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cmmde-gui modification

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Aditya Wibawa Sakti 3 years ago
parent 05684f9cf6
commit 29116e3053
724 changed files with 1473935 additions and 45274 deletions
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  1. 2
      bin/cmmdepre.py
  2. 64
      cmmde_gui/gui.py
  3. 34
      cmmde_gui/test/ala/cmmd.engrad
  4. BIN
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  5. 164
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  8. 7
      cmmde_gui/test/ala/cmmd.xyz
  9. 21
      cmmde_gui/test/ala/cmmd_trj.xyz
  10. 34
      cmmde_gui/test/ala/freq/cmmd.engrad
  11. 192
      cmmde_gui/test/ala/freq/cmmd.hess
  12. BIN
      cmmde_gui/test/ala/freq/cmmd.xtbrestart
  13. 48
      cmmde_gui/test/ala/freq/cmmd_property.txt
  14. 1
      cmmde_gui/test/ala/geom.smi
  15. 7
      cmmde_gui/test/ala/geom.xyz
  16. 0
      cmmde_gui/test/ala/slurm-2914.out
  17. 74
      cmmde_gui/test/alala/alala/cmmd.engrad
  18. BIN
      cmmde_gui/test/alala/alala/cmmd.gbw
  19. 11
      cmmde_gui/test/alala/alala/cmmd.in
  20. 1566
      cmmde_gui/test/alala/alala/cmmd.opt
  21. 2742
      cmmde_gui/test/alala/alala/cmmd.out
  22. BIN
      cmmde_gui/test/alala/alala/cmmd.xtbrestart
  23. 17
      cmmde_gui/test/alala/alala/cmmd.xyz
  24. 102
      cmmde_gui/test/alala/alala/cmmd_trj.xyz
  25. 74
      cmmde_gui/test/alala/alala/freq/cmmd.engrad
  26. 1024
      cmmde_gui/test/alala/alala/freq/cmmd.hess
  27. 13
      cmmde_gui/test/alala/alala/freq/cmmd.in
  28. 1193
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  30. 78
      cmmde_gui/test/alala/alala/freq/cmmd_property.txt
  31. 10
      cmmde_gui/test/alala/alala/freq/run.sh
  32. 0
      cmmde_gui/test/alala/alala/freq/slurm-2890.out
  33. 1
      cmmde_gui/test/alala/alala/geom.smi
  34. 17
      cmmde_gui/test/alala/alala/geom.xyz
  35. 10
      cmmde_gui/test/alala/alala/run.sh
  36. 8
      cmmde_gui/test/alala/alala/run_babel.sh
  37. 1
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  38. 0
      cmmde_gui/test/alala/alala/slurm-2888.out
  39. 74
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  40. 11
      cmmde_gui/test/alala/cmmd.in
  41. 1566
      cmmde_gui/test/alala/cmmd.opt
  42. 2742
      cmmde_gui/test/alala/cmmd.out
  43. BIN
      cmmde_gui/test/alala/cmmd.xtbrestart
  44. 17
      cmmde_gui/test/alala/cmmd.xyz
  45. 102
      cmmde_gui/test/alala/cmmd_trj.xyz
  46. 74
      cmmde_gui/test/alala/freq/cmmd.engrad
  47. 1024
      cmmde_gui/test/alala/freq/cmmd.hess
  48. 13
      cmmde_gui/test/alala/freq/cmmd.in
  49. 1193
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  50. BIN
      cmmde_gui/test/alala/freq/cmmd.xtbrestart
  51. 78
      cmmde_gui/test/alala/freq/cmmd_property.txt
  52. 10
      cmmde_gui/test/alala/freq/run.sh
  53. 0
      cmmde_gui/test/alala/freq/slurm-2889.out
  54. 1
      cmmde_gui/test/alala/geom.smi
  55. 17
      cmmde_gui/test/alala/geom.xyz
  56. 10
      cmmde_gui/test/alala/run.sh
  57. 8
      cmmde_gui/test/alala/run_babel.sh
  58. 1
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  59. 0
      cmmde_gui/test/alala/slurm-2886.out
  60. 62
      cmmde_gui/test/cmmd.engrad
  61. BIN
      cmmde_gui/test/cmmd.gbw
  62. 8
      cmmde_gui/test/cmmd.in
  63. 789
      cmmde_gui/test/cmmd.opt
  64. 1709
      cmmde_gui/test/cmmd.out
  65. BIN
      cmmde_gui/test/cmmd.xtbrestart
  66. 14
      cmmde_gui/test/cmmd.xyz
  67. 56
      cmmde_gui/test/cmmd_trj.xyz
  68. 1
      cmmde_gui/test/geom.smi
  69. 14
      cmmde_gui/test/geom.xyz
  70. 298
      cmmde_gui/test/grafena/cmmd.engrad
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  72. 0
      cmmde_gui/test/grafena/cmmd.in
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  74. 68247
      cmmde_gui/test/grafena/cmmd.out
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  76. 73
      cmmde_gui/test/grafena/cmmd.xyz
  77. 0
      cmmde_gui/test/grafena/cmmd_property.txt
  78. 5037
      cmmde_gui/test/grafena/cmmd_trj.xyz
  79. 71
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  81. 298
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  86. 1
      cmmde_gui/test/grafena/freq/cmmd.hostnames
  87. 2
      cmmde_gui/test/grafena/freq/cmmd.in
  88. 223
      cmmde_gui/test/grafena/freq/cmmd.lastscf
  89. 1362698
      cmmde_gui/test/grafena/freq/cmmd.maininp.tmp
  90. 7
      cmmde_gui/test/grafena/freq/cmmd.numcalcinp.tmp
  91. 527
      cmmde_gui/test/grafena/freq/cmmd.out
  92. 2
      cmmde_gui/test/grafena/freq/cmmd.xtberr
  93. BIN
      cmmde_gui/test/grafena/freq/cmmd.xtbrestart
  94. 160
      cmmde_gui/test/grafena/freq/cmmd.xtbtopo.mol
  95. BIN
      cmmde_gui/test/grafena/freq/cmmd_D00000.gbw
  96. 1
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  97. BIN
      cmmde_gui/test/grafena/freq/cmmd_D00000.res.Dipoles
  98. BIN
      cmmde_gui/test/grafena/freq/cmmd_D00000.res.Gradients
  99. BIN
      cmmde_gui/test/grafena/freq/cmmd_D00000.xtbrestart
  100. 0
      cmmde_gui/test/grafena/freq/cmmd_D00000_property.txt
  101. Some files were not shown because too many files have changed in this diff Show More

2
bin/cmmdepre.py
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@ -21,7 +21,7 @@ import warnings
warnings.filterwarnings("ignore")
parser = argparse.ArgumentParser(description='CMMDEPRE: Program untuk modifikasi input file')
parser.add_argument('-i','--input', type=str, default='',help='Input geometri dalam berbagai format. Format yang didukung: .smi, .mol2, dan semua format yang didukung oleh openbabel.')
parser.add_argument('-i','--input', type=str, default='None',help='Input geometri dalam berbagai format. Format yang didukung: .smi, .mol2, dan semua format yang didukung oleh openbabel.')
parser.add_argument('-j','--job', type=str, default='sp',help='Jenis pekerjaan yang dilakukan.')
parser.add_argument('-s','--size',type=str,help='Ukuran supersel yang ingin dibuat.')
parser.add_argument('-hkl','--hkl',type=str,help='Indeks Miller (hkl) permukaan yang akan dibuat.')

