addition to xTB functions

bin/cmmde.py

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

cmmde_gui/gui.py

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

cmmde_gui/test/ala/cmmd.engrad

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

cmmde_gui/test/ala/cmmd.in

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

cmmde_gui/test/ala/cmmd.opt

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

cmmde_gui/test/ala/cmmd.xyz

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

cmmde_gui/test/ala/cmmd_property.txt

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

cmmde_gui/test/ala/cmmd_trj.xyz

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

cmmde_gui/test/ala/freq/cmmd.engrad

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

cmmde_gui/test/ala/freq/cmmd.hess

@@ -0,0 +1,192 @@
+
+$orca_hessian_file
+
+$act_atom
+  0
+
+$act_coord
+  0
+
+$act_energy
+       -4.175219
+
+$hessian
+15
+                    0                  1                  2                  3                  4        
+    0      5.1329127386E-01  -3.3636519648E-06   2.7836910958E-06  -2.9809786459E-01  -2.0111847410E-07
+    1     -3.3636519648E-06   5.1328774831E-01  -4.1292960070E-07  -2.1994454789E-07  -4.3442763969E-02
+    2      2.7836910958E-06  -4.1292960070E-07   5.1328754864E-01   1.3916768318E-07  -9.6603597691E-09
+    3     -2.9809786459E-01  -2.1994454789E-07   1.3916768318E-07   3.4272726540E-01   2.6835972750E-07
+    4     -2.0111847410E-07  -4.3442763969E-02  -9.6603597691E-09   2.6835972750E-07   4.6441081937E-02
+    5      1.3206793443E-07  -9.6670189178E-09  -4.3442747837E-02  -1.0713789465E-07  -6.1757220961E-08
+    6     -7.1733839407E-02  -5.6161287709E-02   5.7008315131E-02  -1.4874636926E-02  -2.3542514267E-02
+    7     -5.6161183538E-02  -1.5492116032E-01   1.1316381228E-01  -1.6485567775E-03  -9.8151070450E-04
+    8      5.7008202738E-02   1.1316379791E-01  -1.5830910508E-01   1.6733965622E-03   1.1842231955E-03
+    9     -7.1734575351E-02  -2.1289712447E-02  -7.7144027878E-02  -1.4874656620E-02  -8.9246273506E-03
+   10     -2.1289669385E-02  -5.9462115086E-02  -5.8048812159E-02  -6.2501434377E-04   1.7432106214E-05
+   11     -7.7143867707E-02  -5.8048774107E-02  -2.5377698527E-01  -2.2641275020E-03  -6.0733966207E-04
+   12     -7.1734900154E-02   7.7454583479E-02   2.0132790190E-02  -1.4874651446E-02   3.2467074451E-02
+   13      7.7454422495E-02  -2.5547116451E-01  -5.5114568815E-02   2.2731759983E-03  -2.0336583113E-03
+   14      2.0132744638E-02  -5.5114592448E-02  -5.7768143367E-02   5.9102415832E-04  -5.7681327417E-04
+                    5                  6                  7                  8                  9        
+    0      1.3206793443E-07  -7.1733839407E-02  -5.6161183538E-02   5.7008202738E-02  -7.1734575351E-02
+    1     -9.6670189178E-09  -5.6161287709E-02  -1.5492116032E-01   1.1316379791E-01  -2.1289712447E-02
+    2     -4.3442747837E-02   5.7008315131E-02   1.1316381228E-01  -1.5830910508E-01  -7.7144027878E-02
+    3     -1.0713789465E-07  -1.4874636926E-02  -1.6485567775E-03   1.6733965622E-03  -1.4874656620E-02
+    4     -6.1757220961E-08  -2.3542514267E-02  -9.8151070450E-04   1.1842231955E-03  -8.9246273506E-03
+    5      4.6441107085E-02   2.3897558740E-02   1.1842547839E-03  -1.0169431892E-03  -3.2337164017E-02
+    6      2.3897558740E-02   7.9358259250E-02   6.5343154941E-02  -6.6328653384E-02   3.6258428420E-03
+    7      1.1842547839E-03   6.5343154941E-02   1.7614546490E-01  -1.3166436950E-01   2.4437918892E-03
+    8     -1.0169431892E-03  -6.6328653384E-02  -1.3166436950E-01   1.8008726052E-01   9.9401130438E-03
+    9     -3.2337164017E-02   3.6258428420E-03   2.4437918892E-03   9.9401130438E-03   7.9358947320E-02
+   10     -6.0756496012E-04   6.9751642011E-03   4.8745925129E-03   2.1168626472E-02   2.4770458157E-02
+   11     -2.0159862303E-03  -7.4919127771E-03  -4.3037037576E-03  -2.5373371238E-02   8.9755942634E-02
+   12      8.4395802803E-03   3.6258575186E-03  -9.9755627888E-03  -2.2947274765E-03   3.6259250755E-03
+   13     -5.7661955222E-04   7.3867085647E-03  -2.5114204535E-02  -3.8547822493E-03   3.0006239868E-03
+   14      3.5149897336E-05  -7.0865402046E-03   2.1617527214E-02   4.6153930316E-03   9.7865512730E-03
+                   10                 11                 12                 13                 14        
+    0     -2.1289669385E-02  -7.7143867707E-02  -7.1734900154E-02   7.7454422495E-02   2.0132744638E-02
+    1     -5.9462115086E-02  -5.8048774107E-02   7.7454583479E-02  -2.5547116451E-01  -5.5114592448E-02
+    2     -5.8048812159E-02  -2.5377698527E-01   2.0132790190E-02  -5.5114568815E-02  -5.7768143367E-02
+    3     -6.2501434377E-04  -2.2641275020E-03  -1.4874651446E-02   2.2731759983E-03   5.9102415832E-04
+    4      1.7432106214E-05  -6.0733966207E-04   3.2467074451E-02  -2.0336583113E-03  -5.7681327417E-04
+    5     -6.0756496012E-04  -2.0159862303E-03   8.4395802803E-03  -5.7661955222E-04   3.5149897336E-05
+    6      6.9751642011E-03  -7.4919127771E-03   3.6258575186E-03   7.3867085647E-03  -7.0865402046E-03
+    7      4.8745925129E-03  -4.3037037576E-03  -9.9755627888E-03  -2.5114204535E-02   2.1617527214E-02
+    8      2.1168626472E-02  -2.5373371238E-02  -2.2947274765E-03  -3.8547822493E-03   4.6153930316E-03
+    9      2.4770458157E-02   8.9755942634E-02   3.6259250755E-03   3.0006239868E-03   9.7865512730E-03
+   10      6.5079793563E-02   6.7539019241E-02  -9.8303155390E-03  -1.0508688577E-02  -3.0050216659E-02
+   11      6.7539019241E-02   2.9116129859E-01  -2.8537771275E-03  -4.5777014462E-03  -9.9903027647E-03
+   12     -9.8303155390E-03  -2.8537771275E-03   7.9359252291E-02  -9.0117197664E-02  -2.3424369102E-02
+   13     -1.0508688577E-02  -4.5777014462E-03  -9.0117197664E-02   2.9313239407E-01   6.4125091508E-02
+   14     -3.0050216659E-02  -9.9903027647E-03  -2.3424369102E-02   6.4125091508E-02   6.3108869270E-02
+
+$vibrational_frequencies
+15
+    0        0.000000
+    1        0.000000
+    2        0.000000
+    3        0.000000
+    4        0.000000
+    5        0.000000
+    6     1385.802989
+    7     1385.804694
+    8     1385.819131
+    9     1557.265928
+   10     1557.278661
+   11     3090.006354
+   12     3103.914034
+   13     3103.936524
+   14     3103.959260
+
+$normal_modes
+15 15
+                    0                  1                  2                  3                  4        
+    0      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    1      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    2      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    3      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    4      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    5      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    6      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    7      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    8      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    9      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+   10      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+   11      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+   12      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+   13      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+   14      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+                    5                  6                  7                  8                  9        
+    0      0.0000000000E+00   1.1460429268E-01  -3.4379236967E-02  -4.7849264525E-02  -6.2196180136E-08
+    1      0.0000000000E+00   5.8576857374E-02   7.7750867247E-02   8.4434109433E-02   5.7988235870E-06
+    2      0.0000000000E+00  -6.3442646325E-03   9.6842579071E-02  -8.4775157264E-02   5.6540900942E-06
+    3      0.0000000000E+00   5.3322377490E-02  -1.5995533024E-02  -2.2262979463E-02   2.3670438248E-07
+    4      0.0000000000E+00  -2.7535711067E-01  -3.6548194224E-01  -3.9692559975E-01  -3.6560167528E-01
+    5      0.0000000000E+00   2.9827653543E-02  -4.5522985733E-01   3.9852923127E-01  -3.4113931628E-01
+    6      0.0000000000E+00  -3.9889455056E-01   1.1846683962E-01   3.9173216657E-01   1.2781240094E-02
+    7      0.0000000000E+00   2.2582223879E-03  -4.5119127032E-01  -6.5843512581E-02   3.5285840880E-01
+    8      0.0000000000E+00  -2.5200659617E-01  -3.6833527333E-01   6.2452757104E-02   3.5395910859E-01
+    9      0.0000000000E+00  -4.5760273347E-01   3.2700273115E-01   1.0126357845E-01   4.0172057861E-01
+   10      0.0000000000E+00  -2.1431150072E-01  -2.4104848320E-01  -4.8999373348E-01   2.1441650987E-01
+   11      0.0000000000E+00   2.5110611645E-01  -4.2335079059E-03   6.1322674707E-02  -2.0650819767E-01
+   12      0.0000000000E+00  -5.6241255314E-01  -1.9822236936E-02   9.9423500526E-02  -4.1450131430E-01
+   13      0.0000000000E+00  -2.1057238274E-01   1.3126766153E-01  -5.3326527601E-02  -2.0174234028E-01
+   14      0.0000000000E+00   4.6669019129E-02  -3.2614602137E-01   4.8784852530E-01   1.9362103306E-01
+                   10                 11                 12                 13                 14        
+    0     -1.1685424666E-06   1.0305848845E-04  -1.6400025343E-02  -3.1979547838E-03   8.5675284564E-02
+    1     -5.0070919903E-07   5.4593202416E-05  -5.8809524764E-02  -6.3052970933E-02  -1.3611266360E-02
+    2      7.9760804626E-07  -4.9746676876E-05   6.2385950041E-02  -6.0279016142E-02   9.6922378022E-03
+    3     -1.3626230096E-06   4.9897892641E-01   1.6230624130E-01   3.1593465320E-02  -8.4545192635E-01
+    4      3.4111349028E-01   2.6482553553E-05  -2.7197780136E-02  -2.9159539116E-02  -6.2950067490E-03
+    5     -3.6557650895E-01  -2.3880077608E-05   2.8851914775E-02  -2.7876771652E-02   4.4822877101E-03
+    6     -4.7122878139E-01  -1.6697405729E-01   2.8914304946E-01   6.4174313555E-03  -5.0797945399E-03
+    7      1.2657588124E-01  -3.3151699796E-01   5.6180656381E-01  -1.3489457042E-02  -9.5034841166E-02
+    8     -1.0916974631E-01   3.3651927657E-01  -5.6903524917E-01  -4.3792105404E-02   9.4560503801E-02
+    9      2.4669155397E-01  -1.6662718301E-01  -1.3331926298E-01   2.4512947958E-01  -7.7040068406E-02
+   10     -4.3392019027E-01  -1.2539328656E-01  -1.2181111507E-01   1.5640546240E-01  -9.4081351994E-02
+   11      2.9276305623E-02  -4.5446595783E-01  -3.1396261364E-01   6.4450414089E-01  -3.1360477361E-01
+   12      2.2455251402E-01  -1.6660569754E-01  -1.2271266231E-01  -2.4503458766E-01  -9.3307023098E-02
+   13     -3.3763214961E-02   4.5623328713E-01   2.8795749205E-01   6.3756221815E-01   3.5759862079E-01
+   14      4.4546044560E-01   1.1856332655E-01   1.1077526755E-01   1.4542987792E-01   9.9072430276E-02
+
+#
+# The atoms: label  mass x y z (in bohrs)
+#
+$atoms
+5
+ C     12.01100      2.018492210263     0.132035672370     0.041192324579
+ H      1.00800      4.063478598403     0.132037299586     0.041191297887
+ H      1.00800      1.336837066645    -1.221049384893     1.414683138767
+ H      1.00800      1.336828145995    -0.380899654918    -1.817355859331
+ H      1.00800      1.336824342127     1.998051892739     0.526250349434
+
+$actual_temperature
+  0.000000
+
+$frequency_scale_factor
+  1.000000
+
+$dipole_derivatives
+15
+   -0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00   -0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00    0.0000000000E+00   -0.0000000000E+00
+   -2.0000000000E-01    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00   -0.0000000000E+00    0.0000000000E+00
+   -0.0000000000E+00   -0.0000000000E+00    2.0000000000E-01
+    0.0000000000E+00    2.0000000000E-01   -0.0000000000E+00
+    0.0000000000E+00   -0.0000000000E+00   -0.0000000000E+00
+   -0.0000000000E+00    0.0000000000E+00   -0.0000000000E+00
+   -0.0000000000E+00   -0.0000000000E+00   -2.0000000000E-01
+    0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00   -2.0000000000E-01   -0.0000000000E+00
+    0.0000000000E+00   -0.0000000000E+00    0.0000000000E+00
+
+#
+# The IR spectrum
+#  wavenumber eps Int TX TY TZ
+#
+$ir_spectrum
+15
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+   1385.80   0.00043085   2.17736113    -0.002037    -0.001583    -0.009506
+   1385.80   0.00291380  14.72516324     0.000611    -0.019085    -0.017074
+   1385.82   0.00019488   0.98483488     0.000850     0.004423    -0.004858
+   1557.27   0.00475914  24.05072327    -0.000000     0.021765     0.021908
+   1557.28   0.00011600   0.58621836     0.000000    -0.002953     0.003811
+   3090.01   0.00213139  10.77118066    -0.013874    -0.003329     0.003419
+   3103.91   0.01079707  54.56396020    -0.004326    -0.022844     0.023344
+   3103.94   0.00634783  32.07932697    -0.000842    -0.018162    -0.017539
+   3103.96   0.00587823  29.70617211     0.022536    -0.007011     0.005826
+
+
+$end
+

