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CMMDE
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modified gui

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Aditya Wibawa Sakti 3 years ago
parent 69c1a22c6d
commit d06df3d28f
19 changed files with 135 additions and 7974 deletions
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  1. 38
      cmmde_gui/geom.xyz
  2. 119
      cmmde_gui/gui.py
  3. 102
      cmmde_gui/molekul/cmmd.engrad
  4. BIN
      cmmde_gui/molekul/cmmd.gbw
  5. 8
      cmmde_gui/molekul/cmmd.in
  6. 3373
      cmmde_gui/molekul/cmmd.opt
  7. 4203
      cmmde_gui/molekul/cmmd.out
  8. BIN
      cmmde_gui/molekul/cmmd.xtbrestart
  9. 24
      cmmde_gui/molekul/cmmd.xyz
  10. 6
      cmmde_gui/molekul/cmmd_property.txt
  11. 192
      cmmde_gui/molekul/cmmd_trj.xyz
  12. 1
      cmmde_gui/molekul/geom.smi
  13. 24
      cmmde_gui/molekul/geom.xyz
  14. 10
      cmmde_gui/molekul/run.sh
  15. 8
      cmmde_gui/molekul/run_babel.sh
  16. 1
      cmmde_gui/molekul/slurm-2879.out
  17. 0
      cmmde_gui/molekul/slurm-2880.out
  18. 0
      cmmde_gui/test/.xtboptok
  19. BIN
      lib/__pycache__/cmmde_gen2poscar.cpython-39.pyc

38
cmmde_gui/geom.xyz
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@ -0,0 +1,38 @@
Al12 O18
1.0
4.805028 0.000000 0.000000
-2.402514 4.161276 0.000000
0.000000 0.000000 13.116254
Al O
12 18
direct
0.000000 0.000000 0.147904 Al
0.333333 0.666667 0.018763 Al
0.333333 0.666667 0.314571 Al
0.666667 0.333333 0.185429 Al
0.666667 0.333333 0.481237 Al
0.000000 0.000000 0.352096 Al
0.000000 0.000000 0.647904 Al
0.333333 0.666667 0.518763 Al
0.333333 0.666667 0.814571 Al
0.666667 0.333333 0.685429 Al
0.666667 0.333333 0.981237 Al
0.000000 0.000000 0.852096 Al
0.306146 0.000000 0.250000 O
0.666667 0.027187 0.083333 O
0.000000 0.306146 0.250000 O
0.693854 0.693854 0.250000 O
0.972813 0.639479 0.083333 O
0.360521 0.333333 0.083333 O
0.972813 0.333333 0.583333 O
0.333333 0.360521 0.416667 O
0.666667 0.639479 0.583333 O
0.360521 0.027187 0.583333 O
0.639479 0.972813 0.416667 O
0.027187 0.666667 0.416667 O
0.639479 0.666667 0.916667 O
0.000000 0.693854 0.750000 O
0.333333 0.972813 0.916667 O
0.027187 0.360521 0.916667 O
0.306146 0.306146 0.750000 O
0.693854 0.000000 0.750000 O

