_angle_alpha 89.997100
_cell_angle_beta 90.243100
_cell_angle_gamma 120.145800
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
O1 O 0.34875 0.55534 0.29757
O2 O 0.22735 0.55814 0.31441
C3 C 0.19442 0.59326 0.32520
O4 O 0.20430 0.64918 0.29726
O5 O 0.32888 0.77039 0.31468
C6 C 0.39726 0.80342 0.32571
O7 O 0.44349 0.79352 0.29797
O8 O 0.44038 0.66961 0.31505
C9 C 0.40505 0.60151 0.32570
O10 O 0.32873 0.55839 0.18384
O11 O 0.20412 0.55488 0.20066
C12 C 0.19401 0.60077 0.17264
O13 O 0.22708 0.66886 0.18359
O14 O 0.34853 0.79315 0.20104
C15 C 0.40485 0.80335 0.17334
O16 O 0.44025 0.77067 0.18427
O17 O 0.44338 0.64986 0.20136
C18 C 0.39710 0.59374 0.17328
Cr19 Cr 0.27929 0.56079 0.24913
Cr20 Cr 0.27925 0.71835 0.24915
Cr21 Cr 0.43775 0.71885 0.24965
O22 O 0.33211 0.66601 0.24931
O23 O 0.55891 0.33002 0.68481
O24 O 0.55579 0.20610 0.70187
C25 C 0.60200 0.19620 0.67412
O26 O 0.67039 0.22922 0.68515
O27 O 0.79498 0.35041 0.70254
C28 C 0.80489 0.40636 0.67463
O29 O 0.77200 0.44151 0.68545
O30 O 0.65057 0.44428 0.70223
C31 C 0.59425 0.39812 0.67413
O32 O 0.55591 0.34974 0.79850
O33 O 0.55904 0.22893 0.81557
C34 C 0.59445 0.19625 0.82649
O35 O 0.65078 0.20646 0.79879
O36 O 0.77228 0.33074 0.81621
C37 C 0.80525 0.39883 0.82715
O38 O 0.79515 0.44478 0.79922
O39 O 0.67054 0.44127 0.81597
C40 C 0.60218 0.40589 0.82655
Cr41 Cr 0.56154 0.28077 0.75020
Cr42 Cr 0.72004 0.28126 0.75067
Cr43 Cr 0.72001 0.43885 0.75071
O44 O 0.66720 0.33362 0.75054
C45 C 0.46795 0.04163 0.49763
C46 C 0.51613 0.03611 0.45008
C47 C 0.47470 -0.04775 0.45756
C48 C 0.42609 -0.04306 0.50437
C49 C 0.52455 0.04736 0.54227
C50 C 0.48312 -0.03649 0.54975
C51 C 0.57315 0.04267 0.49545
C52 C 0.53130 -0.04201 0.50220
C53 C 0.44697 -0.10076 0.41042
C54 C 0.42423 -0.14445 0.37170
C55 C 0.55228 0.10038 0.58941
C56 C 0.57503 0.14407 0.62813
H57 H 0.44222 0.07661 0.49628
H58 H 0.52938 0.06538 0.40858
H59 H 0.36532 -0.07890 0.50751
H60 H 0.46986 -0.06576 0.59125
H61 H 0.63393 0.07852 0.49232
H62 H 0.55703 -0.07699 0.50355
C63 C 1.03692 0.51838 0.54961
C64 C 1.04118 0.46785 0.50352
C65 C 1.04669 0.52223 0.45736
C66 C 1.04325 0.57315 0.50272
C67 C 0.95261 0.47740 0.54247
C68 C 0.95812 0.53178 0.49631
C69 C 0.95605 0.42648 0.49711
C70 C 0.96238 0.48125 0.45022
C71 C 1.09918 0.54731 0.41003
C72 C 1.14254 0.56814 0.37120
C73 C 0.90012 0.45232 0.58980
C74 C 0.85677 0.43149 0.62863
H75 H 1.06699 0.53338 0.59101
H76 H 1.07591 0.44184 0.50595
