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A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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Tag: Branch: Tree: 05684f9cf6
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Create tag ${ searchTerm }
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CMMDE/cmmde_gui/test/metana5/freq/cmmd.hess

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addition to xTB functions
2 years ago
$orca_hessian_file
$act_atom
0
$act_coord
0
$act_energy
-4.175219
$hessian
15
0 1 2 3 4
0 5.1328904983E-01 4.0104139572E-07 -2.9617036024E-06 -2.9809679856E-01 1.9515321323E-08
1 4.0104139572E-07 5.1328988388E-01 1.2319354815E-07 2.1241556552E-08 -4.3442954994E-02
2 -2.9617036024E-06 1.2319354815E-07 5.1328768391E-01 9.1256739697E-08 -2.7969117270E-10
3 -2.9809679856E-01 2.1241556552E-08 9.1256739697E-08 3.4272636690E-01 1.4640704964E-08
4 1.9515321323E-08 -4.3442954994E-02 -2.7969117270E-10 1.4640704964E-08 4.6441252344E-02
5 9.1788929205E-08 -2.8334016035E-10 -4.3442846289E-02 -3.6035005906E-07 1.1067700287E-08
6 -7.1734140120E-02 -7.1105098004E-02 -3.6719690891E-02 -1.4874695868E-02 -2.9806119290E-02
7 -7.1104941062E-02 -2.2213728053E-01 -9.2283674479E-02 -2.0870043151E-03 -1.6848957919E-03
8 -3.6719658341E-02 -9.2283833789E-02 -9.1097601945E-02 -1.0779036686E-03 -9.6571895625E-04
9 -7.1734204487E-02 6.7353620152E-02 -4.3217000246E-02 -1.4874667032E-02 2.8233637348E-02
10 6.7353471999E-02 -2.0377868043E-01 1.0288211556E-01 1.9769112614E-03 -1.4927477150E-03
11 -4.3216962157E-02 1.0288228123E-01 -1.0945396589E-01 -1.2685924427E-03 1.0766014402E-03
12 -7.1733812729E-02 3.7510556233E-03 7.9939561087E-02 -1.4874718248E-02 1.5724477751E-03
13 3.7510476350E-03 -4.3940158402E-02 -1.0598561382E-02 1.1012450192E-04 1.7991150548E-04
14 7.9939497070E-02 -1.0598568086E-02 -2.6930294669E-01 2.3463039363E-03 -1.1089357381E-04
5 6 7 8 9
0 9.1788929205E-08 -7.1734140120E-02 -7.1104941062E-02 -3.6719658341E-02 -7.1734204487E-02
1 -2.8334016035E-10 -7.1105098004E-02 -2.2213728053E-01 -9.2283833789E-02 6.7353620152E-02
2 -4.3442846289E-02 -3.6719690891E-02 -9.2283674479E-02 -9.1097601945E-02 -4.3217000246E-02
3 -3.6035005906E-07 -1.4874695868E-02 -2.0870043151E-03 -1.0779036686E-03 -1.4874667032E-02
4 1.1067700287E-08 -2.9806119290E-02 -1.6848957919E-03 -9.6571895625E-04 2.8233637348E-02
5 4.6441254224E-02 -1.5392775239E-02 -9.6561006972E-04 -3.1354850181E-04 -1.8116341765E-02
6 -1.5392775239E-02 7.9358619129E-02 8.2729854823E-02 4.2723181184E-02 3.6258437738E-03
7 -9.6561006972E-04 8.2729854823E-02 2.5434926341E-01 1.0737068939E-01 -8.7677409963E-03
8 -3.1354850181E-04 4.2723181184E-02 1.0737068939E-01 1.0188757942E-01 5.2827616702E-03
9 -1.8116341765E-02 3.6258437738E-03 -8.7677409963E-03 5.2827616702E-03 7.9358649927E-02
10 1.0765196222E-03 9.2239047429E-03 -2.7489186231E-02 1.4357641088E-02 -7.8365096448E-02
11 -5.0563684325E-04 4.4384876464E-03 -1.1114552318E-02 6.9904109170E-03 5.0282711026E-02
12 3.3509385650E-02 3.6258460597E-03 -7.6811348287E-04 -1.0207319540E-02 3.6258507992E-03
13 -1.1092068383E-04 8.9587998211E-03 -3.0337524900E-03 -2.8477040386E-02 -8.4557347643E-03
14 -2.1786286698E-03 4.9516934239E-03 -3.0045440927E-03 -1.7464996461E-02 5.7688976542E-03
