addition to xTB functions

Aditya Wibawa Sakti 2 years ago
parent 8f94c4518c
commit 57d8339d20
  1. 2
      bin/cmmde.py
  2. 20
      cmmde_gui/gui.py
  3. 34
      cmmde_gui/test/ala/cmmd.engrad
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      cmmde_gui/test/ala/cmmd.gbw
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      cmmde_gui/test/ala/cmmd.in
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      cmmde_gui/test/ala/cmmd.opt
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      cmmde_gui/test/ala/cmmd.out
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      cmmde_gui/test/ala/cmmd.xtbrestart
  9. 7
      cmmde_gui/test/ala/cmmd.xyz
  10. 6
      cmmde_gui/test/ala/cmmd_property.txt
  11. 21
      cmmde_gui/test/ala/cmmd_trj.xyz
  12. 34
      cmmde_gui/test/ala/freq/cmmd.engrad
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      cmmde_gui/test/ala/freq/cmmd.gbw
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      cmmde_gui/test/ala/freq/cmmd.hess
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      cmmde_gui/test/ala/freq/cmmd.in
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      cmmde_gui/test/ala/freq/cmmd.xtbrestart
  18. 48
      cmmde_gui/test/ala/freq/cmmd_property.txt
  19. 10
      cmmde_gui/test/ala/freq/run.sh
  20. 0
      cmmde_gui/test/ala/freq/slurm-2915.out
  21. 1
      cmmde_gui/test/ala/geom.smi
  22. 7
      cmmde_gui/test/ala/geom.xyz
  23. 10
      cmmde_gui/test/ala/run.sh
  24. 8
      cmmde_gui/test/ala/run_babel.sh
  25. 1
      cmmde_gui/test/ala/slurm-2913.out
  26. 0
      cmmde_gui/test/ala/slurm-2914.out
  27. 74
      cmmde_gui/test/alala/alala/cmmd.engrad
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      cmmde_gui/test/alala/alala/cmmd.gbw
  29. 11
      cmmde_gui/test/alala/alala/cmmd.in
  30. 1566
      cmmde_gui/test/alala/alala/cmmd.opt
  31. 2742
      cmmde_gui/test/alala/alala/cmmd.out
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      cmmde_gui/test/alala/alala/cmmd.xtbrestart
  33. 17
      cmmde_gui/test/alala/alala/cmmd.xyz
  34. 6
      cmmde_gui/test/alala/alala/cmmd_property.txt
  35. 102
      cmmde_gui/test/alala/alala/cmmd_trj.xyz
  36. 74
      cmmde_gui/test/alala/alala/freq/cmmd.engrad
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      cmmde_gui/test/alala/alala/freq/cmmd.gbw
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      cmmde_gui/test/alala/alala/freq/cmmd.in
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      cmmde_gui/test/alala/alala/freq/cmmd.xtbrestart
  42. 78
      cmmde_gui/test/alala/alala/freq/cmmd_property.txt
  43. 10
      cmmde_gui/test/alala/alala/freq/run.sh
  44. 0
      cmmde_gui/test/alala/alala/freq/slurm-2890.out
  45. 1
      cmmde_gui/test/alala/alala/geom.smi
  46. 17
      cmmde_gui/test/alala/alala/geom.xyz
  47. 10
      cmmde_gui/test/alala/alala/run.sh
  48. 8
      cmmde_gui/test/alala/alala/run_babel.sh
  49. 1
      cmmde_gui/test/alala/alala/slurm-2887.out
  50. 0
      cmmde_gui/test/alala/alala/slurm-2888.out
  51. 74
      cmmde_gui/test/alala/cmmd.engrad
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      cmmde_gui/test/alala/cmmd.gbw
  53. 11
      cmmde_gui/test/alala/cmmd.in
  54. 1566
      cmmde_gui/test/alala/cmmd.opt
  55. 2742
      cmmde_gui/test/alala/cmmd.out
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      cmmde_gui/test/alala/cmmd.xtbrestart
  57. 17
      cmmde_gui/test/alala/cmmd.xyz
  58. 6
      cmmde_gui/test/alala/cmmd_property.txt
  59. 102
      cmmde_gui/test/alala/cmmd_trj.xyz
  60. 74
      cmmde_gui/test/alala/freq/cmmd.engrad
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      cmmde_gui/test/alala/freq/cmmd.gbw
  62. 1024
      cmmde_gui/test/alala/freq/cmmd.hess
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      cmmde_gui/test/alala/freq/cmmd.in
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      cmmde_gui/test/alala/freq/cmmd.out
  65. BIN
      cmmde_gui/test/alala/freq/cmmd.xtbrestart
  66. 78
      cmmde_gui/test/alala/freq/cmmd_property.txt
  67. 10
      cmmde_gui/test/alala/freq/run.sh
  68. 0
      cmmde_gui/test/alala/freq/slurm-2889.out
  69. 1
      cmmde_gui/test/alala/geom.smi
  70. 17
      cmmde_gui/test/alala/geom.xyz
  71. 10
      cmmde_gui/test/alala/run.sh
  72. 8
      cmmde_gui/test/alala/run_babel.sh
  73. 1
      cmmde_gui/test/alala/slurm-2885.out
  74. 0
      cmmde_gui/test/alala/slurm-2886.out
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      cmmde_gui/test/metana3/cmmd.engrad
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      cmmde_gui/test/metana3/cmmd.in
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      cmmde_gui/test/metana3/cmmd.opt
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      cmmde_gui/test/metana3/cmmd.out
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      cmmde_gui/test/metana3/cmmd.xtbrestart
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      cmmde_gui/test/metana3/cmmd.xyz
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      cmmde_gui/test/metana3/cmmd_property.txt
  83. 21
      cmmde_gui/test/metana3/cmmd_trj.xyz
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      cmmde_gui/test/metana3/freq/cmmd.engrad
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      cmmde_gui/test/metana3/freq/cmmd.gbw
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      cmmde_gui/test/metana3/freq/cmmd.hess
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      cmmde_gui/test/metana3/freq/cmmd.out
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      cmmde_gui/test/metana3/freq/cmmd.xtbrestart
  90. 48
      cmmde_gui/test/metana3/freq/cmmd_property.txt
  91. 13
      cmmde_gui/test/metana3/freq/freq/cmmd.in
  92. 142
      cmmde_gui/test/metana3/freq/freq/cmmd.out
  93. 10
      cmmde_gui/test/metana3/freq/freq/run.sh
  94. 7
      cmmde_gui/test/metana3/freq/freq/slurm-2909.out
  95. 10
      cmmde_gui/test/metana3/freq/run.sh
  96. 0
      cmmde_gui/test/metana3/freq/slurm-2908.out
  97. 1
      cmmde_gui/test/metana3/geom.smi
  98. 7
      cmmde_gui/test/metana3/geom.xyz
  99. 10
      cmmde_gui/test/metana3/run.sh
  100. 8
      cmmde_gui/test/metana3/run_babel.sh
  101. Some files were not shown because too many files have changed in this diff Show More

@ -400,4 +400,4 @@ if opt.job == 'ligprep' and opt.software == 'gmx':
# Program XTB Standalone
if opt.software == 'xtb':
xtb(opt.job,geom,opt.nproc,opt.produk,opt.temp,opt.nrun,opt.npoint,opt.anopt,opt.kpush,opt.kpull,opt.ppull,opt.alp,opt.distance,opt.angle,opt.dihedral,opt.scanmode,opt.iter,opt.scan,opt.solvent)
xtb(opt.job,geom,opt.nproc,opt.produk,opt.temp,opt.nrun,opt.npoint,opt.anopt,opt.kpush,opt.kpull,opt.ppull,opt.alp,opt.distance,opt.angle,opt.dihedral,opt.scanmode,opt.iter,opt.scan,opt.solvent,opt.charge,opt.mult,opt.method)

@ -59,14 +59,20 @@ def cmmde_gui():
Run_btn.on_click(run)
# Post calculations
post_btn = pn.widgets.MultiChoice(name="Post calculation",value=['Frequency calculation'], options=['Frequency calculation','Radial distribution function', 'Mean Square Displacement','Time-dependent calculation','Thermochemistry calculation'])
post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry':'thermo'}
post_calc = {'Frequency calculation':'freq', 'Radial distribution function':'rdf','Mean Square Displacement':'msd','Time-dependent calculation':'td','Thermochemistry calculation':'thermo'}
# Post Calculation CMMDE software options
post_software_btn = pn.widgets.MultiSelect(name="Software selections for post calculations",value=['Orca'],options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso'])
post_software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'}
# Post CMMDE method options
post_method_btn = pn.widgets.MultiChoice(name="Method selections for post calculations",value=['GFN2-xTB'],options=['GFN2-xTB','GFN1-xTB','DFTB2','DFTB2-gammah','DFTB3','DFTB3-diag'])
post_method = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag'}
def post_calculation(event):
os.makedirs(post_calc[post_btn.value[0]])
os.chdir(post_calc[post_btn.value[0]])
if post_calc[post_btn.value[0]] == 'thermo' and software[software_btn.value[0]] == 'orca':
terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value[0]]),"-s{}".format(software[software_btn.value[0]]))
if post_calc[post_btn.value[0]] == 'thermo' and post_software[post_software_btn.value[0]] == 'orca':
terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value[0]]),"-s{}".format(post_software[post_software_btn.value[0]]))
else:
terminal.subprocess.run("cmmde.py","-i{}".format("../cmmd.xyz"),"-s{}".format(software[software_btn.value[0]]), "-j{}".format(post_calc[post_btn.value[0]]), "-m{}".format(method[method_btn.value[0]]))
os.makedirs(post_calc[post_btn.value[0]])
os.chdir(post_calc[post_btn.value[0]])
terminal.subprocess.run("cmmde.py","-i{}".format("../cmmd.xyz"),"-s{}".format(post_software[post_software_btn.value[0]]), "-j{}".format(post_calc[post_btn.value[0]]), "-m{}".format(post_method[post_method_btn.value[0]]))
runpost_btn = pn.widgets.Button(name="Run post calculation!",button_type='primary')
runpost_btn.on_click(post_calculation)
# Check the progress
@ -116,7 +122,7 @@ def cmmde_gui():
site="CMMDE-GUI",
title="CMMDE Editor",
main=[editor, terminal, terminal.subprocess.param.running,visual_btn,pn.Tabs(xyzviewer)],
sidebar=[pn.Row(software_btn,height=200),Name_input,pn.Column(job_btn, height=400),pn.Column(method_btn,height=400),pn.Row(Run_btn,Progress_btn),pn.Column(post_btn,height=400),pn.Row(runpost_btn,Progress_btn)],
sidebar=[pn.Row(software_btn,height=200),Name_input,pn.Column(job_btn, height=400),pn.Column(method_btn,height=400),pn.Row(Run_btn,Progress_btn),pn.Column(post_btn,height=400),pn.Row(post_software_btn,height=200),pn.Row(post_method_btn,height=400),pn.Row(runpost_btn,Progress_btn)],
header_background=accent, accent_base_color=accent
)

@ -0,0 +1,34 @@
#
# Number of atoms
#
5
#
# The current total energy in Eh
#
-4.175218519970
#
# The current gradient in Eh/bohr
#
0.000000009773
0.000000207326
0.000000451564
0.000099433721
-0.000000459326
0.000000273611
-0.000032618166
-0.000065629718
0.000066668309
-0.000033396983
-0.000024690189
-0.000090646633
-0.000033428344
0.000090571907
0.000023253149
#
# The atomic numbers and current coordinates in Bohr
#
6 2.0184922 0.1320357 0.0411923
1 4.0634786 0.1320373 0.0411913
1 1.3368371 -1.2210494 1.4146831
1 1.3368281 -0.3808997 -1.8173559
1 1.3368243 1.9980519 0.5262503

Binary file not shown.

