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modified README

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Aditya Wibawa Sakti 2 years ago
parent c358e85739
commit 69c1a22c6d
27 changed files with 27 additions and 2429 deletions
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  1. 16
      cmmde_gui/gui.py
  2. 0
      cmmde_gui/test/.xtboptok
  3. 34
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.engrad
  4. BIN
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.gbw
  5. 11
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.in
  6. 164
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.opt
  7. 1136
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.out
  8. BIN
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.xtbrestart
  9. 7
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.xyz
  10. 6
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd_property.txt
  11. 21
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd_trj.xyz
  12. 34
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.engrad
  13. BIN
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.gbw
  14. 192
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.hess
  15. 13
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.in
  16. 711
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.out
  17. BIN
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.xtbrestart
  18. 48
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd_property.txt
  19. 10
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/run.sh
  20. 1
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/geom.smi
  21. 7
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/geom.xyz
  22. 10
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/run.sh
  23. 8
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/run_babel.sh
  24. 1
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/slurm-3027.out
  25. 0
      cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/slurm-3028.out
  26. BIN
      lib/__pycache__/cmmde_xtb.cpython-39.pyc
  27. 26
      lib/cmmde_xtb.py

16
cmmde_gui/gui.py
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@ -64,9 +64,9 @@ def cmmde_gui():
job_list = [job[i] for i in job_btn.value]
jobs = ",".join(job_list)
cmd = subprocess.run(["cmmde.py","-i","{}".format(editor.value),"-s","{}".format(software[software_btn.value]),"-j","{}".format(jobs),"-m","{}".format(method[method_btn.value])],capture_output=True,text=True)
cmd = subprocess.run(["cmmde.py","-i","{}".format(editor.value),"-s","{}".format(software[software_btn.value]),"-j","{}".format(jobs),"-m","{}".format(method[method_btn.value])])
#terminal.subprocess.run("cmmde.py","-i{}".format(editor.value),"-s{}".format(software[software_btn.value]), "-j{}".format(jobs), "-m{}".format(method[method_btn.value]))
TextArea.value = TextArea.value + "\n" + cmd.stdout
TextArea.value = TextArea.value + "\n" + "Perhitungan anda telah tersubmit!"
# RunMessage.value = "Perhitungan telah tersubmit!"
@ -75,6 +75,11 @@ def cmmde_gui():
Run_btn.on_click(run)
# Upload structure button
structure_input = pn.widgets.FileInput()
# Post calculations
post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry calculation':'thermo'}
post_btn = pn.widgets.Select(name="Job Selection",value='Frequency calculation', options=['Frequency calculation','Radial distribution function', 'Mean Square Displacement','Time-dependent calculation','Thermochemistry calculation'])
@ -109,7 +114,12 @@ def cmmde_gui():
Progress_btn = pn.widgets.Button(name="Check calculation",button_type='primary')
Progress_btn.on_click(progress)
# Check the output
def check_out(event):
cmd = subprocess.run(["tail","-f","cmmd.out"],capture_output=True,text=True)
cmd.stdout
checkout_btn = pn.widgets.Button(name="Check output",button_type='primary')
checkout_btn.on_click(check_out)
# Visualize the results
xyzview = py3Dmol.view()
xyzview.setBackgroundColor('0xeeeeee')

0
cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/slurm-3029.out → cmmde_gui/test/.xtboptok
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34
cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.engrad
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@ -1,34 +0,0 @@
#
# Number of atoms
#
5
#
# The current total energy in Eh
#
-4.175218519960
#
# The current gradient in Eh/bohr
#
-0.000001468287
-0.000001452748
-0.000001409928
0.000099625376
0.000000596936
0.000000170656
-0.000032985992
-0.000054178347
0.000076588754
-0.000032654559
-0.000038682622
-0.000084843552
-0.000032516537
0.000093716782
0.000009494069
#
# The atomic numbers and current coordinates in Bohr
#
6 1.9696099 -0.1033438 -0.1365649
1 4.0145972 -0.1033340 -0.1365671
1 1.2879566 -1.2234273 1.4327440
1 1.2879485 -0.9023595 -1.8912376
1 1.2879498 1.8157567 0.0488109

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11
cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.in
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@ -1,11 +0,0 @@
#CMMDE generated Orca input file
!XTB2 opt
%pal
nprocs 1
end
%geom
maxiter 9999
end
*xyzfile 0 1 geom.xyz