H77 H 1.07969 0.63375 0.50449
H78 H 0.92339 0.55780 0.49387
H79 H 0.91961 0.36588 0.49534
H80 H 0.93231 0.46625 0.40882
C81 C 0.48179 0.51824 0.54976
C82 C 0.53223 0.57328 0.50375
C83 C 0.47693 0.52461 0.45756
C84 C 0.42610 0.46999 0.50283
C85 C 0.52237 0.47499 0.54226
C86 C 0.46707 0.42632 0.49607
C87 C 0.57320 0.52961 0.49699
C88 C 0.51751 0.48136 0.45006
C89 C 0.45153 0.55219 0.41041
C90 C 0.43045 0.57478 0.37169
C91 C 0.54777 0.44741 0.58941
C92 C 0.56886 0.42483 0.62814
H93 H 0.46737 0.53308 0.59127
H94 H 0.55874 0.63402 0.50637
H95 H 0.36532 0.44578 0.50470
H96 H 0.44056 0.36558 0.49344
H97 H 0.63398 0.55382 0.49511
H98 H 0.53193 0.46652 0.40854
C99 C 0.48308 -0.03641 0.94991
C100 C 0.53323 -0.04021 0.99696
C101 C 0.47682 -0.04779 1.04206
C102 C 0.42628 -0.04481 0.99574
C103 C 0.52248 0.04738 0.95776
C104 C 0.46607 0.03981 1.00286
C105 C 0.57302 0.04440 1.00408
C106 C 0.51622 0.03600 1.04991
C107 C 0.45133 -0.10083 1.08898
C108 C 0.43021 -0.14453 1.12754
C109 C 0.54798 0.10042 0.91084
C110 C 0.56909 0.14413 0.87229
H111 H 0.46973 -0.06559 0.90827
H112 H 0.56056 -0.07371 0.99506
H113 H 0.36565 -0.08209 0.99284
H114 H 0.43874 0.07330 1.00476
H115 H 0.63365 0.08168 1.00698
H116 H 0.52957 0.06518 1.09155
C117 C 1.03860 0.52070 0.95230
C118 C 1.04255 0.57464 0.99907
C119 C 1.04964 0.52591 1.04455
C120 C 1.04652 0.47240 0.99851
C121 C 0.95442 0.47616 0.95948
C122 C 0.96151 0.42743 1.00496
C123 C 0.95754 0.52967 1.00551
C124 C 0.96546 0.48137 1.05173
C125 C 1.10273 0.55358 1.09188
C126 C 1.14653 0.57630 1.13075
C127 C 0.90133 0.44848 0.91214
C128 C 0.85755 0.42577 0.87328
H129 H 1.06809 0.53656 0.91089
H130 H 1.07646 0.63548 0.99718
H131 H 1.08370 0.44916 0.99617
H132 H 0.92761 0.36658 1.00685
H133 H 0.92036 0.55291 1.00786
H134 H 0.93598 0.46551 1.09314
C135 C 0.48216 0.51858 0.94990
C136 C 0.42596 0.46818 0.99533
C137 C 0.47460 0.52240 1.04203
C138 C 0.53037 0.57320 0.99733
C139 C 0.52466 0.47724 0.95778
C140 C 0.57330 0.53146 1.00448
C141 C 0.46889 0.42644 1.00249
C142 C 0.51710 0.48106 1.04991
C143 C 0.44679 0.54763 1.08893
C144 C 0.42402 0.56856 1.12748
C145 C 0.55247 0.45201 0.91089
C146 C 0.57525 0.43108 0.87235
H147 H 0.46811 0.53374 0.90825
H148 H 0.36507 0.44243 0.99210
H149 H 0.55533 0.63383 0.99574
H150 H 0.63419 0.55721 1.00772
H151 H 0.44393 0.36581 1.00408
H152 H 0.53115 0.46590 1.09156

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