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

@ -0,0 +1,164 @@
$orca_opt_file
$trust
0.300000000000
$epredict
0.000000000000
$ediffsc
1000.000000000000
$ctyp
3
$coordinates
2 15
2.01849207 0.13203516 0.04119603 4.08245096 0.13203516 0.04119603
1.33051838 -1.23359432 1.42742353 1.33049948 -0.38565531 -1.83460282
1.33049948 2.01535513 0.53074848
2.01849229 0.13203602 0.04119252 4.06376085 0.13203517 0.04119289
1.33674541 -1.22123552 1.41487269 1.33673305 -0.38096895 -1.81761288
1.33672876 1.99830910 0.52631602
# 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
-4.1749622725100002
-4.1752184657600004
$gradients
2 15
-0.0000009833906802 -0.0000001119553941 0.0000056024935147 0.0066855474095101
0.0000002580458458 -0.0000003189052208 -0.0022268519256439 -0.0044209628038230
0.0044881548035643 -0.0022296450949106 -0.0016768795046880 -0.0060782365230050
-0.0022280669982754 0.0060976962180593 0.0015847981311467
0.0000000097726303 0.0000002073257427 0.0000004515639351 0.0000994337209119
-0.0000004593262936 0.0000002736105739 -0.0000326181661896 -0.0000656297177652
0.0000666683089600 -0.0000333969829729 -0.0000246901887146 -0.0000906466328031
-0.0000334283443797 0.0000905719070307 0.0000232531493340
$redundant_coords
2 10
2.0639588834687914 2.0639472848570848 2.0639667076849042 2.0639499734306326
1.9106351330402711 1.9106374556324923 1.9106379996267291 1.9106342521654580
1.9106258281440835 1.9106287489029192
2.0452685634715593 2.0452676811671595 2.0452694860764682 2.0452680859704326
1.9106347218710964 1.9106350965581578 1.9106374823377432 1.9106347535765364
1.9106292238372415 1.9106281393229423
$redundant_gradients
2 10
0.0066855474089695 0.0066818646229452 0.0066879145389310 0.0066826466696578
0.0000001194960480 0.0000006856095398 0.0000001503379083 -0.0000001457243627
-0.0000009868782152 0.0000001771603258
0.0000994337211524 0.0000990741203842 0.0000997078101748 0.0000993037484264
0.0000002224784906 0.0000002456789561 0.0000005417275145 0.0000001647442255
-0.0000004988653346 -0.0000006757613803
$hessian_approx
15 15
0 1 2 3 4 5
0 0.839474 -0.000002 -0.000002 -0.357201 -0.000000 -0.000001
1 -0.000002 0.839478 -0.000004 -0.000003 -0.136201 0.000000
2 -0.000002 -0.000004 0.839472 -0.000006 0.000000 -0.136201
3 -0.357201 -0.000003 -0.000006 0.355995 0.000009 -0.000008
4 -0.000000 -0.136201 0.000000 0.000009 0.102151 -0.000000
5 -0.000001 0.000000 -0.136201 -0.000008 -0.000000 0.102151
6 -0.160758 -0.048742 0.049481 0.000400 -0.045063 0.045742
7 -0.048743 -0.232955 0.098218 0.000795 0.011174 -0.011344
8 0.049479 0.098213 -0.235903 -0.000807 -0.011343 0.011515
9 -0.160755 -0.018476 -0.066948 0.000402 -0.017084 -0.061888
10 -0.018477 -0.150102 -0.050376 0.000298 0.001605 0.005823
11 -0.066950 -0.050375 -0.318732 0.001101 0.005812 0.021100
12 -0.160759 0.067223 0.017476 0.000404 0.062138 0.016156
13 0.067222 -0.320219 -0.047838 -0.001100 0.021273 0.005520
14 0.017474 -0.047835 -0.148637 -0.000280 0.005529 0.001435
6 7 8 9 10 11
0 -0.160758 -0.048743 0.049479 -0.160755 -0.018477 -0.066950
1 -0.048742 -0.232955 0.098213 -0.018476 -0.150102 -0.050375
2 0.049481 0.098218 -0.235903 -0.066948 -0.050376 -0.318732
3 0.000400 0.000795 -0.000807 0.000402 0.000298 0.001101
4 -0.045063 0.011174 -0.011343 -0.017084 0.001605 0.005812
5 0.045742 -0.011344 0.011515 -0.061888 0.005823 0.021100
6 0.130358 0.055989 -0.056834 0.015000 0.025278 -0.012919
7 0.055989 0.213290 -0.112815 0.015786 0.026719 -0.014041
8 -0.056834 -0.112815 0.216668 0.023592 0.039308 -0.018611
9 0.015000 0.015786 0.023592 0.130354 0.021225 0.076898
10 0.025278 0.026719 0.039308 0.021225 0.118121 0.057867
11 -0.012919 -0.014041 -0.018611 0.076898 0.057867 0.311806
12 0.015000 -0.023827 -0.015430 0.014998 -0.028323 0.001870
13 0.012538 -0.018226 -0.013364 -0.001449 0.003659 0.000735
14 -0.025469 0.039981 0.026330 0.028348 -0.052623 0.004435
12 13 14
0 -0.160759 0.067222 0.017474
1 0.067223 -0.320219 -0.047835
2 0.017476 -0.047838 -0.148637
3 0.000404 -0.001100 -0.000280
4 0.062138 0.021273 0.005529
5 0.016156 0.005520 0.001435
6 0.015000 0.012538 -0.025469
7 -0.023827 -0.018226 0.039981
8 -0.015430 -0.013364 0.026330
9 0.014998 -0.001449 0.028348
10 -0.028323 0.003659 -0.052623
11 0.001870 0.000735 0.004435
12 0.130357 -0.077211 -0.020072
13 -0.077211 0.313515 0.054947
14 -0.020072 0.054947 0.116436
$bmatrix
10 15
0 1 2 3 4 5
0 -1.000000 0.000000 -0.000000 1.000000 -0.000000 0.000000
1 0.333329 0.661660 -0.671638 0.000000 0.000000 0.000000
2 0.333335 0.250825 0.908832 0.000000 0.000000 0.000000
3 0.333337 -0.912483 -0.237193 0.000000 0.000000 0.000000
4 0.460970 -0.173435 -0.628418 -0.000000 0.130076 0.471313
5 -0.460970 -0.630945 -0.164009 0.000000 0.000000 0.000000
6 0.460970 0.630945 0.164010 -0.000000 -0.473207 -0.123007
7 -0.460971 0.173434 0.628418 0.000000 0.000000 0.000000
8 -0.460972 0.457506 -0.464407 0.000000 0.000000 0.000000
9 0.460972 -0.457507 0.464406 0.000000 0.343131 -0.348306
6 7 8 9 10 11
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1 -0.333329 -0.661660 0.671638 0.000000 0.000000 0.000000
2 0.000000 0.000000 0.000000 -0.333335 -0.250825 -0.908832
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 0.000000 0.000000 0.000000 -0.460970 0.043359 0.157105
5 0.230486 0.244454 0.355211 0.230484 0.386491 -0.191201
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
7 0.230487 -0.358829 -0.239109 0.000000 0.000000 0.000000
8 0.000000 0.000000 0.000000 0.230486 -0.429848 0.034096
9 -0.460972 0.114376 -0.116100 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 -0.333337 0.912483 0.237193
4 0.000000 0.000000 0.000000
5 0.000000 0.000000 0.000000
6 -0.460970 -0.157738 -0.041003
7 0.230484 0.185396 -0.389309
8 0.230486 -0.027658 0.430311
9 0.000000 0.000000 0.000000

File diff suppressed because it is too large Load Diff

@ -0,0 +1,7 @@
5
Coordinates from ORCA-job cmmd
C 1.06814007280221 0.06987026850103 0.02179803932415
H 2.15030026068978 0.06987112958641 0.02179749602221
H 0.70742370687918 -0.64615150469397 0.74861807400167
H 0.70741898627439 -0.20156341603182 -0.96170330012855
H 0.70741697335444 1.05732352263836 0.27847969078052

@ -0,0 +1,6 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,21 @@
5
Coordinates from ORCA-job cmmd E -4.174962272510
C 1.068140 0.069870 0.021800
H 2.160340 0.069870 0.021800
H 0.704080 -0.652790 0.755360
H 0.704070 -0.204080 -0.970830
H 0.704070 1.066480 0.280860
5
Coordinates from ORCA-job cmmd E -4.175218465760
C 1.068140 0.069870 0.021798
H 2.150450 0.069870 0.021798
H 0.707375 -0.646250 0.748718
H 0.707369 -0.201600 -0.961839
H 0.707366 1.057460 0.278514
5
Coordinates from ORCA-job cmmd E -4.175218519970
C 1.068140 0.069870 0.021798
H 2.150300 0.069871 0.021797
H 0.707424 -0.646152 0.748618
H 0.707419 -0.201563 -0.961703
H 0.707417 1.057324 0.278480

@ -0,0 +1,34 @@
#
# Number of atoms
#
5
#
# The current total energy in Eh
#
-4.175218519980
#
# The current gradient in Eh/bohr
#
0.000000045326
0.000000167733
0.000000029765
-0.000003309957
-0.000000249790
0.000000129141
0.000001317460
0.000002127091
-0.000002151036
0.000001016219
0.000001006359
0.000002966352
0.000000930952
-0.000003051392
-0.000000974223
#
# The atomic numbers and current coordinates in Bohr
#
6 2.0184922 0.1320357 0.0411923
1 4.0634786 0.1320373 0.0411913
1 1.3368371 -1.2210494 1.4146831
1 1.3368281 -0.3808997 -1.8173559
1 1.3368243 1.9980519 0.5262503

Binary file not shown.

