modified gui

cmmde_gui/geom.xyz

@@ -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

cmmde_gui/gui.py

@@ -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):
+# Check the calculation progress
-        cmd = subprocess.run(["tail","-f","cmmd.out"],capture_output=True,text=True)
+    def calc_progress(event):
-        cmd.stdout
+        cmd = subprocess.run(["tail", "-n", "10", "cmmd.out"],capture_output=True,text=True)
-    checkout_btn = pn.widgets.Button(name="Check output",button_type='primary')
+        TextArea.value = TextArea.value + "\n" + cmd.stdout 
-    checkout_btn.on_click(check_out)
+    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)],
+        main=[editor, TextArea, 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)],
+        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
     )    
 

cmmde_gui/molekul/cmmd.engrad

@@ -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 

cmmde_gui/molekul/cmmd.in

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

cmmde_gui/molekul/cmmd.xyz

@@ -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

cmmde_gui/molekul/cmmd_property.txt

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

cmmde_gui/molekul/cmmd_trj.xyz

@@ -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

cmmde_gui/molekul/geom.smi

@@ -1 +0,0 @@
-C2CC1CCCC1C2

cmmde_gui/molekul/geom.xyz

@@ -1,24 +0,0 @@
-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

cmmde_gui/molekul/run.sh

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

cmmde_gui/molekul/run_babel.sh

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

cmmde_gui/molekul/slurm-2879.out

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