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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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Create tag ${ searchTerm }
Create branch ${ searchTerm }
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CMMDE/examples/energetics/ch4/cmmd.hess

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$orca_hessian_file
$act_atom
0
$act_coord
0
$act_energy
-4.174453
$hessian
15
0 1 2 3 4
0 4.7636737984E-01 9.8065926338E-06 4.0509474611E-05 -2.6387163902E-01 -4.9481781065E-06
1 9.8065926338E-06 4.7636874797E-01 -3.5322753161E-05 -4.4553523828E-06 -4.6712723347E-02
2 4.0509474611E-05 -3.5322753161E-05 4.7642267416E-01 -1.2244706595E-05 1.3445702371E-06
3 -2.6387163902E-01 -4.4553523828E-06 -1.2244706595E-05 3.0569963803E-01 3.1934909046E-06
4 -4.9481781065E-06 -4.6712723347E-02 1.3445702371E-06 3.1934909046E-06 4.9654687555E-02
5 -1.3149822728E-05 1.3436762125E-06 -4.6713637453E-02 1.0441682149E-05 5.2350354108E-07
6 -7.0839334605E-02 2.3174998109E-02 -6.4209878747E-02 -1.3938723600E-02 1.0841749785E-02
7 2.3175171407E-02 -6.8961088744E-02 6.1660244645E-02 6.2463766555E-04 -1.9733379734E-04
8 -6.4209650586E-02 6.1659527473E-02 -2.1753160526E-01 -1.7300159651E-03 6.4963338353E-04
9 -7.0831022262E-02 4.3995634311E-02 5.2150044298E-02 -1.3942892159E-02 2.0594374742E-02
10 4.3995912265E-02 -1.2696536462E-01 -9.5129410929E-02 1.1882102059E-03 -8.0894314407E-04
11 5.2150455969E-02 -9.5129546775E-02 -1.5947516242E-01 1.4084470151E-03 -1.0045758742E-03
12 -7.0837646203E-02 -6.7175983361E-02 1.2031570067E-02 -1.3939157729E-02 -3.1434370036E-02
13 -6.7175915060E-02 -2.3374165050E-01 3.3503139526E-02 -1.8110895566E-03 -1.9348846781E-03
14 1.2031855740E-02 3.3503990448E-02 -5.2714172578E-02 3.2464202323E-04 3.5307530516E-04
5 6 7 8 9
0 -1.3149822728E-05 -7.0839334605E-02 2.3175171407E-02 -6.4209650586E-02 -7.0831022262E-02
1 1.3436762125E-06 2.3174998109E-02 -6.8961088744E-02 6.1659527473E-02 4.3995634311E-02
2 -4.6713637453E-02 -6.4209878747E-02 6.1660244645E-02 -2.1753160526E-01 5.2150044298E-02
3 1.0441682149E-05 -1.3938723600E-02 6.2463766555E-04 -1.7300159651E-03 -1.3942892159E-02
4 5.2350354108E-07 1.0841749785E-02 -1.9733379734E-04 6.4963338353E-04 2.0594374742E-02
5 4.9655550291E-02 -3.0037506737E-02 6.5000245392E-04 -1.7635556184E-03 2.4410415586E-02
6 -3.0037506737E-02 7.8101558840E-02 -2.7323500177E-02 7.5703379066E-02 3.3391028845E-03
7 6.5000245392E-04 -2.7323500177E-02 7.5886724901E-02 -7.2696444954E-02 -6.1280276453E-03
8 -1.7635556184E-03 7.5703379066E-02 -7.2696444954E-02 2.5105105304E-01 -7.7284477870E-03
9 2.4410415586E-02 3.3391028845E-03 -6.1280276453E-03 -7.7284477870E-03 7.8097057948E-02
10 -1.0046717260E-03 -3.0650673504E-03 5.6305999555E-03 6.6430798619E-03 -5.1877079575E-02
11 -1.1518223626E-03 9.3745302500E-03 -1.7929175053E-02 -2.4869250248E-02 -6.1492402669E-02