@ -0,0 +1,192 @@
$orca_hessian_file
$act_atom
0
$act_coord
0
$act_energy
-4.175219
$hessian
15
0 1 2 3 4
0 5.1329127386E-01 -3.3636519648E-06 2.7836910958E-06 -2.9809786459E-01 -2.0111847410E-07
1 -3.3636519648E-06 5.1328774831E-01 -4.1292960070E-07 -2.1994454789E-07 -4.3442763969E-02
2 2.7836910958E-06 -4.1292960070E-07 5.1328754864E-01 1.3916768318E-07 -9.6603597691E-09
3 -2.9809786459E-01 -2.1994454789E-07 1.3916768318E-07 3.4272726540E-01 2.6835972750E-07
4 -2.0111847410E-07 -4.3442763969E-02 -9.6603597691E-09 2.6835972750E-07 4.6441081937E-02
5 1.3206793443E-07 -9.6670189178E-09 -4.3442747837E-02 -1.0713789465E-07 -6.1757220961E-08
6 -7.1733839407E-02 -5.6161287709E-02 5.7008315131E-02 -1.4874636926E-02 -2.3542514267E-02
7 -5.6161183538E-02 -1.5492116032E-01 1.1316381228E-01 -1.6485567775E-03 -9.8151070450E-04
8 5.7008202738E-02 1.1316379791E-01 -1.5830910508E-01 1.6733965622E-03 1.1842231955E-03
9 -7.1734575351E-02 -2.1289712447E-02 -7.7144027878E-02 -1.4874656620E-02 -8.9246273506E-03
10 -2.1289669385E-02 -5.9462115086E-02 -5.8048812159E-02 -6.2501434377E-04 1.7432106214E-05
11 -7.7143867707E-02 -5.8048774107E-02 -2.5377698527E-01 -2.2641275020E-03 -6.0733966207E-04
12 -7.1734900154E-02 7.7454583479E-02 2.0132790190E-02 -1.4874651446E-02 3.2467074451E-02
13 7.7454422495E-02 -2.5547116451E-01 -5.5114568815E-02 2.2731759983E-03 -2.0336583113E-03
14 2.0132744638E-02 -5.5114592448E-02 -5.7768143367E-02 5.9102415832E-04 -5.7681327417E-04
5 6 7 8 9
0 1.3206793443E-07 -7.1733839407E-02 -5.6161183538E-02 5.7008202738E-02 -7.1734575351E-02
1 -9.6670189178E-09 -5.6161287709E-02 -1.5492116032E-01 1.1316379791E-01 -2.1289712447E-02
2 -4.3442747837E-02 5.7008315131E-02 1.1316381228E-01 -1.5830910508E-01 -7.7144027878E-02
3 -1.0713789465E-07 -1.4874636926E-02 -1.6485567775E-03 1.6733965622E-03 -1.4874656620E-02
4 -6.1757220961E-08 -2.3542514267E-02 -9.8151070450E-04 1.1842231955E-03 -8.9246273506E-03
5 4.6441107085E-02 2.3897558740E-02 1.1842547839E-03 -1.0169431892E-03 -3.2337164017E-02
6 2.3897558740E-02 7.9358259250E-02 6.5343154941E-02 -6.6328653384E-02 3.6258428420E-03
7 1.1842547839E-03 6.5343154941E-02 1.7614546490E-01 -1.3166436950E-01 2.4437918892E-03
8 -1.0169431892E-03 -6.6328653384E-02 -1.3166436950E-01 1.8008726052E-01 9.9401130438E-03
9 -3.2337164017E-02 3.6258428420E-03 2.4437918892E-03 9.9401130438E-03 7.9358947320E-02
10 -6.0756496012E-04 6.9751642011E-03 4.8745925129E-03 2.1168626472E-02 2.4770458157E-02
11 -2.0159862303E-03 -7.4919127771E-03 -4.3037037576E-03 -2.5373371238E-02 8.9755942634E-02
12 8.4395802803E-03 3.6258575186E-03 -9.9755627888E-03 -2.2947274765E-03 3.6259250755E-03
13 -5.7661955222E-04 7.3867085647E-03 -2.5114204535E-02 -3.8547822493E-03 3.0006239868E-03
14 3.5149897336E-05 -7.0865402046E-03 2.1617527214E-02 4.6153930316E-03 9.7865512730E-03
10 11 12 13 14
0 -2.1289669385E-02 -7.7143867707E-02 -7.1734900154E-02 7.7454422495E-02 2.0132744638E-02
1 -5.9462115086E-02 -5.8048774107E-02 7.7454583479E-02 -2.5547116451E-01 -5.5114592448E-02
2 -5.8048812159E-02 -2.5377698527E-01 2.0132790190E-02 -5.5114568815E-02 -5.7768143367E-02
3 -6.2501434377E-04 -2.2641275020E-03 -1.4874651446E-02 2.2731759983E-03 5.9102415832E-04
4 1.7432106214E-05 -6.0733966207E-04 3.2467074451E-02 -2.0336583113E-03 -5.7681327417E-04
5 -6.0756496012E-04 -2.0159862303E-03 8.4395802803E-03 -5.7661955222E-04 3.5149897336E-05
6 6.9751642011E-03 -7.4919127771E-03 3.6258575186E-03 7.3867085647E-03 -7.0865402046E-03
7 4.8745925129E-03 -4.3037037576E-03 -9.9755627888E-03 -2.5114204535E-02 2.1617527214E-02
8 2.1168626472E-02 -2.5373371238E-02 -2.2947274765E-03 -3.8547822493E-03 4.6153930316E-03
9 2.4770458157E-02 8.9755942634E-02 3.6259250755E-03 3.0006239868E-03 9.7865512730E-03
10 6.5079793563E-02 6.7539019241E-02 -9.8303155390E-03 -1.0508688577E-02 -3.0050216659E-02
11 6.7539019241E-02 2.9116129859E-01 -2.8537771275E-03 -4.5777014462E-03 -9.9903027647E-03
12 -9.8303155390E-03 -2.8537771275E-03 7.9359252291E-02 -9.0117197664E-02 -2.3424369102E-02
13 -1.0508688577E-02 -4.5777014462E-03 -9.0117197664E-02 2.9313239407E-01 6.4125091508E-02
14 -3.0050216659E-02 -9.9903027647E-03 -2.3424369102E-02 6.4125091508E-02 6.3108869270E-02
$vibrational_frequencies
15
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 1385.802989
7 1385.804694
8 1385.819131
9 1557.265928
10 1557.278661
11 3090.006354
12 3103.914034
13 3103.936524
14 3103.959260
$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 1.1460429268E-01 -3.4379236967E-02 -4.7849264525E-02 -6.2196180136E-08
1 0.0000000000E+00 5.8576857374E-02 7.7750867247E-02 8.4434109433E-02 5.7988235870E-06
2 0.0000000000E+00 -6.3442646325E-03 9.6842579071E-02 -8.4775157264E-02 5.6540900942E-06
3 0.0000000000E+00 5.3322377490E-02 -1.5995533024E-02 -2.2262979463E-02 2.3670438248E-07
4 0.0000000000E+00 -2.7535711067E-01 -3.6548194224E-01 -3.9692559975E-01 -3.6560167528E-01
5 0.0000000000E+00 2.9827653543E-02 -4.5522985733E-01 3.9852923127E-01 -3.4113931628E-01
6 0.0000000000E+00 -3.9889455056E-01 1.1846683962E-01 3.9173216657E-01 1.2781240094E-02
7 0.0000000000E+00 2.2582223879E-03 -4.5119127032E-01 -6.5843512581E-02 3.5285840880E-01
8 0.0000000000E+00 -2.5200659617E-01 -3.6833527333E-01 6.2452757104E-02 3.5395910859E-01
9 0.0000000000E+00 -4.5760273347E-01 3.2700273115E-01 1.0126357845E-01 4.0172057861E-01
10 0.0000000000E+00 -2.1431150072E-01 -2.4104848320E-01 -4.8999373348E-01 2.1441650987E-01
11 0.0000000000E+00 2.5110611645E-01 -4.2335079059E-03 6.1322674707E-02 -2.0650819767E-01
12 0.0000000000E+00 -5.6241255314E-01 -1.9822236936E-02 9.9423500526E-02 -4.1450131430E-01
13 0.0000000000E+00 -2.1057238274E-01 1.3126766153E-01 -5.3326527601E-02 -2.0174234028E-01
14 0.0000000000E+00 4.6669019129E-02 -3.2614602137E-01 4.8784852530E-01 1.9362103306E-01
10 11 12 13 14
0 -1.1685424666E-06 1.0305848845E-04 -1.6400025343E-02 -3.1979547838E-03 8.5675284564E-02
1 -5.0070919903E-07 5.4593202416E-05 -5.8809524764E-02 -6.3052970933E-02 -1.3611266360E-02
2 7.9760804626E-07 -4.9746676876E-05 6.2385950041E-02 -6.0279016142E-02 9.6922378022E-03
3 -1.3626230096E-06 4.9897892641E-01 1.6230624130E-01 3.1593465320E-02 -8.4545192635E-01
4 3.4111349028E-01 2.6482553553E-05 -2.7197780136E-02 -2.9159539116E-02 -6.2950067490E-03
5 -3.6557650895E-01 -2.3880077608E-05 2.8851914775E-02 -2.7876771652E-02 4.4822877101E-03
6 -4.7122878139E-01 -1.6697405729E-01 2.8914304946E-01 6.4174313555E-03 -5.0797945399E-03
7 1.2657588124E-01 -3.3151699796E-01 5.6180656381E-01 -1.3489457042E-02 -9.5034841166E-02
8 -1.0916974631E-01 3.3651927657E-01 -5.6903524917E-01 -4.3792105404E-02 9.4560503801E-02
9 2.4669155397E-01 -1.6662718301E-01 -1.3331926298E-01 2.4512947958E-01 -7.7040068406E-02
10 -4.3392019027E-01 -1.2539328656E-01 -1.2181111507E-01 1.5640546240E-01 -9.4081351994E-02
11 2.9276305623E-02 -4.5446595783E-01 -3.1396261364E-01 6.4450414089E-01 -3.1360477361E-01
12 2.2455251402E-01 -1.6660569754E-01 -1.2271266231E-01 -2.4503458766E-01 -9.3307023098E-02
13 -3.3763214961E-02 4.5623328713E-01 2.8795749205E-01 6.3756221815E-01 3.5759862079E-01
14 4.4546044560E-01 1.1856332655E-01 1.1077526755E-01 1.4542987792E-01 9.9072430276E-02
#
# The atoms: label mass x y z (in bohrs)
#
$atoms
5
C 12.01100 2.018492210263 0.132035672370 0.041192324579
H 1.00800 4.063478598403 0.132037299586 0.041191297887
H 1.00800 1.336837066645 -1.221049384893 1.414683138767
H 1.00800 1.336828145995 -0.380899654918 -1.817355859331
H 1.00800 1.336824342127 1.998051892739 0.526250349434
$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 2.0000000000E-01
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 -2.0000000000E-01
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 0.00043085 2.17736113 -0.002037 -0.001583 -0.009506
1385.80 0.00291380 14.72516324 0.000611 -0.019085 -0.017074
1385.82 0.00019488 0.98483488 0.000850 0.004423 -0.004858
1557.27 0.00475914 24.05072327 -0.000000 0.021765 0.021908
1557.28 0.00011600 0.58621836 0.000000 -0.002953 0.003811
3090.01 0.00213139 10.77118066 -0.013874 -0.003329 0.003419
3103.91 0.01079707 54.56396020 -0.004326 -0.022844 0.023344
3103.94 0.00634783 32.07932697 -0.000842 -0.018162 -0.017539
3103.96 0.00587823 29.70617211 0.022536 -0.007011 0.005826
$end

