cmmde-gui modification

bin/cmmdepre.py

@@ -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.')

cmmde_gui/gui.py

@@ -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(
+    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",
-        "Computational Molecular and Material Design Environment\n Authors:\n Universitas Pertamina\n Institut Teknologi Sumatera\n Masyarakat Komputasi Indonesia\n\n",
+        height = 500
-        options = {"cursorBlink": True},
-        height = 200, sizing_mode = 'stretch_width'
         )
 # 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.clear()
-            terminal.subprocess.run("cmmdepost.py","-j{}".format(post_calc[post_btn.value[0]]),"-s{}".format(post_software[post_software_btn.value[0]]))  
+        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.makedirs(post_calc[post_btn.value])
-            os.chdir(post_calc[post_btn.value[0]])
+            os.chdir(post_calc[post_btn.value])
-            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]]))
+            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)],
+        main=[editor, TextArea, 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)],
+        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
     )    
 

cmmde_gui/test/ala/cmmd.engrad

@@ -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 

cmmde_gui/test/ala/cmmd.opt

@@ -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
-

cmmde_gui/test/ala/cmmd.xyz

@@ -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

cmmde_gui/test/ala/cmmd_trj.xyz

@@ -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

cmmde_gui/test/ala/freq/cmmd.engrad

@@ -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 

cmmde_gui/test/ala/freq/cmmd.hess

@@ -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
-

cmmde_gui/test/ala/freq/cmmd_property.txt

@@ -1,48 +0,0 @@
--------------------------------------------------------------
------------------------ !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! ------------------------
-# -------------------------------------------------------------

cmmde_gui/test/ala/geom.smi

@@ -1 +0,0 @@
-C

cmmde_gui/test/ala/geom.xyz

@@ -1,7 +0,0 @@
-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

cmmde_gui/test/alala/alala/cmmd.engrad

@@ -1,74 +0,0 @@
-#
-# 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 

cmmde_gui/test/alala/alala/cmmd.in

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

cmmde_gui/test/alala/alala/cmmd.xyz

@@ -1,17 +0,0 @@
-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

cmmde_gui/test/alala/alala/cmmd_trj.xyz

@@ -1,102 +0,0 @@
-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

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

@@ -1,74 +0,0 @@
-#
-# 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 

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

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

cmmde_gui/test/alala/alala/freq/cmmd_property.txt

@@ -1,78 +0,0 @@
--------------------------------------------------------------
------------------------ !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! ------------------------
-# -------------------------------------------------------------

cmmde_gui/test/alala/alala/freq/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/test/alala/alala/geom.smi

@@ -1 +0,0 @@
-C1CCCC1

cmmde_gui/test/alala/alala/geom.xyz

@@ -1,17 +0,0 @@
-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

cmmde_gui/test/alala/alala/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/test/alala/alala/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/test/alala/alala/slurm-2887.out

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

cmmde_gui/test/alala/cmmd.engrad

@@ -1,74 +0,0 @@
-#
-# 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 

cmmde_gui/test/alala/cmmd.in

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

cmmde_gui/test/alala/cmmd.xyz

@@ -1,17 +0,0 @@
-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

cmmde_gui/test/alala/cmmd_trj.xyz

@@ -1,102 +0,0 @@
-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

cmmde_gui/test/alala/freq/cmmd.engrad

@@ -1,74 +0,0 @@
-#
-# 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 

cmmde_gui/test/alala/freq/cmmd.in

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

cmmde_gui/test/alala/freq/cmmd_property.txt

@@ -1,78 +0,0 @@
--------------------------------------------------------------
------------------------ !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! ------------------------
-# -------------------------------------------------------------

cmmde_gui/test/alala/freq/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/test/alala/geom.smi

@@ -1 +0,0 @@
-C1CCCC1

cmmde_gui/test/alala/geom.xyz

@@ -1,17 +0,0 @@
-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

cmmde_gui/test/alala/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/test/alala/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/test/alala/slurm-2885.out