164
cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.opt
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@ -1,164 +0,0 @@
$orca_opt_file
$trust
0.300000000000
$epredict
0.000000000000
$ediffsc
1000.000000000000
$ctyp
3
$coordinates
2 15
1.96960486 -0.10334912 -0.13657051 4.03356374 -0.10333023 -0.13657051
1.28163116 -1.23382109 1.44730345 1.28163116 -0.90977085 -1.90750846
1.28163116 1.83356347 0.05053128
1.96960809 -0.10334555 -0.13656646 4.01487809 -0.10333190 -0.13656706
1.28786237 -1.22358138 1.43296133 1.28785515 -0.90247073 -1.89148051
1.28785837 1.81602174 0.04883795
# redundant internal coordinates
# nbonds nangles ndihedrals nimpropers ncartesians
# bond definitions A B
# angle definitions A B C
# dihedral definitions A B C D
# improper torsion definitions A B C D
# cartesian definitions A x/y/z
$redundant_internals
4 6 0 0 0
1 0 0
2 0 0
3 0 0
4 0 0
1 0 3 0 0
2 0 3 0 0
1 0 4 0 0
2 0 4 0 0
3 0 4 0 0
1 0 2 0 0
$energies
2
-4.1749622801599999
-4.1752184657600004
$gradients
2 15
-0.0000027886034344 -0.0000043518393354 -0.0000060472176322 0.0066850309380137
0.0000008881278605 0.0000000440083344 -0.0022284396811313 -0.0036618597626871
0.0051310474440805 -0.0022260362495245 -0.0026101268472735 -0.0057316617241839
-0.0022277664039233 0.0062754503214355 0.0006066174894011
-0.0000014682870466 -0.0000014527480153 -0.0000014099279061 0.0000996253756442
0.0000005969356365 0.0000001706562852 -0.0000329859920495 -0.0000541783471346
0.0000765887541975 -0.0000326545594519 -0.0000386826222359 -0.0000848435517582
-0.0000325165370961 0.0000937167817493 0.0000094940691815
$redundant_coords
2 10
2.0639588835553004 2.0639601244554804 2.0639392030244004 2.0639634897792400
1.9106339276550293 1.9106418999213668 1.9106168596569035 1.9106313676756239
1.9106434938538384 1.9106318685398802
2.0452700066184040 2.0452684490353756 2.0452656178615110 2.0452697281465047
1.9106345549334645 1.9106391086153649 1.9106230642023705 1.9106310752882207
1.9106396714048268 1.9106319429665910
$redundant_gradients
2 10
0.0066850309457483 0.0066860158599383 0.0066798162630520 0.0066867184136725
-0.0000001823075762 0.0000008112283392 -0.0000018032042837 0.0000000849723980
0.0000011109061823 -0.0000000216333131
0.0000996253795746 0.0000994435536643 0.0000987977985070 0.0000996471539910
0.0000001372361801 0.0000006886868494 -0.0000012431323971 -0.0000002458445154
0.0000007916373290 -0.0000001286033218
$hessian_approx
15 15
0 1 2 3 4 5
0 0.839467 0.000006 0.000005 -0.357182 -0.000002 0.000000
1 0.000006 0.839472 0.000006 0.000017 -0.136199 -0.000001
2 0.000005 0.000006 0.839488 0.000019 -0.000001 -0.136202
3 -0.357182 0.000017 0.000019 0.355990 -0.000006 -0.000002
4 -0.000002 -0.136199 -0.000001 -0.000006 0.102150 0.000001
5 0.000000 -0.000001 -0.136202 -0.000002 0.000001 0.102151
6 -0.160760 -0.040355 0.056523 0.000401 -0.037297 0.052261
7 -0.040361 -0.202511 0.092879 0.000658 0.007665 -0.010732
8 0.056545 0.092904 -0.266334 -0.000931 -0.010740 0.015038
9 -0.160765 -0.028791 -0.063217 0.000397 -0.026605 -0.058433
10 -0.028793 -0.169952 -0.074101 0.000470 0.003901 0.008562
11 -0.063228 -0.074110 -0.298935 0.001031 0.008569 0.018804
12 -0.160758 0.069124 0.006671 0.000393 0.063911 0.006174
13 0.069149 -0.330810 -0.018783 -0.001140 0.022483 0.002170
14 0.006679 -0.018798 -0.138016 -0.000116 0.002171 0.000210
6 7 8 9 10 11
0 -0.160760 -0.040361 0.056545 -0.160765 -0.028793 -0.063228
1 -0.040355 -0.202511 0.092904 -0.028791 -0.169952 -0.074110
2 0.056523 0.092879 -0.266334 -0.063217 -0.074101 -0.298935
3 0.000401 0.000658 -0.000931 0.000397 0.000470 0.001031
4 -0.037297 0.007665 -0.010740 -0.026605 0.003901 0.008569
5 0.052261 -0.010732 0.015038 -0.058433 0.008562 0.018804
6 0.130354 0.046348 -0.064932 0.015002 0.022930 -0.016732
7 0.046348 0.178307 -0.106695 0.019305 0.029523 -0.021703
8 -0.064932 -0.106695 0.251633 0.020811 0.031642 -0.021418
9 0.015002 0.019305 0.020811 0.130362 0.033066 0.072612
10 0.022930 0.029523 0.031642 0.033066 0.140910 0.085110
11 -0.016732 -0.021703 -0.021418 0.072612 0.085110 0.289060
12 0.015003 -0.025951 -0.011493 0.015004 -0.027673 0.006316
13 0.008375 -0.012984 -0.007111 0.003025 -0.004381 0.002136
14 -0.027120 0.046252 0.021081 0.028226 -0.051213 0.012490
12 13 14
0 -0.160758 0.069149 0.006679
1 0.069124 -0.330810 -0.018798
2 0.006671 -0.018783 -0.138016
3 0.000393 -0.001140 -0.000116
4 0.063911 0.022483 0.002171
5 0.006174 0.002170 0.000210
6 0.015003 0.008375 -0.027120
7 -0.025951 -0.012984 0.046252
8 -0.011493 -0.007111 0.021081
9 0.015004 0.003025 0.028226
10 -0.027673 -0.004381 -0.051213
11 0.006316 0.002136 0.012490
12 0.130359 -0.079410 -0.007668
13 -0.079410 0.325693 0.021588
14 -0.007668 0.021588 0.104236
$bmatrix
10 15
0 1 2 3 4 5
0 -1.000000 -0.000007 0.000000 1.000000 0.000007 -0.000000
1 0.333328 0.547721 -0.767395 0.000000 0.000000 0.000000
2 0.333332 0.390720 0.858037 0.000000 0.000000 0.000000
3 0.333330 -0.938442 -0.090650 0.000000 0.000000 0.000000
4 0.460973 -0.270161 -0.593296 -0.000001 0.202623 0.444971
5 -0.460970 -0.648895 -0.062676 0.000000 0.000000 0.000000
6 0.460968 0.648889 0.062680 0.000003 -0.486668 -0.047010
7 -0.460964 0.270166 0.593299 0.000000 0.000000 0.000000
8 -0.460971 0.378729 -0.530618 0.000000 0.000000 0.000000
9 0.460974 -0.378720 0.530618 -0.000002 0.284042 -0.397964
6 7 8 9 10 11
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1 -0.333328 -0.547721 0.767395 0.000000 0.000000 0.000000
2 0.000000 0.000000 0.000000 -0.333332 -0.390720 -0.858037
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 0.000000 0.000000 0.000000 -0.460972 0.067538 0.148325
5 0.230485 0.297307 0.312315 0.230484 0.351587 -0.249639
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
7 0.230482 -0.391988 -0.179665 0.000000 0.000000 0.000000
8 0.000000 0.000000 0.000000 0.230485 -0.419128 0.101316
9 -0.460972 0.094677 -0.132654 0.000000 0.000000 0.000000
12 13 14
0 0.000000 0.000000 0.000000
1 0.000000 0.000000 0.000000
2 0.000000 0.000000 0.000000
3 -0.333330 0.938442 0.090650
4 0.000000 0.000000 0.000000
5 0.000000 0.000000 0.000000
6 -0.460971 -0.162221 -0.015670
7 0.230482 0.121822 -0.413634
8 0.230486 0.040398 0.429302
9 0.000000 0.000000 0.000000

1136
cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.out
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cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd.xyz
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@ -1,7 +0,0 @@
5
Coordinates from ORCA-job cmmd
C 1.04227269060310 -0.05468719364080 -0.07226703535934
H 2.12443335379334 -0.05468200026993 -0.07226820060049
H 0.68155725235486 -0.64740982631557 0.75817547407569
H 0.68155300087124 -0.47750805702477 -1.00079985809395
H 0.68155370237746 0.96085707725107 0.02582961997808

6
cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd_property.txt
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@ -1,6 +0,0 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