10 11 12 13 14
0 6.7353471999E-02 -4.3216962157E-02 -7.1733812729E-02 3.7510476350E-03 7.9939497070E-02
1 -2.0377868043E-01 1.0288228123E-01 3.7510556233E-03 -4.3940158402E-02 -1.0598568086E-02
2 1.0288211556E-01 -1.0945396589E-01 7.9939561087E-02 -1.0598561382E-02 -2.6930294669E-01
3 1.9769112614E-03 -1.2685924427E-03 -1.4874718248E-02 1.1012450192E-04 2.3463039363E-03
4 -1.4927477150E-03 1.0766014402E-03 1.5724477751E-03 1.7991150548E-04 -1.1089357381E-04
5 1.0765196222E-03 -5.0563684325E-04 3.3509385650E-02 -1.1092068383E-04 -2.1786286698E-03
6 9.2239047429E-03 4.4384876464E-03 3.6258460597E-03 8.9587998211E-03 4.9516934239E-03
7 -2.7489186231E-02 -1.1114552318E-02 -7.6811348287E-04 -3.0337524900E-03 -3.0045440927E-03
8 1.4357641088E-02 6.9904109170E-03 -1.0207319540E-02 -2.8477040386E-02 -1.7464996461E-02
9 -7.8365096448E-02 5.0282711026E-02 3.6258507992E-03 -8.4557347643E-03 5.7688976542E-03
10 2.3298964564E-01 -1.1970182129E-01 -1.9113815989E-04 -2.2513330162E-04 1.3830430022E-03
11 -1.1970182129E-01 1.2324514112E-01 -1.0234394966E-02 2.6855477542E-02 -2.0273670666E-02
12 -1.9113815989E-04 -1.0234394966E-02 7.9358307039E-02 -4.3643455992E-03 -9.3008702083E-02
13 -2.2513330162E-04 2.6855477542E-02 -4.3643455992E-03 4.7019711491E-02 1.2331236539E-02
14 1.3830430022E-03 -2.0273670666E-02 -9.3008702083E-02 1.2331236539E-02 3.0922520339E-01
$vibrational_frequencies
15
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 1385.800357
7 1385.808548
8 1385.817911
9 1557.266971
10 1557.277618
11 3090.006346
12 3103.918017
13 3103.935339
14 3103.956484
$normal_modes
15 15
0 1 2 3 4
0 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
2 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
6 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
7 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
8 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
9 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
10 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
11 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
12 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
13 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
14 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
5 6 7 8 9
0 0.0000000000E+00 1.0167012233E-01 -7.8578999511E-02 -9.7049398634E-03 -1.4559172305E-06
1 0.0000000000E+00 3.5139553219E-03 2.0257912907E-02 -1.2721147824E-01 -1.2094324497E-06
2 0.0000000000E+00 7.9098001402E-02 1.0010277739E-01 1.8125792971E-02 -9.0847217695E-06
3 0.0000000000E+00 4.7303187800E-02 -3.6561396386E-02 -4.5157057234E-03 -2.6034477222E-07
4 0.0000000000E+00 -1.6516398084E-02 -9.5227271973E-02 5.9801646362E-01 6.3674525520E-02
5 0.0000000000E+00 -3.7180838507E-01 -4.7055235356E-01 -8.5208664091E-02 4.9597577522E-01
6 0.0000000000E+00 -3.5560952616E-01 4.2807726522E-01 -1.2995464812E-01 -2.6788493062E-01
7 0.0000000000E+00 2.9099460503E-01 5.2286366308E-02 1.5676980114E-01 2.7291280052E-01
8 0.0000000000E+00 -2.1306253368E-01 -3.9442808543E-01 -3.1309282747E-01 -3.2206546012E-01
9 0.0000000000E+00 -3.5505152961E-01 3.8437266310E-01 2.2977400381E-01 -2.0198790287E-01
10 0.0000000000E+00 -3.0913561181E-01 -1.3091832357E-01 1.5964008458E-01 -3.0405607972E-01