64
cmmde_gui/gui.py
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@ -11,6 +11,7 @@ from panel_chemistry.pane import NGLViewer
from panel_chemistry.pane.ngl_viewer import EXTENSIONS
import py3Dmol
from panel_chemistry.pane import Py3DMol
import subprocess
# from iodata import IOData
@ -27,22 +28,20 @@ def cmmde_gui():
# Terminal widget
terminal = pn.widgets.Terminal(
"Computational Molecular and Material Design Environment\n Authors:\n Universitas Pertamina\n Institut Teknologi Sumatera\n Masyarakat Komputasi Indonesia\n\n",
options = {"cursorBlink": True},
height = 200, sizing_mode = 'stretch_width'
TextArea= pn.widgets.TextAreaInput(value = "Computational Molecular and Material Design Environment\n Authors:\n Universitas Pertamina\n Institut Teknologi Sumatera\n Masyarakat Komputasi Indonesia\n\n",
height = 500
)
# CMMDE software options
software_btn = pn.widgets.MultiSelect(name="Software selections",value=['Orca'],options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso'])
software_btn = pn.widgets.Select(name="Software selections",value='Orca',options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso'])
software = {'Orca':'orca','GROMACS':'gromacs','Dcdftbmd':'dcdftb','Quantum Espresso':'qe'}
# CMMDE job options
job_btn = pn.widgets.MultiChoice(name="Job selections",value=['Single point calculation'],options=['Single point calculation','Geometry optimization','Frequency calculation','Molecular dynamics','Metadynamics'])
job_btn = pn.widgets.MultiSelect(name="Job selections",value=['Single point calculation'],options=['Single point calculation','Geometry optimization','Frequency calculation','Molecular dynamics','Metadynamics'])
job = {'Single point calculation':'sp','Geometry optimization':'opt','Frequency calculation':'freq','Molecular dynamics':'md','Metadynamics':'mtd'}
# CMMDE method options
method_btn = pn.widgets.MultiChoice(name="Method selections",value=['GFN2-xTB'],options=['GFN2-xTB','GFN1-xTB','DFTB2','DFTB2-gammah','DFTB3','DFTB3-diag'])
method_btn = pn.widgets.Select(name="Method selections",value='GFN2-xTB',options=['GFN2-xTB','GFN1-xTB','DFTB2','DFTB2-gammah','DFTB3','DFTB3-diag'])
method = {'GFN2-xTB':'XTB2', 'GFN1-xTB':'XTB1','DFTB2':'DFTB2','DFTB2-gammah':'DFTB2_gammah','DFTB3':'DFTB3','DFTB3-diag':'DFTB3-diag'}
# Name your molecule/Materialmaterial
@ -50,34 +49,58 @@ def cmmde_gui():
# CMMDE running button
Run_btn = pn.widgets.Button(name="Run CMMDE!",button_type='primary')
# RunMessage = pn.widgets.StaticText()
def run(event):
# RunMessage.value = " "
# terminal.clear()
os.makedirs(Name_input.value)
os.chdir(Name_input.value)
terminal.subprocess.run("cmmde.py","-i{}".format(editor.value),"-s{}".format(software[software_btn.value[0]]), "-j{}".format(job[job_btn.value[0]]), "-m{}".format(method[method_btn.value[0]]))
job_list = [job[i] for i in job_btn.value]
jobs = ",".join(job_list)
cmd = subprocess.run(["cmmde.py","-i","{}".format(editor.value),"-s","{}".format(software[software_btn.value]),"-j","{}".format(jobs),"-m","{}".format(method[method_btn.value])],capture_output=True,text=True)
#terminal.subprocess.run("cmmde.py","-i{}".format(editor.value),"-s{}".format(software[software_btn.value]), "-j{}".format(jobs), "-m{}".format(method[method_btn.value]))
TextArea.value = TextArea.value + "\n" + cmd.stdout
# RunMessage.value = "Perhitungan telah tersubmit!"
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 calculation':'thermo'}
post_btn = pn.widgets.Select(name="Job Selection",value='Frequency calculation', options=['Frequency calculation','Radial distribution function', 'Mean Square Displacement','Time-dependent calculation','Thermochemistry calculation'])
# 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_btn = pn.widgets.Select(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_btn = pn.widgets.Select(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):
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]]))
# terminal.clear()
if post_calc[post_btn.value] == 'thermo' and post_software[post_software_btn.value] == 'orca':
cmd = subprocess.run(["cmmdepost.py","-j","{}".format(post_calc[post_btn.value]),"-s","{}".format(post_software[post_software_btn.value])],capture_output=True,text=True)
TextArea.value = TextArea.value + "\n" + cmd.stdout
# terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value]),"-s{}".format(post_software[post_software_btn.value]))
else:
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]]))
os.makedirs(post_calc[post_btn.value])
os.chdir(post_calc[post_btn.value])
cmd = subprocess.run(["cmmde.py","-i","{}".format("../cmmd.xyz"),"-s","{}".format(post_software[post_software_btn.value]),"-j","{}".format(post_calc[post_btn.value]),"-m","{}".format(post_method[post_method_btn.value])],capture_output=True,text=True)
# terminal.subprocess.run("cmmde.py","-i{}".format("../cmmd.xyz"),"-s{}".format(post_software[post_software_btn.value]), "-j{}".format(post_calc[post_btn.value]), "-m{}".format(post_method[post_method_btn.value]))
TextArea.value = TextArea.value + "\n" + cmd.stdout
runpost_btn = pn.widgets.Button(name="Run post calculation!",button_type='primary')
runpost_btn.on_click(post_calculation)
# Check the progress
def progress(event):
terminal.subprocess.run("squeue")
# terminal.clear()
# terminal.subprocess.run("squeue")
cmd = subprocess.run(["squeue"],capture_output=True,text=True)
TextArea.value = TextArea.value + "\n" + cmd.stdout
Progress_btn = pn.widgets.Button(name="Check calculation",button_type='primary')
Progress_btn.on_click(progress)
@ -118,11 +141,12 @@ def cmmde_gui():
#### Wrap them all together ##########
return pn.template.MaterialTemplate(
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(post_software_btn,height=200),pn.Row(post_method_btn,height=400),pn.Row(runpost_btn,Progress_btn)],
main=[editor, TextArea, visual_btn, pn.Tabs(xyzviewer)],
sidebar=[pn.Row(software_btn),Name_input,pn.Card(job_btn,method_btn,pn.Row(Run_btn,Progress_btn),title="Main Calculation",collapsed=True),pn.Card(post_btn,post_software_btn,post_method_btn,pn.Row(runpost_btn,Progress_btn),title="Post Calculation",collapsed=True)],
header_background=accent, accent_base_color=accent
)

34
cmmde_gui/test/ala/cmmd.engrad
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@ -1,34 +0,0 @@
#
# Number of atoms
#
5
#
# The current total energy in Eh
#
-4.175218519970
#
# The current gradient in Eh/bohr
#
0.000000009773
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

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cmmde_gui/test/ala/cmmd.gbw
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164
cmmde_gui/test/ala/cmmd.opt
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@ -1,164 +0,0 @@
$orca_opt_file
$trust
0.300000000000
$epredict
0.000000000000
$ediffsc
1000.000000000000
$ctyp
3
$coordinates
2 15
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

1136
cmmde_gui/test/ala/cmmd.out
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BIN
cmmde_gui/test/ala/cmmd.xtbrestart
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Binary file not shown.

7
cmmde_gui/test/ala/cmmd.xyz
Unescape View File

@ -1,7 +0,0 @@
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

21
cmmde_gui/test/ala/cmmd_trj.xyz
Unescape View File

@ -1,21 +0,0 @@
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

34
cmmde_gui/test/ala/freq/cmmd.engrad
Unescape View File

@ -1,34 +0,0 @@
#
# 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

192
cmmde_gui/test/ala/freq/cmmd.hess
Unescape View File

@ -1,192 +0,0 @@
$orca_hessian_file
$act_atom
0
$act_coord
0
$act_energy
-4.175219
$hessian
15
0 1 2 3 4
0 5.1329127386E-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

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cmmde_gui/test/ala/freq/cmmd_property.txt
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-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -----------------------------------------------------------
$ THERMOCHEMISTRY_Energies
description: The Thermochemistry energies
geom. index: 0
prop. index: 1
Temperature (Kelvin) : 298.1500000000
Pressure (atm) : 1.0000000000
Total Mass (AMU) : 16.0430000000
Spin Degeneracy : 1.0000000000
Electronic Energy (Hartree) : -4.1752185200
Translational Energy (Hartree) : 0.0014162714
Rotational Energy (Hartree) : 0.0014162714
Vibrational Energy (Hartree) : 0.0000314005
Number of frequencies : 15
Scaling Factor for frequencies : 1.0000000000
Vibrational frequencies :
0
0 0.000000
1 0.000000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 1385.802989
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! ------------------------
# -------------------------------------------------------------

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C

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cmmde_gui/test/ala/geom.xyz
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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

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cmmde_gui/test/ala/slurm-2914.out
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cmmde_gui/test/alala/alala/cmmd.engrad
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#
# 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

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cmmde_gui/test/alala/alala/cmmd.in
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#CMMDE generated Orca input file
!XTB2 opt
%pal
nprocs 1
end
%geom
maxiter 9999
end
*xyzfile 0 1 geom.xyz

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cmmde_gui/test/alala/alala/cmmd.xyz
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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

102
cmmde_gui/test/alala/alala/cmmd_trj.xyz
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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

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cmmde_gui/test/alala/alala/freq/cmmd.engrad
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#
# 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

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cmmde_gui/test/alala/alala/freq/cmmd.in
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#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