21
cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/cmmd_trj.xyz
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@ -1,21 +0,0 @@
5
Coordinates from ORCA-job cmmd E -4.174962280160
C 1.042270 -0.054690 -0.072270
H 2.134470 -0.054680 -0.072270
H 0.678210 -0.652910 0.765880
H 0.678210 -0.481430 -1.009410
H 0.678210 0.970280 0.026740
5
Coordinates from ORCA-job cmmd E -4.175218465760
C 1.042272 -0.054688 -0.072268
H 2.124582 -0.054681 -0.072268
H 0.681507 -0.647491 0.758290
H 0.681504 -0.477567 -1.000928
H 0.681505 0.960997 0.025844
5
Coordinates from ORCA-job cmmd E -4.175218519960
C 1.042273 -0.054687 -0.072267
H 2.124433 -0.054682 -0.072268
H 0.681557 -0.647410 0.758175
H 0.681553 -0.477508 -1.000800
H 0.681554 0.960857 0.025830

34
cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.engrad
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@ -1,34 +0,0 @@
#
# Number of atoms
#
5
#
# The current total energy in Eh
#
-4.175218519970
#
# The current gradient in Eh/bohr
#
-0.000000827076
-0.000000755023
-0.000000656419
-0.000003175114
0.000000343769
0.000000115603
0.000001211919
0.000002001758
-0.000002385710
0.000001315120
0.000001321331
0.000002945203
0.000001475151
-0.000002911836
-0.000000018677
#
# The atomic numbers and current coordinates in Bohr
#
6 1.9696099 -0.1033438 -0.1365649
1 4.0145972 -0.1033340 -0.1365671
1 1.2879566 -1.2234273 1.4327440
1 1.2879485 -0.9023595 -1.8912376
1 1.2879498 1.8157567 0.0488109