12 5.6297988854E-03 3.3390756247E-03 9.6509362855E-03 -2.0330968182E-03 3.3394321869E-03
13 3.5280279411E-04 -3.6290316847E-03 -1.2357232660E-02 3.7418875799E-03 -6.5863631195E-03
14 -2.5744191699E-05 9.1708936904E-03 2.8314023659E-02 -6.8818696287E-03 -7.3415421228E-03
10 11 12 13 14
0 4.3995912265E-02 5.2150455969E-02 -7.0837646203E-02 -6.7175915060E-02 1.2031855740E-02
1 -1.2696536462E-01 -9.5129546775E-02 -6.7175983361E-02 -2.3374165050E-01 3.3503990448E-02
2 -9.5129410929E-02 -1.5947516242E-01 1.2031570067E-02 3.3503139526E-02 -5.2714172578E-02
3 1.1882102059E-03 1.4084470151E-03 -1.3939157729E-02 -1.8110895566E-03 3.2464202323E-04
4 -8.0894314407E-04 -1.0045758742E-03 -3.1434370036E-02 -1.9348846781E-03 3.5307530516E-04
5 -1.0046717260E-03 -1.1518223626E-03 5.6297988854E-03 3.5280279411E-04 -2.5744191699E-05
6 -3.0650673504E-03 9.3745302500E-03 3.3390756247E-03 -3.6290316847E-03 9.1708936904E-03
7 5.6305999555E-03 -1.7929175053E-02 9.6509362855E-03 -1.2357232660E-02 2.8314023659E-02
8 6.6430798619E-03 -2.4869250248E-02 -2.0330968182E-03 3.7418875799E-03 -6.8818696287E-03
9 -5.1877079575E-02 -6.1492402669E-02 3.3394321869E-03 -6.5863631195E-03 -7.3415421228E-03
10 1.4428067706E-01 1.1216627263E-01 9.7565379841E-03 -2.2133354919E-02 -2.2671723378E-02
11 1.1216627263E-01 1.8260820267E-01 -1.4427922682E-03 1.9002273053E-03 2.8931816346E-03
12 9.7565379841E-03 -1.4427922682E-03 7.8099975098E-02 7.9204668253E-02 -1.4186255518E-02
13 -2.2133354919E-02 1.9002273053E-03 7.9204668253E-02 2.7017311542E-01 -3.9500247375E-02
14 -2.2671723378E-02 2.8931816346E-03 -1.4186255518E-02 -3.9500247375E-02 5.6729796094E-02
$vibrational_frequencies
15
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 1411.894158
7 1411.942387
8 1411.989208
9 1567.724975
10 1567.756664
11 2918.147432
12 2930.722274
13 2930.813685
14 2930.996046
$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 9.6477903682E-02 6.9838285112E-02 5.0247657476E-02 1.0285495508E-05
1 0.0000000000E+00 -6.5244195857E-02 1.0860033168E-01 -2.5674116800E-02 -1.0798405126E-05
2 0.0000000000E+00 -5.6088574999E-02 -6.1989041273E-03 1.1629676616E-01 -7.5696185494E-06
3 0.0000000000E+00 4.2224433199E-02 3.0585059656E-02 2.2027491770E-02 1.1770838068E-05
4 0.0000000000E+00 3.0574268985E-01 -5.0895242725E-01 1.2037823767E-01 4.2177266162E-01
5 0.0000000000E+00 2.6292699701E-01 2.9150057128E-02 -5.4508701960E-01 -2.6859136081E-01
6 0.0000000000E+00 -4.4663913988E-01 -3.5644404675E-01 -1.6705301932E-02 3.7314153890E-01
7 0.0000000000E+00 3.0044265391E-01 -4.8132377619E-01 -8.9851299978E-02 -2.4247029500E-01
8 0.0000000000E+00 2.7795616746E-01 -4.8141902391E-02 3.7122287366E-02 -2.2777215718E-01
9 0.0000000000E+00 -2.6047059427E-01 -3.9261870970E-01 -3.2337347124E-01 6.2793968834E-02
10 0.0000000000E+00 -4.3850669339E-02 -3.8972868840E-01 2.8067701807E-01 -3.6444449307E-01