cmmde_gui/test/ala/freq/cmmd.in

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

cmmde_gui/test/ala/freq/cmmd.out

@@ -0,0 +1,711 @@
+
+                                 *****************
+                                 * O   R   C   A *
+                                 *****************
+
+                                            #,                                       
+                                            ###                                      
+                                            ####                                     
+                                            #####                                    
+                                            ######                                   
+                                           ########,                                 
+                                     ,,################,,,,,                         
+                               ,,#################################,,                 
+                          ,,##########################################,,             
+                       ,#########################################, ''#####,          
+                    ,#############################################,,   '####,        
+                  ,##################################################,,,,####,       
+                ,###########''''           ''''###############################       
+              ,#####''   ,,,,##########,,,,          '''####'''          '####       
+            ,##' ,,,,###########################,,,                        '##       
+           ' ,,###''''                  '''############,,,                           
+         ,,##''                                '''############,,,,        ,,,,,,###''
+      ,#''                                            '''#######################'''  
+     '                                                          ''''####''''         
+             ,#######,   #######,   ,#######,      ##                                
+            ,#'     '#,  ##    ##  ,#'     '#,    #''#        ######   ,####,        
+            ##       ##  ##   ,#'  ##            #'  '#       #        #'  '#        
+            ##       ##  #######   ##           ,######,      #####,   #    #        
+            '#,     ,#'  ##    ##  '#,     ,#' ,#      #,         ##   #,  ,#        
+             '#######'   ##     ##  '#######'  #'      '#     #####' # '####'        
+
+
+
+                  #######################################################
+                  #                        -***-                        #
+                  #          Department of theory and spectroscopy      #
+                  #    Directorship and core code : Frank Neese         #
+                  #        Max Planck Institute fuer Kohlenforschung    #
+                  #                Kaiser Wilhelm Platz 1               #
+                  #                 D-45470 Muelheim/Ruhr               #
+                  #                      Germany                        #
+                  #                                                     #
+                  #                  All rights reserved                #
+                  #                        -***-                        #
+                  #######################################################
+
+
+                         Program Version 5.0.2 -  RELEASE  -
+
+
+ With contributions from (in alphabetic order):
+   Daniel Aravena         : Magnetic Suceptibility
+   Michael Atanasov       : Ab Initio Ligand Field Theory (pilot matlab implementation)
+   Alexander A. Auer      : GIAO ZORA, VPT2 properties, NMR spectrum
+   Ute Becker             : Parallelization
+   Giovanni Bistoni       : ED, misc. LED, open-shell LED, HFLD
+   Martin Brehm           : Molecular dynamics
+   Dmytro Bykov           : SCF Hessian
+   Vijay G. Chilkuri      : MRCI spin determinant printing, contributions to CSF-ICE
+   Dipayan Datta          : RHF DLPNO-CCSD density
+   Achintya Kumar Dutta   : EOM-CC, STEOM-CC
+   Dmitry Ganyushin       : Spin-Orbit,Spin-Spin,Magnetic field MRCI
+   Miquel Garcia          : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme
+   Yang Guo               : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization
+   Andreas Hansen         : Spin unrestricted coupled pair/coupled cluster methods
+   Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals
+   Lee Huntington         : MR-EOM, pCC
+   Robert Izsak           : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM
+   Marcus Kettner         : VPT2
+   Christian Kollmar      : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K
+   Simone Kossmann        : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian
+   Martin Krupicka        : Initial AUTO-CI
+   Lucas Lang             : DCDCAS
+   Marvin Lechner         : AUTO-CI (C++ implementation), FIC-MRCC
+   Dagmar Lenk            : GEPOL surface, SMD
+   Dimitrios Liakos       : Extrapolation schemes; Compound Job, initial MDCI parallelization
+   Dimitrios Manganas     : Further ROCIS development; embedding schemes
+   Dimitrios Pantazis     : SARC Basis sets
+   Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients
+   Taras Petrenko         : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS
+   Peter Pinski           : DLPNO-MP2, DLPNO-MP2 Gradient
+   Christoph Reimann      : Effective Core Potentials
+   Marius Retegan         : Local ZFS, SOC
+   Christoph Riplinger    : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples
+   Tobias Risthaus        : Range-separated hybrids, TD-DFT gradient, RPA, STAB
+   Michael Roemelt        : Original ROCIS implementation
+   Masaaki Saitow         : Open-shell DLPNO-CCSD energy and density
+   Barbara Sandhoefer     : DKH picture change effects
+   Avijit Sen             : IP-ROCIS
+   Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI
+   Bernardo de Souza      : ESD, SOC TD-DFT
+   Georgi Stoychev        : AutoAux, RI-MP2 NMR, DLPNO-MP2 response
+   Willem Van den Heuvel  : Paramagnetic NMR
+   Boris Wezisla          : Elementary symmetry handling
+   Frank Wennmohs         : Technical directorship
+
+
+ We gratefully acknowledge several colleagues who have allowed us to
+ interface, adapt or use parts of their codes:
+   Stefan Grimme, W. Hujo, H. Kruse, P. Pracht,  : VdW corrections, initial TS optimization,
+                  C. Bannwarth, S. Ehlert          DFT functionals, gCP, sTDA/sTD-DF
+   Ed Valeev, F. Pavosevic, A. Kumar             : LibInt (2-el integral package), F12 methods
+   Garnet Chan, S. Sharma, J. Yang, R. Olivares  : DMRG
+   Ulf Ekstrom                                   : XCFun DFT Library
+   Mihaly Kallay                                 : mrcc  (arbitrary order and MRCC methods)
+   Jiri Pittner, Ondrej Demel                    : Mk-CCSD
+   Frank Weinhold                                : gennbo (NPA and NBO analysis)
+   Christopher J. Cramer and Donald G. Truhlar   : smd solvation model
+   Lars Goerigk                                  : TD-DFT with DH, B97 family of functionals
+   V. Asgeirsson, H. Jonsson                     : NEB implementation
+   FAccTs GmbH                                   : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT
+                                                   MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM,
+                                                   LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT,
+                                                   nearIR, NL-DFT gradient (VV10), updates on ESD,
+                                                   ML-optimized integration grids
+   S Lehtola, MJT Oliveira, MAL Marques          : LibXC Library
+   Liviu Ungur et al                             : ANISO software
+
+
+ Your calculation uses the libint2 library for the computation of 2-el integrals
+ For citations please refer to: http://libint.valeyev.net
+
+ Your ORCA version has been built with support for libXC version: 5.1.0
+ For citations please refer to: https://tddft.org/programs/libxc/
+
+ This ORCA versions uses:
+   CBLAS   interface :  Fast vector & matrix operations
+   LAPACKE interface :  Fast linear algebra routines
+   SCALAPACK package :  Parallel linear algebra routines
+   Shared memory     :  Shared parallel matrices
+   BLAS/LAPACK       :  OpenBLAS 0.3.15  USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED
+        Core in use  :  SkylakeX
+   Copyright (c) 2011-2014, The OpenBLAS Project
+
+
+
+
+***************************************
+The coordinates will be read from file: ../cmmd.xyz
+***************************************
+
+
+Your calculation utilizes the semiempirical GFN2-xTB method
+Please cite in your paper:
+C. Bannwarth, Ehlert S., S. Grimme,  J. Chem. Theory Comput., 15, (2019), 1652.
+   
+
+================================================================================
+
+================================================================================
+                                        WARNINGS
+                       Please study these warnings very carefully!
+================================================================================
+
+WARNING: Gradients needed for Numerical Frequencies
+  ===> : Setting RunTyp to EnGrad
+
+WARNING: Found dipole moment calculation with XTB calculation
+  ===> : Switching off dipole moment calculation
+
+
+WARNING: TRAH-SCF for XTB is not implemented!
+  ===> : Turning TRAH off!
+
+================================================================================
+                                       INPUT FILE
+================================================================================
+NAME = cmmd.in
+|  1> #CMMDE generated Orca input file
+|  2> !XTB2 Numfreq
+|  3> %pal 
+|  4>  nprocs 1 
+|  5> end
+|  6>      
+|  7> *xyzfile 0 1 ../cmmd.xyz
+|  8> 
+|  9> %freq 
+| 10>  scalfreq 1 
+| 11>  Temp 298.15
+| 12>  Pressure 1.0
+| 13> end
+| 14> 
+| 15>                          ****END OF INPUT****
+================================================================================
+
+                     *******************************
+                     * Energy+Gradient Calculation *
+                     *******************************
+
+      -----------------------------------------------------------      
+     |                   =====================                   |     
+     |                           x T B                           |     
+     |                   =====================                   |     
+     |                         S. Grimme                         |     
+     |          Mulliken Center for Theoretical Chemistry        |     
+     |                    University of Bonn                     |     
+     |                      Aditya W. Sakti                      |     
+     |                     Departemen Kimia                      |     
+     |                  Universitas Pertamina                    |     
+      -----------------------------------------------------------      
+
+   * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
+
+   xtb is free software: you can redistribute it and/or modify it under
+   the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+   
+   xtb is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+   
+   Cite this work as:
+   * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