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-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -----------------------------------------------------------
$ THERMOCHEMISTRY_Energies
description: The Thermochemistry energies
geom. index: 0
prop. index: 1
Temperature (Kelvin) : 298.1500000000
Pressure (atm) : 1.0000000000
Total Mass (AMU) : 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! ------------------------
# -------------------------------------------------------------

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

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cmmde_gui/test/alala/alala/geom.smi
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C1CCCC1

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cmmde_gui/test/alala/alala/geom.xyz
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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

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

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

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1 molecule converted

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#
# 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

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

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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

102
cmmde_gui/test/alala/cmmd_trj.xyz
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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

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cmmde_gui/test/alala/freq/cmmd.engrad
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#
# 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

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cmmde_gui/test/alala/freq/cmmd.hess
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cmmde_gui/test/alala/freq/cmmd.in
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#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

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cmmde_gui/test/alala/freq/cmmd.xtbrestart
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cmmde_gui/test/alala/freq/cmmd_property.txt
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-------------------------------------------------------------
----------------------- !PROPERTIES! ------------------------
-------------------------------------------------------------
# -----------------------------------------------------------
$ THERMOCHEMISTRY_Energies
description: The Thermochemistry energies
geom. index: 0
prop. index: 1
Temperature (Kelvin) : 298.1500000000
Pressure (atm) : 1.0000000000
Total Mass (AMU) : 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! ------------------------
# -------------------------------------------------------------

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

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cmmde_gui/test/alala/freq/slurm-2889.out
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cmmde_gui/test/alala/geom.smi
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C1CCCC1

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cmmde_gui/test/alala/geom.xyz
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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

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

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

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cmmde_gui/test/alala/slurm-2885.out
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1 molecule converted

0
cmmde_gui/test/alala/slurm-2886.out
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cmmde_gui/test/cmmd.engrad
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#
# Number of atoms
#
12
#
# The current total energy in Eh
#
-15.879640652450
#
# The current gradient in Eh/bohr
#
0.000083151256
0.000032627904
-0.000000801280
-0.000011773444
-0.000092719019
-0.000008798638
0.000004092498
-0.000045349095
0.000008265502
-0.000095719643
0.000023986034
-0.000000346361
-0.000010542094
0.000056660251
-0.000008827102
0.000027808309
0.000031909554
0.000010537622
-0.000055844305
-0.000000629739
0.000001035977
-0.000012931289
0.000055053936
0.000010215618
0.000028823167
0.000043789233
-0.000010112181
0.000056885559
-0.000009417128
0.000000682946
0.000014817015
-0.000052034477
0.000010200866
-0.000028767027
-0.000043877452
-0.000012052970
#
# The atomic numbers and current coordinates in Bohr
#
6 2.5938463 -0.4162363 0.0103377
6 0.9500210 -2.4517633 -0.0164952
6 -1.6347236 -2.0458335 -0.0259782
6 -2.5758034 0.3955182 -0.0084365
6 -0.9319776 2.4309707 0.0184779
6 1.6528189 2.0250743 0.0277733
1 4.6108664 -0.7330783 0.0176863
1 1.6844131 -4.3568328 -0.0299365
1 -2.9175367 -3.6341720 -0.0471728
1 -4.5928432 0.7121836 -0.0157500
1 -1.6662937 4.3360760 0.0323392
1 2.9355884 3.6134472 0.0485120

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cmmde_gui/test/cmmd.in
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#CMMDE generated Orca input file
!XTB2 opt
%pal
nprocs 1
end
*xyzfile 0 1 geom.xyz

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cmmde_gui/test/cmmd.opt
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$orca_opt_file
$trust
0.300000000000
$epredict
0.000000000000
$ediffsc
1000.000000000000
$ctyp
3
$coordinates
3 36
2.61288653 -0.41908456 0.01052577 0.95684393 -2.46996654 -0.01536347
-1.64670735 -2.06091642 -0.02753331 -2.59502862 0.39856214 -0.00842818
-0.93887264 2.44900948 0.01999330 1.66482983 2.04001605 0.02668293
4.64154533 -0.73782467 0.01814137 1.69553788 -4.38584649 -0.02672073
-2.93691787 -3.65837751 -0.05119268 -4.62334727 0.71699989 -0.01574142
-1.67749099 4.36532406 0.03615046 2.95509704 3.63745825 0.04484320
2.59550649 -0.41643815 0.01036785 0.95059732 -2.45337629 -0.01616171
-1.63568287 -2.04709654 -0.02637120 -2.57753162 0.39582279 -0.00841789
-0.93258418 2.43251905 0.01884428 1.65382183 2.02632143 0.02742870
4.61219663 -0.73330531 0.01783196 1.68493943 -4.35810299 -0.02863830
-2.91832796 -3.63515895 -0.04859871 -4.59420509 0.71241063 -0.01568095
-1.66681407 4.33733453 0.03371620 2.93645989 3.61442347 0.04703701
2.59388908 -0.41622532 0.01034226 0.95003032 -2.45180768 -0.01642596
-1.63471042 -2.04583567 -0.02605385 -2.57586432 0.39554159 -0.00842982
-0.93199846 2.43099668 0.01854548 1.65282602 2.02508075 0.02770048
4.61075286 -0.73308274 0.01772377 1.68439784 -4.35672268 -0.02958857
-2.91745011 -3.63404503 -0.04754841 -4.59274904 0.71216783 -0.01572644
-1.66627328 4.33595684 0.03269999 2.93552530 3.61332910 0.04811831
# 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
12 18 24 0 0
1 0 0
2 1 0
3 2 0
4 3 0
5 4 0
5 0 0
6 0 0
7 1 0
8 2 0
9 3 0
10 4 0
11 5 0
1 0 5 0 0
1 0 6 0 0
5 0 6 0 0
2 1 7 0 0
0 1 2 0 0
0 1 7 0 0
3 2 8 0 0
1 2 8 0 0
1 2 3 0 0
4 3 9 0 0
2 3 9 0 0
2 3 4 0 0
3 4 10 0 0
3 4 5 0 0
5 4 10 0 0
0 5 4 0 0
4 5 11 0 0
0 5 11 0 0
7 1 0 5 0
7 1 0 6 0
2 1 0 6 0
2 1 0 5 0
8 2 1 0 0
3 2 1 0 0
3 2 1 7 0
8 2 1 7 0
9 3 2 8 0
9 3 2 1 0
4 3 2 8 0
4 3 2 1 0
10 4 3 2 0
5 4 3 9 0
5 4 3 2 0
10 4 3 9 0
11 5 4 10 0
0 5 4 10 0
0 5 4 3 0
11 5 0 6 0
11 5 0 1 0
11 5 4 3 0
4 5 0 6 0
4 5 0 1 0
$energies
3
-15.8788484754799999
-15.8796359048200006
-15.8796406113999993
$gradients
3 36
0.0064018160793736 -0.0008229451415805 0.0000260966823487 0.0021803146107729
-0.0061542978497816 0.0000049452388562 -0.0039050482885651 -0.0050614621002014
-0.0001218965954347 -0.0065626845075318 0.0010371472824853 -0.0000251452776693
-0.0021547143969915 0.0059717090910768 0.0001045708426146 0.0039680418697520
0.0049535638574042 0.0000176960611633 0.0043782680781490 -0.0006979952561195
0.0000224205130562 0.0015811699369878 -0.0040851994213401 0.0000094067688575
-0.0027764670085239 -0.0034396855777557 -0.0000856428740190 -0.0042656113389818
0.0006730817772657 -0.0000155060301103 -0.0016234011707950 0.0042026080424502
0.0000707744157942 0.0027783161363538 0.0034234752960966 -0.0000077197454574
0.0010040025823895 -0.0000670205344290 0.0000018036084095 0.0002867953631190
-0.0009842350184835 -0.0000137658828775 -0.0005390260895022 -0.0007728409062354
-0.0000030723682150 -0.0010444805899158 0.0001789077900104 -0.0000040206256170
-0.0003098934823978 0.0009135483550405 -0.0000006879957278 0.0005877852508803
0.0007306345414987 0.0000200289790264 -0.0000661848886922 -0.0000012381340454
0.0000029372635074 -0.0000171236024680 0.0000701496281870 0.0000220386669648
0.0000365685375400 0.0000528706378343 -0.0000223758573212 0.0000796162050068
-0.0000114134291758 0.0000011533483257 0.0000140486721613 -0.0000560579426239
0.0000228663559333 -0.0000321079581210 -0.0000533049875778 -0.0000269054924086
0.0000831512555905 0.0000326279035727 -0.0000008012802187 -0.0000117734440296
-0.0000927190185813 -0.0000087986377071 0.0000040924975157 -0.0000453490952724
0.0000082655018806 -0.0000957196433499 0.0000239860337539 -0.0000003463606999
-0.0000105420939887 0.0000566602506760 -0.0000088271019431 0.0000278083088741
0.0000319095541218 0.0000105376222142 -0.0000558443048920 -0.0000006297393995
0.0000010359767700 -0.0000129312894485 0.0000550539357266 0.0000102156181436
0.0000288231670055 0.0000437892334748 -0.0000101121807344 0.0000568855589559
-0.0000094171283497 0.0000006829462579 0.0000148170145674 -0.0000520344773025
0.0000102008661905 -0.0000287670268006 -0.0000438774524204 -0.0000120529701534
$redundant_coords
3 54
2.6361457162075697 2.6355169116962252 2.6360411666939112 2.6359049155609657
2.6356378515282941 2.6355736411282118 2.0535602686671370 2.0533859089446578
2.0535542068948041 2.0531762283892818 2.0537964121469758 2.0535191323951199
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10 -0.359652 0.933061 0.006933 0.000000 0.000000 0.000000
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26 -0.457025 -0.176133 -0.003940 0.000000 0.000000 0.000000
27 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
28 0.000000 0.000000 0.000000 0.381057 -0.307738 -0.000849
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30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
31 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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40 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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43 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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52 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
53 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000