119
cmmde_gui/gui.py
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@ -30,7 +30,7 @@ def cmmde_gui():
# Terminal widget
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
height = 500, disabled=True
)
# CMMDE software options
software_btn = pn.widgets.Select(name="Software selections",value='Orca',options=['Orca','GROMACS','Dcdftbmd','Quantum Espresso'])
@ -45,26 +45,43 @@ def cmmde_gui():
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
# Name your molecule/Material
Name_input = pn.widgets.TextInput(name="Molecule name")
id_input = pn.widgets.TextInput(name="Input your name")
workdir = os.getenv("HOME") + "/" + "scr"
# File input (if you don't want to draw the structure)
FileInput = pn.widgets.FileInput(title='Input structure',accept='.xyz, .vasp, CONTCAR, POSCAR, .pdb')
def fileinput(event):
if FileInput.value is not None:
FileInput.save("geom.xyz")
FileInput.param.watch(fileinput,'value')
# CMMDE running button
Run_btn = pn.widgets.Button(name="Run CMMDE!",button_type='primary')
# RunMessage = pn.widgets.StaticText()
charge = pn.widgets.TextInput(name="Charge",value="0")
mult = pn.widgets.TextInput(name="Spin multiplicity",value="1")
def run(event):
# RunMessage.value = " "
# terminal.clear()
unik = str(uuid.uuid4().hex)
# unik = str(uuid.uuid4().hex)
Folder = workdir + "/" + id_input.value + "/" + Name_input.value
Folder = Name_input.value + "_" + unik
os.makedirs(Folder)
os.chdir(Folder)
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])])
if editor == JSMEEditor(value=" "):
geom = save(FileInput.filename)
else:
geom = editor.value
TextArea.value = TextArea.value + "\n" + "Mempersiapkan Struktur 3 Dimensi!"
cmd = subprocess.run(["cmmde.py","-i","{}".format(geom),"-s","{}".format(software[software_btn.value]),"-j","{}".format(jobs),"-m","{}".format(method[method_btn.value]),"-c","{}".format(charge.value),"-mult","{}".format(mult.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" + "Perhitungan anda telah tersubmit!"
@ -75,9 +92,22 @@ def cmmde_gui():
Run_btn.on_click(run)
# Upload structure button
# Check directory button
checkdir_btn = pn.widgets.Button(name="Generate work directory",type="primary")
TextWarning = pn.widgets.StaticText()
def checkdir(event):
Folder = workdir + "/" + id_input.value + "/" + Name_input.value
isExist = os.path.exists(Folder)
TextWarning.value = ""
if isExist:
TextWarning.value = "Directory exists! Change the molecule name!"
else:
os.makedirs(Folder)
TextWarning.value = "Successfully create the directory!"
checkdir_btn.on_click(checkdir)
structure_input = pn.widgets.FileInput()
# Post calculations
@ -96,6 +126,8 @@ def cmmde_gui():
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:
Folder = workdir + "/" + id_input.value + "/" + Name_input.value
os.chdir(Folder)
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)
@ -103,7 +135,7 @@ def cmmde_gui():
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
# Check the queue progress
def progress(event):
# terminal.clear()
# terminal.subprocess.run("squeue")
@ -112,27 +144,70 @@ def cmmde_gui():
Progress_btn = pn.widgets.Button(name="Check calculation",button_type='primary')
Progress_btn = pn.widgets.Button(name="Check queue",button_type='primary')
Progress_btn.on_click(progress)
# Check the output
def check_out(event):
cmd = subprocess.run(["tail","-f","cmmd.out"],capture_output=True,text=True)
cmd.stdout
checkout_btn = pn.widgets.Button(name="Check output",button_type='primary')
checkout_btn.on_click(check_out)
# Check the calculation progress
def calc_progress(event):
cmd = subprocess.run(["tail", "-n", "10", "cmmd.out"],capture_output=True,text=True)
TextArea.value = TextArea.value + "\n" + cmd.stdout
Checkcalc_btn = pn.widgets.Button(name="Check calculation",button_type='primary')
Checkcalc_btn.on_click(calc_progress)
# # Download Button
download_xyz = pn.widgets.FileDownload(file="cmmd.xyz",filename="cmmd.xyz")
download_slab = pn.widgets.FileDownload(file="slab.vasp",filename="slab.vasp")
# Slab Builder
hkl_input = pn.widgets.TextInput(name="Miller index (hkl)",placeholder="Example: 100")
size_input = pn.widgets.TextInput(name="Dimension",placeholder="Example: 2x2")
layer_input = pn.widgets.TextInput(name="Layer",placeholder="Example: 2")
slabbuilder_btn = pn.widgets.Button(name="Build it!",button_type="primary")
def slab_builder(event):
Folder = workdir + "/" + id_input.value + "/" + Name_input.value
os.chdir(Folder)
os.system("mv geom.xyz POSCAR")
hkl = hkl_input.value
size = size_input.value
layer = layer_input.value
cmd = subprocess.run(["cmmdepre.py","-j","surface","-hkl","{}".format(hkl),"-s","{}".format(size),"-n","{}".format(layer),"-i","POSCAR"])
os.system("mv slab_{}.xyz cmmd.xyz".format(hkl))
os.system("mv slab_{}.vasp slab.vasp".format(hkl))
cmd = subprocess.run(["echo","({})-surface construction done!".format(hkl)],capture_output=True,text=True)
TextArea.value = TextArea.value + "\n" + cmd.stdout
# xyzview = py3Dmol.view()
# with open('slab_{}.xyz'.format(hkl),'r') as f:
# xyz = f.read()
# xyzview.addModel(xyz,'xyz')
# xyzview.setStyle('stick')
# xyzviewer.object = xyzview
slabbuilder_btn.on_click(slab_builder)
# Solution Builder
# fileinput_solute = pn.widgets.FileInput(accept=".xyz",multiple=True)
# fileinput_solvent = pn.widgets.FileInput(accept=".xyz")
# def SolutionBuilder(event):
# solute = fileinput_solute.value
# solvent = fileinput_solute.value
# Visualize the results
xyzview = py3Dmol.view()
xyzview.setBackgroundColor('0xeeeeee')
xyzview.zoomTo()
xyzviewer = Py3DMol(xyzview, height=400, sizing_mode="stretch_width",name="CMMDE viewer")
def visualize(event):
xyzview = py3Dmol.view()
Folder = workdir + "/" + id_input.value + "/" + Name_input.value
os.chdir(Folder)
with open('cmmd.xyz','r') as f:
xyz = f.read()
xyzview.addModel(xyz,'xyz')
xyzview.setStyle('stick')
xyzviewer.object = xyzview
# xyzviewer.object = xyzview
visual_btn = pn.widgets.Button(name="Visualize!", button_type='primary')
visual_btn.on_click(visualize)
@ -161,8 +236,8 @@ def cmmde_gui():
return pn.template.MaterialTemplate(
site="CMMDE-GUI",
title="CMMDE Editor",
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)],
main=[editor, TextArea, pn.Tabs(xyzviewer)],
sidebar=[pn.Card(id_input,Name_input,charge,mult,checkdir_btn,TextWarning,pn.Card(FileInput,title="Upload molecule",collapsed=True),pn.Card(pn.Card(FileInput,title="Unit cell",collapsed=True),hkl_input,size_input,layer_input,pn.Row(slabbuilder_btn,visual_btn),pn.Row(download_xyz,download_slab),title="Surface Builder",collapsed=True),title="Pre-Calculation",collapsed=True),pn.Card(pn.Card(software_btn,job_btn,method_btn,pn.Row(Run_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),title="General calculation",collapsed=True),title="Main Calculation",collapsed=True),pn.Card(post_software_btn,post_btn,post_method_btn,pn.Row(runpost_btn,Progress_btn),pn.Row(Checkcalc_btn,visual_btn),title="Post-Calculation",collapsed=True)],
header_background=accent, accent_base_color=accent
)