+     J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
+     e01493. DOI: 10.1002/wcms.1493
+   
+   for GFN2-xTB:
+   * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
+     15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
+   for GFN1-xTB:
+   * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
+     13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
+   for GFN0-xTB:
+   * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
+     DOI: 10.26434/chemrxiv.8326202.v1
+   for GFN-FF:
+   * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
+     DOI: 10.1002/anie.202004239
+   
+   for ALPB and GBSA implicit solvation:
+   * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
+     2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
+   
+   for DFT-D4:
+   * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
+     147, 034112. DOI: 10.1063/1.4993215
+   * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
+     C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
+     DOI: 10.1063/1.5090222
+   * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
+     2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
+   
+   for sTDA-xTB:
+   * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
+     DOI: 10.1063/1.4959605
+   
+   in the mass-spec context:
+   * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
+     DOI: 10.1039/c7sc00601b
+   * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
+     DOI: 10.1021/acsomega.9b02011
+   
+   for metadynamics refer to:
+   * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
+     DOI: 10.1021/acs.jctc.9b00143
+   
+   for SPH calculations refer to:
+   * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
+     DOI: 10.1021/acs.jctc.0c01306
+   
+   with help from (in alphabetical order)
+   P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
+   M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
+   C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
+   J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
+   M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
+   
+ * started run on 2022/07/22 at 20:31:34.411     
+
+           -------------------------------------------------
+          |                Calculation Setup                |
+           -------------------------------------------------
+
+          program call               : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000
+          hostname                   : compute
+          calculation namespace      : cmmd
+          coordinate file            : cmmd_XTB.xyz
+          number of atoms            :                     5
+          number of electrons        :                     8
+          charge                     :                     0
+          spin                       :                   0.0
+          first test random number   :      0.60690392607394
+
+   ID    Z sym.   atoms
+    1    6 C      1
+    2    1 H      2-5
+
+           -------------------------------------------------
+          |                 G F N 2 - x T B                 |
+           -------------------------------------------------
+
+        Reference                      10.1021/acs.jctc.8b01176
+      * Hamiltonian:
+        H0-scaling (s, p, d)           1.850000    2.230000    2.230000
+        zeta-weighting                 0.500000
+      * Dispersion:
+        s8                             2.700000
+        a1                             0.520000
+        a2                             5.000000
+        s9                             5.000000
+      * Repulsion:
+        kExp                           1.500000    1.000000
+        rExp                           1.000000
+      * Coulomb:
+        alpha                          2.000000
+        third order                    shell-resolved
+        anisotropic                    true
+        a3                             3.000000
+        a5                             4.000000
+        cn-shift                       1.200000
+        cn-exp                         4.000000
+        max-rad                        5.000000
+
+
+          ...................................................
+          :                      SETUP                      :
+          :.................................................:
+          :  # basis functions                   8          :
+          :  # atomic orbitals                   8          :
+          :  # shells                            6          :
+          :  # electrons                         8          :
+          :  max. iterations                   250          :
+          :  Hamiltonian                  GFN2-xTB          :
+          :  restarted?                      false          :
+          :  GBSA solvation                  false          :
+          :  PC potential                    false          :
+          :  electronic temp.          300.0000000     K    :
+          :  accuracy                    1.0000000          :
+          :  -> integral cutoff          0.2500000E+02      :
+          :  -> integral neglect         0.1000000E-07      :
+          :  -> SCF convergence          0.1000000E-05 Eh   :
+          :  -> wf. convergence          0.1000000E-03 e    :
+          :  Broyden damping             0.4000000          :
+          ...................................................
+
+ iter      E             dE          RMSdq      gap      omega  full diag
+   1     -4.2352961 -0.423530E+01  0.243E+00   17.75       0.0  T
+   2     -4.2472613 -0.119651E-01  0.928E-01   17.57       1.0  T
+   3     -4.2474252 -0.163901E-03  0.500E-01   17.46       1.0  T
+   4     -4.2474673 -0.421128E-04  0.924E-02   17.36       1.0  T
+   5     -4.2474672  0.111480E-06  0.698E-03   17.35       6.4  T
+   6     -4.2474673 -0.145702E-06  0.191E-04   17.35     233.9  T
+   7     -4.2474673 -0.109869E-09  0.432E-06   17.35   10350.2  T
+
+   *** convergence criteria satisfied after 7 iterations ***
+
+         #    Occupation            Energy/Eh            Energy/eV
+      -------------------------------------------------------------
+         1        2.0000           -0.5818361             -15.8326
+         2        2.0000           -0.4674583             -12.7202
+         3        2.0000           -0.4674579             -12.7202
+         4        2.0000           -0.4674579             -12.7202 (HOMO)
+         5                          0.1702647               4.6331 (LUMO)
+         6                          0.2292565               6.2384
+         7                          0.2292569               6.2384
+         8                          0.2292585               6.2384
+      -------------------------------------------------------------
+                  HL-Gap            0.6377226 Eh           17.3533 eV
+             Fermi-level           -0.1485966 Eh           -4.0435 eV
+
+ SCC (total)                   0 d,  0 h,  0 min,  0.023 sec
+ SCC setup                      ...        0 min,  0.000 sec (  0.165%)
+ Dispersion                     ...        0 min,  0.000 sec (  0.028%)
+ classical contributions        ...        0 min,  0.000 sec (  0.021%)
+ integral evaluation            ...        0 min,  0.000 sec (  0.275%)
+ iterations                     ...        0 min,  0.023 sec ( 97.223%)
+ molecular gradient             ...        0 min,  0.000 sec (  1.597%)
+ printout                       ...        0 min,  0.000 sec (  0.655%)
+
+         :::::::::::::::::::::::::::::::::::::::::::::::::::::
+         ::                     SUMMARY                     ::
+         :::::::::::::::::::::::::::::::::::::::::::::::::::::
+         :: total energy              -4.175218519975 Eh    ::
+         :: gradient norm              0.000006627564 Eh/a0 ::
+         :: HOMO-LUMO gap             17.353313970090 eV    ::
+         ::.................................................::
+         :: SCC energy                -4.247467308188 Eh    ::
+         :: -> isotropic ES            0.002035567944 Eh    ::
+         :: -> anisotropic ES          0.002321540929 Eh    ::
+         :: -> anisotropic XC          0.003585096736 Eh    ::
+         :: -> dispersion             -0.000661011606 Eh    ::
+         :: repulsion energy           0.072248782622 Eh    ::
+         :: add. restraining           0.000000000000 Eh    ::
+         :: total charge               0.000000000000 e     ::
+         :::::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+Property printout bound to 'properties.out'
+
+           -------------------------------------------------
+          | TOTAL ENERGY               -4.175218519975 Eh   |
+          | GRADIENT NORM               0.000006627564 Eh/α |
+          | HOMO-LUMO GAP              17.353313970090 eV   |
+           -------------------------------------------------
+
+------------------------------------------------------------------------
+ * finished run on 2022/07/22 at 20:31:34.439     
+------------------------------------------------------------------------
+ total:
+ * wall-time:     0 d,  0 h,  0 min,  0.028 sec
+ *  cpu-time:     0 d,  0 h,  0 min,  0.007 sec
+ * ratio c/w:     0.264 speedup
+ SCF:
+ * wall-time:     0 d,  0 h,  0 min,  0.023 sec
+ *  cpu-time:     0 d,  0 h,  0 min,  0.003 sec
+ * ratio c/w:     0.126 speedup
+
+
+-------------------------   --------------------
+FINAL SINGLE POINT ENERGY        -4.175218519980
+-------------------------   --------------------
+
+
+----------------------------------------------------------------------------
+                           ORCA NUMERICAL FREQUENCIES
+----------------------------------------------------------------------------
+
+Number of atoms                ... 5
+Central differences            ... used
+Number of displacements        ... 30
+Numerical increment            ... 5.000e-03 bohr
+IR-spectrum generation         ... on
+Raman-spectrum generation      ... off
+Surface Crossing Hessian       ... off
+
+The output will be reduced. Please look at the following files:
+SCF program output             ... >cmmd.lastscf
+Integral program output        ... >cmmd.lastint
+Gradient program output        ... >cmmd.lastgrad
+Dipole moment program output   ... >cmmd.lastmom
+AutoCI program output          ... >cmmd.lastautoci
+
+	<< Calculating on displaced geometry   1 (of  30) >>
+	<< Calculating on displaced geometry   2 (of  30) >>
+	<< Calculating on displaced geometry   3 (of  30) >>
+	<< Calculating on displaced geometry   4 (of  30) >>
+	<< Calculating on displaced geometry   5 (of  30) >>
+	<< Calculating on displaced geometry   6 (of  30) >>
+	<< Calculating on displaced geometry   7 (of  30) >>
+	<< Calculating on displaced geometry   8 (of  30) >>
+	<< Calculating on displaced geometry   9 (of  30) >>
+	<< Calculating on displaced geometry  10 (of  30) >>
+	<< Calculating on displaced geometry  11 (of  30) >>
+	<< Calculating on displaced geometry  12 (of  30) >>
+	<< Calculating on displaced geometry  13 (of  30) >>
+	<< Calculating on displaced geometry  14 (of  30) >>
+	<< Calculating on displaced geometry  15 (of  30) >>
+	<< Calculating on displaced geometry  16 (of  30) >>
+	<< Calculating on displaced geometry  17 (of  30) >>
+	<< Calculating on displaced geometry  18 (of  30) >>
+	<< Calculating on displaced geometry  19 (of  30) >>
+	<< Calculating on displaced geometry  20 (of  30) >>
+	<< Calculating on displaced geometry  21 (of  30) >>
+	<< Calculating on displaced geometry  22 (of  30) >>