1709
cmmde_gui/test/cmmd.out
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cmmde_gui/test/cmmd.xtbrestart
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14
cmmde_gui/test/cmmd.xyz
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@ -1,14 +0,0 @@
12
Coordinates from ORCA-job cmmd
C 1.37260436112356 -0.22026276421215 0.00547047023826
C 0.50272945880886 -1.29741725617100 -0.00872890193775
C -0.86505848472206 -1.08260844519038 -0.01374705758241
C -1.36305644841968 0.20929919814959 -0.00446438511787
C -0.49318132097366 1.28641428149678 0.00977806727944
C 0.87463411368352 1.07162318446095 0.01469701658624
H 2.43996541860591 -0.38792834851432 0.00935918376693
H 0.89135300032527 -2.30553664453777 -0.01584172099556
H -1.54389392375015 -1.92312101358440 -0.02496277241009
H -2.43042795974921 0.37687130997575 -0.00833452091932
H -0.88176466598630 2.29455258686373 0.01711318587593
H 1.55344645105395 1.91215391126322 0.02567143521620

56
cmmde_gui/test/cmmd_trj.xyz
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@ -1,56 +0,0 @@
12
Coordinates from ORCA-job cmmd E -15.878848475480
C 1.382680 -0.221770 0.005570
C 0.506340 -1.307050 -0.008130
C -0.871400 -1.090590 -0.014570
C -1.373230 0.210910 -0.004460
C -0.496830 1.295960 0.010580
C 0.880990 1.079530 0.014120
H 2.456200 -0.390440 0.009600
H 0.897240 -2.320890 -0.014140
H -1.554150 -1.935930 -0.027090
H -2.446570 0.379420 -0.008330
H -0.887690 2.310030 0.019130
H 1.563770 1.924860 0.023730
12
Coordinates from ORCA-job cmmd E -15.879635904820
C 1.373483 -0.220370 0.005486
C 0.503034 -1.298271 -0.008552
C -0.865566 -1.083277 -0.013955
C -1.363971 0.209460 -0.004455
C -0.493502 1.287234 0.009972
C 0.875165 1.072283 0.014515
H 2.440669 -0.388048 0.009436
H 0.891632 -2.306209 -0.015155
H -1.544313 -1.923643 -0.025717
H -2.431149 0.376991 -0.008298
H -0.882040 2.295219 0.017842
H 1.553908 1.912671 0.024891
12
Coordinates from ORCA-job cmmd E -15.879640611400
C 1.372627 -0.220257 0.005473
C 0.502734 -1.297441 -0.008692
C -0.865051 -1.082610 -0.013787
C -1.363089 0.209312 -0.004461
C -0.493192 1.286428 0.009814
C 0.874638 1.071627 0.014658
H 2.439905 -0.387931 0.009379
H 0.891345 -2.305478 -0.015658
H -1.543848 -1.923054 -0.025162
H -2.430378 0.376863 -0.008322
H -0.881754 2.294490 0.017304
H 1.553413 1.912091 0.025463
12
Coordinates from ORCA-job cmmd E -15.879640652450
C 1.372604 -0.220263 0.005470
C 0.502729 -1.297417 -0.008729
C -0.865058 -1.082608 -0.013747
C -1.363056 0.209299 -0.004464
C -0.493181 1.286414 0.009778
C 0.874634 1.071623 0.014697
H 2.439965 -0.387928 0.009359
H 0.891353 -2.305537 -0.015842
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H -2.430428 0.376871 -0.008335
H -0.881765 2.294553 0.017113
H 1.553446 1.912154 0.025671

1
cmmde_gui/test/geom.smi
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c1ccccc1

14
cmmde_gui/test/geom.xyz
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12
C 1.38268 -0.22177 0.00557
C 0.50634 -1.30705 -0.00813
C -0.87140 -1.09059 -0.01457
C -1.37323 0.21091 -0.00446
C -0.49683 1.29596 0.01058
C 0.88099 1.07953 0.01412
H 2.45620 -0.39044 0.00960
H 0.89724 -2.32089 -0.01414
H -1.55415 -1.93593 -0.02709
H -2.44657 0.37942 -0.00833
H -0.88769 2.31003 0.01913
H 1.56377 1.92486 0.02373