102
cmmde_gui/molekul/cmmd.engrad
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@ -1,102 +0,0 @@
#
# Number of atoms
#
22
#
# The current total energy in Eh
#
-24.300689883530
#
# The current gradient in Eh/bohr
#
-0.000078011731
0.000077990155
-0.000172228341
0.000077300972
-0.000042371283
0.000161175655
-0.000052245246
-0.000103228073
0.000049462422
0.000001820626
0.000105051957
0.000094782729
0.000086221104
-0.000080609774
-0.000172014815
-0.000078903466
0.000042802807
0.000160254314
0.000050604245
0.000099415702
0.000049911283
-0.000002512022
-0.000100677629
0.000095940374
0.000056324030
-0.000026054592
0.000017365028
-0.000013951222
-0.000000307285
-0.000009022819
0.000004009247
0.000094374895
-0.000051467186
-0.000008807355
-0.000037453860
-0.000046442953
0.000063131670
-0.000001043091
-0.000026363600
0.000023364226
0.000005993197
-0.000031768002
-0.000049385865
-0.000001522204
0.000014911885
0.000012879917
-0.000000298953
-0.000007152993
-0.000062772195
0.000028037742
0.000014978945
-0.000006117115
-0.000093207811
-0.000053946988
0.000010826250
0.000036672974
-0.000043812282
-0.000063088326
0.000003364246
-0.000026478385
-0.000022753307
-0.000009224066
-0.000032077644
0.000052065564
0.000002294948
0.000013993374
#
# The atomic numbers and current coordinates in Bohr
#
6 -3.1707575 0.2177972 1.6020414
6 -2.8099636 -1.9153359 -0.2995915
6 -0.1693597 -1.4539744 -1.3830761
6 1.9809828 -2.5062842 0.2758215
6 3.1608987 -0.2282573 1.6062985
6 2.8030447 1.9100763 -0.2900301
6 0.1641039 1.4516803 -1.3788482
6 -1.9888064 2.4994425 0.2795973
1 -2.1624375 -0.2154170 3.3453092
1 -5.1516399 0.5292905 2.0710045
1 -4.2110958 -1.7429666 -1.8049678
1 -3.0006371 -3.7835331 0.5439859
1 -0.0290829 -2.2380751 -3.2862394
1 3.3966523 -3.4147175 -0.9171384
1 1.2960176 -3.9106360 1.6159815
1 5.1410759 -0.5410329 2.0774044
1 2.1499317 0.2001714 3.3492010
1 4.2064587 1.7419051 -1.7937487
1 2.9924414 3.7759296 0.5590142
1 0.0267864 2.2409994 -3.2800674
1 -3.4027000 3.4110120 -0.9131000
1 -1.3059498 3.9002107 1.6245537