+	<< Calculating on displaced geometry  23 (of  30) >>
+	<< Calculating on displaced geometry  24 (of  30) >>
+	<< Calculating on displaced geometry  25 (of  30) >>
+	<< Calculating on displaced geometry  26 (of  30) >>
+	<< Calculating on displaced geometry  27 (of  30) >>
+	<< Calculating on displaced geometry  28 (of  30) >>
+	<< Calculating on displaced geometry  29 (of  30) >>
+	<< Calculating on displaced geometry  30 (of  30) >>
+
+-----------------------
+VIBRATIONAL FREQUENCIES
+-----------------------
+
+Scaling factor for frequencies =  1.000000000 (already applied!)
+
+   0:         0.00 cm**-1
+   1:         0.00 cm**-1
+   2:         0.00 cm**-1
+   3:         0.00 cm**-1
+   4:         0.00 cm**-1
+   5:         0.00 cm**-1
+   6:      1385.80 cm**-1
+   7:      1385.80 cm**-1
+   8:      1385.82 cm**-1
+   9:      1557.27 cm**-1
+  10:      1557.28 cm**-1
+  11:      3090.01 cm**-1
+  12:      3103.91 cm**-1
+  13:      3103.94 cm**-1
+  14:      3103.96 cm**-1
+
+
+------------
+NORMAL MODES
+------------
+
+These modes are the cartesian displacements weighted by the diagonal matrix
+M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom
+Thus, these vectors are normalized but *not* orthogonal
+
+                  0          1          2          3          4          5    
+      0       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      1       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      2       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      3       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      4       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      5       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      6       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      7       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      8       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      9       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+     10       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+     11       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+     12       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+     13       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+     14       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+                  6          7          8          9         10         11    
+      0       0.114604  -0.034379  -0.047849  -0.000000  -0.000001   0.000103
+      1       0.058577   0.077751   0.084434   0.000006  -0.000001   0.000055
+      2      -0.006344   0.096843  -0.084775   0.000006   0.000001  -0.000050
+      3       0.053322  -0.015996  -0.022263   0.000000  -0.000001   0.498979
+      4      -0.275357  -0.365482  -0.396926  -0.365602   0.341113   0.000026
+      5       0.029828  -0.455230   0.398529  -0.341139  -0.365577  -0.000024
+      6      -0.398895   0.118467   0.391732   0.012781  -0.471229  -0.166974
+      7       0.002258  -0.451191  -0.065844   0.352858   0.126576  -0.331517
+      8      -0.252007  -0.368335   0.062453   0.353959  -0.109170   0.336519
+      9      -0.457603   0.327003   0.101264   0.401721   0.246692  -0.166627
+     10      -0.214312  -0.241048  -0.489994   0.214417  -0.433920  -0.125393
+     11       0.251106  -0.004234   0.061323  -0.206508   0.029276  -0.454466
+     12      -0.562413  -0.019822   0.099424  -0.414501   0.224553  -0.166606
+     13      -0.210572   0.131268  -0.053327  -0.201742  -0.033763   0.456233
+     14       0.046669  -0.326146   0.487849   0.193621   0.445460   0.118563
+                 12         13         14    
+      0      -0.016400  -0.003198   0.085675
+      1      -0.058810  -0.063053  -0.013611
+      2       0.062386  -0.060279   0.009692
+      3       0.162306   0.031593  -0.845452
+      4      -0.027198  -0.029160  -0.006295
+      5       0.028852  -0.027877   0.004482
+      6       0.289143   0.006417  -0.005080
+      7       0.561807  -0.013489  -0.095035
+      8      -0.569035  -0.043792   0.094561
+      9      -0.133319   0.245129  -0.077040
+     10      -0.121811   0.156405  -0.094081
+     11      -0.313963   0.644504  -0.313605
+     12      -0.122713  -0.245035  -0.093307
+     13       0.287957   0.637562   0.357599
+     14       0.110775   0.145430   0.099072
+
+
+-----------
+IR SPECTRUM
+-----------
+
+ Mode   freq       eps      Int      T**2         TX        TY        TZ
+       cm**-1   L/(mol*cm) km/mol    a.u.
+----------------------------------------------------------------------------
+  6:   1385.80   0.000431    2.18  0.000097  (-0.002037 -0.001583 -0.009506)
+  7:   1385.80   0.002914   14.73  0.000656  ( 0.000611 -0.019085 -0.017074)
+  8:   1385.82   0.000195    0.98  0.000044  ( 0.000850  0.004423 -0.004858)
+  9:   1557.27   0.004759   24.05  0.000954  (-0.000000  0.021765  0.021908)
+ 10:   1557.28   0.000116    0.59  0.000023  ( 0.000000 -0.002953  0.003811)
+ 11:   3090.01   0.002131   10.77  0.000215  (-0.013874 -0.003329  0.003419)
+ 12:   3103.91   0.010797   54.56  0.001086  (-0.004326 -0.022844  0.023344)
+ 13:   3103.94   0.006348   32.08  0.000638  (-0.000842 -0.018162 -0.017539)
+ 14:   3103.96   0.005878   29.71  0.000591  ( 0.022536 -0.007011  0.005826)
+
+* The epsilon (eps) is given for a Dirac delta lineshape.
+** The dipole moment derivative (T) already includes vibrational overlap.
+
+The first frequency considered to be a vibration is 6
+The total number of vibrations considered is 9
+
+
+--------------------------
+THERMOCHEMISTRY AT 298.15K
+--------------------------
+
+Temperature         ... 298.15 K
+Pressure            ... 1.00 atm
+Total Mass          ... 16.04 AMU
+
+Throughout the following assumptions are being made:
+  (1) The electronic state is orbitally nondegenerate
+  (2) There are no thermally accessible electronically excited states
+  (3) Hindered rotations indicated by low frequency modes are not
+      treated as such but are treated as vibrations and this may
+      cause some error
+  (4) All equations used are the standard statistical mechanics
+      equations for an ideal gas
+  (5) All vibrations are strictly harmonic
+
+freq.    1385.80  E(vib)   ...       0.00 
+freq.    1385.80  E(vib)   ...       0.00 
+freq.    1385.82  E(vib)   ...       0.00 
+freq.    1557.27  E(vib)   ...       0.00 
+freq.    1557.28  E(vib)   ...       0.00 
+freq.    3090.01  E(vib)   ...       0.00 
+freq.    3103.91  E(vib)   ...       0.00 
+freq.    3103.94  E(vib)   ...       0.00 
+freq.    3103.96  E(vib)   ...       0.00 
+
+------------
+INNER ENERGY
+------------
+
+The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans)
+    E(el)   - is the total energy from the electronic structure calculation
+              = E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc)
+    E(ZPE)  - the the zero temperature vibrational energy from the frequency calculation
+    E(vib)  - the the finite temperature correction to E(ZPE) due to population
+              of excited vibrational states
+    E(rot)  - is the rotational thermal energy
+    E(trans)- is the translational thermal energy
+
+Summary of contributions to the inner energy U:
+Electronic energy                ...     -4.17521852 Eh
+Zero point energy                ...      0.04482019 Eh      28.13 kcal/mol
+Thermal vibrational correction   ...      0.00003140 Eh       0.02 kcal/mol
+Thermal rotational correction    ...      0.00141627 Eh       0.89 kcal/mol
+Thermal translational correction ...      0.00141627 Eh       0.89 kcal/mol
+-----------------------------------------------------------------------
+Total thermal energy                     -4.12753439 Eh
+
+
+Summary of corrections to the electronic energy:
+(perhaps to be used in another calculation)
+Total thermal correction                  0.00286394 Eh       1.80 kcal/mol
+Non-thermal (ZPE) correction              0.04482019 Eh      28.13 kcal/mol
+-----------------------------------------------------------------------
+Total correction                          0.04768413 Eh      29.92 kcal/mol
+
+
+--------
+ENTHALPY
+--------
+
+The enthalpy is H = U + kB*T
+                kB is Boltzmann's constant
+Total free energy                 ...     -4.12753439 Eh 
+Thermal Enthalpy correction       ...      0.00094421 Eh       0.59 kcal/mol
+-----------------------------------------------------------------------
+Total Enthalpy                    ...     -4.12659018 Eh
+
+
+Note: Rotational entropy computed according to Herzberg 
+Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 
+Point Group:  Td, Symmetry Number:  12  
+Rotational constants in cm-1:     5.355318     5.355306     5.355302 
+
+Vibrational entropy computed according to the QRRHO of S. Grimme
+Chem.Eur.J. 2012 18 9955
+
+
+-------
+ENTROPY
+-------
+
+The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans))
+     S(el)   - electronic entropy
+     S(vib)  - vibrational entropy
+     S(rot)  - rotational entropy
+     S(trans)- translational entropy
+The entropies will be listed as multiplied by the temperature to get
+units of energy
+
+Electronic entropy                ...      0.00000000 Eh      0.00 kcal/mol
+Vibrational entropy               ...      0.00003597 Eh      0.02 kcal/mol
+Rotational entropy                ...      0.00478798 Eh      3.00 kcal/mol
+Translational entropy             ...      0.01627961 Eh     10.22 kcal/mol
+-----------------------------------------------------------------------
+Final entropy term                ...      0.02110356 Eh     13.24 kcal/mol
+
+In case the symmetry of your molecule has not been determined correctly
+or in case you have a reason to use a different symmetry number we print 
+out the resulting rotational entropy values for sn=1,12 :
+ --------------------------------------------------------
+|  sn= 1 | S(rot)=       0.00713418 Eh      4.48 kcal/mol|
+|  sn= 2 | S(rot)=       0.00647973 Eh      4.07 kcal/mol|
+|  sn= 3 | S(rot)=       0.00609689 Eh      3.83 kcal/mol|
+|  sn= 4 | S(rot)=       0.00582527 Eh      3.66 kcal/mol|
+|  sn= 5 | S(rot)=       0.00561458 Eh      3.52 kcal/mol|
+|  sn= 6 | S(rot)=       0.00544244 Eh      3.42 kcal/mol|
+|  sn= 7 | S(rot)=       0.00529689 Eh      3.32 kcal/mol|
+|  sn= 8 | S(rot)=       0.00517081 Eh      3.24 kcal/mol|
+|  sn= 9 | S(rot)=       0.00505960 Eh      3.17 kcal/mol|
+|  sn=10 | S(rot)=       0.00496012 Eh      3.11 kcal/mol|
+|  sn=11 | S(rot)=       0.00487013 Eh      3.06 kcal/mol|
+|  sn=12 | S(rot)=       0.00478798 Eh      3.00 kcal/mol|
+ --------------------------------------------------------
+
+
+-------------------
+GIBBS FREE ENERGY
+-------------------
+
+The Gibbs free energy is G = H - T*S
+
+Total enthalpy                    ...     -4.12659018 Eh 
+Total entropy correction          ...     -0.02110356 Eh    -13.24 kcal/mol
+-----------------------------------------------------------------------
+Final Gibbs free energy         ...     -4.14769375 Eh
+
+For completeness - the Gibbs free energy minus the electronic energy
+G-E(el)                           ...      0.02752477 Eh     17.27 kcal/mol
+
+
+
+Timings for individual modules:
+
+Sum of individual times         ...       63.185 sec (=   1.053 min)
+Numerical frequency calculation ...       63.123 sec (=   1.052 min)  99.9 %
+XTB module                      ...        0.061 sec (=   0.001 min)   0.1 %
+                             ****ORCA TERMINATED NORMALLY****
+TOTAL RUN TIME: 0 days 0 hours 1 minutes 3 seconds 196 msec