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cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.hess
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@ -1,192 +0,0 @@
$orca_hessian_file
$act_atom
0
$act_coord
0
$act_energy
-4.175219
$hessian
15
0 1 2 3 4
0 5.1328905741E-01 -1.8813124925E-06 1.5285832446E-06 -2.9809680213E-01 -1.2481010430E-06
1 -1.8813124925E-06 5.1328676748E-01 1.0141633996E-06 -1.2196382094E-06 -4.3442806323E-02
2 1.5285832446E-06 1.0141633996E-06 5.1329078129E-01 2.8178652120E-07 -2.5661061108E-08
3 -2.9809680213E-01 -1.2196382094E-06 2.8178652120E-07 3.4272636990E-01 1.0203571411E-06
4 -1.2481010430E-06 -4.3442806323E-02 -2.5661061108E-08 1.0203571411E-06 4.6441270146E-02
5 2.4970183537E-07 -2.5621379862E-08 -4.3442993520E-02 -3.5252078753E-07 3.1016397346E-08
6 -7.1733642620E-02 -4.6489873493E-02 6.5136478040E-02 -1.4874508419E-02 -1.9488509389E-02
7 -4.6489819409E-02 -1.1983224963E-01 1.0703267810E-01 -1.3646955029E-03 -6.1431748846E-04
8 6.5136349474E-02 1.0703256689E-01 -1.9339988478E-01 1.9118931572E-03 1.1200060927E-03
9 -7.1734348504E-02 -3.3163990785E-02 -7.2832305527E-02 -1.4874647696E-02 -1.3902140096E-02
10 -3.3163949631E-02 -8.2314662161E-02 -8.5371270341E-02 -9.7355683515E-04 -2.2171180812E-04
11 -7.2832140811E-02 -8.5371143887E-02 -2.3092188761E-01 -2.1375924019E-03 -8.9322868307E-04
12 -7.1734170269E-02 7.9656964644E-02 7.6940171216E-03 -1.4874924566E-02 3.3390877327E-02
13 7.9656904875E-02 -2.6770669774E-01 -2.1662391844E-02 2.3380226055E-03 -2.1618422618E-03
14 7.6940112824E-03 -2.1662406422E-02 -4.5535239713E-02 2.2592323447E-04 -2.2678343983E-04
5 6 7 8 9
0 2.4970183537E-07 -7.1733642620E-02 -4.6489819409E-02 6.5136349474E-02 -7.1734348504E-02
1 -2.5621379862E-08 -4.6489873493E-02 -1.1983224963E-01 1.0703256689E-01 -3.3163990785E-02
2 -4.3442993520E-02 6.5136478040E-02 1.0703267810E-01 -1.9339988478E-01 -7.2832305527E-02
3 -3.5252078753E-07 -1.4874508419E-02 -1.3646955029E-03 1.9118931572E-03 -1.4874647696E-02
4 3.1016397346E-08 -1.9488509389E-02 -6.1431748846E-04 1.1200060927E-03 -1.3902140096E-02
5 4.6441235331E-02 2.7304586099E-02 1.1201082305E-03 -1.3841743700E-03 -3.0529798620E-02
6 2.7304586099E-02 7.9357956137E-02 5.4090646353E-02 -7.5785513987E-02 3.6258065418E-03
7 1.1201082305E-03 5.4090646353E-02 1.3532032998E-01 -1.2453084083E-01 3.9775442999E-03
8 -1.3841743700E-03 -7.5785513987E-02 -1.2453084083E-01 2.2091418254E-01 9.4316885472E-03
9 -3.0529798620E-02 3.6258065418E-03 3.9775442999E-03 9.4316885472E-03 7.9358789672E-02
10 -8.9346754024E-04 5.7093049371E-03 6.7463940969E-03 1.6050313975E-02 3.8586105367E-02
11 -1.7767478996E-03 -8.4962173439E-03 -9.4219371480E-03 -2.7245125890E-02 8.4739297257E-02
12 3.2253153082E-03 3.6258613739E-03 -1.0212331942E-02 -6.9629984106E-04 3.6258730430E-03
13 -2.2664667572E-04 6.1795128356E-03 -2.1617659979E-02 3.2541370840E-04 4.5032921910E-03
14 1.6324783834E-04 -8.1606384269E-03 2.5797834931E-02 1.1187730715E-03 9.1924706303E-03
10 11 12 13 14
0 -3.3163949631E-02 -7.2832140811E-02 -7.1734170269E-02 7.9656904875E-02 7.6940112824E-03
1 -8.2314662161E-02 -8.5371143887E-02 7.9656964644E-02 -2.6770669774E-01 -2.1662406422E-02
2 -8.5371270341E-02 -2.3092188761E-01 7.6940171216E-03 -2.1662391844E-02 -4.5535239713E-02
3 -9.7355683515E-04 -2.1375924019E-03 -1.4874924566E-02 2.3380226055E-03 2.2592323447E-04
4 -2.2171180812E-04 -8.9322868307E-04 3.3390877327E-02 -2.1618422618E-03 -2.2678343983E-04
5 -8.9346754024E-04 -1.7767478996E-03 3.2253153082E-03 -2.2664667572E-04 1.6324783834E-04
6 5.7093049371E-03 -8.4962173439E-03 3.6258613739E-03 6.1795128356E-03 -8.1606384269E-03
7 6.7463940969E-03 -9.4219371480E-03 -1.0212331942E-02 -2.1617659979E-02 2.5797834931E-02
8 1.6050313975E-02 -2.7245125890E-02 -6.9629984106E-04 3.2541370840E-04 1.1187730715E-03
9 3.8586105367E-02 8.4739297257E-02 3.6258730430E-03 4.5032921910E-03 9.1924706303E-03
10 9.1668620309E-02 9.9327957080E-02 -1.0156945223E-02 -1.5877025382E-02 -2.9111956311E-02
11 9.9327957080E-02 2.6456970708E-01 -1.2712416705E-03 -3.6395042200E-03 -4.6216847948E-03
12 -1.0156945223E-02 -1.2712416705E-03 7.9358833381E-02 -9.2680034434E-02 -8.9519890716E-03
13 -1.5877025382E-02 -3.6395042200E-03 -9.2680034434E-02 3.0736816946E-01 2.5203704444E-02
14 -2.9111956311E-02 -4.6216847948E-03 -8.9519890716E-03 2.5203704444E-02 4.8875529098E-02
$vibrational_frequencies
15
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 1385.801368
7 1385.807055
8 1385.818393
9 1557.267394
10 1557.277196
11 3090.006345
12 3103.917565
13 3103.936793
14 3103.955476
$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 -1.0522380429E-01 7.1926850074E-02 1.8977292979E-02 -1.9213598946E-06
1 0.0000000000E+00 -7.4384998929E-02 -1.0203984118E-01 -2.5697356965E-02 -9.1458445686E-06
2 0.0000000000E+00 6.8379081575E-04 -3.1937815854E-02 1.2483986839E-01 -2.1042842766E-06
3 0.0000000000E+00 -4.8958509759E-02 3.3463985344E-02 8.8286458306E-03 -2.4474256739E-06
4 0.0000000000E+00 3.4965092692E-01 4.7965845299E-01 1.2080417716E-01 4.8163341852E-01
5 0.0000000000E+00 -3.2185549380E-03 1.5013119824E-01 -5.8686871577E-01 1.3444934690E-01
6 0.0000000000E+00 3.6320544779E-01 -3.5086958291E-01 -2.6753226731E-01 -1.6060826546E-01
7 0.0000000000E+00 1.3368615134E-01 4.5875836547E-01 -1.7221936430E-01 -3.4960191712E-01
8 0.0000000000E+00 2.9946405912E-01 1.7951912997E-01 -1.7634254451E-01 -3.1928324596E-01
9 0.0000000000E+00 3.8523460216E-01 -4.1267227574E-01 8.8852833333E-02 -3.0351961154E-01
10 0.0000000000E+00 2.2142626156E-01 3.9231247427E-01 3.2953390855E-01 -3.0367097945E-01
11 0.0000000000E+00 -2.8494402080E-01 -4.1806165335E-02 -1.2850248619E-01 2.5618530386E-01
12 0.0000000000E+00 5.5433107230E-01 -1.2697906740E-01 -5.6276459837E-02 4.6415321872E-01
13 0.0000000000E+00 1.8158410278E-01 -1.1485574868E-01 2.8082622332E-02 1.7174845695E-01
14 0.0000000000E+00 -1.9449312243E-02 9.2716458384E-02 -5.9583750281E-01 -7.1326330842E-02
10 11 12 13 14
0 2.6627445365E-07 -9.2465528650E-05 -1.2392804697E-02 -1.5777178984E-02 -8.4952426649E-02
1 7.6420126515E-07 -6.0382317016E-05 -3.8001795953E-02 -7.6080830644E-02 1.9673297139E-02
2 -1.1373327037E-06 2.8933120330E-05 7.7600466571E-02 -3.9777771804E-02 -3.9330151542E-03
3 1.2399571826E-06 -4.9908209222E-01 1.2262267864E-01 1.5594148384E-01 8.3825091479E-01
4 -1.3444228464E-01 -3.0339721201E-05 -1.7574466793E-02 -3.5184448973E-02 9.1012344449E-03
5 4.8159367532E-01 1.4242294503E-05 3.5887637599E-02 -1.8395850186E-02 -1.8197234278E-03
6 4.4320256200E-01 1.6691715919E-01 2.8491106346E-01 4.9042483503E-02 1.0534938301E-02
7 -2.2968569630E-01 2.7432124992E-01 4.6000479877E-01 5.7387058460E-02 9.0971785732E-02
8 2.8572925384E-02 -3.8436939116E-01 -6.3323291108E-01 -1.4810466961E-01 -1.1652870621E-01
9 -3.6069470191E-01 1.6672499246E-01 -1.6969360392E-01 2.3044093055E-01 4.3166124965E-02
10 3.4582583817E-01 1.9545046246E-01 -2.0976549547E-01 2.4347887274E-01 1.0575001080E-01
11 -1.7352728000E-02 4.2929823266E-01 -3.8616812782E-01 5.9357259509E-01 2.1043489954E-01
12 -8.2512272887E-02 1.6654172972E-01 -9.0171509999E-02 -2.4742916696E-01 1.2031349464E-01
13 1.8293036796E-02 -4.6902187661E-01 2.2015219841E-01 6.4087293927E-01 -4.4024363806E-01
14 -4.9280032062E-01 -4.5287841445E-02 5.8851492583E-02 4.6906909965E-02 -4.5221941107E-02
#
# The atoms: label mass x y z (in bohrs)
#
$atoms
5
C 12.01100 1.969609942105 -0.103343819014 -0.136564905340
H 1.00800 4.014597228437 -0.103334004965 -0.136567107326
H 1.00800 1.287956551539 -1.223427268146 1.432744007459
H 1.00800 1.287948517399 -0.902359454518 -1.891237646665
H 1.00800 1.287949843053 1.815756729845 0.048810907902
$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 -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
1385.80 0.00022921 1.15834033 0.001870 -0.006937 0.000000
1385.81 0.00009275 0.46870034 -0.001278 0.004388 0.000000
1385.82 0.00000562 0.02838005 -0.000337 -0.001073 0.000000
1557.27 0.00022581 1.14113331 0.000000 -0.006727 0.000000
1557.28 0.00000256 0.01294560 -0.000000 -0.000716 0.000000
3090.01 0.00359073 18.14609414 0.013877 0.013041 0.000000
3103.92 0.00044880 2.26803333 -0.003269 -0.005868 0.000000
3103.94 0.00307453 15.53740262 -0.004157 -0.017083 0.000000
3103.96 0.00633569 32.01796816 -0.022344 0.011735 0.000000
$end