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

cmmde_gui/test/cmmd.engrad

@@ -1,62 +0,0 @@
-#
-# 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 

cmmde_gui/test/cmmd.in

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

cmmde_gui/test/cmmd.opt

@@ -1,789 +0,0 @@
-
-$orca_opt_file
-
-$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
-$redundant_internals
- 12 18 24 0 0
-   1   0   0
-   2   1   0
-   3   2   0
-   4   3   0
-   5   4   0
-   5   0   0
-   6   0   0
-   7   1   0
-   8   2   0
-   9   3   0
-  10   4   0
-  11   5   0
-   1   0   5   0   0
-   1   0   6   0   0
-   5   0   6   0   0
-   2   1   7   0   0
-   0   1   2   0   0
-   0   1   7   0   0
-   3   2   8   0   0
-   1   2   8   0   0
-   1   2   3   0   0
-   4   3   9   0   0
-   2   3   9   0   0
-   2   3   4   0   0
-   3   4  10   0   0
-   3   4   5   0   0
-   5   4  10   0   0
-   0   5   4   0   0
-   4   5  11   0   0
-   0   5  11   0   0
-   7   1   0   5   0
-   7   1   0   6   0
-   2   1   0   6   0
-   2   1   0   5   0
-   8   2   1   0   0
-   3   2   1   0   0
-   3   2   1   7   0
-   8   2   1   7   0
-   9   3   2   8   0
-   9   3   2   1   0
-   4   3   2   8   0
-   4   3   2   1   0
-  10   4   3   2   0
-   5   4   3   9   0
-   5   4   3   2   0
-  10   4   3   9   0
-  11   5   4  10   0
-   0   5   4  10   0
-   0   5   4   3   0
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-$energies
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-$redundant_gradients
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-$hessian_approx
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-     14       0.005344   0.010883   0.138715  -0.001323  -0.001999  -0.063285
-     15      -0.605276   0.033707  -0.001323   1.218166  -0.102481   0.002914
-     16       0.040370  -0.370548  -0.001999  -0.102481   1.174360   0.007516
-     17      -0.001467  -0.003623  -0.063285   0.002914   0.007516   0.138731
-     18      -0.001438   0.004164  -0.000001   0.012148   0.007002   0.000095
-     19      -0.000104   0.000320  -0.000061   0.060328   0.023427   0.000447
-     20       0.000016  -0.000177   0.006425   0.000440   0.000049   0.008242
-     21      -0.000268   0.000765   0.000010   0.000500   0.000621  -0.000029
-     22       0.001449  -0.004215  -0.000025  -0.002730  -0.003392  -0.000118
-     23       0.000369  -0.001111   0.000009  -0.000739  -0.000928   0.006375
-     24       0.000680  -0.001963  -0.000057  -0.001277  -0.001587  -0.000025
-     25       0.001122  -0.003253  -0.000088  -0.002112  -0.002625  -0.000047
-     26      -0.000407   0.001068   0.006398   0.000718   0.000887   0.000033
-     27      -0.006358   0.001943  -0.000042  -0.002853  -0.003542  -0.000107
-     28      -0.050388   0.041225   0.000061   0.000474   0.000590  -0.000051
-     29      -0.000549   0.000281   0.008233  -0.000070  -0.000120   0.006412
-     30      -0.249308   0.043303  -0.000454   0.008847   0.059374   0.000603
-     31       0.042906  -0.343492  -0.002820   0.006094   0.026221   0.000211
-     32      -0.000072  -0.003969  -0.045788  -0.000680  -0.000492   0.008209
-     33      -0.008542  -0.048208  -0.000455  -0.283475  -0.062882  -0.001449
-     34       0.005234   0.043756   0.000315  -0.062315  -0.309812  -0.002389
-     35      -0.000445   0.001386   0.008231  -0.000643  -0.001415  -0.045792
-                 18         19         20         21         22         23    
-      0      -0.356756   0.020569  -0.001578   0.048181   0.013624  -0.000877
-      1       0.019862  -0.235820  -0.001514  -0.038300  -0.014394  -0.000362
-      2      -0.001424  -0.001517  -0.045777  -0.000088  -0.000094   0.008217
-      3      -0.006519  -0.050027  -0.000541  -0.249513   0.042938  -0.001127
-      4       0.001907   0.040113   0.000446   0.043456  -0.343013  -0.000994
-      5      -0.000061   0.000010   0.008223  -0.000822  -0.002166  -0.045772
-      6      -0.002514  -0.000174   0.000029   0.008978   0.006162   0.000650
-      7      -0.003525  -0.000270   0.000055   0.059489   0.026750   0.001420
-      8      -0.000079  -0.000051   0.006404   0.000490   0.000186   0.008249
-      9      -0.004728  -0.000375   0.000149  -0.000866   0.004805   0.001266
-     10       0.000797   0.000068  -0.000027   0.000144  -0.000814  -0.000298
-     11      -0.000019  -0.000001   0.000000  -0.000042  -0.000035   0.006429
-     12      -0.001438  -0.000104   0.000016  -0.000268   0.001449   0.000369
-     13       0.004164   0.000320  -0.000177   0.000765  -0.004215  -0.001111
-     14      -0.000001  -0.000061   0.006425   0.000010  -0.000025   0.000009