cmmde_gui/test/ala/freq/cmmd_property.txt

@@ -0,0 +1,48 @@
+-------------------------------------------------------------
+----------------------- !PROPERTIES! ------------------------
+-------------------------------------------------------------
+# -----------------------------------------------------------
+$ THERMOCHEMISTRY_Energies
+   description: The Thermochemistry energies
+   geom. index: 0
+   prop. index: 1
+        Temperature (Kelvin)           :        298.1500000000
+        Pressure (atm)                 :          1.0000000000
+        Total Mass (AMU)               :         16.0430000000
+        Spin Degeneracy                :          1.0000000000
+        Electronic Energy (Hartree)    :         -4.1752185200
+        Translational Energy (Hartree) :          0.0014162714
+        Rotational Energy (Hartree)    :          0.0014162714
+        Vibrational Energy (Hartree)   :          0.0000314005
+        Number of frequencies          :     15      
+        Scaling Factor for frequencies :          1.0000000000
+        Vibrational frequencies        :     
+                  0    
+      0       0.000000
+      1       0.000000
+      2       0.000000
+      3       0.000000
+      4       0.000000
+      5       0.000000
+      6     1385.802989
+      7     1385.804694
+      8     1385.819131
+      9     1557.265928
+     10     1557.278661
+     11     3090.006354
+     12     3103.914034
+     13     3103.936524
+     14     3103.959260
+        Zero Point Energy (Hartree)    :          0.0448201860
+        Inner Energy (Hartree)         :         -4.1275343906
+        Enthalpy (Hartree)             :         -4.1265901815
+        Electronic entropy             :          0.0000000000
+        Rotational entropy             :          0.0047879801
+        Vibrational entropy            :          0.0000359731
+        Translational entropy          :          0.0047879801
+        Entropy                        :          0.0211035637
+        Gibbs Energy (Hartree)         :         -4.1476937452
+        Is Linear                      :                 false
+# -------------------------------------------------------------
+----------------------- !GEOMETRIES! ------------------------
+# -------------------------------------------------------------

cmmde_gui/test/ala/freq/run.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
+export PATH=/home/adit/opt/openmpi411/bin:$PATH
+export OMP_NUM_THREADS=1
+cd $PWD
+$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

cmmde_gui/test/ala/geom.smi

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

cmmde_gui/test/ala/geom.xyz

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

cmmde_gui/test/ala/run.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
+export PATH=/home/adit/opt/openmpi411/bin:$PATH
+export OMP_NUM_THREADS=1
+cd $PWD
+$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

cmmde_gui/test/ala/run_babel.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export OMP_NUM_THREADS=1
+cd $PWD
+obabel geom.smi -O geom.xyz --gen3d

cmmde_gui/test/ala/slurm-2913.out

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

cmmde_gui/test/alala/alala/cmmd.engrad

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

cmmde_gui/test/alala/alala/cmmd.in

@@ -0,0 +1,11 @@
+#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

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

cmmde_gui/test/alala/alala/cmmd_property.txt

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

cmmde_gui/test/alala/alala/cmmd_trj.xyz

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

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

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

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

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

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

@@ -0,0 +1,78 @@
+-------------------------------------------------------------
+----------------------- !PROPERTIES! ------------------------
+-------------------------------------------------------------
+# -----------------------------------------------------------
+$ THERMOCHEMISTRY_Energies
+   description: The Thermochemistry energies
+   geom. index: 0
+   prop. index: 1
+        Temperature (Kelvin)           :        298.1500000000
+        Pressure (atm)                 :          1.0000000000
+        Total Mass (AMU)               :         70.1350000000
+        Spin Degeneracy                :          1.0000000000
+        Electronic Energy (Hartree)    :        -15.8143133661
+        Translational Energy (Hartree) :          0.0014162714
+        Rotational Energy (Hartree)    :          0.0014162714
+        Vibrational Energy (Hartree)   :          0.0014286410
+        Number of frequencies          :     45      
+        Scaling Factor for frequencies :          1.0000000000
+        Vibrational frequencies        :     
+                  0    
+      0       0.000000
+      1       0.000000
+      2       0.000000
+      3       0.000000
+      4       0.000000
+      5       0.000000
+      6     -13.351568
+      7     252.244123
+      8     557.175881
+      9     613.241874
+     10     803.096513
+     11     840.536598
+     12     876.377253
+     13     954.582365
+     14     965.585932
+     15     980.313366
+     16     1000.249668
+     17     1030.244023
+     18     1101.221133
+     19     1125.950241
+     20     1163.245212
+     21     1191.481572
+     22     1205.003583
+     23     1219.576673
+     24     1239.150145
+     25     1296.431408
+     26     1307.223911
+     27     1323.325759
+     28     1324.021436
+     29     1324.985289
+     30     1483.494156
+     31     1487.616972
+     32     1497.580040
+     33     1498.376661
+     34     1516.087224
+     35     2971.917990
+     36     2972.553003
+     37     2984.877385
+     38     2986.620750
+     39     2999.161041
+     40     3000.307663
+     41     3005.881613
+     42     3008.879158
+     43     3009.438792
+     44     3012.882898
+        Zero Point Energy (Hartree)    :          0.1392665271
+        Inner Energy (Hartree)         :        -15.6707856551
+        Enthalpy (Hartree)             :        -15.6698414460
+        Electronic entropy             :          0.0000000000
+        Rotational entropy             :          0.0119173746
+        Vibrational entropy            :          0.0020062037
+        Translational entropy          :          0.0119173746
+        Entropy                        :          0.0322924006
+        Gibbs Energy (Hartree)         :        -15.7021338467
+        Is Linear                      :                 false
+# -------------------------------------------------------------
+----------------------- !GEOMETRIES! ------------------------
+# -------------------------------------------------------------

cmmde_gui/test/alala/alala/freq/run.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
+export PATH=/home/adit/opt/openmpi411/bin:$PATH
+export OMP_NUM_THREADS=1
+cd $PWD
+$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

cmmde_gui/test/alala/alala/geom.smi

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

cmmde_gui/test/alala/alala/geom.xyz

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

cmmde_gui/test/alala/alala/run.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
+export PATH=/home/adit/opt/openmpi411/bin:$PATH
+export OMP_NUM_THREADS=1
+cd $PWD
+$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

cmmde_gui/test/alala/alala/run_babel.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export OMP_NUM_THREADS=1
+cd $PWD
+obabel geom.smi -O geom.xyz --gen3d

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

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

cmmde_gui/test/alala/cmmd.engrad

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

cmmde_gui/test/alala/cmmd.in

@@ -0,0 +1,11 @@
+#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

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

cmmde_gui/test/alala/cmmd_property.txt

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

cmmde_gui/test/alala/cmmd_trj.xyz

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

cmmde_gui/test/alala/freq/cmmd.engrad

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

cmmde_gui/test/alala/freq/cmmd.in

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

cmmde_gui/test/alala/freq/cmmd_property.txt

@@ -0,0 +1,78 @@
+-------------------------------------------------------------
+----------------------- !PROPERTIES! ------------------------
+-------------------------------------------------------------
+# -----------------------------------------------------------
+$ THERMOCHEMISTRY_Energies
+   description: The Thermochemistry energies
+   geom. index: 0
+   prop. index: 1
+        Temperature (Kelvin)           :        298.1500000000
+        Pressure (atm)                 :          1.0000000000
+        Total Mass (AMU)               :         70.1350000000
+        Spin Degeneracy                :          1.0000000000
+        Electronic Energy (Hartree)    :        -15.8143133661
+        Translational Energy (Hartree) :          0.0014162714
+        Rotational Energy (Hartree)    :          0.0014162714
+        Vibrational Energy (Hartree)   :          0.0014286410
+        Number of frequencies          :     45      
+        Scaling Factor for frequencies :          1.0000000000
+        Vibrational frequencies        :     
+                  0    
+      0       0.000000
+      1       0.000000
+      2       0.000000
+      3       0.000000
+      4       0.000000
+      5       0.000000
+      6     -13.351568
+      7     252.244123
+      8     557.175881
+      9     613.241874
+     10     803.096513
+     11     840.536598
+     12     876.377253
+     13     954.582365
+     14     965.585932
+     15     980.313366
+     16     1000.249668
+     17     1030.244023
+     18     1101.221133
+     19     1125.950241
+     20     1163.245212
+     21     1191.481572
+     22     1205.003583
+     23     1219.576673
+     24     1239.150145
+     25     1296.431408
+     26     1307.223911
+     27     1323.325759
+     28     1324.021436
+     29     1324.985289
+     30     1483.494156
+     31     1487.616972
+     32     1497.580040
+     33     1498.376661
+     34     1516.087224
+     35     2971.917990
+     36     2972.553003
+     37     2984.877385
+     38     2986.620750
+     39     2999.161041
+     40     3000.307663
+     41     3005.881613
+     42     3008.879158
+     43     3009.438792
+     44     3012.882898
+        Zero Point Energy (Hartree)    :          0.1392665271
+        Inner Energy (Hartree)         :        -15.6707856551
+        Enthalpy (Hartree)             :        -15.6698414460
+        Electronic entropy             :          0.0000000000
+        Rotational entropy             :          0.0119173746
+        Vibrational entropy            :          0.0020062037
+        Translational entropy          :          0.0119173746
+        Entropy                        :          0.0322924006
+        Gibbs Energy (Hartree)         :        -15.7021338467
+        Is Linear                      :                 false
+# -------------------------------------------------------------
+----------------------- !GEOMETRIES! ------------------------
+# -------------------------------------------------------------