13
cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.in
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@ -1,13 +0,0 @@
#CMMDE generated Orca input file
!XTB2 Numfreq
%pal
nprocs 1
end
*xyzfile 0 1 ../cmmd.xyz
%freq
scalfreq 1
Temp 298.15
Pressure 1.0
end

711
cmmde_gui/test/metana_02514d87e9c74c04985fb73ba2b46a97/freq/cmmd.out
Unescape View File

@ -1,711 +0,0 @@
*****************
* O R C A *
*****************
#,
###
####
#####
######
########,
,,################,,,,,
,,#################################,,
,,##########################################,,
,#########################################, ''#####,
,#############################################,, '####,
,##################################################,,,,####,
,###########'''' ''''###############################
,#####'' ,,,,##########,,,, '''####''' '####
,##' ,,,,###########################,,, '##
' ,,###'''' '''############,,,
,,##'' '''############,,,, ,,,,,,###''
,#'' '''#######################'''
' ''''####''''
,#######, #######, ,#######, ##
,#' '#, ## ## ,#' '#, #''# ###### ,####,
## ## ## ,#' ## #' '# # #' '#
## ## ####### ## ,######, #####, # #
'#, ,#' ## ## '#, ,#' ,# #, ## #, ,#
'#######' ## ## '#######' #' '# #####' # '####'
#######################################################
# -***- #
# Department of theory and spectroscopy #
# Directorship and core code : Frank Neese #
# Max Planck Institute fuer Kohlenforschung #
# Kaiser Wilhelm Platz 1 #
# D-45470 Muelheim/Ruhr #
# Germany #
# #
# All rights reserved #
# -***- #
#######################################################
Program Version 5.0.2 - RELEASE -
With contributions from (in alphabetic order):
Daniel Aravena : Magnetic Suceptibility
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation)
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum
Ute Becker : Parallelization
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD
Martin Brehm : Molecular dynamics
Dmytro Bykov : SCF Hessian
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE
Dipayan Datta : RHF DLPNO-CCSD density
Achintya Kumar Dutta : EOM-CC, STEOM-CC
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI
Miquel Garcia : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods
Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals
Lee Huntington : MR-EOM, pCC
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM
Marcus Kettner : VPT2
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian
Martin Krupicka : Initial AUTO-CI
Lucas Lang : DCDCAS
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC
Dagmar Lenk : GEPOL surface, SMD
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization
Dimitrios Manganas : Further ROCIS development; embedding schemes
Dimitrios Pantazis : SARC Basis sets
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient
Christoph Reimann : Effective Core Potentials
Marius Retegan : Local ZFS, SOC
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples
Tobias Risthaus : Range-separated hybrids, TD-DFT gradient, RPA, STAB
Michael Roemelt : Original ROCIS implementation
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density
Barbara Sandhoefer : DKH picture change effects
Avijit Sen : IP-ROCIS
Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI
Bernardo de Souza : ESD, SOC TD-DFT
Georgi Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response
Willem Van den Heuvel : Paramagnetic NMR
Boris Wezisla : Elementary symmetry handling
Frank Wennmohs : Technical directorship
We gratefully acknowledge several colleagues who have allowed us to
interface, adapt or use parts of their codes:
Stefan Grimme, W. Hujo, H. Kruse, P. Pracht, : VdW corrections, initial TS optimization,
C. Bannwarth, S. Ehlert DFT functionals, gCP, sTDA/sTD-DF
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG
Ulf Ekstrom : XCFun DFT Library
Mihaly Kallay : mrcc (arbitrary order and MRCC methods)
Jiri Pittner, Ondrej Demel : Mk-CCSD
Frank Weinhold : gennbo (NPA and NBO analysis)
Christopher J. Cramer and Donald G. Truhlar : smd solvation model
Lars Goerigk : TD-DFT with DH, B97 family of functionals
V. Asgeirsson, H. Jonsson : NEB implementation
FAccTs GmbH : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT
MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM,
LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT,
nearIR, NL-DFT gradient (VV10), updates on ESD,
ML-optimized integration grids
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library
Liviu Ungur et al : ANISO software
Your calculation uses the libint2 library for the computation of 2-el integrals
For citations please refer to: http://libint.valeyev.net
Your ORCA version has been built with support for libXC version: 5.1.0
For citations please refer to: https://tddft.org/programs/libxc/
This ORCA versions uses:
CBLAS interface : Fast vector & matrix operations
LAPACKE interface : Fast linear algebra routines
SCALAPACK package : Parallel linear algebra routines
Shared memory : Shared parallel matrices
BLAS/LAPACK : OpenBLAS 0.3.15 USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED
Core in use : SkylakeX
Copyright (c) 2011-2014, The OpenBLAS Project
***************************************
The coordinates will be read from file: ../cmmd.xyz
***************************************
Your calculation utilizes the semiempirical GFN2-xTB method
Please cite in your paper:
C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652.
================================================================================
================================================================================
WARNINGS
Please study these warnings very carefully!
================================================================================
WARNING: Gradients needed for Numerical Frequencies
===> : Setting RunTyp to EnGrad
WARNING: Found dipole moment calculation with XTB calculation
===> : Switching off dipole moment calculation
WARNING: TRAH-SCF for XTB is not implemented!
===> : Turning TRAH off!
================================================================================
INPUT FILE
================================================================================
NAME = cmmd.in
| 1> #CMMDE generated Orca input file
| 2> !XTB2 Numfreq
| 3> %pal
| 4> nprocs 1
| 5> end
| 6>
| 7> *xyzfile 0 1 ../cmmd.xyz
| 8>
| 9> %freq
| 10> scalfreq 1
| 11> Temp 298.15
| 12> Pressure 1.0
| 13> end
| 14>
| 15> ****END OF INPUT****
================================================================================
*******************************
* Energy+Gradient Calculation *
*******************************
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
| Aditya W. Sakti |
| Departemen Kimia |
| Universitas Pertamina |
-----------------------------------------------------------
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/08/05 at 08:10:00.277
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 5
number of electrons : 8
charge : 0
spin : 0.0
first test random number : 0.76798836703338
ID Z sym. atoms
1 6 C 1
2 1 H 2-5
-------------------------------------------------
| G F N 2 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.8b01176
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.230000 2.230000
zeta-weighting 0.500000
* Dispersion:
s8 2.700000
a1 0.520000
a2 5.000000
s9 5.000000
* Repulsion:
kExp 1.500000 1.000000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order shell-resolved
anisotropic true
a3 3.000000
a5 4.000000
cn-shift 1.200000
cn-exp 4.000000
max-rad 5.000000
...................................................
: SETUP :
:.................................................:
: # basis functions 8 :
: # atomic orbitals 8 :
: # shells 6 :
: # electrons 8 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: restarted? false :
: GBSA solvation false :
: PC potential false :
: electronic temp. 300.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -4.2352961 -0.423530E+01 0.243E+00 17.75 0.0 T
2 -4.2472613 -0.119651E-01 0.928E-01 17.57 1.0 T
3 -4.2474252 -0.163901E-03 0.500E-01 17.46 1.0 T
4 -4.2474673 -0.421128E-04 0.924E-02 17.36 1.0 T
5 -4.2474672 0.111480E-06 0.698E-03 17.35 6.4 T
6 -4.2474673 -0.145702E-06 0.191E-04 17.35 233.9 T
7 -4.2474673 -0.109876E-09 0.432E-06 17.35 10340.8 T
*** convergence criteria satisfied after 7 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.5818361 -15.8326
2 2.0000 -0.4674583 -12.7202
3 2.0000 -0.4674580 -12.7202
4 2.0000 -0.4674577 -12.7202 (HOMO)
5 0.1702647 4.6331 (LUMO)
6 0.2292553 6.2384
7 0.2292573 6.2384
8 0.2292593 6.2385
-------------------------------------------------------------
HL-Gap 0.6377224 Eh 17.3533 eV
Fermi-level -0.1485965 Eh -4.0435 eV
SCC (total) 0 d, 0 h, 0 min, 0.020 sec
SCC setup ... 0 min, 0.000 sec ( 0.578%)
Dispersion ... 0 min, 0.000 sec ( 0.119%)
classical contributions ... 0 min, 0.000 sec ( 0.083%)
integral evaluation ... 0 min, 0.000 sec ( 0.958%)
iterations ... 0 min, 0.019 sec ( 95.735%)
molecular gradient ... 0 min, 0.000 sec ( 1.769%)
printout ... 0 min, 0.000 sec ( 0.706%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -4.175218519973 Eh ::
:: gradient norm 0.000006772752 Eh/a0 ::
:: HOMO-LUMO gap 17.353310653954 eV ::
::.................................................::
:: SCC energy -4.247467308169 Eh ::
:: -> isotropic ES 0.002035567931 Eh ::
:: -> anisotropic ES 0.002321540934 Eh ::
:: -> anisotropic XC 0.003585096737 Eh ::
:: -> dispersion -0.000661011606 Eh ::
:: repulsion energy 0.072248782606 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge -0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -4.175218519973 Eh |
| GRADIENT NORM 0.000006772752 Eh/α |
| HOMO-LUMO GAP 17.353310653954 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/08/05 at 08:10:00.308
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.031 sec
* cpu-time: 0 d, 0 h, 0 min, 0.014 sec
* ratio c/w: 0.453 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.020 sec
* cpu-time: 0 d, 0 h, 0 min, 0.003 sec
* ratio c/w: 0.166 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -4.175218519970
------------------------- --------------------
----------------------------------------------------------------------------
ORCA NUMERICAL FREQUENCIES
----------------------------------------------------------------------------
Number of atoms ... 5