-     15       0.012148   0.060328   0.000440   0.000500  -0.002730  -0.000739
-     16       0.007002   0.023427   0.000049   0.000621  -0.003392  -0.000928
-     17       0.000095   0.000447   0.008242  -0.000029  -0.000118   0.006375
-     18       0.360650  -0.030410   0.001424   0.000356  -0.000822   0.000122
-     19      -0.030410   0.172190   0.001034  -0.000064   0.000179   0.000082
-     20       0.001424   0.001034   0.032946   0.000050   0.000050  -0.008226
-     21       0.000356  -0.000064   0.000050   0.193111  -0.066510   0.000398
-     22      -0.000822   0.000179   0.000050  -0.066510   0.339829   0.002028
-     23       0.000122   0.000082  -0.008226   0.000398   0.002028   0.032926
-     24      -0.000599   0.000116  -0.000008  -0.000230   0.000548   0.000015
-     25      -0.000713   0.000149  -0.000013  -0.000279   0.000644   0.000018
-     26      -0.000101  -0.000010   0.000004   0.000030   0.000174  -0.008208
-     27      -0.000840   0.000192  -0.000018  -0.000341   0.000752  -0.000096
-     28       0.000135  -0.000029   0.000003   0.000054  -0.000121   0.000014
-     29      -0.000000   0.000001  -0.000000  -0.000001  -0.000001  -0.000002
-     30      -0.000373   0.000064  -0.000004  -0.000136   0.000345  -0.000011
-     31       0.000896  -0.000176   0.000015   0.000344  -0.000814   0.000066
-     32       0.000099   0.000010  -0.000004   0.000018  -0.000104  -0.000038
-     33       0.000613  -0.000114   0.000040   0.000231  -0.000561   0.000031
-     34       0.000707  -0.000149   0.000080   0.000278  -0.000639   0.000064
-     35      -0.000055   0.000056  -0.008237  -0.000015   0.000105   0.000043
-                 24         25         26         27         28         29    
-      0      -0.002150  -0.003564   0.001231  -0.004859   0.000801  -0.000075
-      1       0.000174   0.000280  -0.000088   0.000333  -0.000061   0.000003
-      2      -0.000046  -0.000072   0.006422  -0.000011   0.000002  -0.000000
-      3      -0.008514   0.005306   0.000281  -0.001392   0.000235  -0.000060
-      4      -0.048036   0.043971  -0.001254   0.004760  -0.000782   0.000009
-      5      -0.000578   0.000382   0.008225   0.000013  -0.000069   0.006412
-      6      -0.283492  -0.062475  -0.002693   0.012049   0.059686   0.000634
-      7      -0.062758  -0.309671  -0.003970   0.007370   0.022560   0.000222
-      8      -0.002061  -0.003000  -0.045810   0.000079   0.000447   0.008229
-      9       0.049566  -0.034531  -0.001482  -0.356532   0.019409  -0.001348
-     10       0.017873  -0.015361   0.000114   0.019374  -0.235771  -0.001761
-     11       0.000423  -0.000442   0.008220  -0.001405  -0.001750  -0.045779
-     12       0.000680   0.001122  -0.000407  -0.006358  -0.050388  -0.000549
-     13      -0.001963  -0.003253   0.001068   0.001943   0.041225   0.000281
-     14      -0.000057  -0.000088   0.006398  -0.000042   0.000061   0.008233
-     15      -0.001277  -0.002112   0.000718  -0.002853   0.000474  -0.000070
-     16      -0.001587  -0.002625   0.000887  -0.003542   0.000590  -0.000120
-     17      -0.000025  -0.000047   0.000033  -0.000107  -0.000051   0.006412
-     18      -0.000599  -0.000713  -0.000101  -0.000840   0.000135  -0.000000
-     19       0.000116   0.000149  -0.000010   0.000192  -0.000029   0.000001
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-     21      -0.000230  -0.000279   0.000030  -0.000341   0.000054  -0.000001
-     22       0.000548   0.000644   0.000174   0.000752  -0.000121  -0.000001
-     23       0.000015   0.000018  -0.008208  -0.000096   0.000014  -0.000002
-     24       0.245610   0.096776   0.002290   0.000565  -0.000090   0.000050
-     25       0.096776   0.287230   0.003180   0.000658  -0.000107   0.000083
-     26       0.002290   0.003180   0.032944   0.000160   0.000062  -0.008225
-     27       0.000565   0.000658   0.000160   0.360784  -0.030354   0.001384
-     28      -0.000090  -0.000107   0.000062  -0.030354   0.172259   0.001201
-     29       0.000050   0.000083  -0.008225   0.001384   0.001201   0.032950
-     30       0.000239   0.000293   0.000018   0.000358  -0.000056   0.000038
-     31      -0.000585  -0.000702  -0.000086  -0.000833   0.000134   0.000084
-     32      -0.000048  -0.000077   0.000039  -0.000073   0.000097  -0.008233
-     33      -0.000397  -0.000480  -0.000044  -0.000580   0.000092  -0.000001
-     34      -0.000467  -0.000555  -0.000080  -0.000653   0.000105   0.000000
-     35       0.000043   0.000076  -0.000044   0.000117  -0.000018   0.000003