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cmmde_gui/molekul/cmmd.gbw
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cmmde_gui/molekul/cmmd.in
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@ -1,8 +0,0 @@
#CMMDE generated Orca input file
!XTB2 opt
%pal
nprocs 1
end
*xyzfile 0 1 geom.xyz

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cmmde_gui/molekul/cmmd.opt
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cmmde_gui/molekul/cmmd.out
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cmmde_gui/molekul/cmmd.xtbrestart
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24
cmmde_gui/molekul/cmmd.xyz
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@ -1,24 +0,0 @@
22
Coordinates from ORCA-job cmmd
C -1.67789262482362 0.11525329869831 0.84776377059116
C -1.48696869578108 -1.01355209578752 -0.15853701195241
C -0.08962128164374 -0.76941009503983 -0.73189236960181
C 1.04829096618154 -1.32626849868764 0.14595842599341
C 1.67267554494252 -0.12078858357241 0.85001656867164
C 1.48330738130646 1.01076883814883 -0.15347731629115
C 0.08684005579747 0.76819612789448 -0.72965504301328
C -1.05243100784612 1.32264799435766 0.14795651490402
H -1.14431262086837 -0.11399375088709 1.77026137692973
H -2.72613042030156 0.28008844485899 1.09592839250909
H -2.22841592956031 -0.92233820827076 -0.95514782836367
H -1.58786878660918 -2.00215949404559 0.28786493139880
H -0.01538998189394 -1.18433834677691 -1.73900299660471
H 1.79743095555466 -1.80699066458022 -0.48532872804034
H 0.68582296618717 -2.06941944989369 0.85514056319983
H 2.72054019275969 -0.28630229679690 1.09931508645209
H 1.13769483539212 0.10592615728604 1.77232082684411
H 2.22596209405418 0.92177649029586 -0.94921094504504
H 1.58353180060076 1.99813590573103 0.29581758406903
H 0.01417474663286 1.18588579823564 -1.73573690178012
H -1.80063130399002 1.80502981213503 -0.48319168424581
H -0.69107888609148 2.06390261669669 0.85967678337543