cmmde_gui/test/alala/freq/run.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
+export PATH=/home/adit/opt/openmpi411/bin:$PATH
+export OMP_NUM_THREADS=1
+cd $PWD
+$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

cmmde_gui/test/alala/geom.smi

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

cmmde_gui/test/alala/geom.xyz

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

cmmde_gui/test/alala/run.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
+export PATH=/home/adit/opt/openmpi411/bin:$PATH
+export OMP_NUM_THREADS=1
+cd $PWD
+$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

cmmde_gui/test/alala/run_babel.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export OMP_NUM_THREADS=1
+cd $PWD
+obabel geom.smi -O geom.xyz --gen3d

cmmde_gui/test/alala/slurm-2885.out

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

cmmde_gui/test/metana3/cmmd.engrad

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

cmmde_gui/test/metana3/cmmd.in

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

cmmde_gui/test/metana3/cmmd.opt

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

cmmde_gui/test/metana3/cmmd.xyz

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

cmmde_gui/test/metana3/cmmd_property.txt

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

cmmde_gui/test/metana3/cmmd_trj.xyz

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

cmmde_gui/test/metana3/freq/cmmd.engrad

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

cmmde_gui/test/metana3/freq/cmmd.hess

@@ -0,0 +1,192 @@
+
+$orca_hessian_file
+
+$act_atom
+  0
+
+$act_coord
+  0
+
+$act_energy
+       -4.175219
+
+$hessian
+15
+                    0                  1                  2                  3                  4        
+    0      5.1329012148E-01  -2.6663567559E-06   8.3835566296E-07  -2.9809731316E-01  -1.9784696379E-06
+    1     -2.6663567559E-06   5.1328712912E-01  -2.6497366205E-08  -1.9726025329E-06  -4.3442777277E-02
+    2      8.3835566296E-07  -2.6497366205E-08   5.1328935767E-01  -1.7634020912E-08   7.2276242091E-09
+    3     -2.9809731316E-01  -1.9726025329E-06  -1.7634020912E-08   3.4272680101E-01   2.0211245618E-06
+    4     -1.9784696379E-06  -4.3442777277E-02   7.2276242091E-09   2.0211245618E-06   4.6441179291E-02
+    5     -1.7116830436E-08   7.2320836845E-09  -4.3442884873E-02   1.0454268310E-07   1.5596984091E-08
+    6     -7.1733742694E-02  -4.6783019481E-02   6.4926425576E-02  -1.4874469674E-02  -1.9611323313E-02
+    7     -4.6782960343E-02  -1.2079849231E-01   1.0735996309E-01  -1.3733460307E-03  -6.2451045673E-04
+    8      6.4926271962E-02   1.0735982095E-01  -1.9243359408E-01   1.9056658411E-03   1.1233724602E-03
+    9     -7.1733749665E-02  -3.2835255893E-02  -7.2979874524E-02  -1.4874557137E-02  -1.3764589681E-02
+   10     -3.2835212863E-02  -8.1549006178E-02  -8.4698552890E-02  -9.6399521602E-04  -2.1374725375E-04
+   11     -7.2979703320E-02  -8.4698425775E-02  -2.3168748610E-01  -2.1420126424E-03  -8.8624128993E-04
+   12     -7.1735221884E-02   7.9622913833E-02   8.0526283576E-03  -1.4874988941E-02   3.3375870456E-02
+   13      7.9622824479E-02  -2.6750649802E-01  -2.2661386241E-02   2.3368513654E-03  -2.1595522467E-03
+   14      8.0526082358E-03  -2.2661370610E-02  -4.5734620980E-02   2.3640040325E-04  -2.3715469799E-04
+                    5                  6                  7                  8                  9        
+    0     -1.7116830436E-08  -7.1733742694E-02  -4.6782960343E-02   6.4926271962E-02  -7.1733749665E-02
+    1      7.2320836845E-09  -4.6783019481E-02  -1.2079849231E-01   1.0735982095E-01  -3.2835255893E-02
+    2     -4.3442884873E-02   6.4926425576E-02   1.0735996309E-01  -1.9243359408E-01  -7.2979874524E-02
+    3      1.0454268310E-07  -1.4874469674E-02  -1.3733460307E-03   1.9056658411E-03  -1.4874557137E-02
+    4      1.5596984091E-08  -1.9611323313E-02  -6.2451045673E-04   1.1233724602E-03  -1.3764589681E-02
+    5      4.6441174206E-02   2.7216470791E-02   1.1236342607E-03  -1.3739986007E-03  -3.0592163721E-02
+    6      2.7216470791E-02   7.9358012224E-02   5.4431671651E-02  -7.5541061727E-02   3.6257810679E-03
+    7      1.1236342607E-03   5.4431671651E-02   1.3644442522E-01  -1.2491155865E-01   3.9350425729E-03
+    8     -1.3739986007E-03  -7.5541061727E-02  -1.2491155865E-01   2.1979006093E-01   9.4495234104E-03
+    9     -3.0592163721E-02   3.6257810679E-03   3.9350425729E-03   9.4495234104E-03   7.9358100288E-02
+   10     -8.8657495192E-04   5.7474554883E-03   6.7159136625E-03   1.6203333770E-02   3.8203656742E-02
+   11     -1.7848534176E-03  -8.4702978109E-03  -9.2690123799E-03  -2.7214652258E-02   8.4911071790E-02
+   12      3.3756054802E-03   3.6258970273E-03  -1.0209047413E-02  -7.4228743024E-04   3.6259033802E-03
+   13     -2.3708276366E-04   6.2163065628E-03  -2.1734810904E-02   2.2247745899E-04   4.4619543959E-03
+   14      1.6113030257E-04  -8.1328347074E-03   2.5694815653E-02   1.2359268027E-03   9.2128031272E-03
+                   10                 11                 12                 13                 14        
+    0     -3.2835212863E-02  -7.2979703320E-02  -7.1735221884E-02   7.9622824479E-02   8.0526082358E-03
+    1     -8.1549006178E-02  -8.4698425775E-02   7.9622913833E-02  -2.6750649802E-01  -2.2661370610E-02
+    2     -8.4698552890E-02  -2.3168748610E-01   8.0526283576E-03  -2.2661386241E-02  -4.5734620980E-02
+    3     -9.6399521602E-04  -2.1420126424E-03  -1.4874988941E-02   2.3368513654E-03   2.3640040325E-04
+    4     -2.1374725375E-04  -8.8624128993E-04   3.3375870456E-02  -2.1595522467E-03  -2.3715469799E-04
+    5     -8.8657495192E-04  -1.7848534176E-03   3.3756054802E-03  -2.3708276366E-04   1.6113030257E-04
+    6      5.7474554883E-03  -8.4702978109E-03   3.6258970273E-03   6.2163065628E-03  -8.1328347074E-03
+    7      6.7159136625E-03  -9.2690123799E-03  -1.0209047413E-02  -2.1734810904E-02   2.5694815653E-02
+    8      1.6203333770E-02  -2.7214652258E-02  -7.4228743024E-04   2.2247745899E-04   1.2359268027E-03
+    9      3.8203656742E-02   8.4911071790E-02   3.6259033802E-03   4.4619543959E-03   9.2128031272E-03
+   10      9.0777856163E-02   9.8545399446E-02  -1.0150949331E-02  -1.5729415534E-02  -2.9162035420E-02
+   11      9.8545399446E-02   2.6546069193E-01  -1.3169360375E-03  -3.6895800365E-03  -4.7694116180E-03
+   12     -1.0150949331E-02  -1.3169360375E-03   7.9359888349E-02  -9.2640251677E-02  -9.3692112021E-03
+   13     -1.5729415534E-02  -3.6895800365E-03  -9.2640251677E-02   3.0713520326E-01   2.6366155060E-02
+   14     -2.9162035420E-02  -4.7694116180E-03  -9.3692112021E-03   2.6366155060E-02   4.9107604906E-02
+
+$vibrational_frequencies
+15
+    0        0.000000
+    1        0.000000
+    2        0.000000
+    3        0.000000
+    4        0.000000
+    5        0.000000
+    6     1385.801243
+    7     1385.807833
+    8     1385.817738
+    9     1557.267071
+   10     1557.277517
+   11     3090.006354
+   12     3103.916950
+   13     3103.935349
+   14     3103.957551
+
+$normal_modes
+15 15
+                    0                  1                  2                  3                  4        
+    0      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    1      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    2      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    3      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    4      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    5      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    6      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    7      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    8      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+    9      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+   10      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+   11      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+   12      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+   13      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+   14      0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00   0.0000000000E+00
+                    5                  6                  7                  8                  9        
+    0      0.0000000000E+00   9.6797657942E-02   8.2365346046E-02  -2.1255744557E-02   1.3565503999E-06
+    1      0.0000000000E+00   8.4411040010E-02  -8.9025947952E-02   3.9430470446E-02   8.4463207128E-06
+    2      0.0000000000E+00   1.0518163403E-02  -4.3542418206E-02  -1.2082603904E-01   2.5431002121E-06
+    3      0.0000000000E+00   4.5039867057E-02   3.8319275010E-02  -9.8888064412E-03   4.0940917893E-06
+    4      0.0000000000E+00  -3.9678163781E-01   4.1848772921E-01  -1.8536275006E-01  -4.7936966115E-01
+    5      0.0000000000E+00  -4.9439500527E-02   2.0468256538E-01   5.6800147233E-01  -1.4229946023E-01
+    6      0.0000000000E+00  -3.3323101216E-01  -3.6705927428E-01   2.8430357692E-01   1.5535215297E-01
+    7      0.0000000000E+00  -1.9539178912E-01   4.5182775143E-01   1.1952435584E-01   3.5085591294E-01
+    8      0.0000000000E+00  -3.2903426800E-01   1.5850581178E-01   1.4488860669E-01   3.2050854553E-01
+    9      0.0000000000E+00  -3.2769383579E-01  -4.6367987556E-01  -6.4905337996E-02   3.0776788299E-01
+   10      0.0000000000E+00  -2.4901821935E-01   3.2974389776E-01  -3.7666601478E-01   3.0071279184E-01
+   11      0.0000000000E+00   2.7910711546E-01   7.3591678003E-03   1.4284036761E-01  -2.5461243337E-01
+   12      0.0000000000E+00  -5.3752441350E-01  -1.8901878724E-01   4.3767103099E-02  -4.6314029427E-01
+   13      0.0000000000E+00  -1.6462283940E-01  -1.3925515138E-01  -2.7336246289E-02  -1.7229968725E-01
+   14      0.0000000000E+00  -2.5964359463E-02   1.4828974182E-01   5.8399331822E-01   7.6373045314E-02
+                   10                 11                 12                 13                 14        
+    0     -7.9127379703E-07   9.7553325878E-05  -9.3441729587E-03   2.0992456319E-02  -8.4210637714E-02
+    1     -2.6770649591E-07   6.5147540638E-05  -3.0512090500E-02   7.8495911765E-02   2.2953731977E-02
+    2      1.0298204828E-06  -2.1731165731E-05   8.1248104559E-02   3.1893066657E-02  -1.0650293390E-03
+    3     -1.2447062918E-06   4.9903254676E-01   9.2484178440E-02  -2.0748948882E-01   8.3094350740E-01
+    4      1.4228805621E-01   3.4317001329E-05  -1.4110337985E-02   3.6300337934E-02   1.0620974834E-02
+    5     -4.7933265552E-01  -1.0101399734E-05   3.7574805097E-02   1.4749333888E-02  -4.9217932073E-04
+    6     -4.4506967419E-01  -1.6691136091E-01   2.7803414614E-01  -7.9154449480E-02   1.1150877196E-02
+    7      2.2567287332E-01  -2.7604255955E-01   4.5277635485E-01  -1.1063369599E-01   9.3455982976E-02
+    8     -3.1334047752E-02   3.8312432019E-01  -6.1036905838E-01   2.1867547957E-01  -1.1545783368E-01
+    9      3.5708300928E-01  -1.6675280959E-01  -1.9349240750E-01  -2.1308515106E-01   3.0085401986E-02
+   10     -3.4948440847E-01  -1.9355090358E-01  -2.3365818721E-01  -2.2226371481E-01   9.0732549420E-02
+   11      1.8809950526E-02  -4.3025387674E-01  -4.5037152473E-01  -5.5992947067E-01   1.7757149370E-01
+   12      8.7997338176E-02  -1.6653078994E-01  -6.5683792677E-02   2.4958981073E-01   1.3124677054E-01
+   13     -1.8473331162E-02   4.6878286924E-01   1.5856431221E-01  -6.3873466941E-01  -4.6831870839E-01
+   14      4.9184448174E-01   4.7398599447E-02   5.5039801961E-02  -5.3522747167E-02  -4.8930937645E-02
+
+#
+# The atoms: label  mass x y z (in bohrs)
+#
+$atoms
+5
+ C     12.01100      1.973519147593     0.155168174767     0.067897849931
+ H      1.00800      4.018506001741     0.155183961786     0.067897981884
+ H      1.00800      1.291864972606    -0.971976276432     1.632142434168
+ H      1.00800      1.291864856257    -0.635940211091    -1.690357908924
+ H      1.00800      1.291846872562     2.073410312513     0.261908942900
+
+$actual_temperature
+  0.000000
+
+$frequency_scale_factor
+  1.000000
+
+$dipole_derivatives
+15
+   -0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00   -0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00    0.0000000000E+00   -0.0000000000E+00
+   -2.0000000000E-01    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00   -0.0000000000E+00    0.0000000000E+00
+   -0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00    0.0000000000E+00   -0.0000000000E+00
+    0.0000000000E+00   -0.0000000000E+00   -0.0000000000E+00
+   -0.0000000000E+00    0.0000000000E+00   -0.0000000000E+00
+   -0.0000000000E+00   -0.0000000000E+00   -0.0000000000E+00
+    0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00   -2.0000000000E-01   -0.0000000000E+00
+    0.0000000000E+00   -0.0000000000E+00    0.0000000000E+00
+
+#
+# The IR spectrum
+#  wavenumber eps Int TX TY TZ
+#
+$ir_spectrum
+15
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+      0.00   0.00000000   0.00000000     0.000000     0.000000     0.000000
+   1385.80   0.00018877   0.95396870    -0.001721     0.006289     0.000000
+   1385.81   0.00013518   0.68316648    -0.001464     0.005320     0.000000
+   1385.82   0.00000548   0.02767528     0.000378     0.001044     0.000000
+   1557.27   0.00022726   1.14847005    -0.000000     0.006748     0.000000
+   1557.28   0.00000261   0.01320204     0.000000     0.000724     0.000000
+   3090.01   0.00358864  18.13550971    -0.013875    -0.013034     0.000000
+   3103.92   0.00023814   1.20345796    -0.002465    -0.004227     0.000000
+   3103.94   0.00318759  16.10877850     0.005531     0.017026     0.000000
+   3103.96   0.00642976  32.49334901    -0.022149     0.012483     0.000000
+
+
+$end
+