-                 30         31         32         33         34         35    
-      0      -0.000978   0.004117  -0.001301   0.049449  -0.034666   0.001320
-      1       0.000103  -0.000353  -0.000015   0.018067  -0.015022  -0.000157
-      2      -0.000030  -0.000053   0.006419   0.000311  -0.000331   0.008242
-      3      -0.000313   0.001246  -0.000320   0.000640   0.001057   0.000337
-      4       0.000947  -0.004012   0.001265  -0.002040  -0.003495  -0.001516
-      5       0.000001  -0.000024   0.000025  -0.000036  -0.000079   0.006391
-      6       0.000570  -0.002303   0.000591  -0.001181  -0.001967  -0.000722
-      7       0.000766  -0.003194   0.000897  -0.001629  -0.002764  -0.001107
-      8      -0.000012  -0.000112   0.006405  -0.000028  -0.000035   0.000005
-      9       0.048341   0.013977   0.001700  -0.002169  -0.003712  -0.001574
-     10      -0.038392  -0.014017  -0.000647   0.000361   0.000628   0.000210
-     11      -0.000207  -0.000168   0.008237  -0.000034  -0.000067   0.006414
-     12      -0.249308   0.042906  -0.000072  -0.008542   0.005234  -0.000445
-     13       0.043303  -0.343492  -0.003969  -0.048208   0.043756   0.001386
-     14      -0.000454  -0.002820  -0.045788  -0.000455   0.000315   0.008231
-     15       0.008847   0.006094  -0.000680  -0.283475  -0.062315  -0.000643
-     16       0.059374   0.026221  -0.000492  -0.062882  -0.309812  -0.001415
-     17       0.000603   0.000211   0.008209  -0.001449  -0.002389  -0.045792
-     18      -0.000373   0.000896   0.000099   0.000613   0.000707  -0.000055
-     19       0.000064  -0.000176   0.000010  -0.000114  -0.000149   0.000056
-     20      -0.000004   0.000015  -0.000004   0.000040   0.000080  -0.008237
-     21      -0.000136   0.000344   0.000018   0.000231   0.000278  -0.000015
-     22       0.000345  -0.000814  -0.000104  -0.000561  -0.000639   0.000105
-     23      -0.000011   0.000066  -0.000038   0.000031   0.000064   0.000043
-     24       0.000239  -0.000585  -0.000048  -0.000397  -0.000467   0.000043
-     25       0.000293  -0.000702  -0.000077  -0.000480  -0.000555   0.000076
-     26       0.000018  -0.000086   0.000039  -0.000044  -0.000080  -0.000044
-     27       0.000358  -0.000833  -0.000073  -0.000580  -0.000653   0.000117
-     28      -0.000056   0.000134   0.000097   0.000092   0.000105  -0.000018
-     29       0.000038   0.000084  -0.008233  -0.000001   0.000000   0.000003
-     30       0.192995  -0.066455   0.000010  -0.000240  -0.000291   0.000048
-     31      -0.066455   0.339711   0.002887   0.000597   0.000696   0.000002
-     32       0.000010   0.002887   0.032924   0.000074   0.000146  -0.008194
-     33      -0.000240   0.000597   0.000074   0.245653   0.096798   0.001587
-     34      -0.000291   0.000696   0.000146   0.096798   0.287249   0.002378
-     35       0.000048   0.000002  -0.008194   0.001587   0.002378   0.032938
-
-$bmatrix
- 54 36
-                  0          1          2          3          4          5    
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-     48       0.002188   0.003981  -0.441310   0.000000   0.000000   0.000000
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-     53      -0.004445  -0.007989   0.882577   0.002234   0.003999  -0.441268
-                  6          7          8          9         10         11    
-      0       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
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-     19       0.321762  -0.685299  -0.004730   0.000000   0.000000   0.000000
-     20       0.415883   0.514999   0.006895  -0.356596  -0.137446  -0.003111
-     21       0.000000   0.000000   0.000000  -0.221392   0.723989   0.005518
-     22       0.356597   0.137446   0.003064  -0.432540  -0.621311  -0.007884
-     23      -0.356597  -0.137446  -0.003064   0.653933  -0.102678   0.002366
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-     25       0.000000   0.000000   0.000000  -0.297336   0.240124   0.000731
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-     28       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
-     29       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
-     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
-     32       0.002268   0.003972  -0.441288   0.000000   0.000000   0.000000
-     33       0.002268   0.003972  -0.441288   0.000000   0.000000   0.000000
-     34       0.002948   0.005358  -0.565578   0.000000   0.000000   0.000000
-     35      -0.004557  -0.008085   0.882627   0.002282   0.004066  -0.441303
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-