@ -0,0 +1,13 @@
#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

@ -0,0 +1,711 @@
*****************
* 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 2022/07/22 at 20:31:34.411
-------------------------------------------------
| 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 : 0.60690392607394
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 -0.109869E-09 0.432E-06 17.35 10350.2 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 -0.4674579 -12.7202
4 2.0000 -0.4674579 -12.7202 (HOMO)
5 0.1702647 4.6331 (LUMO)
6 0.2292565 6.2384
7 0.2292569 6.2384
8 0.2292585 6.2384
-------------------------------------------------------------
HL-Gap 0.6377226 Eh 17.3533 eV
Fermi-level -0.1485966 Eh -4.0435 eV
SCC (total) 0 d, 0 h, 0 min, 0.023 sec
SCC setup ... 0 min, 0.000 sec ( 0.165%)
Dispersion ... 0 min, 0.000 sec ( 0.028%)
classical contributions ... 0 min, 0.000 sec ( 0.021%)
integral evaluation ... 0 min, 0.000 sec ( 0.275%)
iterations ... 0 min, 0.023 sec ( 97.223%)
molecular gradient ... 0 min, 0.000 sec ( 1.597%)
printout ... 0 min, 0.000 sec ( 0.655%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -4.175218519975 Eh ::
:: gradient norm 0.000006627564 Eh/a0 ::
:: HOMO-LUMO gap 17.353313970090 eV ::
::.................................................::
:: SCC energy -4.247467308188 Eh ::
:: -> isotropic ES 0.002035567944 Eh ::
:: -> anisotropic ES 0.002321540929 Eh ::
:: -> anisotropic XC 0.003585096736 Eh ::
:: -> dispersion -0.000661011606 Eh ::
:: repulsion energy 0.072248782622 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -4.175218519975 Eh |
| GRADIENT NORM 0.000006627564 Eh/α |
| HOMO-LUMO GAP 17.353313970090 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/07/22 at 20:31:34.439
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.028 sec
* cpu-time: 0 d, 0 h, 0 min, 0.007 sec
* ratio c/w: 0.264 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.023 sec
* cpu-time: 0 d, 0 h, 0 min, 0.003 sec
* ratio c/w: 0.126 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -4.175218519980
------------------------- --------------------
----------------------------------------------------------------------------
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: 1385.80 cm**-1
8: 1385.82 cm**-1
9: 1557.27 cm**-1
10: 1557.28 cm**-1
11: 3090.01 cm**-1
12: 3103.91 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 0.114604 -0.034379 -0.047849 -0.000000 -0.000001 0.000103
1 0.058577 0.077751 0.084434 0.000006 -0.000001 0.000055
2 -0.006344 0.096843 -0.084775 0.000006 0.000001 -0.000050
3 0.053322 -0.015996 -0.022263 0.000000 -0.000001 0.498979
4 -0.275357 -0.365482 -0.396926 -0.365602 0.341113 0.000026
5 0.029828 -0.455230 0.398529 -0.341139 -0.365577 -0.000024
6 -0.398895 0.118467 0.391732 0.012781 -0.471229 -0.166974
7 0.002258 -0.451191 -0.065844 0.352858 0.126576 -0.331517
8 -0.252007 -0.368335 0.062453 0.353959 -0.109170 0.336519
9 -0.457603 0.327003 0.101264 0.401721 0.246692 -0.166627
10 -0.214312 -0.241048 -0.489994 0.214417 -0.433920 -0.125393
11 0.251106 -0.004234 0.061323 -0.206508 0.029276 -0.454466
12 -0.562413 -0.019822 0.099424 -0.414501 0.224553 -0.166606
13 -0.210572 0.131268 -0.053327 -0.201742 -0.033763 0.456233
14 0.046669 -0.326146 0.487849 0.193621 0.445460 0.118563
12 13 14
0 -0.016400 -0.003198 0.085675
1 -0.058810 -0.063053 -0.013611
2 0.062386 -0.060279 0.009692
3 0.162306 0.031593 -0.845452
4 -0.027198 -0.029160 -0.006295
5 0.028852 -0.027877 0.004482
6 0.289143 0.006417 -0.005080
7 0.561807 -0.013489 -0.095035
8 -0.569035 -0.043792 0.094561
9 -0.133319 0.245129 -0.077040
10 -0.121811 0.156405 -0.094081
11 -0.313963 0.644504 -0.313605
12 -0.122713 -0.245035 -0.093307
13 0.287957 0.637562 0.357599
14 0.110775 0.145430 0.099072
-----------
IR SPECTRUM
-----------
Mode freq eps Int T**2 TX TY TZ
cm**-1 L/(mol*cm) km/mol a.u.
----------------------------------------------------------------------------
6: 1385.80 0.000431 2.18 0.000097 (-0.002037 -0.001583 -0.009506)
7: 1385.80 0.002914 14.73 0.000656 ( 0.000611 -0.019085 -0.017074)
8: 1385.82 0.000195 0.98 0.000044 ( 0.000850 0.004423 -0.004858)
9: 1557.27 0.004759 24.05 0.000954 (-0.000000 0.021765 0.021908)
10: 1557.28 0.000116 0.59 0.000023 ( 0.000000 -0.002953 0.003811)
11: 3090.01 0.002131 10.77 0.000215 (-0.013874 -0.003329 0.003419)
12: 3103.91 0.010797 54.56 0.001086 (-0.004326 -0.022844 0.023344)
13: 3103.94 0.006348 32.08 0.000638 (-0.000842 -0.018162 -0.017539)
14: 3103.96 0.005878 29.71 0.000591 ( 0.022536 -0.007011 0.005826)
* 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. 1385.80 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. 3103.91 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: 5.355318 5.355306 5.355302
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 ... 63.185 sec (= 1.053 min)
Numerical frequency calculation ... 63.123 sec (= 1.052 min) 99.9 %
XTB module ... 0.061 sec (= 0.001 min) 0.1 %
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 1 minutes 3 seconds 196 msec

@ -0,0 +1,48 @@
-------------------------------------------------------------
----------------------- !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 1385.802989
7 1385.804694
8 1385.819131
9 1557.265928
10 1557.278661
11 3090.006354
12 3103.914034
13 3103.936524
14 3103.959260
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! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,10 @@
#!/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

@ -0,0 +1,7 @@
5
C 1.06814 0.06987 0.02180
H 2.16034 0.06987 0.02180
H 0.70408 -0.65279 0.75536
H 0.70407 -0.20408 -0.97083
H 0.70407 1.06648 0.28086

@ -0,0 +1,10 @@
#!/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

@ -0,0 +1,8 @@
#!/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

@ -0,0 +1 @@
1 molecule converted

@ -0,0 +1,74 @@
#
# Number of atoms
#
15
#
# The current total energy in Eh
#
-15.814313366050
#
# The current gradient in Eh/bohr
#
0.000227495798
-0.000049478208
0.000259008811
0.000082454763
-0.000273081820
-0.000428388240
-0.000389851164
-0.000263790724
0.000131258810
-0.000267765264
0.000279977188
0.000405328706
0.000065519654
0.000232417966
-0.000346430104
-0.000091428520
-0.000003594258
-0.000047833688
0.000020375247
0.000036476347
-0.000092535766
-0.000051248393
0.000118951949
0.000073438073
0.000077590295
0.000013581623
0.000136037554
0.000084963869
-0.000004747271
-0.000102722280
0.000081476300
0.000093731217
0.000038224552
0.000050966115
0.000038809074
-0.000147860440
0.000094397666
-0.000112630042
-0.000050618890
-0.000060968602
-0.000087995984
0.000064681824
0.000076022236
-0.000018627056
0.000108411078
#
# The atomic numbers and current coordinates in Bohr
#
6 2.3703954 -0.1651194 0.4670557
6 0.6244121 -2.3149509 -0.3431616
6 -2.0569278 -1.2859578 0.0884502
6 -1.7932022 1.6093409 0.2505151
6 0.9572467 2.1759662 -0.4424772
1 4.2547410 -0.3279597 -0.3452135
1 2.5424148 -0.1255682 2.5217455
1 0.9699948 -4.0479168 0.7122810
1 0.9164144 -2.7164515 -2.3442578
1 -2.8470130 -2.0337184 1.8372841
1 -3.3119226 -1.8405746 -1.4465563
1 -2.1702788 2.2491381 2.1728818
1 -3.1105539 2.5739965 -1.0028484
1 1.6415786 3.9116989 0.4268932
1 1.1549780 2.3508701 -2.4877364

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

File diff suppressed because it is too large Load Diff

File diff suppressed because it is too large Load Diff

@ -0,0 +1,17 @@
15
Coordinates from ORCA-job cmmd
C 1.25435919537090 -0.08737739876512 0.24715524632648
C 0.33042466881332 -1.22501927170804 -0.18159328410705
C -1.08847928950794 -0.68049957284919 0.04680580985473
C -0.94892173529753 0.85162652438004 0.13256689033968
C 0.50655312120543 1.15147170068949 -0.23414885516456
H 2.25151196078735 -0.17354879054452 -0.18267911191086
H 1.34538795520408 -0.06644782326499 1.33445026657908
H 0.51329912580071 -2.14206529372394 0.37692286104836
H 0.48494562341946 -1.43748420682295 -1.24052779233776
H -1.50657437511684 -1.07619744223052 0.97224888296167
H -1.75259393059400 -0.97399011796120 -0.76548462512947
H -1.14846207491294 1.19019262513953 1.14983951261691
H -1.64603424175245 1.36210030835772 -0.53068454217281
H 0.86868596585501 2.06998188715470 0.22590214224166
H 0.61118803072543 1.24402687214901 -1.31645340114607

@ -0,0 +1,6 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,102 @@
15
Coordinates from ORCA-job cmmd E -15.813823527310
C 1.253970 -0.087850 0.236110
C 0.326710 -1.222030 -0.169190
C -1.082040 -0.675110 0.043510
C -0.946150 0.845120 0.122080
C 0.504630 1.150760 -0.222060
H 2.240750 -0.172920 -0.227570
H 1.384620 -0.073870 1.324710
H 0.508830 -2.133100 0.408370
H 0.473010 -1.462750 -1.229290
H -1.513940 -1.062630 0.972820
H -1.743910 -0.977410 -0.775000
H -1.169630 1.182400 1.141400
H -1.640100 1.355580 -0.553100
H 0.864040 2.060640 0.266980
H 0.614500 1.279940 -1.305450
15
Coordinates from ORCA-job cmmd E -15.814241222380
C 1.257123 -0.088091 0.238226
C 0.328826 -1.226976 -0.172935
C -1.088491 -0.679714 0.044787
C -0.950523 0.850465 0.125720
C 0.506368 1.154273 -0.224938
H 2.245041 -0.172991 -0.215333
H 1.379029 -0.071943 1.323172
H 0.512114 -2.137358 0.398053
H 0.479548 -1.461348 -1.229026
H -1.516833 -1.070415 0.969225
H -1.749798 -0.979717 -0.769026
H -1.167689 1.190610 1.140388
H -1.642768 1.360747 -0.544398
H 0.866704 2.064442 0.255169
H 0.616638 1.274786 -1.304765
15
Coordinates from ORCA-job cmmd E -15.814284975000
C 1.256840 -0.087971 0.240929
C 0.329515 -1.227180 -0.176191
C -1.089636 -0.680681 0.045702
C -0.950883 0.851597 0.128554
C 0.506606 1.153997 -0.227959
H 2.247193 -0.173216 -0.204973
H 1.369029 -0.069993 1.325991
H 0.512598 -2.138785 0.390994
H 0.482449 -1.454647 -1.232210
H -1.514223 -1.073592 0.969408
H -1.751405 -0.977871 -0.767095
H -1.162122 1.192254 1.142832
H -1.643824 1.361220 -0.539544
H 0.867356 2.066207 0.245741
H 0.615797 1.265430 -1.307858
15
Coordinates from ORCA-job cmmd E -15.814304882810
C 1.255759 -0.087735 0.244138
C 0.330030 -1.226385 -0.179456
C -1.089550 -0.680907 0.046501
C -0.950251 0.851938 0.131194
C 0.506593 1.152913 -0.231316
H 2.249411 -0.173472 -0.193485
H 1.356785 -0.067973 1.330167
H 0.512793 -2.140292 0.383710
H 0.484505 -1.445960 -1.236559
H -1.510226 -1.075841 0.970688
H -1.752335 -0.975396 -0.766044
H -1.155056 1.192253 1.146436
H -1.644903 1.361314 -0.534953
H 0.867883 2.068121 0.235501
H 0.613852 1.254194 -1.312201
15
Coordinates from ORCA-job cmmd E -15.814311679880
C 1.254764 -0.087506 0.246357
C 0.330312 -1.225457 -0.181258
C -1.088902 -0.680693 0.046834
C -0.949381 0.851790 0.132471
C 0.506536 1.151901 -0.233475
H 2.250907 -0.173582 -0.185613
H 1.348285 -0.066771 1.333273
H 0.513007 -2.141451 0.378820
H 0.485140 -1.439720 -1.239568
H -1.507362 -1.076489 0.971842
H -1.752602 -0.974004 -0.765631
H -1.150114 1.191161 1.149001
H -1.645670 1.361592 -0.531936
H 0.868338 2.069444 0.228533
H 0.612033 1.246555 -1.315330
15
Coordinates from ORCA-job cmmd E -15.814313366050
C 1.254359 -0.087377 0.247155
C 0.330425 -1.225019 -0.181593
C -1.088479 -0.680500 0.046806
C -0.948922 0.851627 0.132567
C 0.506553 1.151472 -0.234149
H 2.251512 -0.173549 -0.182679
H 1.345388 -0.066448 1.334450
H 0.513299 -2.142065 0.376923
H 0.484946 -1.437484 -1.240528
H -1.506574 -1.076197 0.972249
H -1.752594 -0.973990 -0.765485
H -1.148462 1.190193 1.149840
H -1.646034 1.362100 -0.530685
H 0.868686 2.069982 0.225902
H 0.611188 1.244027 -1.316453