Central differences ... used
Number of displacements ... 30
Numerical increment ... 5.000e-03 bohr
IR-spectrum generation ... on
Raman-spectrum generation ... off
Surface Crossing Hessian ... off
The output will be reduced. Please look at the following files:
SCF program output ... >cmmd.lastscf
Integral program output ... >cmmd.lastint
Gradient program output ... >cmmd.lastgrad
Dipole moment program output ... >cmmd.lastmom
AutoCI program output ... >cmmd.lastautoci
<< Calculating on displaced geometry 1 (of 30) >>
<< Calculating on displaced geometry 2 (of 30) >>
<< Calculating on displaced geometry 3 (of 30) >>
<< Calculating on displaced geometry 4 (of 30) >>
<< Calculating on displaced geometry 5 (of 30) >>
<< Calculating on displaced geometry 6 (of 30) >>
<< Calculating on displaced geometry 7 (of 30) >>
<< Calculating on displaced geometry 8 (of 30) >>
<< Calculating on displaced geometry 9 (of 30) >>
<< Calculating on displaced geometry 10 (of 30) >>
<< Calculating on displaced geometry 11 (of 30) >>
<< Calculating on displaced geometry 12 (of 30) >>
<< Calculating on displaced geometry 13 (of 30) >>
<< Calculating on displaced geometry 14 (of 30) >>
<< Calculating on displaced geometry 15 (of 30) >>
<< Calculating on displaced geometry 16 (of 30) >>
<< Calculating on displaced geometry 17 (of 30) >>
<< Calculating on displaced geometry 18 (of 30) >>
<< Calculating on displaced geometry 19 (of 30) >>
<< Calculating on displaced geometry 20 (of 30) >>
<< Calculating on displaced geometry 21 (of 30) >>
<< Calculating on displaced geometry 22 (of 30) >>
<< Calculating on displaced geometry 23 (of 30) >>
<< Calculating on displaced geometry 24 (of 30) >>
<< Calculating on displaced geometry 25 (of 30) >>
<< Calculating on displaced geometry 26 (of 30) >>
<< Calculating on displaced geometry 27 (of 30) >>
<< Calculating on displaced geometry 28 (of 30) >>
<< Calculating on displaced geometry 29 (of 30) >>
<< Calculating on displaced geometry 30 (of 30) >>
-----------------------
VIBRATIONAL FREQUENCIES
-----------------------
Scaling factor for frequencies = 1.000000000 (already applied!)
0: 0.00 cm**-1
1: 0.00 cm**-1
2: 0.00 cm**-1
3: 0.00 cm**-1
4: 0.00 cm**-1
5: 0.00 cm**-1
6: 1385.80 cm**-1
7: 1385.81 cm**-1
8: 1385.82 cm**-1
9: 1557.27 cm**-1
10: 1557.28 cm**-1
11: 3090.01 cm**-1
12: 3103.92 cm**-1
13: 3103.94 cm**-1
14: 3103.96 cm**-1
------------
NORMAL MODES
------------
These modes are the cartesian displacements weighted by the diagonal matrix
M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom
Thus, these vectors are normalized but *not* orthogonal
0 1 2 3 4 5
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
9 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
10 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
11 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
12 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
13 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
14 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
6 7 8 9 10 11
0 -0.105224 0.071927 0.018977 -0.000002 0.000000 -0.000092
1 -0.074385 -0.102040 -0.025697 -0.000009 0.000001 -0.000060
2 0.000684 -0.031938 0.124840 -0.000002 -0.000001 0.000029
3 -0.048959 0.033464 0.008829 -0.000002 0.000001 -0.499082
4 0.349651 0.479658 0.120804 0.481633 -0.134442 -0.000030
5 -0.003219 0.150131 -0.586869 0.134449 0.481594 0.000014
6 0.363205 -0.350870 -0.267532 -0.160608 0.443203 0.166917
7 0.133686 0.458758 -0.172219 -0.349602 -0.229686 0.274321
8 0.299464 0.179519 -0.176343 -0.319283 0.028573 -0.384369
9 0.385235 -0.412672 0.088853 -0.303520 -0.360695 0.166725
10 0.221426 0.392312 0.329534 -0.303671 0.345826 0.195450
11 -0.284944 -0.041806 -0.128502 0.256185 -0.017353 0.429298
12 0.554331 -0.126979 -0.056276 0.464153 -0.082512 0.166542
13 0.181584 -0.114856 0.028083 0.171748 0.018293 -0.469022
14 -0.019449 0.092716 -0.595838 -0.071326 -0.492800 -0.045288
12 13 14
0 -0.012393 -0.015777 -0.084952
1 -0.038002 -0.076081 0.019673
2 0.077600 -0.039778 -0.003933
3 0.122623 0.155941 0.838251
4 -0.017574 -0.035184 0.009101
5 0.035888 -0.018396 -0.001820
6 0.284911 0.049042 0.010535
7 0.460005 0.057387 0.090972
8 -0.633233 -0.148105 -0.116529
9 -0.169694 0.230441 0.043166
10 -0.209765 0.243479 0.105750
11 -0.386168 0.593573 0.210435
12 -0.090172 -0.247429 0.120313
13 0.220152 0.640873 -0.440244
14 0.058851 0.046907 -0.045222
-----------
IR SPECTRUM
-----------
Mode freq eps Int T**2 TX TY TZ
cm**-1 L/(mol*cm) km/mol a.u.
----------------------------------------------------------------------------
6: 1385.80 0.000229 1.16 0.000052 ( 0.001870 -0.006937 0.000000)
7: 1385.81 0.000093 0.47 0.000021 (-0.001278 0.004388 0.000000)
8: 1385.82 0.000006 0.03 0.000001 (-0.000337 -0.001073 0.000000)
9: 1557.27 0.000226 1.14 0.000045 ( 0.000000 -0.006727 0.000000)
10: 1557.28 0.000003 0.01 0.000001 (-0.000000 -0.000716 0.000000)
11: 3090.01 0.003591 18.15 0.000363 ( 0.013877 0.013041 0.000000)
12: 3103.92 0.000449 2.27 0.000045 (-0.003269 -0.005868 0.000000)
13: 3103.94 0.003075 15.54 0.000309 (-0.004157 -0.017083 0.000000)
14: 3103.96 0.006336 32.02 0.000637 (-0.022344 0.011735 0.000000)
* The epsilon (eps) is given for a Dirac delta lineshape.
** The dipole moment derivative (T) already includes vibrational overlap.
The first frequency considered to be a vibration is 6
The total number of vibrations considered is 9
--------------------------
THERMOCHEMISTRY AT 298.15K
--------------------------
Temperature ... 298.15 K
Pressure ... 1.00 atm
Total Mass ... 16.04 AMU
Throughout the following assumptions are being made:
(1) The electronic state is orbitally nondegenerate
(2) There are no thermally accessible electronically excited states
(3) Hindered rotations indicated by low frequency modes are not
treated as such but are treated as vibrations and this may
cause some error
(4) All equations used are the standard statistical mechanics
equations for an ideal gas
(5) All vibrations are strictly harmonic
freq. 1385.80 E(vib) ... 0.00
freq. 1385.81 E(vib) ... 0.00
freq. 1385.82 E(vib) ... 0.00
freq. 1557.27 E(vib) ... 0.00
freq. 1557.28 E(vib) ... 0.00
freq. 3090.01 E(vib) ... 0.00
freq. 3103.92 E(vib) ... 0.00
freq. 3103.94 E(vib) ... 0.00
freq. 3103.96 E(vib) ... 0.00
------------
INNER ENERGY
------------
The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans)
E(el) - is the total energy from the electronic structure calculation
= E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc)
E(ZPE) - the the zero temperature vibrational energy from the frequency calculation
E(vib) - the the finite temperature correction to E(ZPE) due to population
of excited vibrational states
E(rot) - is the rotational thermal energy
E(trans)- is the translational thermal energy
Summary of contributions to the inner energy U:
Electronic energy ... -4.17521852 Eh
Zero point energy ... 0.04482019 Eh 28.13 kcal/mol
Thermal vibrational correction ... 0.00003140 Eh 0.02 kcal/mol
Thermal rotational correction ... 0.00141627 Eh 0.89 kcal/mol
Thermal translational correction ... 0.00141627 Eh 0.89 kcal/mol
-----------------------------------------------------------------------
Total thermal energy -4.12753439 Eh
Summary of corrections to the electronic energy:
(perhaps to be used in another calculation)
Total thermal correction 0.00286394 Eh 1.80 kcal/mol
Non-thermal (ZPE) correction 0.04482019 Eh 28.13 kcal/mol
-----------------------------------------------------------------------
Total correction 0.04768413 Eh 29.92 kcal/mol
--------
ENTHALPY
--------
The enthalpy is H = U + kB*T
kB is Boltzmann's constant
Total free energy ... -4.12753439 Eh
Thermal Enthalpy correction ... 0.00094421 Eh 0.59 kcal/mol
-----------------------------------------------------------------------
Total Enthalpy ... -4.12659018 Eh
Note: Rotational entropy computed according to Herzberg
Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945
Point Group: Td, Symmetry Number: 12
Rotational constants in cm-1: 5.355317 5.355310 5.355299
Vibrational entropy computed according to the QRRHO of S. Grimme
Chem.Eur.J. 2012 18 9955
-------
ENTROPY
-------
The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans))
S(el) - electronic entropy
S(vib) - vibrational entropy
S(rot) - rotational entropy
S(trans)- translational entropy
The entropies will be listed as multiplied by the temperature to get
units of energy
Electronic entropy ... 0.00000000 Eh 0.00 kcal/mol
Vibrational entropy ... 0.00003597 Eh 0.02 kcal/mol
Rotational entropy ... 0.00478798 Eh 3.00 kcal/mol
Translational entropy ... 0.01627961 Eh 10.22 kcal/mol
-----------------------------------------------------------------------
Final entropy term ... 0.02110356 Eh 13.24 kcal/mol
In case the symmetry of your molecule has not been determined correctly
or in case you have a reason to use a different symmetry number we print
out the resulting rotational entropy values for sn=1,12 :
--------------------------------------------------------
| sn= 1 | S(rot)= 0.00713418 Eh 4.48 kcal/mol|
| sn= 2 | S(rot)= 0.00647973 Eh 4.07 kcal/mol|
| sn= 3 | S(rot)= 0.00609689 Eh 3.83 kcal/mol|
| sn= 4 | S(rot)= 0.00582527 Eh 3.66 kcal/mol|
| sn= 5 | S(rot)= 0.00561458 Eh 3.52 kcal/mol|
| sn= 6 | S(rot)= 0.00544244 Eh 3.42 kcal/mol|
| sn= 7 | S(rot)= 0.00529689 Eh 3.32 kcal/mol|
| sn= 8 | S(rot)= 0.00517081 Eh 3.24 kcal/mol|
| sn= 9 | S(rot)= 0.00505960 Eh 3.17 kcal/mol|
| sn=10 | S(rot)= 0.00496012 Eh 3.11 kcal/mol|
| sn=11 | S(rot)= 0.00487013 Eh 3.06 kcal/mol|
| sn=12 | S(rot)= 0.00478798 Eh 3.00 kcal/mol|
--------------------------------------------------------
-------------------
GIBBS FREE ENERGY
-------------------
The Gibbs free energy is G = H - T*S
Total enthalpy ... -4.12659018 Eh
Total entropy correction ... -0.02110356 Eh -13.24 kcal/mol
-----------------------------------------------------------------------
Final Gibbs free energy ... -4.14769375 Eh
For completeness - the Gibbs free energy minus the electronic energy
G-E(el) ... 0.02752477 Eh 17.27 kcal/mol
Timings for individual modules:
Sum of individual times ... 51.424 sec (= 0.857 min)
Numerical frequency calculation ... 51.346 sec (= 0.856 min) 99.8 %
XTB module ... 0.078 sec (= 0.001 min) 0.2 %
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 0 minutes 51 seconds 463 msec