cmmde_gui/test/cmmd.xyz

@@ -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

cmmde_gui/test/cmmd_trj.xyz

@@ -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
-  H      -1.543894     -1.923121     -0.024963
-  H      -2.430428      0.376871     -0.008335
-  H      -0.881765      2.294553      0.017113
-  H       1.553446      1.912154      0.025671

cmmde_gui/test/geom.smi

@@ -1 +0,0 @@
-c1ccccc1

cmmde_gui/test/geom.xyz

@@ -1,14 +0,0 @@
-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

cmmde_gui/test/grafena/cmmd.engrad

@@ -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
+      -0.000045941580
+       0.000017547022
+      -0.000042417750
+       0.000013701618
+       0.000028931679
+       0.000006626910
+      -0.000004777434
+      -0.000018973001
+       0.000006815630
+      -0.000012566777
+       0.000003961274
+      -0.000000290495
+       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
+      -0.000000782613
+       0.000005493576
+       0.000001443301
+      -0.000003562666
+      -0.000002247086
+       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
+      -0.000008506876
+      -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 

cmmde_gui/test/grafena/cmmd.xyz

@@ -0,0 +1,73 @@
+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
+  C   9.32430737085525     -0.53819516247474      1.21713753339898
+  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
+  C   14.27592490742450     -0.65228980512658      5.35699445263271
+  C   13.07405711851004     -0.75734295262974      4.65068097814951
+  C   11.91248454724954     -1.26882361302687      5.29086217556897
+  H   5.16185143514081     -3.15882215729037      4.95403949008511
+  H   4.91802467599078     -2.24201913845910      2.68846591450517
+  H   6.85500679826839     -0.33496448330993      2.83836530526916
+  H   5.98461386444324     -1.26630869356802      0.64387641820013
+  H   7.17638852989058     -2.55999758194727      0.78374501060828
+  H   7.60932040336028      0.42028974688182      0.42724433109965
+  H   8.21330108761868     -0.89715441920766     -0.57533346212512
+  H   9.24808071143430      1.17741152364752     -0.82465256537855
+  H   10.44476012626449      0.06262393035398     -1.48544516274204
+  H   11.14891940878957      2.41580026352334     -1.80884434866177
+  H   11.02662027705112      2.70074828394699     -0.06758141173515
+  H   12.91119250845211      0.72777163749630     -1.43004131122708
+  H   13.35917297596527      2.27418042402556     -0.70000147983408
+  H   15.31961363016889      2.33037115147470      0.96571086165418
+  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

cmmde_gui/test/grafena/freq/cmmd.charges

@@ -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

cmmde_gui/test/grafena/freq/cmmd.engrad

@@ -0,0 +1,298 @@
+#
+# 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 

cmmde_gui/test/grafena/freq/cmmd.hostnames

@@ -0,0 +1 @@
+compute

cmmde_gui/test/grafena/freq/cmmd.in

@@ -1,5 +1,5 @@
 #CMMDE generated Orca input file
-!XTB2 Numfreq
+!XTB1 Numfreq
 %pal 
  nprocs 1 
 end

cmmde_gui/test/grafena/freq/cmmd.lastscf

@@ -0,0 +1,223 @@
+      -----------------------------------------------------------      
+     |                   =====================                   |     
+     |                           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
+

cmmde_gui/test/grafena/freq/cmmd.numcalcinp.tmp

@@ -0,0 +1,7 @@
+cmmd        # BaseName
+cmmd        # GBWName
+426       # number of calculations
+1       # number of CPUs        
+1       # program flag
+0       # printing flag
+1       # free_end

cmmde_gui/test/grafena/freq/cmmd.out

@@ -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 atoms            :                    71
-          number of electrons        :                     8
+          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
+    1    6 C      1-43
-    2    1 H      2-5
+    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
+        H0-scaling (s, p, d)           1.850000    2.250000    2.000000
-        zeta-weighting                 0.500000
+        zeta-weighting                 0.000000
       * Dispersion:
-        s8                             2.700000
+        s8                             2.400000
-        a1                             0.520000
+        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
+        third order                    atomic
-        anisotropic                    true
+        anisotropic                    false
-        a3                             3.000000
+      * Halogen bond correction:
-        a5                             4.000000
+        rad-scale                      1.300000
-        cn-shift                       1.200000
+        damping                        0.440000
-        cn-exp                         4.000000
-        max-rad                        5.000000
 