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

192
cmmde_gui/molekul/cmmd_trj.xyz
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@ -1,192 +0,0 @@
22
Coordinates from ORCA-job cmmd E -24.299620455070
C -1.725240 0.119920 0.813870
C -1.484880 -1.019420 -0.160120
C -0.085570 -0.765670 -0.712320
C 1.044960 -1.324190 0.165240
C 1.718310 -0.124670 0.817500
C 1.480690 1.016080 -0.155250
C 0.082270 0.763840 -0.710460
C -1.047980 1.320790 0.167740
H -1.260210 -0.102750 1.781010
H -2.791150 0.295240 0.986430
H -2.217220 -0.965940 -0.975640
H -1.588450 -1.998500 0.316400
H 0.001250 -1.183270 -1.721800
H 1.770250 -1.843610 -0.474190
H 0.699930 -2.046300 0.911040
H 2.784520 -0.299540 0.991200
H 1.251920 0.094270 1.784860
H 2.214410 0.963270 -0.969600
H 1.584150 1.994690 0.322370
H -0.003520 1.183550 -1.719180
H -1.770860 1.845420 -0.469780
H -0.702050 2.038840 0.917520
22
Coordinates from ORCA-job cmmd E -24.300403307080
C -1.709132 0.115048 0.826880
C -1.487578 -1.020249 -0.164171
C -0.087098 -0.768140 -0.722859
C 1.044630 -1.326248 0.159829
C 1.702747 -0.120052 0.829946
C 1.483786 1.017132 -0.159357
C 0.084088 0.766620 -0.720867
C -1.048130 1.322791 0.162264
H -1.220711 -0.112775 1.776421
H -2.767293 0.286107 1.027865
H -2.223486 -0.956290 -0.969999
H -1.586266 -2.001512 0.300410
H -0.002435 -1.182897 -1.730211
H 1.776008 -1.841904 -0.467851
H 0.685755 -2.046335 0.894657
H 2.760757 -0.291127 1.032519
H 1.212674 0.104640 1.779268
H 2.221057 0.953970 -0.964009
H 1.582348 1.997725 0.306717
H 0.000571 1.183628 -1.727369
H -1.777706 1.842783 -0.463950
H -0.689056 2.039136 0.900706
22
Coordinates from ORCA-job cmmd E -24.300625110610
C -1.688892 0.110555 0.838929
C -1.487880 -1.018290 -0.167108
C -0.088001 -0.769291 -0.731798
C 1.043682 -1.325583 0.154806
C 1.683125 -0.115834 0.841502
C 1.484275 1.015358 -0.162300
C 0.085172 0.767987 -0.729671
C -1.047503 1.322045 0.157119
H -1.173838 -0.122387 1.770474
H -2.740485 0.277951 1.068830
H -2.227954 -0.939663 -0.965143
H -1.583761 -2.004133 0.285749
H -0.005328 -1.182022 -1.738588
H 1.784243 -1.833370 -0.464143
H 0.671687 -2.047435 0.879948
H 2.734248 -0.283624 1.073308
H 1.166063 0.114491 1.772522
H 2.225628 0.937925 -0.959263
H 1.579857 2.000291 0.292581
H 0.003743 1.183225 -1.735509
H -1.786675 1.833075 -0.460894
H -0.675878 2.040782 0.885491
22
Coordinates from ORCA-job cmmd E -24.300658534300
C -1.683044 0.109671 0.842540
C -1.487918 -1.016665 -0.166983
C -0.088217 -0.769447 -0.733107
C 1.044132 -1.324679 0.153495
C 1.677508 -0.115054 0.844955
C 1.484328 1.013785 -0.162146
C 0.085421 0.768184 -0.730926
C -1.048036 1.321107 0.155745
H -1.159198 -0.124866 1.768748
H -2.733089 0.276104 1.081191
H -2.228551 -0.930780 -0.963992
H -1.585189 -2.004851 0.281233
H -0.006427 -1.182147 -1.740251
H 1.788442 -1.826774 -0.465552
H 0.670352 -2.050064 0.874996
H 2.727029 -0.281989 1.085508
H 1.151587 0.116998 1.770600
H 2.226192 0.929376 -0.958172
H 1.581191 2.000949 0.288380
H 0.004934 1.183520 -1.737080
H -1.791083 1.825917 -0.462620
H -0.674835 2.043756 0.880278
22
Coordinates from ORCA-job cmmd E -24.300678425300
C -1.679506 0.109965 0.845350
C -1.487907 -1.014891 -0.165490
C -0.088461 -0.769531 -0.732743
C 1.045298 -1.324031 0.152235
C 1.674171 -0.115440 0.847637
C 1.484310 1.012056 -0.160594
C 0.085683 0.768292 -0.730515
C -1.049284 1.320426 0.154403
H -1.149225 -0.125125 1.768088
H -2.728516 0.275701 1.090181
H -2.228031 -0.922067 -0.962812
H -1.588094 -2.005009 0.278512
H -0.008091 -1.182838 -1.740143
H 1.792681 -1.818304 -0.469956
H 0.673286 -2.055248 0.869460
H 2.722660 -0.281771 1.094218
H 1.141890 0.117227 1.769860
H 2.225618 0.921062 -0.957034
H 1.583975 2.001035 0.286042
H 0.006702 1.184357 -1.736891
H -1.795546 1.816846 -0.467384
H -0.678084 2.049339 0.874415
22
Coordinates from ORCA-job cmmd E -24.300683906960
C -1.679004 0.111083 0.846262
C -1.487774 -1.014271 -0.163796
C -0.088697 -0.769539 -0.732111
C 1.046183 -1.324330 0.151061
C 1.673727 -0.116588 0.848520
C 1.484164 1.011456 -0.158851
C 0.085921 0.768309 -0.729871
C -1.050218 1.320713 0.153178
H -1.147302 -0.123035 1.768607
H -2.727718 0.276560 1.092502
H -2.227597 -0.919980 -0.961478
H -1.589297 -2.004506 0.279483
H -0.009687 -1.183453 -1.739420
H 1.794361 -1.814113 -0.474068
H 0.677052 -2.059360 0.865783
H 2.721959 -0.282692 1.096332
H 1.140182 0.115087 1.770437
H 2.225163 0.919161 -0.955679
H 1.585116 2.000505 0.287191
H 0.008358 1.185007 -1.736149
H -1.797349 1.812418 -0.471664
H -0.682013 2.053620 0.870572
22
Coordinates from ORCA-job cmmd E -24.300687361530
C -1.678599 0.112925 0.847033
C -1.487456 -1.013868 -0.161409
C -0.089093 -0.769496 -0.731792
C 1.047194 -1.325156 0.148943
C 1.673355 -0.118447 0.849285
C 1.483824 1.011070 -0.156406
C 0.086316 0.768274 -0.729552
C -1.051283 1.321534 0.151000
H -1.146019 -0.119120 1.769453
H -2.727060 0.278101 1.094226
H -2.227681 -0.920293 -0.958895
H -1.589279 -2.003498 0.282769
H -0.012172 -1.184023 -1.738944
H 1.795860 -1.810369 -0.479379
H 0.681533 -2.064271 0.860927
H 2.721389 -0.284278 1.097826
H 1.139154 0.111110 1.771394
H 2.225235 0.919623 -0.953037
H 1.585027 1.999483 0.290618
H 0.010904 1.185580 -1.735672
H -1.798966 1.808511 -0.477121
H -0.686652 2.058658 0.865573
22
Coordinates from ORCA-job cmmd E -24.300689883530
C -1.677893 0.115253 0.847764
C -1.486969 -1.013552 -0.158537
C -0.089621 -0.769410 -0.731892
C 1.048291 -1.326268 0.145958
C 1.672676 -0.120789 0.850017
C 1.483307 1.010769 -0.153477
C 0.086840 0.768196 -0.729655
C -1.052431 1.322648 0.147957
H -1.144313 -0.113994 1.770261
H -2.726130 0.280088 1.095928
H -2.228416 -0.922338 -0.955148
H -1.587869 -2.002159 0.287865
H -0.015390 -1.184338 -1.739003
H 1.797431 -1.806991 -0.485329
H 0.685823 -2.069419 0.855141
H 2.720540 -0.286302 1.099315
H 1.137695 0.105926 1.772321
H 2.225962 0.921776 -0.949211
H 1.583532 1.998136 0.295818
H 0.014175 1.185886 -1.735737
H -1.800631 1.805030 -0.483192
H -0.691079 2.063903 0.859677