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-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -----------------------------------------------------------
$ THERMOCHEMISTRY_Energies
description: The Thermochemistry energies
geom. index: 0
prop. index: 1
Temperature (Kelvin) : 298.1500000000
Pressure (atm) : 1.0000000000
Total Mass (AMU) : 16.0430000000
Spin Degeneracy : 1.0000000000
Electronic Energy (Hartree) : -4.1752185200
Translational Energy (Hartree) : 0.0014162714
Rotational Energy (Hartree) : 0.0014162714
Vibrational Energy (Hartree) : 0.0000314005
Number of frequencies : 15
Scaling Factor for frequencies : 1.0000000000
Vibrational frequencies :
0
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 1385.801368
7 1385.807055
8 1385.818393
9 1557.267394
10 1557.277196
11 3090.006345
12 3103.917565
13 3103.936793
14 3103.955476
Zero Point Energy (Hartree) : 0.0448201860
Inner Energy (Hartree) : -4.1275343906
Enthalpy (Hartree) : -4.1265901815
Electronic entropy : 0.0000000000
Rotational entropy : 0.0047879801
Vibrational entropy : 0.0000359731
Translational entropy : 0.0047879801
Entropy : 0.0211035637
Gibbs Energy (Hartree) : -4.1476937452
Is Linear : false
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