298
cmmde_gui/test/grafena/cmmd.engrad
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@ -0,0 +1,298 @@
#
# Number of atoms
#
71
#
# The current total energy in Eh
#
-106.584609849900
#
# The current gradient in Eh/bohr
#
0.000012434938
0.000003391057
-0.000003321356
-0.000008112395
-0.000019366935
-0.000007027411
0.000007702114
0.000028151841
-0.000027730849
0.000020687858
0.000008675811
-0.000005742211
-0.000003903790
-0.000048421805
0.000047709565
0.000048246564
-0.000061127583
-0.000026271659
-0.000053925571
0.000001575583
-0.000028196995
0.000031648291
0.000032801706
0.000033036343
0.000004141107
-0.000007283302
-0.000038075314
-0.000021083590
-0.000005497721
0.000049420434
-0.000017643399
-0.000038472445
-0.000054995889
0.000018370442
0.000096795823
0.000120899036
0.000044028453
-0.000126763553
-0.000194650689
0.000053839849
0.000205225883
0.000002118298
0.000018980627
-0.000128205259
-0.000007485304
-0.000021195777
0.000034682283
0.000015893514
-0.000023781656
-0.000012719725
-0.000011931615
0.000033871956
0.000011669556
0.000000386219
-0.000002368742
-0.000015009876
-0.000017593337
-0.000005979656
-0.000000847897
-0.000009767010
0.000008394600
0.000005492788
0.000014347190
-0.000014986012
-0.000011121906
-0.000020725502
0.000028144657
0.000005693398
0.000007215545
-0.000001836192
-0.000004941521
0.000004275985
-0.000012167056
-0.000002000396
0.000003681707
0.000028555709
0.000004748171
0.000002822717
-0.000014198526
-0.000000946476
-0.000012165884
-0.000009099833
-0.000011377097
0.000013512852
0.000017045835
0.000008970975
0.000028257524
-0.000004051596
0.000008277547
-0.000026984700
-0.000009038531
0.000010110245
0.000000197894
0.000020728949
0.000016549328
-0.000025451848
-0.000025549662
0.000004278239
0.000057828924
0.000004777463
-0.000006121602
-0.000044295569
-0.000055432087
-0.000030842844
0.000040500942
0.000104267579
0.000029917255
-0.000020155499
0.000004952904
0.000003744939
-0.000009932713
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0.000017547022
-0.000042417750
0.000013701618
0.000028931679
0.000006626910
-0.000004777434
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0.000006815630
-0.000012566777
0.000003961274
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0.000023762434
-0.000000680331
0.000012167392
-0.000021489741
-0.000005129746
-0.000003186058
-0.000001420915
-0.000000183604
-0.000000379390
0.000001455137
-0.000006116840
0.000000234290
-0.000007236940
-0.000008772200
0.000030181576
0.000000661606
0.000021309682
0.000010348427
-0.000017662625
-0.000006468910
0.000000526887
0.000007442540
0.000009541652
-0.000020497364
-0.000006940906
0.000007347513
-0.000012573760
-0.000009734241
0.000014933254
0.000038977278
-0.000026645418
0.000000488223
-0.000012232614
0.000011965820
-0.000004627710
-0.000002394198
-0.000010603484
0.000007846102
-0.000009920215
-0.000016237820
-0.000014228781
0.000004245497
-0.000001564989
-0.000012650798
-0.000041025624
-0.000025167468
0.000006722300
0.000046596824
-0.000019310143
0.000029395265
0.000045374628
-0.000025632836
-0.000033267220
0.000011713308
-0.000002140626
-0.000025639450
0.000059997407
0.000009319352
-0.000017151742
0.000000217840
0.000007257631
0.000003887648
-0.000004172665
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0.000005493576
0.000001443301
-0.000003562666
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0.000006128976
-0.000007962565
-0.000008306052
0.000009109571
0.000007573836
0.000011780771
0.000003616352
0.000003652743
0.000002111423
0.000002437966
-0.000005402791
0.000000266564
-0.000000670810
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-0.000000943392
0.000000110232
0.000001979165
0.000002851888
0.000004688478
-0.000013946253
0.000001286540
-0.000001401167
#
# The atomic numbers and current coordinates in Bohr
#
6 11.2976954 -5.0017672 8.4371308
6 11.0509311 -4.0792889 6.1090126
6 13.1540058 -2.6430107 4.8625477
6 13.1597995 -2.8777150 1.9936868
6 15.1546219 -1.1263409 0.8637619
6 17.6203873 -1.0170415 2.3000566
6 19.6564325 0.2491804 1.2241563
6 19.3913950 1.5060812 -1.3092213
6 21.2541549 3.6794332 -1.5635075
6 23.9337083 2.7129031 -1.1910463
6 24.2045614 1.4245254 1.3293362
6 26.5115020 1.2866485 2.5048470
6 28.8489214 2.3977280 1.3144035
6 31.2520199 1.0766343 2.1982040
6 31.3449754 0.9087994 5.0205233
6 33.5472880 1.1850790 6.3640989
6 33.5637083 0.9112333 8.9901628
6 31.4207001 0.1818695 10.2586412
6 31.3458939 -0.0462455 13.0844216
6 29.6808842 -2.2555045 13.8892542
6 27.1271596 -2.1300246 12.6595943
6 25.0168125 -2.9903880 13.8426831
6 22.6404610 -3.1071390 12.5965218
6 20.4742185 -3.9238279 13.8245708
6 18.1716319 -4.1394626 12.5523201
6 15.9418606 -4.9688687 13.7721626
6 13.7360138 -5.2207298 12.4684839
6 13.6244071 -4.6908479 9.8573353
6 15.7769574 -3.8755586 8.6190088
6 18.0646532 -3.5590489 9.9264230
6 20.2407107 -2.6461696 8.6668692
6 20.0799929 -1.8191309 6.0801622
6 17.8425748 -2.0751015 4.7116232
6 15.7113081 -3.6024583 5.7981547
6 22.2124751 -0.6888503 4.9315975
6 22.0130884 0.3363498 2.4696658
6 24.5556623 -0.6063741 6.2267317
6 26.7219958 0.2671703 4.9788244
6 29.0871413 0.3008503 6.2918244
6 29.1697686 -0.2476772 8.8963453
6 26.9775884 -1.2326491 10.1232524
6 24.7063874 -1.4311708 8.7885134
6 22.5113334 -2.3977291 9.9982805
1 9.7544856 -5.9693088 9.3617779
1 9.2937198 -4.2368022 5.0804643
1 12.9540855 -0.6329911 5.3637331
1 11.3092812 -2.3929766 1.2167501
1 13.5614090 -4.8376943 1.4810634
1 14.3795316 0.7942325 0.8073748
1 15.5208897 -1.6953762 -1.0872227
1 17.4763398 2.2249853 -1.5583675
1 19.7377362 0.1183421 -2.8070845
1 21.0684044 4.5652009 -3.4182204
1 20.8372925 5.1036746 -0.1277104
1 24.3986179 1.3752891 -2.7023864
1 25.2451783 4.2975782 -1.3228111
1 28.9498742 4.4037633 1.8249291
1 28.7473058 2.2707274 -0.7395327
1 31.2780246 -0.8490839 1.4348896
1 32.9135704 2.0609555 1.4716791
1 35.2831294 1.6431850 5.3896627
1 35.2927237 1.2488418 10.0242375
1 30.5604894 1.7082233 13.8570036
1 33.2523021 -0.2666997 13.8417996
1 30.5846345 -4.0249842 13.3013778
1 29.4863693 -2.3052609 15.9426435
1 25.1198110 -3.6551926 15.7728153
1 20.5674127 -4.4160414 15.8055454
1 16.0297784 -5.4105727 15.7642288
1 12.0384136 -5.8504567 13.4144756
1 15.9384454 -5.5454457 5.0555804

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cmmde_gui/test/ala/cmmd.in → cmmde_gui/test/grafena/cmmd.in
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36038
cmmde_gui/test/grafena/cmmd.opt
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cmmde_gui/test/grafena/cmmd.out
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cmmde_gui/test/grafena/cmmd.xtbrestart
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cmmde_gui/test/grafena/cmmd.xyz
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71
Coordinates from ORCA-job cmmd
C 5.97848292227904 -2.64682122276911 4.46473733913830
C 5.84790084724943 -2.15866672146033 3.23275021415626
C 6.96080005815379 -1.39862102621101 2.57314942053880
C 6.96386594614745 -1.52282120155028 1.05501363093393
C 8.01948053588850 -0.59603395259741 0.45708310508559
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C 10.40173605767687 0.13186057020019 0.64779562191024
C 10.26148427591736 0.79698386697550 -0.69281006629740
C 11.24721433432398 1.94707216289516 -0.82737253044232
C 12.66517295020455 1.43560651499299 -0.63027453120388
C 12.80850223257784 0.75382639523883 0.70345443684858
C 14.02928262082641 0.68086508196686 1.32550791795183
C 15.26619168199529 1.26882298316129 0.69555237740619
C 16.53785665556502 0.56973034535385 1.16323947693111
C 16.58704658600130 0.48091595264054 2.65674651101873
C 17.75246023074004 0.62711680775512 3.36773608410543
C 17.76114946247022 0.48220387222681 4.75738922945350
C 16.62711838321354 0.09624117050565 5.42863910220794
C 16.58753261377575 -0.02447208294616 6.92397771989722
C 15.70644744063530 -1.19356156918612 7.34987676603452
C 14.35507456107774 -1.12716046730315 6.69916874499826
C 13.23832700657148 -1.58244519711857 7.32523241601003
C 11.98081595795971 -1.64422714244578 6.66579222406349
C 10.83448978337768 -2.07640029731820 7.31564776809629
C 9.61601342462801 -2.19050924838847 6.64240169897696
C 8.43606928602578 -2.62941209208893 7.28791457516977
C 7.26878545045833 -2.76269121637430 6.59803747846171
C 7.20972573453389 -2.48228979441454 5.21627717090888
C 8.34880625528048 -2.05085726538503 4.56098301260707
C 9.55940277123032 -1.88336758566790 5.25283679344501
C 10.71092279368064 -1.40029264276640 4.58630964227842
C 10.62587457726097 -0.96264262550886 3.21748328506328
C 9.44188394504274 -1.09809639581324 2.49328362980176
C 8.31406613942317 -1.90633885016553 3.06825129746761
C 11.75433555668981 -0.36452388611557 2.60968898332605
C 11.64882464129668 0.17798865470172 1.30689085634491
C 12.99429682216915 -0.32087933760251 3.29504450611523
C 14.14067115232695 0.14138044646240 2.63468040283324
C 15.39225224524583 0.15920311616137 3.32949007692182
C 15.43597673333186 -0.13106510802484 4.70774317896792
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C 11.91248454724954 -1.26882361302687 5.29086217556897
H 5.16185143514081 -3.15882215729037 4.95403949008511
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H 15.21241904613515 1.20161717795566 -0.39134387501925
H 16.55161773026214 -0.44931583271431 0.75931087110127
H 17.41711129166774 1.09061065318135 0.77877902014267
H 18.67102790036752 0.86953605388811 2.85208666734182
H 18.67610500266945 0.66085864065976 5.30459803675925
H 16.17191446950705 0.90395283201875 7.33281050670623
H 17.59636041899511 -0.14113141823571 7.32476486198412
H 16.18469147913577 -2.12992990498067 7.03878599101778
H 15.60351461488460 -1.21989151110030 8.43648360238666
H 13.29283143296124 -1.93424461794932 8.34661439239236
H 10.88380604831301 -2.33686848565543 8.36393437140590
H 8.48259336596857 -2.86315175237683 8.34207056876517
H 6.37045410726021 -3.09592833661734 7.09863476621227
H 8.43426204174167 -2.93452346439970 2.67529792180339