1
cmmde_gui/molekul/geom.smi
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C2CC1CCCC1C2

24
cmmde_gui/molekul/geom.xyz
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22
C -1.72524 0.11992 0.81387
C -1.48488 -1.01942 -0.16012
C -0.08557 -0.76567 -0.71232
C 1.04496 -1.32419 0.16524
C 1.71831 -0.12467 0.81750
C 1.48069 1.01608 -0.15525
C 0.08227 0.76384 -0.71046
C -1.04798 1.32079 0.16774
H -1.26021 -0.10275 1.78101
H -2.79115 0.29524 0.98643
H -2.21722 -0.96594 -0.97564
H -1.58845 -1.99850 0.31640
H 0.00125 -1.18327 -1.72180
H 1.77025 -1.84361 -0.47419
H 0.69993 -2.04630 0.91104
H 2.78452 -0.29954 0.99120
H 1.25192 0.09427 1.78486
H 2.21441 0.96327 -0.96960
H 1.58415 1.99469 0.32237
H -0.00352 1.18355 -1.71918
H -1.77086 1.84542 -0.46978
H -0.70205 2.03884 0.91752

10
cmmde_gui/molekul/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

8
cmmde_gui/molekul/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

1
cmmde_gui/molekul/slurm-2879.out
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1 molecule converted

0
cmmde_gui/molekul/slurm-2880.out
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0
cmmde_gui/test/.xtboptok
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lib/__pycache__/cmmde_gen2poscar.cpython-39.pyc
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