cmmde_gui/test/metana3/freq/cmmd.in

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

cmmde_gui/test/metana3/freq/cmmd.out

@@ -0,0 +1,711 @@
+
+                                 *****************
+                                 * O   R   C   A *
+                                 *****************
+
+                                            #,                                       
+                                            ###                                      
+                                            ####                                     
+                                            #####                                    
+                                            ######                                   
+                                           ########,                                 
+                                     ,,################,,,,,                         
+                               ,,#################################,,                 
+                          ,,##########################################,,             
+                       ,#########################################, ''#####,          
+                    ,#############################################,,   '####,        
+                  ,##################################################,,,,####,       
+                ,###########''''           ''''###############################       
+              ,#####''   ,,,,##########,,,,          '''####'''          '####       
+            ,##' ,,,,###########################,,,                        '##       
+           ' ,,###''''                  '''############,,,                           
+         ,,##''                                '''############,,,,        ,,,,,,###''
+      ,#''                                            '''#######################'''  
+     '                                                          ''''####''''         
+             ,#######,   #######,   ,#######,      ##                                
+            ,#'     '#,  ##    ##  ,#'     '#,    #''#        ######   ,####,        
+            ##       ##  ##   ,#'  ##            #'  '#       #        #'  '#        
+            ##       ##  #######   ##           ,######,      #####,   #    #        
+            '#,     ,#'  ##    ##  '#,     ,#' ,#      #,         ##   #,  ,#        
+             '#######'   ##     ##  '#######'  #'      '#     #####' # '####'        
+
+
+
+                  #######################################################
+                  #                        -***-                        #
+                  #          Department of theory and spectroscopy      #
+                  #    Directorship and core code : Frank Neese         #
+                  #        Max Planck Institute fuer Kohlenforschung    #
+                  #                Kaiser Wilhelm Platz 1               #
+                  #                 D-45470 Muelheim/Ruhr               #
+                  #                      Germany                        #
+                  #                                                     #
+                  #                  All rights reserved                #
+                  #                        -***-                        #
+                  #######################################################
+
+
+                         Program Version 5.0.2 -  RELEASE  -
+
+
+ With contributions from (in alphabetic order):
+   Daniel Aravena         : Magnetic Suceptibility
+   Michael Atanasov       : Ab Initio Ligand Field Theory (pilot matlab implementation)
+   Alexander A. Auer      : GIAO ZORA, VPT2 properties, NMR spectrum
+   Ute Becker             : Parallelization
+   Giovanni Bistoni       : ED, misc. LED, open-shell LED, HFLD
+   Martin Brehm           : Molecular dynamics
+   Dmytro Bykov           : SCF Hessian
+   Vijay G. Chilkuri      : MRCI spin determinant printing, contributions to CSF-ICE
+   Dipayan Datta          : RHF DLPNO-CCSD density
+   Achintya Kumar Dutta   : EOM-CC, STEOM-CC
+   Dmitry Ganyushin       : Spin-Orbit,Spin-Spin,Magnetic field MRCI
+   Miquel Garcia          : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme
+   Yang Guo               : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization
+   Andreas Hansen         : Spin unrestricted coupled pair/coupled cluster methods
+   Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals
+   Lee Huntington         : MR-EOM, pCC
+   Robert Izsak           : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM
+   Marcus Kettner         : VPT2
+   Christian Kollmar      : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K
+   Simone Kossmann        : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian
+   Martin Krupicka        : Initial AUTO-CI
+   Lucas Lang             : DCDCAS
+   Marvin Lechner         : AUTO-CI (C++ implementation), FIC-MRCC
+   Dagmar Lenk            : GEPOL surface, SMD
+   Dimitrios Liakos       : Extrapolation schemes; Compound Job, initial MDCI parallelization
+   Dimitrios Manganas     : Further ROCIS development; embedding schemes
+   Dimitrios Pantazis     : SARC Basis sets
+   Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients
+   Taras Petrenko         : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS
+   Peter Pinski           : DLPNO-MP2, DLPNO-MP2 Gradient
+   Christoph Reimann      : Effective Core Potentials
+   Marius Retegan         : Local ZFS, SOC
+   Christoph Riplinger    : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples
+   Tobias Risthaus        : Range-separated hybrids, TD-DFT gradient, RPA, STAB
+   Michael Roemelt        : Original ROCIS implementation
+   Masaaki Saitow         : Open-shell DLPNO-CCSD energy and density
+   Barbara Sandhoefer     : DKH picture change effects
+   Avijit Sen             : IP-ROCIS
+   Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI
+   Bernardo de Souza      : ESD, SOC TD-DFT
+   Georgi Stoychev        : AutoAux, RI-MP2 NMR, DLPNO-MP2 response
+   Willem Van den Heuvel  : Paramagnetic NMR
+   Boris Wezisla          : Elementary symmetry handling
+   Frank Wennmohs         : Technical directorship
+
+
+ We gratefully acknowledge several colleagues who have allowed us to
+ interface, adapt or use parts of their codes:
+   Stefan Grimme, W. Hujo, H. Kruse, P. Pracht,  : VdW corrections, initial TS optimization,
+                  C. Bannwarth, S. Ehlert          DFT functionals, gCP, sTDA/sTD-DF
+   Ed Valeev, F. Pavosevic, A. Kumar             : LibInt (2-el integral package), F12 methods
+   Garnet Chan, S. Sharma, J. Yang, R. Olivares  : DMRG
+   Ulf Ekstrom                                   : XCFun DFT Library
+   Mihaly Kallay                                 : mrcc  (arbitrary order and MRCC methods)
+   Jiri Pittner, Ondrej Demel                    : Mk-CCSD
+   Frank Weinhold                                : gennbo (NPA and NBO analysis)
+   Christopher J. Cramer and Donald G. Truhlar   : smd solvation model
+   Lars Goerigk                                  : TD-DFT with DH, B97 family of functionals
+   V. Asgeirsson, H. Jonsson                     : NEB implementation
+   FAccTs GmbH                                   : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT
+                                                   MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM,
+                                                   LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT,
+                                                   nearIR, NL-DFT gradient (VV10), updates on ESD,
+                                                   ML-optimized integration grids
+   S Lehtola, MJT Oliveira, MAL Marques          : LibXC Library
+   Liviu Ungur et al                             : ANISO software
+
+
+ Your calculation uses the libint2 library for the computation of 2-el integrals
+ For citations please refer to: http://libint.valeyev.net
+
+ Your ORCA version has been built with support for libXC version: 5.1.0
+ For citations please refer to: https://tddft.org/programs/libxc/
+
+ This ORCA versions uses:
+   CBLAS   interface :  Fast vector & matrix operations
+   LAPACKE interface :  Fast linear algebra routines
+   SCALAPACK package :  Parallel linear algebra routines
+   Shared memory     :  Shared parallel matrices
+   BLAS/LAPACK       :  OpenBLAS 0.3.15  USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED
+        Core in use  :  SkylakeX
+   Copyright (c) 2011-2014, The OpenBLAS Project
+
+
+
+
+***************************************
+The coordinates will be read from file: ../cmmd.xyz
+***************************************
+
+
+Your calculation utilizes the semiempirical GFN2-xTB method
+Please cite in your paper:
+C. Bannwarth, Ehlert S., S. Grimme,  J. Chem. Theory Comput., 15, (2019), 1652.
+   
+
+================================================================================
+
+================================================================================
+                                        WARNINGS
+                       Please study these warnings very carefully!
+================================================================================
+
+WARNING: Gradients needed for Numerical Frequencies
+  ===> : Setting RunTyp to EnGrad
+
+WARNING: Found dipole moment calculation with XTB calculation
+  ===> : Switching off dipole moment calculation
+
+
+WARNING: TRAH-SCF for XTB is not implemented!
+  ===> : Turning TRAH off!
+
+================================================================================
+                                       INPUT FILE
+================================================================================
+NAME = cmmd.in