0
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cmmde_gui/test/grafena/cmmd_trj.xyz
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71
cmmde_gui/test/grafena/freq/cmmd.charges
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@ -0,0 +1,71 @@
-0.04217847
-0.04290674
-0.00833544
-0.04834424
-0.04824291
-0.01567417
-0.00886872
-0.04859533
-0.04058975
-0.04807889
-0.01102690
-0.01236832
-0.04508654
-0.04405994
-0.00031105
-0.04300191
-0.04183275
-0.00125066
-0.04430427
-0.04436281
0.00681281
-0.05585292
0.01188300
-0.05195054
0.00909741
-0.04259012
-0.03244423
-0.00845218
-0.00331346
-0.00741485
-0.00122354
-0.00910097
-0.00726897
-0.01358112
-0.00457262
-0.01109382
-0.00504026
-0.00548182
-0.00845894
-0.00669753
-0.01186227
-0.00085888
-0.00847907
0.03163018
0.03081475
0.03480601
0.02872946
0.02700014
0.03474261
0.03314557
0.03165048
0.03540163
0.02609424
0.02874119
0.03456874
0.03199368
0.03664342
0.03070310
0.03684641
0.02999382
0.02819675
0.02831425
0.03724966
0.03047089
0.03798862
0.03151872
0.03049641
0.03187238
0.03052359
0.02980316
0.04742482

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cmmde_gui/test/grafena/freq/cmmd.engrad
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#
# Number of atoms
#
71
#
# The current total energy in Eh
#
-106.196831730670
#
# The current gradient in Eh/bohr
#
0.000674227956
0.000680444598
-0.000621186098
0.001616919200
0.000452590030
0.001106420163
-0.000331875650
-0.003766368988
-0.000920006064
0.000552182022
0.001510645235
0.001497012134
0.001155354300
-0.001532226013
0.000984783012
-0.000568179895
-0.000046601034
-0.000517010439
-0.000061055401
0.000795138662
-0.001331170225
0.000264848844
0.001060222727
0.002361365830
0.000692250217
-0.002344109916
-0.000208407174
-0.000841845562
0.000888569825
0.002135620281
-0.000492952695
0.000622951310
-0.000916780243
0.000890703542
0.000543161148
-0.000353464846
-0.000629810546
-0.002423559792
0.000239437400
-0.001383784608
0.001029843702
0.002088063072
0.001297200269
0.000232855919
-0.001369415920
-0.001538861413
-0.000406800302
0.001953764316
-0.001423170738
-0.000299736581
-0.002010535112
0.001221807696
0.000320479951
0.001462345388
-0.000573103651
-0.001567618653
-0.001919534563
-0.001275903593
0.001911570932
-0.001203076478
0.000852740021
-0.000809414147
0.002033476622
-0.000840225924
0.000711748649
-0.002846580877
0.000327778682
-0.000483676034
0.001697544033
-0.000329215074
0.000453413512
-0.002234600124
0.000039347681
-0.000373354707
0.001630186534
-0.000554000242
0.000240485021
-0.001568734425
0.001591999708
0.000304688525
-0.000271873765
-0.001147353652
-0.000114076198
0.000329494468
0.000666711916
0.000260413582
-0.001310991848
-0.000272557884
-0.000201021748
0.000219282328
-0.000185675804
0.000201365226
-0.000355359878
0.000469259216
0.000236371437
-0.000094750991
-0.000670098056
-0.000382643905
0.000653453990
-0.000106180509
0.002808074660
0.001252724466
0.000241209149
-0.000002837353
0.000305548635
0.000267522340
-0.000010442664
0.000150849711
-0.000487198141
-0.000251280421
0.000280259036
0.000258960633
0.000378830486
-0.000158373267
0.000176347289
0.000140295005
-0.000116005045
0.000215869330
0.000011474622
0.000098099163
0.000110930373
-0.000185380719
0.000283172717
-0.000435356264
0.000093839187
-0.000370892491
0.000168091211
0.000138285114
-0.000185785903
0.002481785016
0.001203829079
-0.001062727571
0.002480644873
0.000269609705
0.001509367765
0.000394551009
-0.001109718451
-0.000040711253
0.000774378703
-0.000617269228
0.000317011161
-0.000120474272
0.001477502339
0.000894005337
0.000654745008
-0.000639647752
0.000706281819
0.000319539640
0.000553662910
0.001229862639
0.001511780954
-0.000871744005
0.000565687802
0.000300550028
0.000524559535
0.001041233511
-0.000005920964
-0.000019088603
0.001079955000
0.000489413086
-0.001626088079
-0.000745379269
-0.000667113572
0.000127697979
0.000996572235
-0.000910573302
-0.001313144674
0.000644173881
-0.000338135533
-0.000904375066
0.000659953845
-0.000348241768
-0.000150943133
0.001548975949
-0.000457891780
0.000640386799
0.000764492375
-0.000608245787
-0.000863288259
0.000964407254
-0.002625852378
-0.000664439863
0.000984196489
-0.002623847741
-0.000550082411
-0.001080096568
-0.000183001346
-0.000726152499
-0.000721430853
-0.000907216317
0.000545642701
-0.000946654513
-0.000531366740
0.000807431985
-0.000409195783
-0.000478822589
-0.000326310394
-0.001325318294
-0.000182611548
0.001001948384
-0.002754299389
-0.000115345797
0.000694234257
-0.002772804129
0.000229660758
0.000697944269
-0.002825157839
0.002164757283
0.000898137312
-0.001549300120
-0.000301001215
0.000113095273
0.000448530991
#
# The atomic numbers and current coordinates in Bohr
#
6 11.2976954 -5.0017672 8.4371308
6 11.0509311 -4.0792889 6.1090126
6 13.1540058 -2.6430107 4.8625477
6 13.1597995 -2.8777150 1.9936868
6 15.1546219 -1.1263409 0.8637619
6 17.6203873 -1.0170415 2.3000566
6 19.6564325 0.2491804 1.2241563
6 19.3913950 1.5060812 -1.3092213
6 21.2541549 3.6794332 -1.5635075
6 23.9337083 2.7129031 -1.1910463
6 24.2045614 1.4245254 1.3293362
6 26.5115020 1.2866485 2.5048470
6 28.8489214 2.3977280 1.3144035
6 31.2520199 1.0766343 2.1982040
6 31.3449754 0.9087994 5.0205233
6 33.5472880 1.1850790 6.3640989
6 33.5637083 0.9112333 8.9901628
6 31.4207001 0.1818695 10.2586412
6 31.3458939 -0.0462455 13.0844216
6 29.6808842 -2.2555045 13.8892542
6 27.1271596 -2.1300246 12.6595943
6 25.0168125 -2.9903880 13.8426831
6 22.6404610 -3.1071390 12.5965218
6 20.4742185 -3.9238279 13.8245708
6 18.1716319 -4.1394626 12.5523201
6 15.9418606 -4.9688687 13.7721626
6 13.7360138 -5.2207298 12.4684839
6 13.6244071 -4.6908479 9.8573353
6 15.7769574 -3.8755586 8.6190088
6 18.0646532 -3.5590489 9.9264230
6 20.2407107 -2.6461696 8.6668692
6 20.0799929 -1.8191309 6.0801622
6 17.8425748 -2.0751015 4.7116232
6 15.7113081 -3.6024583 5.7981547
6 22.2124751 -0.6888503 4.9315975
6 22.0130884 0.3363498 2.4696658
6 24.5556623 -0.6063741 6.2267317
6 26.7219958 0.2671703 4.9788244
6 29.0871413 0.3008503 6.2918244
6 29.1697686 -0.2476772 8.8963453
6 26.9775884 -1.2326491 10.1232524
6 24.7063874 -1.4311708 8.7885134
6 22.5113334 -2.3977291 9.9982805
1 9.7544856 -5.9693088 9.3617779
1 9.2937198 -4.2368022 5.0804643
1 12.9540855 -0.6329911 5.3637331
1 11.3092812 -2.3929766 1.2167501
1 13.5614090 -4.8376943 1.4810634
1 14.3795316 0.7942325 0.8073748
1 15.5208897 -1.6953762 -1.0872227
1 17.4763398 2.2249853 -1.5583675
1 19.7377362 0.1183421 -2.8070845
1 21.0684044 4.5652009 -3.4182204
1 20.8372925 5.1036746 -0.1277104
1 24.3986179 1.3752891 -2.7023864
1 25.2451783 4.2975782 -1.3228111
1 28.9498742 4.4037633 1.8249291
1 28.7473058 2.2707274 -0.7395327
1 31.2780246 -0.8490839 1.4348896
1 32.9135704 2.0609555 1.4716791
1 35.2831294 1.6431850 5.3896627
1 35.2927237 1.2488418 10.0242375
1 30.5604894 1.7082233 13.8570036
1 33.2523021 -0.2666997 13.8417996
1 30.5846345 -4.0249842 13.3013778
1 29.4863693 -2.3052609 15.9426435
1 25.1198110 -3.6551926 15.7728153
1 20.5674127 -4.4160414 15.8055454
1 16.0297784 -5.4105727 15.7642288
1 12.0384136 -5.8504567 13.4144756
1 15.9384454 -5.5454457 5.0555804