@ -0,0 +1,74 @@
#
# Number of atoms
#
15
#
# The current total energy in Eh
#
-15.814313366040
#
# The current gradient in Eh/bohr
#
0.000093445366
-0.000037800737
0.000096275051
-0.000010073323
-0.000088198644
-0.000211507452
-0.000119959751
-0.000072369051
0.000067753667
-0.000096319713
0.000061047473
0.000209392125
-0.000005836629
0.000099601016
-0.000152648923
-0.000025194460
-0.000007170976
-0.000052903955
-0.000025753319
0.000023389775
-0.000004352513
-0.000035015166
0.000041014721
0.000094162535
0.000040652610
0.000035452112
0.000025317956
0.000072635153
-0.000012646097
0.000007408023
0.000031305419
0.000073594694
-0.000046643386
0.000054142600
0.000014078792
-0.000025462090
0.000029656457
-0.000065370350
-0.000093857042
-0.000032119204
-0.000021523008
0.000072705280
0.000028433961
-0.000043099721
0.000014360724
#
# The atomic numbers and current coordinates in Bohr
#
6 2.3703954 -0.1651194 0.4670557
6 0.6244121 -2.3149509 -0.3431616
6 -2.0569278 -1.2859578 0.0884502
6 -1.7932022 1.6093409 0.2505151
6 0.9572467 2.1759662 -0.4424772
1 4.2547410 -0.3279597 -0.3452135
1 2.5424148 -0.1255682 2.5217455
1 0.9699948 -4.0479168 0.7122810
1 0.9164144 -2.7164515 -2.3442578
1 -2.8470130 -2.0337184 1.8372841
1 -3.3119226 -1.8405746 -1.4465563
1 -2.1702788 2.2491381 2.1728818
1 -3.1105539 2.5739965 -1.0028484
1 1.6415786 3.9116989 0.4268932
1 1.1549780 2.3508701 -2.4877364

File diff suppressed because it is too large Load Diff

@ -0,0 +1,13 @@
#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

File diff suppressed because it is too large Load Diff

@ -0,0 +1,78 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -----------------------------------------------------------
$ THERMOCHEMISTRY_Energies
description: The Thermochemistry energies
geom. index: 0
prop. index: 1
Temperature (Kelvin) : 298.1500000000
Pressure (atm) : 1.0000000000
Total Mass (AMU) : 70.1350000000
Spin Degeneracy : 1.0000000000
Electronic Energy (Hartree) : -15.8143133661
Translational Energy (Hartree) : 0.0014162714
Rotational Energy (Hartree) : 0.0014162714
Vibrational Energy (Hartree) : 0.0014286410
Number of frequencies : 45
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 -13.351568
7 252.244123
8 557.175881
9 613.241874
10 803.096513
11 840.536598
12 876.377253
13 954.582365
14 965.585932
15 980.313366
16 1000.249668
17 1030.244023
18 1101.221133
19 1125.950241
20 1163.245212
21 1191.481572
22 1205.003583
23 1219.576673
24 1239.150145
25 1296.431408
26 1307.223911
27 1323.325759
28 1324.021436
29 1324.985289
30 1483.494156
31 1487.616972
32 1497.580040
33 1498.376661
34 1516.087224
35 2971.917990
36 2972.553003
37 2984.877385
38 2986.620750
39 2999.161041
40 3000.307663
41 3005.881613
42 3008.879158
43 3009.438792
44 3012.882898
Zero Point Energy (Hartree) : 0.1392665271
Inner Energy (Hartree) : -15.6707856551
Enthalpy (Hartree) : -15.6698414460
Electronic entropy : 0.0000000000
Rotational entropy : 0.0119173746
Vibrational entropy : 0.0020062037
Translational entropy : 0.0119173746
Entropy : 0.0322924006
Gibbs Energy (Hartree) : -15.7021338467
Is Linear : false
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,10 @@
#!/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

@ -0,0 +1,17 @@
15
C 1.25397 -0.08785 0.23611
C 0.32671 -1.22203 -0.16919
C -1.08204 -0.67511 0.04351
C -0.94615 0.84512 0.12208
C 0.50463 1.15076 -0.22206
H 2.24075 -0.17292 -0.22757
H 1.38462 -0.07387 1.32471
H 0.50883 -2.13310 0.40837
H 0.47301 -1.46275 -1.22929
H -1.51394 -1.06263 0.97282
H -1.74391 -0.97741 -0.77500
H -1.16963 1.18240 1.14140
H -1.64010 1.35558 -0.55310
H 0.86404 2.06064 0.26698
H 0.61450 1.27994 -1.30545

@ -0,0 +1,10 @@
#!/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

@ -0,0 +1,8 @@
#!/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

@ -0,0 +1,74 @@
#
# Number of atoms
#
15
#
# The current total energy in Eh
#
-15.814313366050
#
# The current gradient in Eh/bohr
#
0.000227495798
-0.000049478208
0.000259008811
0.000082454763
-0.000273081820
-0.000428388240
-0.000389851164
-0.000263790724
0.000131258810
-0.000267765264
0.000279977188
0.000405328706
0.000065519654
0.000232417966
-0.000346430104
-0.000091428520
-0.000003594258
-0.000047833688
0.000020375247
0.000036476347
-0.000092535766
-0.000051248393
0.000118951949
0.000073438073
0.000077590295
0.000013581623
0.000136037554
0.000084963869
-0.000004747271
-0.000102722280
0.000081476300
0.000093731217
0.000038224552
0.000050966115
0.000038809074
-0.000147860440
0.000094397666
-0.000112630042
-0.000050618890
-0.000060968602
-0.000087995984
0.000064681824
0.000076022236
-0.000018627056
0.000108411078
#
# The atomic numbers and current coordinates in Bohr
#
6 2.3703954 -0.1651194 0.4670557
6 0.6244121 -2.3149509 -0.3431616
6 -2.0569278 -1.2859578 0.0884502
6 -1.7932022 1.6093409 0.2505151
6 0.9572467 2.1759662 -0.4424772
1 4.2547410 -0.3279597 -0.3452135
1 2.5424148 -0.1255682 2.5217455
1 0.9699948 -4.0479168 0.7122810
1 0.9164144 -2.7164515 -2.3442578
1 -2.8470130 -2.0337184 1.8372841
1 -3.3119226 -1.8405746 -1.4465563
1 -2.1702788 2.2491381 2.1728818
1 -3.1105539 2.5739965 -1.0028484
1 1.6415786 3.9116989 0.4268932
1 1.1549780 2.3508701 -2.4877364

Binary file not shown.

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

File diff suppressed because it is too large Load Diff

File diff suppressed because it is too large Load Diff

@ -0,0 +1,17 @@
15
Coordinates from ORCA-job cmmd
C 1.25435919537090 -0.08737739876512 0.24715524632648
C 0.33042466881332 -1.22501927170804 -0.18159328410705
C -1.08847928950794 -0.68049957284919 0.04680580985473
C -0.94892173529753 0.85162652438004 0.13256689033968
C 0.50655312120543 1.15147170068949 -0.23414885516456
H 2.25151196078735 -0.17354879054452 -0.18267911191086
H 1.34538795520408 -0.06644782326499 1.33445026657908
H 0.51329912580071 -2.14206529372394 0.37692286104836
H 0.48494562341946 -1.43748420682295 -1.24052779233776
H -1.50657437511684 -1.07619744223052 0.97224888296167
H -1.75259393059400 -0.97399011796120 -0.76548462512947
H -1.14846207491294 1.19019262513953 1.14983951261691
H -1.64603424175245 1.36210030835772 -0.53068454217281
H 0.86868596585501 2.06998188715470 0.22590214224166
H 0.61118803072543 1.24402687214901 -1.31645340114607

@ -0,0 +1,6 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,102 @@
15
Coordinates from ORCA-job cmmd E -15.813823527310
C 1.253970 -0.087850 0.236110
C 0.326710 -1.222030 -0.169190
C -1.082040 -0.675110 0.043510
C -0.946150 0.845120 0.122080
C 0.504630 1.150760 -0.222060
H 2.240750 -0.172920 -0.227570
H 1.384620 -0.073870 1.324710
H 0.508830 -2.133100 0.408370
H 0.473010 -1.462750 -1.229290
H -1.513940 -1.062630 0.972820
H -1.743910 -0.977410 -0.775000
H -1.169630 1.182400 1.141400
H -1.640100 1.355580 -0.553100
H 0.864040 2.060640 0.266980
H 0.614500 1.279940 -1.305450
15
Coordinates from ORCA-job cmmd E -15.814241222380
C 1.257123 -0.088091 0.238226
C 0.328826 -1.226976 -0.172935
C -1.088491 -0.679714 0.044787
C -0.950523 0.850465 0.125720
C 0.506368 1.154273 -0.224938
H 2.245041 -0.172991 -0.215333
H 1.379029 -0.071943 1.323172
H 0.512114 -2.137358 0.398053
H 0.479548 -1.461348 -1.229026
H -1.516833 -1.070415 0.969225
H -1.749798 -0.979717 -0.769026
H -1.167689 1.190610 1.140388
H -1.642768 1.360747 -0.544398
H 0.866704 2.064442 0.255169
H 0.616638 1.274786 -1.304765
15
Coordinates from ORCA-job cmmd E -15.814284975000
C 1.256840 -0.087971 0.240929
C 0.329515 -1.227180 -0.176191
C -1.089636 -0.680681 0.045702
C -0.950883 0.851597 0.128554
C 0.506606 1.153997 -0.227959
H 2.247193 -0.173216 -0.204973
H 1.369029 -0.069993 1.325991
H 0.512598 -2.138785 0.390994
H 0.482449 -1.454647 -1.232210
H -1.514223 -1.073592 0.969408
H -1.751405 -0.977871 -0.767095
H -1.162122 1.192254 1.142832
H -1.643824 1.361220 -0.539544
H 0.867356 2.066207 0.245741
H 0.615797 1.265430 -1.307858
15
Coordinates from ORCA-job cmmd E -15.814304882810
C 1.255759 -0.087735 0.244138
C 0.330030 -1.226385 -0.179456
C -1.089550 -0.680907 0.046501
C -0.950251 0.851938 0.131194
C 0.506593 1.152913 -0.231316
H 2.249411 -0.173472 -0.193485
H 1.356785 -0.067973 1.330167
H 0.512793 -2.140292 0.383710
H 0.484505 -1.445960 -1.236559
H -1.510226 -1.075841 0.970688
H -1.752335 -0.975396 -0.766044
H -1.155056 1.192253 1.146436
H -1.644903 1.361314 -0.534953
H 0.867883 2.068121 0.235501
H 0.613852 1.254194 -1.312201
15
Coordinates from ORCA-job cmmd E -15.814311679880
C 1.254764 -0.087506 0.246357
C 0.330312 -1.225457 -0.181258
C -1.088902 -0.680693 0.046834
C -0.949381 0.851790 0.132471
C 0.506536 1.151901 -0.233475
H 2.250907 -0.173582 -0.185613
H 1.348285 -0.066771 1.333273
H 0.513007 -2.141451 0.378820
H 0.485140 -1.439720 -1.239568
H -1.507362 -1.076489 0.971842
H -1.752602 -0.974004 -0.765631
H -1.150114 1.191161 1.149001
H -1.645670 1.361592 -0.531936
H 0.868338 2.069444 0.228533
H 0.612033 1.246555 -1.315330
15
Coordinates from ORCA-job cmmd E -15.814313366050
C 1.254359 -0.087377 0.247155
C 0.330425 -1.225019 -0.181593
C -1.088479 -0.680500 0.046806
C -0.948922 0.851627 0.132567
C 0.506553 1.151472 -0.234149
H 2.251512 -0.173549 -0.182679
H 1.345388 -0.066448 1.334450
H 0.513299 -2.142065 0.376923
H 0.484946 -1.437484 -1.240528
H -1.506574 -1.076197 0.972249
H -1.752594 -0.973990 -0.765485
H -1.148462 1.190193 1.149840
H -1.646034 1.362100 -0.530685
H 0.868686 2.069982 0.225902
H 0.611188 1.244027 -1.316453