11 0.0000000000E+00 -1.8411528768E-01 -4.4772038599E-01 1.9608827343E-01 -3.4163278167E-01
12 0.0000000000E+00 -5.4811022662E-01 1.6043325688E-01 2.0337255488E-02 4.6989044207E-01
13 0.0000000000E+00 -7.2137433220E-03 -6.7527469103E-02 6.0138423114E-01 -3.2516835117E-02
14 0.0000000000E+00 -1.7351984003E-01 1.1990870272E-01 -1.3767832842E-02 1.6783071716E-01
10 11 12 13 14
0 3.1994872509E-07 -9.2432081897E-05 -5.4343359797E-03 -2.8446098991E-02 -8.2345029786E-02
1 -1.5108210556E-06 1.0770600240E-05 8.5682011078E-02 -1.6677843455E-02 1.0678227446E-04
2 1.4964506359E-07 -6.8753951946E-05 -1.5767957277E-02 -8.0821547902E-02 2.8960646009E-02
3 7.9423020652E-08 -4.9908240777E-01 5.3770757743E-02 2.8109924355E-01 8.1247173594E-01
4 4.9593792877E-01 5.0587520831E-06 3.9625362479E-02 -7.7129039652E-03 4.9442937052E-05
5 -6.3669189237E-02 -3.2026734230E-05 -7.2923242998E-03 -3.7377773813E-02 1.3391944848E-02
6 -3.8789758809E-01 1.6679977207E-01 -2.1987020400E-01 1.8768978701E-01 1.2818429973E-02
7 -8.5213488594E-03 4.1930269185E-01 -5.0661386304E-01 4.9703773487E-01 1.2797468300E-01
8 3.1537773018E-01 2.1650437726E-01 -2.8938826281E-01 2.2328633840E-01 7.9457830564E-02
9 4.2593938445E-01 1.6687857714E-01 2.6526509960E-01 1.1535825898E-01 5.7892675694E-03
10 1.1045794906E-02 -3.9735996097E-01 -5.9782550379E-01 -3.1364808990E-01 -1.0439388788E-01
11 -2.6163413879E-01 2.5493902886E-01 4.0173391290E-01 1.5892227387E-01 8.0410742753E-02
12 -3.8045688189E-02 1.6650544917E-01 -3.4411874126E-02 -2.4519283024E-01 1.5011714664E-01
13 -4.9844437237E-01 -2.2076128599E-02 4.3855041007E-02 2.3051014690E-02 -2.4902620899E-02
14 9.9238147318E-03 -4.7059212967E-01 8.2832522273E-02 6.1821242727E-01 -5.1834615230E-01
#
# The atoms: label mass x y z (in bohrs)
#
$atoms
5
C 12.01100 2.043441533093 0.014361775768 -0.108977471450
H 1.00800 4.088428822464 0.014361600955 -0.108978286738
H 1.00800 1.361782268872 -1.698716011169 -0.993665474494
H 1.00800 1.361781467806 1.637064463077 -1.150199588032
H 1.00800 1.361785990560 0.104737764458 1.816937187259
$actual_temperature
0.000000
$frequency_scale_factor
1.000000
$dipole_derivatives
15
-0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00
-2.0000000000E-01 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00
-0.0000000000E+00 -0.0000000000E+00 -0.0000000000E+00
-0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00
0.0000000000E+00 -0.0000000000E+00 0.0000000000E+00
-0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 -0.0000000000E+00
0.0000000000E+00 -0.0000000000E+00 -2.0000000000E-01
#
# The IR spectrum
# wavenumber eps Int TX TY TZ
#
$ir_spectrum
15
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
0.00 0.00000000 0.00000000 0.000000 0.000000 0.000000
1385.80 0.00020962 1.05933867 -0.001807 0.000000 0.006629
1385.81 0.00010184 0.51465292 0.001397 0.000000 -0.004581
1385.82 0.00000136 0.00687560 0.000173 0.000000 0.000526
1557.27 0.00021562 1.08966649 0.000000 0.000000 -0.006573
1557.28 0.00000075 0.00380985 -0.000000 0.000000 -0.000389
3090.01 0.00360203 18.20318438 0.013877 0.000000 0.013085
3103.92 0.00006892 0.34831316 -0.001433 0.000000 -0.002208
3103.94 0.00325946 16.47198631 -0.007493 0.000000 -0.016479
3103.96 0.00656406 33.17206637 -0.021657 0.000000 0.013817
$end