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cmmde_gui/test/grafena/freq/cmmd.hostnames
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compute

2
cmmde_gui/test/ala/freq/cmmd.in → cmmde_gui/test/grafena/freq/cmmd.in
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@ -1,5 +1,5 @@
#CMMDE generated Orca input file
!XTB2 Numfreq
!XTB1 Numfreq
%pal
nprocs 1
end

223
cmmde_gui/test/grafena/freq/cmmd.lastscf
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-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
| Aditya W. Sakti |
| Departemen Kimia |
| Universitas Pertamina |
-----------------------------------------------------------
* xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/08/04 at 09:43:13.535
-------------------------------------------------
| 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 --gfn 1 --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 71
number of electrons : 200
charge : 0
spin : 0.0
first test random number : 0.11018891849212
ID Z sym. atoms
1 6 C 1-43
2 1 H 44-71
-------------------------------------------------
| G F N 1 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.7b00118
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.250000 2.000000
zeta-weighting 0.000000
* Dispersion:
s8 2.400000
a1 0.630000
a2 5.000000
s9 0.000000
* Repulsion:
kExp 1.500000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order atomic
anisotropic false
* Halogen bond correction:
rad-scale 1.300000
damping 0.440000
q/qsh data taken from xtbrestart
...................................................
: SETUP :
:.................................................:
: # basis functions 228 :
: # atomic orbitals 228 :
: # shells 142 :
: # electrons 200 :
: # halogen bonds 0 :
: max. iterations 250 :
: Hamiltonian GFN1-xTB :
: restarted? true :
: 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 0.2000000E-04 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -107.9721901 -0.107972E+03 0.178E-05 1.49 0.0 T
2 -107.9721901 -0.515854E-11 0.840E-06 1.49 1412.6 T
3 -107.9721901 -0.626699E-11 0.690E-06 1.49 1720.5 T
*** convergence criteria satisfied after 3 iterations ***
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.6780197 -18.4499
... ... ... ...
94 2.0000 -0.4299532 -11.6996
95 2.0000 -0.4242112 -11.5434
96 2.0000 -0.4217085 -11.4753
97 2.0000 -0.4141609 -11.2699
98 2.0000 -0.4065524 -11.0629
99 2.0000 -0.4025241 -10.9532
100 2.0000 -0.3741491 -10.1811 (HOMO)
101 -0.3193036 -8.6887 (LUMO)
102 -0.2855655 -7.7706
103 -0.2802990 -7.6273
104 -0.2694395 -7.3318
105 -0.2598321 -7.0704
... ... ...
228 0.6943959 18.8955
-------------------------------------------------------------
HL-Gap 0.0548455 Eh 1.4924 eV
Fermi-level -0.3467264 Eh -9.4349 eV
SCC (total) 0 d, 0 h, 0 min, 0.284 sec
SCC setup ... 0 min, 0.001 sec ( 0.327%)
Dispersion ... 0 min, 0.002 sec ( 0.752%)
classical contributions ... 0 min, 0.000 sec ( 0.124%)
integral evaluation ... 0 min, 0.058 sec ( 20.367%)
iterations ... 0 min, 0.034 sec ( 12.056%)
molecular gradient ... 0 min, 0.187 sec ( 65.718%)
printout ... 0 min, 0.002 sec ( 0.644%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -106.196831730824 Eh ::
:: gradient norm 0.015896246397 Eh/a0 ::
:: HOMO-LUMO gap 1.492421979466 eV ::
::.................................................::
:: SCC energy -107.972190143497 Eh ::
:: -> electrostatic 0.004053563662 Eh ::
:: repulsion energy 1.841954650940 Eh ::
:: dispersion energy -0.066596238268 Eh ::
:: halogen bond corr. 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge -0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -106.196831730824 Eh |
| GRADIENT NORM 0.015896246397 Eh/α |
| HOMO-LUMO GAP 1.492421979466 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/08/04 at 09:43:13.869
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.334 sec
* cpu-time: 0 d, 0 h, 0 min, 0.333 sec
* ratio c/w: 0.997 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.284 sec
* cpu-time: 0 d, 0 h, 0 min, 0.284 sec
* ratio c/w: 0.997 speedup

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cmmd # BaseName
cmmd # GBWName
426 # number of calculations
1 # number of CPUs
1 # program flag
0 # printing flag
1 # free_end