 
           ...................................................
           :                      SETUP                      :
           :.................................................:
-          :  # basis functions                   8          :
+          :  # basis functions                 228          :
-          :  # atomic orbitals                   8          :
+          :  # atomic orbitals                 228          :
-          :  # shells                            6          :
+          :  # shells                          142          :
-          :  # electrons                         8          :
+          :  # 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
+   1   -107.8847039 -0.107885E+03  0.104E+01    1.52       0.0  T
-   2     -4.2472613 -0.119651E-01  0.928E-01   17.57       1.0  T
+   2   -107.9625255 -0.778216E-01  0.628E+00    1.49       1.0  T
-   3     -4.2474252 -0.163901E-03  0.500E-01   17.46       1.0  T
+   3   -107.9286345  0.338911E-01  0.684E-01    1.54       1.0  T
-   4     -4.2474673 -0.421128E-04  0.924E-02   17.36       1.0  T
+   4   -107.9667855 -0.381510E-01  0.207E-01    1.49       1.0  T
-   5     -4.2474672  0.111480E-06  0.698E-03   17.35       6.4  T
+   5   -107.9716052 -0.481967E-02  0.610E-02    1.49       1.0  T
-   6     -4.2474673 -0.145702E-06  0.191E-04   17.35     233.9  T
+   6   -107.9721688 -0.563640E-03  0.109E-02    1.49       1.1  T
-   7     -4.2474673 -0.109869E-09  0.432E-06   17.35   10350.2  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
-   *** convergence criteria satisfied after 7 iterations ***
+   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
+         1        2.0000           -0.6780191             -18.4498
-         2        2.0000           -0.4674583             -12.7202
+       ...           ...                  ...                  ...
-         3        2.0000           -0.4674579             -12.7202
+        94        2.0000           -0.4299532             -11.6996
-         4        2.0000           -0.4674579             -12.7202 (HOMO)
+        95        2.0000           -0.4242112             -11.5434
-         5                          0.1702647               4.6331 (LUMO)
+        96        2.0000           -0.4217088             -11.4753
-         6                          0.2292565               6.2384
+        97        2.0000           -0.4141608             -11.2699
-         7                          0.2292569               6.2384
+        98        2.0000           -0.4065523             -11.0629
-         8                          0.2292585               6.2384
+        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
+                  HL-Gap            0.0548455 Eh            1.4924 eV
-             Fermi-level           -0.1485966 Eh           -4.0435 eV
+             Fermi-level           -0.3467265 Eh           -9.4349 eV
-
+
- SCC (total)                   0 d,  0 h,  0 min,  0.023 sec
+ SCC (total)                   0 d,  0 h,  0 min,  0.235 sec
- SCC setup                      ...        0 min,  0.000 sec (  0.165%)
+ SCC setup                      ...        0 min,  0.001 sec (  0.366%)
- Dispersion                     ...        0 min,  0.000 sec (  0.028%)
+ Dispersion                     ...        0 min,  0.002 sec (  0.739%)
- classical contributions        ...        0 min,  0.000 sec (  0.021%)
+ classical contributions        ...        0 min,  0.000 sec (  0.147%)
- integral evaluation            ...        0 min,  0.000 sec (  0.275%)
+ integral evaluation            ...        0 min,  0.045 sec ( 18.969%)
- iterations                     ...        0 min,  0.023 sec ( 97.223%)
+ iterations                     ...        0 min,  0.073 sec ( 30.918%)
- molecular gradient             ...        0 min,  0.000 sec (  1.597%)
+ molecular gradient             ...        0 min,  0.113 sec ( 47.933%)
- printout                       ...        0 min,  0.000 sec (  0.655%)
+ printout                       ...        0 min,  0.002 sec (  0.914%)
 