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#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
export PATH=/home/adit/opt/openmpi411/bin:$PATH
export OMP_NUM_THREADS=1
cd $PWD
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

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C

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5
C 1.04227 -0.05469 -0.07227
H 2.13447 -0.05468 -0.07227
H 0.67821 -0.65291 0.76588
H 0.67821 -0.48143 -1.00941
H 0.67821 0.97028 0.02674

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#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
export PATH=/home/adit/opt/openmpi411/bin:$PATH
export OMP_NUM_THREADS=1
cd $PWD
$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

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#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
obabel geom.smi -O geom.xyz --gen3d

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@ -20,34 +20,34 @@ cd $PWD""".format(nproc),file=fout)
meth += '--gfn0'
if 'opt' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --opt -P {} --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge,mult-1,meth),file=fout)
print("$XTB_COMMAND {} --opt -P {} --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth),file=fout)
else:
print("$XTB_COMMAND {} --opt -P {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth),file=fout)
print("$XTB_COMMAND {} --opt -P {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth),file=fout)
if 'fix' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --opt -P {} --alpb {} --chrg {} --uhf {} {} --input cmmd.in > xtb.out".format(geom,nproc,solvent,charge,mult-1,meth),file=fout)
print("$XTB_COMMAND {} --opt -P {} --alpb {} --chrg {} --uhf {} {} --input cmmd.in > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth),file=fout)
else:
print("$XTB_COMMAND {} --opt -P {} --chrg {} --uhf {} {} --input cmmd.in > xtb.out".format(geom,nproc,charge,mult-1,meth),file=fout)
print("$XTB_COMMAND {} --opt -P {} --chrg {} --uhf {} {} --input cmmd.in > cmmd.out".format(geom,nproc,charge,mult-1,meth),file=fout)
if 'freq' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout)
print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout)
else:
print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth), file=fout)
print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth), file=fout)
if 'opt' in job and 'freq' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge, mult-1,meth),file=fout)
print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge, mult-1,meth),file=fout)
else:
print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth),file=fout)
print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth),file=fout)
if 'path' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --alpb {} --chrg {} --uhf {} ,method > xtb.out".format(geom,product,nproc,solvent,charge,mult-1,meth),file=fout)
print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --alpb {} --chrg {} --uhf {} ,method > cmmd.out".format(geom,product,nproc,solvent,charge,mult-1,meth),file=fout)
else:
print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --chrg {} --uhf {} {} > xtb.out".format(geom,product,nproc,charge,mult-1,meth),file=fout)
print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --chrg {} --uhf {} {} > cmmd.out".format(geom,product,nproc,charge,mult-1,meth),file=fout)
if 'scan' in job:
if solvent != 'none':
print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout)
print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --alpb {} --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,solvent,charge,mult-1,meth), file=fout)
else:
print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --chrg {} --uhf {} {} > xtb.out".format(geom,nproc,charge,mult-1,meth), file=fout)
print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --chrg {} --uhf {} {} > cmmd.out".format(geom,nproc,charge,mult-1,meth), file=fout)
if 'freq' in job:
with open('cmmd.in', 'w') as f:
print("""$thermo
@ -112,3 +112,5 @@ $end""".format(nrun,npoint,anopt,kpush,kpull,ppull,alp),file=f)
os.system('sbatch run.sh')

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