@ -0,0 +1,74 @@
#
# Number of atoms
#
15
#
# The current total energy in Eh
#
-15.814313366040
#
# The current gradient in Eh/bohr
#
0.000093445366
-0.000037800737
0.000096275051
-0.000010073323
-0.000088198644
-0.000211507452
-0.000119959751
-0.000072369051
0.000067753667
-0.000096319713
0.000061047473
0.000209392125
-0.000005836629
0.000099601016
-0.000152648923
-0.000025194460
-0.000007170976
-0.000052903955
-0.000025753319
0.000023389775
-0.000004352513
-0.000035015166
0.000041014721
0.000094162535
0.000040652610
0.000035452112
0.000025317956
0.000072635153
-0.000012646097
0.000007408023
0.000031305419
0.000073594694
-0.000046643386
0.000054142600
0.000014078792
-0.000025462090
0.000029656457
-0.000065370350
-0.000093857042
-0.000032119204
-0.000021523008
0.000072705280
0.000028433961
-0.000043099721
0.000014360724
#
# The atomic numbers and current coordinates in Bohr
#
6 2.3703954 -0.1651194 0.4670557
6 0.6244121 -2.3149509 -0.3431616
6 -2.0569278 -1.2859578 0.0884502
6 -1.7932022 1.6093409 0.2505151
6 0.9572467 2.1759662 -0.4424772
1 4.2547410 -0.3279597 -0.3452135
1 2.5424148 -0.1255682 2.5217455
1 0.9699948 -4.0479168 0.7122810
1 0.9164144 -2.7164515 -2.3442578
1 -2.8470130 -2.0337184 1.8372841
1 -3.3119226 -1.8405746 -1.4465563
1 -2.1702788 2.2491381 2.1728818
1 -3.1105539 2.5739965 -1.0028484
1 1.6415786 3.9116989 0.4268932
1 1.1549780 2.3508701 -2.4877364

File diff suppressed because it is too large Load Diff

@ -0,0 +1,13 @@
#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

File diff suppressed because it is too large Load Diff

@ -0,0 +1,78 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -----------------------------------------------------------
$ THERMOCHEMISTRY_Energies
description: The Thermochemistry energies
geom. index: 0
prop. index: 1
Temperature (Kelvin) : 298.1500000000
Pressure (atm) : 1.0000000000
Total Mass (AMU) : 70.1350000000
Spin Degeneracy : 1.0000000000
Electronic Energy (Hartree) : -15.8143133661
Translational Energy (Hartree) : 0.0014162714
Rotational Energy (Hartree) : 0.0014162714
Vibrational Energy (Hartree) : 0.0014286410
Number of frequencies : 45
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 -13.351568
7 252.244123
8 557.175881
9 613.241874
10 803.096513
11 840.536598
12 876.377253
13 954.582365
14 965.585932
15 980.313366
16 1000.249668
17 1030.244023
18 1101.221133
19 1125.950241
20 1163.245212
21 1191.481572
22 1205.003583
23 1219.576673
24 1239.150145
25 1296.431408
26 1307.223911
27 1323.325759
28 1324.021436
29 1324.985289
30 1483.494156
31 1487.616972
32 1497.580040
33 1498.376661
34 1516.087224
35 2971.917990
36 2972.553003
37 2984.877385
38 2986.620750
39 2999.161041
40 3000.307663
41 3005.881613
42 3008.879158
43 3009.438792
44 3012.882898
Zero Point Energy (Hartree) : 0.1392665271
Inner Energy (Hartree) : -15.6707856551
Enthalpy (Hartree) : -15.6698414460
Electronic entropy : 0.0000000000
Rotational entropy : 0.0119173746
Vibrational entropy : 0.0020062037
Translational entropy : 0.0119173746
Entropy : 0.0322924006
Gibbs Energy (Hartree) : -15.7021338467
Is Linear : false
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,10 @@
#!/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

@ -0,0 +1,17 @@
15
C 1.25397 -0.08785 0.23611
C 0.32671 -1.22203 -0.16919
C -1.08204 -0.67511 0.04351
C -0.94615 0.84512 0.12208
C 0.50463 1.15076 -0.22206
H 2.24075 -0.17292 -0.22757
H 1.38462 -0.07387 1.32471
H 0.50883 -2.13310 0.40837
H 0.47301 -1.46275 -1.22929
H -1.51394 -1.06263 0.97282
H -1.74391 -0.97741 -0.77500
H -1.16963 1.18240 1.14140
H -1.64010 1.35558 -0.55310
H 0.86404 2.06064 0.26698
H 0.61450 1.27994 -1.30545

@ -0,0 +1,10 @@
#!/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

@ -0,0 +1,8 @@
#!/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

@ -0,0 +1 @@
1 molecule converted

@ -0,0 +1,34 @@
#
# Number of atoms
#
5
#
# The current total energy in Eh
#
-4.175218519970
#
# The current gradient in Eh/bohr
#
-0.000000733096
-0.000000718518
0.000000020579
0.000099514185
0.000000241014
-0.000000088710
-0.000033024105
-0.000054585621
0.000075974379
-0.000032878360
-0.000038400839
-0.000085447395
-0.000032878624
0.000093463963
0.000009541147
#
# The atomic numbers and current coordinates in Bohr
#
6 1.9735191 0.1551682 0.0678978
1 4.0185060 0.1551840 0.0678980
1 1.2918650 -0.9719763 1.6321424
1 1.2918649 -0.6359402 -1.6903579
1 1.2918469 2.0734103 0.2619089

Binary file not shown.

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

@ -0,0 +1,164 @@
$orca_opt_file
$trust
0.300000000000
$epredict
0.000000000000
$ediffsc
1000.000000000000
$ctyp
3
$coordinates
2 15
1.97351659 0.15516541 0.06789786 4.03747547 0.15518431 0.06789786
1.28554289 -0.98243082 1.64665066 1.28554289 -0.64328167 -1.70666836
1.28552400 2.09120873 0.26371128
1.97351823 0.15516737 0.06789785 4.01878749 0.15518474 0.06789756
1.29177082 -0.97213160 1.63235852 1.29177148 -0.63604970 -1.69060084
1.29175384 2.07367515 0.26193621
# 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
-4.1749622430100004
-4.1752184657600004
$gradients
2 15
-0.0000014989475235 -0.0000029641967182 0.0000005089667544 0.0066853000519982
0.0000002931963416 0.0000000295532466 -0.0022275693320578 -0.0036835039735562
0.0051121489868166 -0.0022278030172314 -0.0025860825632740 -0.0057473124295500
-0.0022284287551855 0.0062722575372068 0.0006346249227325
-0.0000007330957995 -0.0000007185178272 0.0000000205785172 0.0000995141850074
0.0000002410139902 -0.0000000887100310 -0.0000330241046346 -0.0000545856207558
0.0000759743788589 -0.0000328783600969 -0.0000384008386753 -0.0000854473945138
-0.0000328786244764 0.0000934639632680 0.0000095411471688
$redundant_coords
2 10
2.0639588835553018 2.0639509221905303 2.0639551441538115 2.0639623173969524
1.9106311594293877 1.9106371741585475 1.9106267757352700 1.9106336068354863
1.9106372229078048 1.9106334783960390
2.0452692580590215 2.0452676296801728 2.0452678932521779 2.0452690923577119
1.9106318134115725 1.9106361158092082 1.9106289640702252 1.9106335225769691
1.9106350761295567 1.9106339254827431
$redundant_gradients
2 10
0.0066853000544024 0.0066831380271350 0.0066844991834355 0.0066865430418864
-0.0000001900650910 0.0000003075848132 -0.0000006359875241 0.0000000244873687
0.0000006239099189 -0.0000001299358990
0.0000995141870624 0.0000992082093941 0.0000992814911456 0.0000995361271033
-0.0000001785324037 0.0000003366760758 -0.0000005162540254 0.0000000319823672
0.0000002391742728 0.0000000869504141
$hessian_approx
15 15
0 1 2 3 4 5
0 0.839469 0.000003 -0.000001 -0.357191 -0.000002 -0.000000
1 0.000003 0.839472 -0.000001 0.000007 -0.136200 -0.000000
2 -0.000001 -0.000001 0.839479 -0.000000 -0.000000 -0.136201
3 -0.357191 0.000007 -0.000000 0.355993 -0.000001 0.000002
4 -0.000002 -0.136200 -0.000000 -0.000001 0.102150 0.000000
5 -0.000000 -0.000000 -0.136201 0.000002 0.000000 0.102151
6 -0.160760 -0.040607 0.056349 0.000400 -0.037534 0.052091
7 -0.040609 -0.203347 0.093176 0.000662 0.007760 -0.010767
8 0.056356 0.093183 -0.265512 -0.000922 -0.010769 0.014943
9 -0.160759 -0.028501 -0.063337 0.000399 -0.026344 -0.058553
10 -0.028503 -0.169280 -0.073508 0.000466 0.003823 0.008492
11 -0.063345 -0.073516 -0.299575 0.001037 0.008497 0.018877
12 -0.160758 0.069098 0.006989 0.000398 0.063880 0.006460
13 0.069110 -0.330645 -0.019667 -0.001135 0.022467 0.002274
14 0.006990 -0.019666 -0.138190 -0.000116 0.002273 0.000230
6 7 8 9 10 11
0 -0.160760 -0.040609 0.056356 -0.160759 -0.028503 -0.063345
1 -0.040607 -0.203347 0.093183 -0.028501 -0.169280 -0.073516
2 0.056349 0.093176 -0.265512 -0.063337 -0.073508 -0.299575
3 0.000400 0.000662 -0.000922 0.000399 0.000466 0.001037
4 -0.037534 0.007760 -0.010769 -0.026344 0.003823 0.008497
5 0.052091 -0.010767 0.014943 -0.058553 0.008492 0.018877
6 0.130357 0.046640 -0.064725 0.015001 0.023004 -0.016631
7 0.046640 0.179273 -0.107026 0.019209 0.029476 -0.021478
8 -0.064725 -0.107026 0.250680 0.020899 0.031871 -0.021372
9 0.015001 0.019209 0.020899 0.130357 0.032735 0.072753
10 0.023004 0.029476 0.031871 0.032735 0.140141 0.084433
11 -0.016631 -0.021478 -0.021372 0.072753 0.084433 0.289806
12 0.015001 -0.025903 -0.011608 0.015001 -0.027703 0.006186
13 0.008497 -0.013161 -0.007258 0.002901 -0.004160 0.002064
14 -0.027085 0.046095 0.021261 0.028237 -0.051289 0.012265
12 13 14
0 -0.160758 0.069110 0.006990
1 0.069098 -0.330645 -0.019666
2 0.006989 -0.019667 -0.138190
3 0.000398 -0.001135 -0.000116
4 0.063880 0.022467 0.002273
5 0.006460 0.002274 0.000230
6 0.015001 0.008497 -0.027085
7 -0.025903 -0.013161 0.046095
8 -0.011608 -0.007258 0.021261
9 0.015001 0.002901 0.028237
10 -0.027703 -0.004160 -0.051289
11 0.006186 0.002064 0.012265
12 0.130357 -0.079374 -0.008028
13 -0.079374 0.325498 0.022588
14 -0.008028 0.022588 0.104435
$bmatrix
10 15
0 1 2 3 4 5
0 -1.000000 -0.000008 0.000000 1.000000 0.000008 -0.000000
1 0.333329 0.551174 -0.764917 0.000000 0.000000 0.000000
2 0.333329 0.386853 0.859789 0.000000 0.000000 0.000000
3 0.333337 -0.938022 -0.094872 0.000000 0.000000 0.000000
4 0.460973 -0.267485 -0.594505 -0.000002 0.200617 0.445879
5 -0.460966 -0.648607 -0.065600 0.000000 0.000000 0.000000
6 0.460966 0.648604 0.065599 0.000004 -0.486451 -0.049200
7 -0.460971 0.267489 0.594507 0.000000 0.000000 0.000000
8 -0.460971 0.381111 -0.528908 0.000000 0.000000 0.000000
9 0.460974 -0.381107 0.528907 -0.000002 0.285833 -0.396680
6 7 8 9 10 11
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1 -0.333329 -0.551174 0.764917 0.000000 0.000000 0.000000
2 0.000000 0.000000 0.000000 -0.333329 -0.386853 -0.859789
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 0.000000 0.000000 0.000000 -0.460972 0.066868 0.148626
5 0.230483 0.295898 0.313652 0.230483 0.352709 -0.248053
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
7 0.230487 -0.391173 -0.181427 0.000000 0.000000 0.000000
8 0.000000 0.000000 0.000000 0.230487 -0.419578 0.099428
9 -0.460972 0.095274 -0.132227 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 -0.333337 0.938022 0.094872
4 0.000000 0.000000 0.000000
5 0.000000 0.000000 0.000000
6 -0.460970 -0.162152 -0.016400
7 0.230484 0.123684 -0.413080
8 0.230484 0.038468 0.429480
9 0.000000 0.000000 0.000000