          :::::::::::::::::::::::::::::::::::::::::::::::::::::
          ::                     SUMMARY                     ::
          :::::::::::::::::::::::::::::::::::::::::::::::::::::
-         :: total energy              -4.175218519975 Eh    ::
+         :: total energy            -106.196831730665 Eh    ::
-         :: gradient norm              0.000006627564 Eh/a0 ::
+         :: gradient norm              0.015896196187 Eh/a0 ::
-         :: HOMO-LUMO gap             17.353313970090 eV    ::
+         :: HOMO-LUMO gap              1.492422010339 eV    ::
          ::.................................................::
-         :: SCC energy                -4.247467308188 Eh    ::
+         :: SCC energy              -107.972190143337 Eh    ::
-         :: -> isotropic ES            0.002035567944 Eh    ::
+         :: -> electrostatic           0.004053721879 Eh    ::
-         :: -> anisotropic ES          0.002321540929 Eh    ::
+         :: repulsion energy           1.841954650940 Eh    ::
-         :: -> anisotropic XC          0.003585096736 Eh    ::
+         :: dispersion energy         -0.066596238268 Eh    ::
-         :: -> dispersion             -0.000661011606 Eh    ::
+         :: halogen bond corr.         0.000000000000 Eh    ::
-         :: repulsion energy           0.072248782622 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   |
+          | TOTAL ENERGY             -106.196831730665 Eh   |
-          | GRADIENT NORM               0.000006627564 Eh/α |
+          | GRADIENT NORM               0.015896196187 Eh/α |
-          | HOMO-LUMO GAP              17.353313970090 eV   |
+          | 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
+ * wall-time:     0 d,  0 h,  0 min,  0.293 sec
- *  cpu-time:     0 d,  0 h,  0 min,  0.007 sec
+ *  cpu-time:     0 d,  0 h,  0 min,  0.284 sec
- * ratio c/w:     0.264 speedup
+ * ratio c/w:     0.969 speedup
  SCF:
- * wall-time:     0 d,  0 h,  0 min,  0.023 sec
+ * wall-time:     0 d,  0 h,  0 min,  0.235 sec
- *  cpu-time:     0 d,  0 h,  0 min,  0.003 sec
+ *  cpu-time:     0 d,  0 h,  0 min,  0.234 sec
- * ratio c/w:     0.126 speedup
+ * 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   1 (of 426) >>
-	<< Calculating on displaced geometry   2 (of  30) >>
+	<< Calculating on displaced geometry   2 (of 426) >>
-	<< Calculating on displaced geometry   3 (of  30) >>
+	<< Calculating on displaced geometry   3 (of 426) >>
-	<< Calculating on displaced geometry   4 (of  30) >>
+	<< Calculating on displaced geometry   4 (of 426) >>
-	<< Calculating on displaced geometry   5 (of  30) >>
+	<< Calculating on displaced geometry   5 (of 426) >>
-	<< Calculating on displaced geometry   6 (of  30) >>
+	<< Calculating on displaced geometry   6 (of 426) >>
-	<< Calculating on displaced geometry   7 (of  30) >>
+	<< Calculating on displaced geometry   7 (of 426) >>
-	<< Calculating on displaced geometry   8 (of  30) >>
+	<< Calculating on displaced geometry   8 (of 426) >>
-	<< Calculating on displaced geometry   9 (of  30) >>
+	<< Calculating on displaced geometry   9 (of 426) >>
-	<< Calculating on displaced geometry  10 (of  30) >>
+	<< Calculating on displaced geometry  10 (of 426) >>
-	<< Calculating on displaced geometry  11 (of  30) >>
+	<< Calculating on displaced geometry  11 (of 426) >>
-	<< Calculating on displaced geometry  12 (of  30) >>
+	<< Calculating on displaced geometry  12 (of 426) >>
-	<< Calculating on displaced geometry  13 (of  30) >>
+	<< Calculating on displaced geometry  13 (of 426) >>
-	<< Calculating on displaced geometry  14 (of  30) >>
+	<< Calculating on displaced geometry  14 (of 426) >>
-	<< Calculating on displaced geometry  15 (of  30) >>
+	<< Calculating on displaced geometry  15 (of 426) >>
-	<< Calculating on displaced geometry  16 (of  30) >>
+	<< Calculating on displaced geometry  16 (of 426) >>
-	<< Calculating on displaced geometry  17 (of  30) >>
+	<< Calculating on displaced geometry  17 (of 426) >>
-	<< Calculating on displaced geometry  18 (of  30) >>
+	<< Calculating on displaced geometry  18 (of 426) >>
-	<< Calculating on displaced geometry  19 (of  30) >>
+	<< Calculating on displaced geometry  19 (of 426) >>
-	<< Calculating on displaced geometry  20 (of  30) >>
+	<< Calculating on displaced geometry  20 (of 426) >>
-	<< Calculating on displaced geometry  21 (of  30) >>
+	<< Calculating on displaced geometry  21 (of 426) >>
-	<< Calculating on displaced geometry  22 (of  30) >>
+	<< Calculating on displaced geometry  22 (of 426) >>
-	<< Calculating on displaced geometry  23 (of  30) >>
+	<< Calculating on displaced geometry  23 (of 426) >>
-	<< Calculating on displaced geometry  24 (of  30) >>
+	<< Calculating on displaced geometry  24 (of 426) >>
-	<< Calculating on displaced geometry  25 (of  30) >>
+	<< Calculating on displaced geometry  25 (of 426) >>
-	<< Calculating on displaced geometry  26 (of  30) >>