11 0.0000000000E+00 -1.5166137869E-01 1.7045603953E-01 -3.5509072322E-01 3.3649266944E-01
12 0.0000000000E+00 -4.8471400571E-01 -1.1369258345E-01 -2.8068345465E-01 -4.3606983719E-01
13 0.0000000000E+00 2.1509393316E-01 8.5958677760E-02 -5.2795342450E-03 1.8527079673E-01
14 0.0000000000E+00 2.7911142286E-01 -7.7600069791E-02 -5.2269896754E-01 1.5996104566E-01
10 11 12 13 14
0 1.9204652077E-05 -5.4805850258E-05 -4.1798508139E-02 -6.7803732330E-02 3.4456264823E-02
1 2.0564924792E-05 6.8646694199E-05 6.0729309089E-02 -5.3425545265E-02 -3.1456376564E-02
2 9.6100321186E-06 -6.9645773690E-04 4.5782854569E-02 8.9593147936E-03 7.3181607166E-02
3 2.5534976406E-05 5.0051084360E-01 4.1636224744E-01 6.7286481475E-01 -3.3775125382E-01
4 -2.6872468668E-01 3.7454611147E-05 2.9774155047E-02 -2.6169302021E-02 -1.5414189686E-02
5 -4.2176170002E-01 -3.2676870747E-04 2.2463737380E-02 4.4214525483E-03 3.5838244132E-02
6 2.8791652277E-01 -1.6441255022E-01 -4.6171136093E-02 -4.1860475240E-02 -2.8431296913E-01
7 4.0677554581E-01 1.5789223761E-01 5.4429591353E-02 -1.7893642594E-02 2.7381977344E-01
8 3.8608146478E-02 -4.3768539857E-01 -4.5893125785E-02 -1.8572459712E-02 -7.6545794522E-01
9 -4.6732937548E-01 -1.6820033754E-01 2.6974086174E-01 -4.5257667378E-02 9.2311851128E-02
10 -1.5748775713E-01 3.0678667384E-01 -4.9963292343E-01 -4.2590214260E-03 -1.5299492287E-01
11 -8.3277284963E-02 3.6326100083E-01 -6.0508221964E-01 3.0380954142E-02 -1.2722379425E-01
12 1.7915848135E-01 -1.6724490716E-01 -1.4187455121E-01 2.2218053919E-01 1.1918273215E-01
13 1.9191853047E-02 -4.6553433773E-01 -3.0820150894E-01 6.8492337892E-01 2.6941328644E-01
14 4.6631632849E-01 8.3049930218E-02 8.2978010602E-02 -1.2298622673E-01 -1.5164722587E-02
#
# The atoms: label mass x y z (in bohrs)
#
$atoms
5
C 12.01100 1.808228232708 -0.115503926643 -0.125502358011
H 1.00800 3.886263342700 -0.115457665877 -0.125382884353
H 1.00800 1.115566681275 0.549649980043 -1.968268883378
H 1.00800 1.115645469129 1.147845717277 1.372015106814
H 1.00800 1.115558681105 -2.043996616803 0.219957812341
$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 -2.0000000000E-01
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 -0.0000000000E+00 -1.0000000000E-01
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
#
# 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
1411.89 0.00073546 3.71673613 -0.001597 -0.008137 -0.009685
1411.94 0.00043621 2.20441932 -0.001157 -0.003252 0.009192
1411.99 0.00020721 1.04716171 -0.000833 0.000200 -0.006713
1567.72 0.00154955 7.83078993 -0.000000 -0.007232 0.016004
1567.76 0.00001515 0.07656697 -0.000001 -0.000749 0.001567
2918.15 0.00419539 21.20180047 -0.014320 0.013320 0.008134
2930.72 0.00251671 12.71842438 -0.011427 0.008458 0.008116
2930.81 0.00652390 32.96909208 -0.018466 -0.018797 0.000568
2931.00 0.00633467 32.01283832 0.009269 -0.007394 0.023106
$end