File diff suppressed because it is too large Load Diff

@ -0,0 +1,7 @@
5
Coordinates from ORCA-job cmmd
C 1.04434135305002 0.08211146154040 0.03592999467599
H 2.12650178753787 0.08211981567066 0.03593006450254
H 0.68362549970396 -0.51434769249601 0.86369257686113
H 0.68362543813495 -0.33652506555091 -0.89449887927247
H 0.68361592157322 1.09720148083585 0.13859624323281

@ -0,0 +1,6 @@
-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,21 @@
5
Coordinates from ORCA-job cmmd E -4.174962243010
C 1.044340 0.082110 0.035930
H 2.136540 0.082120 0.035930
H 0.680280 -0.519880 0.871370
H 0.680280 -0.340410 -0.903130
H 0.680270 1.106620 0.139550
5
Coordinates from ORCA-job cmmd E -4.175218465760
C 1.044341 0.082111 0.035930
H 2.126651 0.082120 0.035930
H 0.683576 -0.514430 0.863807
H 0.683576 -0.336583 -0.894627
H 0.683567 1.097342 0.138611
5
Coordinates from ORCA-job cmmd E -4.175218519970
C 1.044341 0.082111 0.035930
H 2.126502 0.082120 0.035930
H 0.683625 -0.514348 0.863693
H 0.683625 -0.336525 -0.894499
H 0.683616 1.097201 0.138596

@ -0,0 +1,34 @@
#
# Number of atoms
#
5
#
# The current total energy in Eh
#
-4.175218519980
#
# The current gradient in Eh/bohr
#
-0.000000408709
-0.000000341181
-0.000000003239
-0.000003240340
0.000000142461
-0.000000050001
0.000001145952
0.000001906967
-0.000002511868
0.000001237903
0.000001306725
0.000002824023
0.000001265194
-0.000003014973
-0.000000258915
#
# The atomic numbers and current coordinates in Bohr
#
6 1.9735191 0.1551682 0.0678978
1 4.0185060 0.1551840 0.0678980
1 1.2918650 -0.9719763 1.6321424
1 1.2918649 -0.6359402 -1.6903579
1 1.2918469 2.0734103 0.2619089

@ -0,0 +1,192 @@
$orca_hessian_file
$act_atom
0
$act_coord
0
$act_energy
-4.175219
$hessian
15
0 1 2 3 4
0 5.1329012148E-01 -2.6663567559E-06 8.3835566296E-07 -2.9809731316E-01 -1.9784696379E-06
1 -2.6663567559E-06 5.1328712912E-01 -2.6497366205E-08 -1.9726025329E-06 -4.3442777277E-02
2 8.3835566296E-07 -2.6497366205E-08 5.1328935767E-01 -1.7634020912E-08 7.2276242091E-09
3 -2.9809731316E-01 -1.9726025329E-06 -1.7634020912E-08 3.4272680101E-01 2.0211245618E-06
4 -1.9784696379E-06 -4.3442777277E-02 7.2276242091E-09 2.0211245618E-06 4.6441179291E-02
5 -1.7116830436E-08 7.2320836845E-09 -4.3442884873E-02 1.0454268310E-07 1.5596984091E-08
6 -7.1733742694E-02 -4.6783019481E-02 6.4926425576E-02 -1.4874469674E-02 -1.9611323313E-02
7 -4.6782960343E-02 -1.2079849231E-01 1.0735996309E-01 -1.3733460307E-03 -6.2451045673E-04
8 6.4926271962E-02 1.0735982095E-01 -1.9243359408E-01 1.9056658411E-03 1.1233724602E-03
9 -7.1733749665E-02 -3.2835255893E-02 -7.2979874524E-02 -1.4874557137E-02 -1.3764589681E-02
10 -3.2835212863E-02 -8.1549006178E-02 -8.4698552890E-02 -9.6399521602E-04 -2.1374725375E-04
11 -7.2979703320E-02 -8.4698425775E-02 -2.3168748610E-01 -2.1420126424E-03 -8.8624128993E-04
12 -7.1735221884E-02 7.9622913833E-02 8.0526283576E-03 -1.4874988941E-02 3.3375870456E-02
13 7.9622824479E-02 -2.6750649802E-01 -2.2661386241E-02 2.3368513654E-03 -2.1595522467E-03
14 8.0526082358E-03 -2.2661370610E-02 -4.5734620980E-02 2.3640040325E-04 -2.3715469799E-04
5 6 7 8 9
0 -1.7116830436E-08 -7.1733742694E-02 -4.6782960343E-02 6.4926271962E-02 -7.1733749665E-02
1 7.2320836845E-09 -4.6783019481E-02 -1.2079849231E-01 1.0735982095E-01 -3.2835255893E-02
2 -4.3442884873E-02 6.4926425576E-02 1.0735996309E-01 -1.9243359408E-01 -7.2979874524E-02
3 1.0454268310E-07 -1.4874469674E-02 -1.3733460307E-03 1.9056658411E-03 -1.4874557137E-02
4 1.5596984091E-08 -1.9611323313E-02 -6.2451045673E-04 1.1233724602E-03 -1.3764589681E-02
5 4.6441174206E-02 2.7216470791E-02 1.1236342607E-03 -1.3739986007E-03 -3.0592163721E-02
6 2.7216470791E-02 7.9358012224E-02 5.4431671651E-02 -7.5541061727E-02 3.6257810679E-03
7 1.1236342607E-03 5.4431671651E-02 1.3644442522E-01 -1.2491155865E-01 3.9350425729E-03
8 -1.3739986007E-03 -7.5541061727E-02 -1.2491155865E-01 2.1979006093E-01 9.4495234104E-03
9 -3.0592163721E-02 3.6257810679E-03 3.9350425729E-03 9.4495234104E-03 7.9358100288E-02
10 -8.8657495192E-04 5.7474554883E-03 6.7159136625E-03 1.6203333770E-02 3.8203656742E-02
11 -1.7848534176E-03 -8.4702978109E-03 -9.2690123799E-03 -2.7214652258E-02 8.4911071790E-02
12 3.3756054802E-03 3.6258970273E-03 -1.0209047413E-02 -7.4228743024E-04 3.6259033802E-03
13 -2.3708276366E-04 6.2163065628E-03 -2.1734810904E-02 2.2247745899E-04 4.4619543959E-03
14 1.6113030257E-04 -8.1328347074E-03 2.5694815653E-02 1.2359268027E-03 9.2128031272E-03
10 11 12 13 14
0 -3.2835212863E-02 -7.2979703320E-02 -7.1735221884E-02 7.9622824479E-02 8.0526082358E-03
1 -8.1549006178E-02 -8.4698425775E-02 7.9622913833E-02 -2.6750649802E-01 -2.2661370610E-02
2 -8.4698552890E-02 -2.3168748610E-01 8.0526283576E-03 -2.2661386241E-02 -4.5734620980E-02
3 -9.6399521602E-04 -2.1420126424E-03 -1.4874988941E-02 2.3368513654E-03 2.3640040325E-04
4 -2.1374725375E-04 -8.8624128993E-04 3.3375870456E-02 -2.1595522467E-03 -2.3715469799E-04
5 -8.8657495192E-04 -1.7848534176E-03 3.3756054802E-03 -2.3708276366E-04 1.6113030257E-04
6 5.7474554883E-03 -8.4702978109E-03 3.6258970273E-03 6.2163065628E-03 -8.1328347074E-03
7 6.7159136625E-03 -9.2690123799E-03 -1.0209047413E-02 -2.1734810904E-02 2.5694815653E-02
8 1.6203333770E-02 -2.7214652258E-02 -7.4228743024E-04 2.2247745899E-04 1.2359268027E-03
9 3.8203656742E-02 8.4911071790E-02 3.6259033802E-03 4.4619543959E-03 9.2128031272E-03
10 9.0777856163E-02 9.8545399446E-02 -1.0150949331E-02 -1.5729415534E-02 -2.9162035420E-02
11 9.8545399446E-02 2.6546069193E-01 -1.3169360375E-03 -3.6895800365E-03 -4.7694116180E-03
12 -1.0150949331E-02 -1.3169360375E-03 7.9359888349E-02 -9.2640251677E-02 -9.3692112021E-03
13 -1.5729415534E-02 -3.6895800365E-03 -9.2640251677E-02 3.0713520326E-01 2.6366155060E-02
14 -2.9162035420E-02 -4.7694116180E-03 -9.3692112021E-03 2.6366155060E-02 4.9107604906E-02
$vibrational_frequencies
15
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 1385.801243
7 1385.807833
8 1385.817738
9 1557.267071
10 1557.277517
11 3090.006354
12 3103.916950
13 3103.935349
14 3103.957551
$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 9.6797657942E-02 8.2365346046E-02 -2.1255744557E-02 1.3565503999E-06
1 0.0000000000E+00 8.4411040010E-02 -8.9025947952E-02 3.9430470446E-02 8.4463207128E-06
2 0.0000000000E+00 1.0518163403E-02 -4.3542418206E-02 -1.2082603904E-01 2.5431002121E-06
3 0.0000000000E+00 4.5039867057E-02 3.8319275010E-02 -9.8888064412E-03 4.0940917893E-06
4 0.0000000000E+00 -3.9678163781E-01 4.1848772921E-01 -1.8536275006E-01 -4.7936966115E-01
5 0.0000000000E+00 -4.9439500527E-02 2.0468256538E-01 5.6800147233E-01 -1.4229946023E-01
6 0.0000000000E+00 -3.3323101216E-01 -3.6705927428E-01 2.8430357692E-01 1.5535215297E-01
7 0.0000000000E+00 -1.9539178912E-01 4.5182775143E-01 1.1952435584E-01 3.5085591294E-01
8 0.0000000000E+00 -3.2903426800E-01 1.5850581178E-01 1.4488860669E-01 3.2050854553E-01
9 0.0000000000E+00 -3.2769383579E-01 -4.6367987556E-01 -6.4905337996E-02 3.0776788299E-01
10 0.0000000000E+00 -2.4901821935E-01 3.2974389776E-01 -3.7666601478E-01 3.0071279184E-01
11 0.0000000000E+00 2.7910711546E-01 7.3591678003E-03 1.4284036761E-01 -2.5461243337E-01
12 0.0000000000E+00 -5.3752441350E-01 -1.8901878724E-01 4.3767103099E-02 -4.6314029427E-01
13 0.0000000000E+00 -1.6462283940E-01 -1.3925515138E-01 -2.7336246289E-02 -1.7229968725E-01
14 0.0000000000E+00 -2.5964359463E-02 1.4828974182E-01 5.8399331822E-01 7.6373045314E-02
10 11 12 13 14
0 -7.9127379703E-07 9.7553325878E-05 -9.3441729587E-03 2.0992456319E-02 -8.4210637714E-02
1 -2.6770649591E-07 6.5147540638E-05 -3.0512090500E-02 7.8495911765E-02 2.2953731977E-02
2 1.0298204828E-06 -2.1731165731E-05 8.1248104559E-02 3.1893066657E-02 -1.0650293390E-03
3 -1.2447062918E-06 4.9903254676E-01 9.2484178440E-02 -2.0748948882E-01 8.3094350740E-01
4 1.4228805621E-01 3.4317001329E-05 -1.4110337985E-02 3.6300337934E-02 1.0620974834E-02
5 -4.7933265552E-01 -1.0101399734E-05 3.7574805097E-02 1.4749333888E-02 -4.9217932073E-04
6 -4.4506967419E-01 -1.6691136091E-01 2.7803414614E-01 -7.9154449480E-02 1.1150877196E-02
7 2.2567287332E-01 -2.7604255955E-01 4.5277635485E-01 -1.1063369599E-01 9.3455982976E-02
8 -3.1334047752E-02 3.8312432019E-01 -6.1036905838E-01 2.1867547957E-01 -1.1545783368E-01
9 3.5708300928E-01 -1.6675280959E-01 -1.9349240750E-01 -2.1308515106E-01 3.0085401986E-02
10 -3.4948440847E-01 -1.9355090358E-01 -2.3365818721E-01 -2.2226371481E-01 9.0732549420E-02
11 1.8809950526E-02 -4.3025387674E-01 -4.5037152473E-01 -5.5992947067E-01 1.7757149370E-01
12 8.7997338176E-02 -1.6653078994E-01 -6.5683792677E-02 2.4958981073E-01 1.3124677054E-01
13 -1.8473331162E-02 4.6878286924E-01 1.5856431221E-01 -6.3873466941E-01 -4.6831870839E-01
14 4.9184448174E-01 4.7398599447E-02 5.5039801961E-02 -5.3522747167E-02 -4.8930937645E-02
#
# The atoms: label mass x y z (in bohrs)
#
$atoms
5
C 12.01100 1.973519147593 0.155168174767 0.067897849931
H 1.00800 4.018506001741 0.155183961786 0.067897981884
H 1.00800 1.291864972606 -0.971976276432 1.632142434168
H 1.00800 1.291864856257 -0.635940211091 -1.690357908924
H 1.00800 1.291846872562 2.073410312513 0.261908942900
$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 0.00018877 0.95396870 -0.001721 0.006289 0.000000
1385.81 0.00013518 0.68316648 -0.001464 0.005320 0.000000
1385.82 0.00000548 0.02767528 0.000378 0.001044 0.000000
1557.27 0.00022726 1.14847005 -0.000000 0.006748 0.000000
1557.28 0.00000261 0.01320204 0.000000 0.000724 0.000000
3090.01 0.00358864 18.13550971 -0.013875 -0.013034 0.000000
3103.92 0.00023814 1.20345796 -0.002465 -0.004227 0.000000
3103.94 0.00318759 16.10877850 0.005531 0.017026 0.000000
3103.96 0.00642976 32.49334901 -0.022149 0.012483 0.000000
$end