+	<< Calculating on displaced geometry  26 (of 426) >>
-	<< Calculating on displaced geometry  27 (of  30) >>
+	<< Calculating on displaced geometry  27 (of 426) >>
-	<< Calculating on displaced geometry  28 (of  30) >>
+	<< Calculating on displaced geometry  28 (of 426) >>
-	<< Calculating on displaced geometry  29 (of  30) >>
+	<< Calculating on displaced geometry  29 (of 426) >>
-	<< Calculating on displaced geometry  30 (of  30) >>
+	<< Calculating on displaced geometry  30 (of 426) >>
-
+	<< Calculating on displaced geometry  31 (of 426) >>
------------------------
+	<< Calculating on displaced geometry  32 (of 426) >>
-VIBRATIONAL FREQUENCIES
+	<< Calculating on displaced geometry  33 (of 426) >>
------------------------
+	<< Calculating on displaced geometry  34 (of 426) >>
-
+	<< Calculating on displaced geometry  35 (of 426) >>
-Scaling factor for frequencies =  1.000000000 (already applied!)
+	<< Calculating on displaced geometry  36 (of 426) >>
-
+	<< Calculating on displaced geometry  37 (of 426) >>
-   0:         0.00 cm**-1
+	<< Calculating on displaced geometry  38 (of 426) >>
-   1:         0.00 cm**-1
+	<< Calculating on displaced geometry  39 (of 426) >>
-   2:         0.00 cm**-1
+	<< Calculating on displaced geometry  40 (of 426) >>
-   3:         0.00 cm**-1
+	<< Calculating on displaced geometry  41 (of 426) >>
-   4:         0.00 cm**-1
+	<< Calculating on displaced geometry  42 (of 426) >>
-   5:         0.00 cm**-1
+	<< Calculating on displaced geometry  43 (of 426) >>
-   6:      1385.80 cm**-1
+	<< Calculating on displaced geometry  44 (of 426) >>
-   7:      1385.80 cm**-1
+	<< Calculating on displaced geometry  45 (of 426) >>
-   8:      1385.82 cm**-1
+	<< Calculating on displaced geometry  46 (of 426) >>
-   9:      1557.27 cm**-1
+	<< Calculating on displaced geometry  47 (of 426) >>
-  10:      1557.28 cm**-1
+	<< Calculating on displaced geometry  48 (of 426) >>
-  11:      3090.01 cm**-1
+	<< Calculating on displaced geometry  49 (of 426) >>
-  12:      3103.91 cm**-1
+	<< Calculating on displaced geometry  50 (of 426) >>
-  13:      3103.94 cm**-1
+	<< Calculating on displaced geometry  51 (of 426) >>
-  14:      3103.96 cm**-1
+	<< 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) >>
-NORMAL MODES
+	<< Calculating on displaced geometry  56 (of 426) >>
-------------
+	<< Calculating on displaced geometry  57 (of 426) >>
-
+	<< Calculating on displaced geometry  58 (of 426) >>
-These modes are the cartesian displacements weighted by the diagonal matrix
+	<< Calculating on displaced geometry  59 (of 426) >>
-M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom
+	<< Calculating on displaced geometry  60 (of 426) >>
-Thus, these vectors are normalized but *not* orthogonal
+	<< Calculating on displaced geometry  61 (of 426) >>
-
+	<< Calculating on displaced geometry  62 (of 426) >>
-                  0          1          2          3          4          5    
+	<< Calculating on displaced geometry  63 (of 426) >>
-      0       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  64 (of 426) >>
-      1       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  65 (of 426) >>
-      2       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  66 (of 426) >>
-      3       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  67 (of 426) >>
-      4       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  68 (of 426) >>
-      5       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  69 (of 426) >>
-      6       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  70 (of 426) >>
-      7       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  71 (of 426) >>
-      8       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  72 (of 426) >>
-      9       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  73 (of 426) >>
-     10       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  74 (of 426) >>
-     11       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  75 (of 426) >>
-     12       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  76 (of 426) >>
-     13       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  77 (of 426) >>
-     14       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+	<< Calculating on displaced geometry  78 (of 426) >>
-                  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

cmmde_gui/test/grafena/freq/cmmd.xtberr

@@ -0,0 +1,2 @@
+Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
+normal termination of xtb

cmmde_gui/test/grafena/freq/cmmd.xtbtopo.mol

@@ -0,0 +1,160 @@
+
+  xtb     08042209433D
+ xtb: 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54)
+ 71 84  0     0  0            999 V2000
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+ 34 71  1  0  0  0  0
+M  END

cmmde_gui/test/grafena/freq/cmmd_D00000.hostnames

@@ -0,0 +1 @@
+compute