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@ -140,9 +140,9 @@ The coordinates will be read from file: ../cmmd.xyz
***************************************
Your calculation utilizes the semiempirical GFN2-xTB method
Your calculation utilizes the semiempirical GFN-xTB method
Please cite in your paper:
C. Bannwarth, Ehlert S., S. Grimme, J. Chem. Theory Comput., 15, (2019), 1652.
S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 13, (2017), 1989.
================================================================================
@ -167,7 +167,7 @@ WARNING: TRAH-SCF for XTB is not implemented!
================================================================================
NAME = cmmd.in
| 1> #CMMDE generated Orca input file
| 2> !XTB2 Numfreq
| 2> !XTB1 Numfreq
| 3> %pal
| 4> nprocs 1
| 5> end
@ -267,62 +267,61 @@ NAME = cmmd.in
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
* started run on 2022/08/04 at 09:43:13.227
-------------------------------------------------
| 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
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 --gfn 1 --acc 1.000000
hostname : compute
calculation namespace : cmmd
coordinate file : cmmd_XTB.xyz
number of atoms : 5
number of electrons : 8
number of atoms : 71
number of electrons : 200
charge : 0
spin : 0.0
first test random number : 0.60690392607394
first test random number : 0.60158050573190
ID Z sym. atoms
1 6 C 1
2 1 H 2-5
1 6 C 1-43
2 1 H 44-71
-------------------------------------------------
| G F N 2 - x T B |
| G F N 1 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.8b01176
Reference 10.1021/acs.jctc.7b00118
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.230000 2.230000
zeta-weighting 0.500000
H0-scaling (s, p, d) 1.850000 2.250000 2.000000
zeta-weighting 0.000000
* Dispersion:
s8 2.700000
a1 0.520000
s8 2.400000
a1 0.630000
a2 5.000000
s9 5.000000
s9 0.000000
* Repulsion:
kExp 1.500000 1.000000
kExp 1.500000
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
third order atomic
anisotropic false
* Halogen bond correction:
rad-scale 1.300000
damping 0.440000
...................................................
: SETUP :
:.................................................:
: # basis functions 8 :
: # atomic orbitals 8 :
: # shells 6 :
: # electrons 8 :
: # basis functions 228 :
: # atomic orbitals 228 :
: # shells 142 :
: # electrons 200 :
: # halogen bonds 0 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: Hamiltonian GFN1-xTB :
: restarted? false :
: GBSA solvation false :
: PC potential false :
@ -331,57 +330,68 @@ NAME = cmmd.in
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: -> wf. convergence 0.2000000E-04 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 ***
1 -107.8847039 -0.107885E+03 0.104E+01 1.52 0.0 T
2 -107.9625255 -0.778216E-01 0.628E+00 1.49 1.0 T
3 -107.9286345 0.338911E-01 0.684E-01 1.54 1.0 T
4 -107.9667855 -0.381510E-01 0.207E-01 1.49 1.0 T
5 -107.9716052 -0.481967E-02 0.610E-02 1.49 1.0 T
6 -107.9721688 -0.563640E-03 0.109E-02 1.49 1.1 T
7 -107.9721891 -0.203189E-04 0.279E-03 1.49 4.3 T
8 -107.9721901 -0.975196E-06 0.986E-04 1.49 12.0 T
9 -107.9721901 -0.487483E-07 0.245E-04 1.49 48.5 T
10 -107.9721901 -0.387629E-08 0.109E-04 1.49 109.2 T
11 -107.9721901 -0.763720E-09 0.575E-05 1.49 206.3 T
*** convergence criteria satisfied after 11 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
1 2.0000 -0.6780191 -18.4498
... ... ... ...
94 2.0000 -0.4299532 -11.6996
95 2.0000 -0.4242112 -11.5434
96 2.0000 -0.4217088 -11.4753
97 2.0000 -0.4141608 -11.2699
98 2.0000 -0.4065523 -11.0629
99 2.0000 -0.4025242 -10.9532
100 2.0000 -0.3741493 -10.1811 (HOMO)
101 -0.3193038 -8.6887 (LUMO)
102 -0.2855657 -7.7706
103 -0.2802989 -7.6273
104 -0.2694394 -7.3318
105 -0.2598322 -7.0704
... ... ...
228 0.6943955 18.8955
-------------------------------------------------------------
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%)
HL-Gap 0.0548455 Eh 1.4924 eV
Fermi-level -0.3467265 Eh -9.4349 eV
SCC (total) 0 d, 0 h, 0 min, 0.235 sec
SCC setup ... 0 min, 0.001 sec ( 0.366%)
Dispersion ... 0 min, 0.002 sec ( 0.739%)
classical contributions ... 0 min, 0.000 sec ( 0.147%)
integral evaluation ... 0 min, 0.045 sec ( 18.969%)
iterations ... 0 min, 0.073 sec ( 30.918%)
molecular gradient ... 0 min, 0.113 sec ( 47.933%)
printout ... 0 min, 0.002 sec ( 0.914%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -4.175218519975 Eh ::
:: gradient norm 0.000006627564 Eh/a0 ::
:: HOMO-LUMO gap 17.353313970090 eV ::
:: total energy -106.196831730665 Eh ::
:: gradient norm 0.015896196187 Eh/a0 ::
:: HOMO-LUMO gap 1.492422010339 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 ::
:: SCC energy -107.972190143337 Eh ::
:: -> electrostatic 0.004053721879 Eh ::
:: repulsion energy 1.841954650940 Eh ::
:: dispersion energy -0.066596238268 Eh ::
:: halogen bond corr. 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
@ -390,26 +400,26 @@ NAME = cmmd.in
Property printout bound to 'properties.out'
-------------------------------------------------
| TOTAL ENERGY -4.175218519975 Eh |
| GRADIENT NORM 0.000006627564 Eh/α |
| HOMO-LUMO GAP 17.353313970090 eV |
| TOTAL ENERGY -106.196831730665 Eh |
| GRADIENT NORM 0.015896196187 Eh/α |
| HOMO-LUMO GAP 1.492422010339 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2022/07/22 at 20:31:34.439
* finished run on 2022/08/04 at 09:43:13.520
------------------------------------------------------------------------
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
* wall-time: 0 d, 0 h, 0 min, 0.293 sec
* cpu-time: 0 d, 0 h, 0 min, 0.284 sec
* ratio c/w: 0.969 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
* wall-time: 0 d, 0 h, 0 min, 0.235 sec
* cpu-time: 0 d, 0 h, 0 min, 0.234 sec
* ratio c/w: 0.995 speedup
------------------------- --------------------
FINAL SINGLE POINT ENERGY -4.175218519980
FINAL SINGLE POINT ENERGY -106.196831730670
------------------------- --------------------
@ -417,9 +427,9 @@ FINAL SINGLE POINT ENERGY -4.175218519980
ORCA NUMERICAL FREQUENCIES
----------------------------------------------------------------------------
Number of atoms ... 5
Number of atoms ... 71
Central differences ... used
Number of displacements ... 30
Number of displacements ... 426
Numerical increment ... 5.000e-03 bohr
IR-spectrum generation ... on
Raman-spectrum generation ... off
@ -432,280 +442,81 @@ 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
<< Calculating on displaced geometry 1 (of 426) >>
<< Calculating on displaced geometry 2 (of 426) >>
<< Calculating on displaced geometry 3 (of 426) >>
<< Calculating on displaced geometry 4 (of 426) >>
<< Calculating on displaced geometry 5 (of 426) >>
<< Calculating on displaced geometry 6 (of 426) >>
<< Calculating on displaced geometry 7 (of 426) >>
<< Calculating on displaced geometry 8 (of 426) >>
<< Calculating on displaced geometry 9 (of 426) >>
<< Calculating on displaced geometry 10 (of 426) >>
<< Calculating on displaced geometry 11 (of 426) >>
<< Calculating on displaced geometry 12 (of 426) >>
<< Calculating on displaced geometry 13 (of 426) >>
<< Calculating on displaced geometry 14 (of 426) >>
<< Calculating on displaced geometry 15 (of 426) >>
<< Calculating on displaced geometry 16 (of 426) >>
<< Calculating on displaced geometry 17 (of 426) >>
<< Calculating on displaced geometry 18 (of 426) >>
<< Calculating on displaced geometry 19 (of 426) >>
<< Calculating on displaced geometry 20 (of 426) >>
<< Calculating on displaced geometry 21 (of 426) >>
<< Calculating on displaced geometry 22 (of 426) >>
<< Calculating on displaced geometry 23 (of 426) >>
<< Calculating on displaced geometry 24 (of 426) >>
<< Calculating on displaced geometry 25 (of 426) >>
<< Calculating on displaced geometry 26 (of 426) >>
<< Calculating on displaced geometry 27 (of 426) >>
<< Calculating on displaced geometry 28 (of 426) >>
<< Calculating on displaced geometry 29 (of 426) >>
<< Calculating on displaced geometry 30 (of 426) >>
<< Calculating on displaced geometry 31 (of 426) >>
<< Calculating on displaced geometry 32 (of 426) >>
<< Calculating on displaced geometry 33 (of 426) >>
<< Calculating on displaced geometry 34 (of 426) >>
<< Calculating on displaced geometry 35 (of 426) >>
<< Calculating on displaced geometry 36 (of 426) >>
<< Calculating on displaced geometry 37 (of 426) >>
<< Calculating on displaced geometry 38 (of 426) >>
<< Calculating on displaced geometry 39 (of 426) >>
<< Calculating on displaced geometry 40 (of 426) >>
<< Calculating on displaced geometry 41 (of 426) >>
<< Calculating on displaced geometry 42 (of 426) >>
<< Calculating on displaced geometry 43 (of 426) >>
<< Calculating on displaced geometry 44 (of 426) >>
<< Calculating on displaced geometry 45 (of 426) >>
<< Calculating on displaced geometry 46 (of 426) >>
<< Calculating on displaced geometry 47 (of 426) >>
<< Calculating on displaced geometry 48 (of 426) >>
<< Calculating on displaced geometry 49 (of 426) >>
<< Calculating on displaced geometry 50 (of 426) >>
<< Calculating on displaced geometry 51 (of 426) >>
<< Calculating on displaced geometry 52 (of 426) >>
<< Calculating on displaced geometry 53 (of 426) >>
<< Calculating on displaced geometry 54 (of 426) >>
<< Calculating on displaced geometry 55 (of 426) >>
<< Calculating on displaced geometry 56 (of 426) >>
<< Calculating on displaced geometry 57 (of 426) >>
<< Calculating on displaced geometry 58 (of 426) >>
<< Calculating on displaced geometry 59 (of 426) >>
<< Calculating on displaced geometry 60 (of 426) >>
<< Calculating on displaced geometry 61 (of 426) >>
<< Calculating on displaced geometry 62 (of 426) >>
<< Calculating on displaced geometry 63 (of 426) >>
<< Calculating on displaced geometry 64 (of 426) >>
<< Calculating on displaced geometry 65 (of 426) >>
<< Calculating on displaced geometry 66 (of 426) >>
<< Calculating on displaced geometry 67 (of 426) >>
<< Calculating on displaced geometry 68 (of 426) >>
<< Calculating on displaced geometry 69 (of 426) >>
<< Calculating on displaced geometry 70 (of 426) >>
<< Calculating on displaced geometry 71 (of 426) >>
<< Calculating on displaced geometry 72 (of 426) >>
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<< Calculating on displaced geometry 74 (of 426) >>
<< Calculating on displaced geometry 75 (of 426) >>
<< Calculating on displaced geometry 76 (of 426) >>
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<< Calculating on displaced geometry 78 (of 426) >>

2
cmmde_gui/test/grafena/freq/cmmd.xtberr
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cmmde_gui/test/grafena/freq/cmmd.xtbtopo.mol
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cmmde_gui/test/metana3/freq/cmmd.gbw → cmmde_gui/test/grafena/freq/cmmd_D00000.gbw
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cmmde_gui/test/grafena/freq/cmmd_D00000.hostnames
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compute

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cmmde_gui/test/grafena/freq/cmmd_D00000.res.Dipoles
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cmmde_gui/test/grafena/freq/cmmd_D00000.res.Gradients
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cmmde_gui/test/grafena/freq/cmmd_D00000.xtbrestart
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0
cmmde_gui/test/alala/alala/cmmd_property.txt → cmmde_gui/test/grafena/freq/cmmd_D00000_property.txt
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