@ -0,0 +1,13 @@
#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

@ -0,0 +1,711 @@
*****************
* 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 2022/07/22 at 20:01:44.804
-------------------------------------------------
| 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 : 0.28638523637135
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 -0.109869E-09 0.432E-06 17.35 10344.8 T
*** convergence criteria satisfied after 7 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.5818361 -15.8326
2 2.0000 -0.4674581 -12.7202
3 2.0000 -0.4674581 -12.7202
4 2.0000 -0.4674579 -12.7202 (HOMO)
5 0.1702647 4.6331 (LUMO)
6 0.2292564 6.2384
7 0.2292575 6.2384
8 0.2292580 6.2384
-------------------------------------------------------------
HL-Gap 0.6377226 Eh 17.3533 eV
Fermi-level -0.1485966 Eh -4.0435 eV
SCC (total) 0 d, 0 h, 0 min, 0.021 sec
SCC setup ... 0 min, 0.000 sec ( 0.604%)
Dispersion ... 0 min, 0.000 sec ( 0.142%)
classical contributions ... 0 min, 0.000 sec ( 0.098%)
integral evaluation ... 0 min, 0.000 sec ( 0.910%)
iterations ... 0 min, 0.020 sec ( 95.478%)
molecular gradient ... 0 min, 0.000 sec ( 1.911%)
printout ... 0 min, 0.000 sec ( 0.795%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -4.175218519976 Eh ::
:: gradient norm 0.000006636122 Eh/a0 ::
:: HOMO-LUMO gap 17.353314919929 eV ::
::.................................................::
:: SCC energy -4.247467308451 Eh ::
:: -> isotropic ES 0.002035567940 Eh ::
:: -> anisotropic ES 0.002321540923 Eh ::
:: -> anisotropic XC 0.003585096725 Eh ::
:: -> dispersion -0.000661011606 Eh ::
:: repulsion energy 0.072248782884 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -4.175218519976 Eh |
| GRADIENT NORM 0.000006636122 Eh/α |
| HOMO-LUMO GAP 17.353314919929 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/07/22 at 20:01:44.835
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.032 sec
* cpu-time: 0 d, 0 h, 0 min, 0.014 sec
* ratio c/w: 0.452 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.021 sec
* cpu-time: 0 d, 0 h, 0 min, 0.004 sec
* ratio c/w: 0.185 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -4.175218519980
------------------------- --------------------
----------------------------------------------------------------------------
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 0.096798 0.082365 -0.021256 0.000001 -0.000001 0.000098
1 0.084411 -0.089026 0.039430 0.000008 -0.000000 0.000065
2 0.010518 -0.043542 -0.120826 0.000003 0.000001 -0.000022
3 0.045040 0.038319 -0.009889 0.000004 -0.000001 0.499033
4 -0.396782 0.418488 -0.185363 -0.479370 0.142288 0.000034
5 -0.049440 0.204683 0.568001 -0.142299 -0.479333 -0.000010
6 -0.333231 -0.367059 0.284304 0.155352 -0.445070 -0.166911
7 -0.195392 0.451828 0.119524 0.350856 0.225673 -0.276043
8 -0.329034 0.158506 0.144889 0.320509 -0.031334 0.383124
9 -0.327694 -0.463680 -0.064905 0.307768 0.357083 -0.166753
10 -0.249018 0.329744 -0.376666 0.300713 -0.349484 -0.193551
11 0.279107 0.007359 0.142840 -0.254612 0.018810 -0.430254
12 -0.537524 -0.189019 0.043767 -0.463140 0.087997 -0.166531
13 -0.164623 -0.139255 -0.027336 -0.172300 -0.018473 0.468783
14 -0.025964 0.148290 0.583993 0.076373 0.491844 0.047399
12 13 14
0 -0.009344 0.020992 -0.084211
1 -0.030512 0.078496 0.022954
2 0.081248 0.031893 -0.001065
3 0.092484 -0.207489 0.830944
4 -0.014110 0.036300 0.010621
5 0.037575 0.014749 -0.000492
6 0.278034 -0.079154 0.011151
7 0.452776 -0.110634 0.093456
8 -0.610369 0.218675 -0.115458
9 -0.193492 -0.213085 0.030085
10 -0.233658 -0.222264 0.090733
11 -0.450372 -0.559929 0.177571
12 -0.065684 0.249590 0.131247
13 0.158564 -0.638735 -0.468319
14 0.055040 -0.053523 -0.048931
-----------
IR SPECTRUM
-----------
Mode freq eps Int T**2 TX TY TZ
cm**-1 L/(mol*cm) km/mol a.u.
----------------------------------------------------------------------------
6: 1385.80 0.000189 0.95 0.000043 (-0.001721 0.006289 0.000000)
7: 1385.81 0.000135 0.68 0.000030 (-0.001464 0.005320 0.000000)
8: 1385.82 0.000005 0.03 0.000001 ( 0.000378 0.001044 0.000000)
9: 1557.27 0.000227 1.15 0.000046 (-0.000000 0.006748 0.000000)
10: 1557.28 0.000003 0.01 0.000001 ( 0.000000 0.000724 0.000000)
11: 3090.01 0.003589 18.14 0.000362 (-0.013875 -0.013034 0.000000)
12: 3103.92 0.000238 1.20 0.000024 (-0.002465 -0.004227 0.000000)
13: 3103.94 0.003188 16.11 0.000320 ( 0.005531 0.017026 0.000000)
14: 3103.96 0.006430 32.49 0.000646 (-0.022149 0.012483 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: 5.355312 5.355310 5.355304
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 ... 51.025 sec (= 0.850 min)
Numerical frequency calculation ... 50.947 sec (= 0.849 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 56 msec

@ -0,0 +1,48 @@
-------------------------------------------------------------
----------------------- !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 1385.801243
7 1385.807833
8 1385.817738
9 1557.267071
10 1557.277517
11 3090.006354
12 3103.916950
13 3103.935349
14 3103.957551
Zero Point Energy (Hartree) : 0.0448201861
Inner Energy (Hartree) : -4.1275343905
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) : -4.1476937451
Is Linear : false
# -------------------------------------------------------------
----------------------- !GEOMETRIES! ------------------------
# -------------------------------------------------------------

@ -0,0 +1,13 @@
#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

@ -0,0 +1,142 @@
*****************
* 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
***************************************

@ -0,0 +1,10 @@
#!/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

@ -0,0 +1,7 @@
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!! FATAL ERROR ENCOUNTERED !!!
!!! ----------------------- !!!
!!! CANNOT OPEN FILE !!!
!!! Filename: ../cmmd.xyz !!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@ -0,0 +1,10 @@
#!/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

@ -0,0 +1,7 @@
5
C 1.04434 0.08211 0.03593
H 2.13654 0.08212 0.03593
H 0.68028 -0.51988 0.87137
H 0.68028 -0.34041 -0.90313
H 0.68027 1.10662 0.13955

@ -0,0 +1,10 @@
#!/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

@ -0,0 +1,8 @@
#!/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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