+|  1> #CMMDE generated Orca input file
+|  2> !XTB2 Numfreq
+|  3> %pal 
+|  4>  nprocs 1 
+|  5> end
+|  6>      
+|  7> *xyzfile 0 1 ../cmmd.xyz
+|  8> 
+|  9> %freq 
+| 10>  scalfreq 1 
+| 11>  Temp 298.15
+| 12>  Pressure 1.0
+| 13> end
+| 14> 
+| 15>                          ****END OF INPUT****
+================================================================================
+
+                     *******************************
+                     * Energy+Gradient Calculation *
+                     *******************************
+
+      -----------------------------------------------------------      
+     |                   =====================                   |     
+     |                           x T B                           |     
+     |                   =====================                   |     
+     |                         S. Grimme                         |     
+     |          Mulliken Center for Theoretical Chemistry        |     
+     |                    University of Bonn                     |     
+     |                      Aditya W. Sakti                      |     
+     |                     Departemen Kimia                      |     
+     |                  Universitas Pertamina                    |     
+      -----------------------------------------------------------      
+
+   * xtb version 6.4.1 (060166e8e329d5f5f0e407f406ce482635821d54) compiled by '@Linux' on 12/03/2021
+
+   xtb is free software: you can redistribute it and/or modify it under
+   the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+   
+   xtb is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+   
+   Cite this work as:
+   * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
+     J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
+     e01493. DOI: 10.1002/wcms.1493
+   
+   for GFN2-xTB:
+   * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
+     15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
+   for GFN1-xTB:
+   * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
+     13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
+   for GFN0-xTB:
+   * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
+     DOI: 10.26434/chemrxiv.8326202.v1
+   for GFN-FF:
+   * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
+     DOI: 10.1002/anie.202004239
+   
+   for ALPB and GBSA implicit solvation:
+   * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
+     2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
+   
+   for DFT-D4:
+   * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
+     147, 034112. DOI: 10.1063/1.4993215
+   * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
+     C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
+     DOI: 10.1063/1.5090222
+   * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
+     2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
+   
+   for sTDA-xTB:
+   * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
+     DOI: 10.1063/1.4959605
+   
+   in the mass-spec context:
+   * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
+     DOI: 10.1039/c7sc00601b
+   * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
+     DOI: 10.1021/acsomega.9b02011
+   
+   for metadynamics refer to:
+   * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
+     DOI: 10.1021/acs.jctc.9b00143
+   
+   for SPH calculations refer to:
+   * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
+     DOI: 10.1021/acs.jctc.0c01306
+   
+   with help from (in alphabetical order)
+   P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
+   M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
+   C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
+   J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
+   M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
+   
+ * started run on 2022/07/22 at 20:01:44.804     
+
+           -------------------------------------------------
+          |                Calculation Setup                |
+           -------------------------------------------------
+
+          program call               : /home/adit/opt/orca/otool_xtb cmmd_XTB.xyz --grad -c 0 -u 0 -P 1 --namespace cmmd --input cmmd_XTB.input.tmp --acc 1.000000
+          hostname                   : compute
+          calculation namespace      : cmmd
+          coordinate file            : cmmd_XTB.xyz
+          number of atoms            :                     5
+          number of electrons        :                     8
+          charge                     :                     0
+          spin                       :                   0.0
+          first test random number   :      0.28638523637135
+
+   ID    Z sym.   atoms
+    1    6 C      1
+    2    1 H      2-5
+
+           -------------------------------------------------
+          |                 G F N 2 - x T B                 |
+           -------------------------------------------------
+
+        Reference                      10.1021/acs.jctc.8b01176
+      * Hamiltonian:
+        H0-scaling (s, p, d)           1.850000    2.230000    2.230000
+        zeta-weighting                 0.500000
+      * Dispersion:
+        s8                             2.700000
+        a1                             0.520000
+        a2                             5.000000
+        s9                             5.000000
+      * Repulsion:
+        kExp                           1.500000    1.000000
+        rExp                           1.000000
+      * Coulomb:
+        alpha                          2.000000
+        third order                    shell-resolved
+        anisotropic                    true
+        a3                             3.000000
+        a5                             4.000000
+        cn-shift                       1.200000
+        cn-exp                         4.000000
+        max-rad                        5.000000
+
+
+          ...................................................
+          :                      SETUP                      :
+          :.................................................:
+          :  # basis functions                   8          :
+          :  # atomic orbitals                   8          :
+          :  # shells                            6          :
+          :  # electrons                         8          :
+          :  max. iterations                   250          :
+          :  Hamiltonian                  GFN2-xTB          :
+          :  restarted?                      false          :
+          :  GBSA solvation                  false          :
+          :  PC potential                    false          :
+          :  electronic temp.          300.0000000     K    :
+          :  accuracy                    1.0000000          :
+          :  -> integral cutoff          0.2500000E+02      :
+          :  -> integral neglect         0.1000000E-07      :
+          :  -> SCF convergence          0.1000000E-05 Eh   :
+          :  -> wf. convergence          0.1000000E-03 e    :
+          :  Broyden damping             0.4000000          :
+          ...................................................
+
+ iter      E             dE          RMSdq      gap      omega  full diag
+   1     -4.2352961 -0.423530E+01  0.243E+00   17.75       0.0  T
+   2     -4.2472613 -0.119651E-01  0.928E-01   17.57       1.0  T
+   3     -4.2474252 -0.163901E-03  0.500E-01   17.46       1.0  T
+   4     -4.2474673 -0.421128E-04  0.924E-02   17.36       1.0  T
+   5     -4.2474672  0.111480E-06  0.698E-03   17.35       6.4  T
+   6     -4.2474673 -0.145702E-06  0.191E-04   17.35     233.9  T
+   7     -4.2474673 -0.109869E-09  0.432E-06   17.35   10344.8  T
+
+   *** convergence criteria satisfied after 7 iterations ***
+
+         #    Occupation            Energy/Eh            Energy/eV
+      -------------------------------------------------------------
+         1        2.0000           -0.5818361             -15.8326
+         2        2.0000           -0.4674581             -12.7202
+         3        2.0000           -0.4674581             -12.7202
+         4        2.0000           -0.4674579             -12.7202 (HOMO)
+         5                          0.1702647               4.6331 (LUMO)
+         6                          0.2292564               6.2384
+         7                          0.2292575               6.2384
+         8                          0.2292580               6.2384
+      -------------------------------------------------------------
+                  HL-Gap            0.6377226 Eh           17.3533 eV
+             Fermi-level           -0.1485966 Eh           -4.0435 eV
+
+ SCC (total)                   0 d,  0 h,  0 min,  0.021 sec
+ SCC setup                      ...        0 min,  0.000 sec (  0.604%)
+ Dispersion                     ...        0 min,  0.000 sec (  0.142%)
+ classical contributions        ...        0 min,  0.000 sec (  0.098%)
+ integral evaluation            ...        0 min,  0.000 sec (  0.910%)
+ iterations                     ...        0 min,  0.020 sec ( 95.478%)
+ molecular gradient             ...        0 min,  0.000 sec (  1.911%)
+ printout                       ...        0 min,  0.000 sec (  0.795%)
+
+         :::::::::::::::::::::::::::::::::::::::::::::::::::::
+         ::                     SUMMARY                     ::
+         :::::::::::::::::::::::::::::::::::::::::::::::::::::
+         :: total energy              -4.175218519976 Eh    ::
+         :: gradient norm              0.000006636122 Eh/a0 ::
+         :: HOMO-LUMO gap             17.353314919929 eV    ::
+         ::.................................................::
+         :: SCC energy                -4.247467308451 Eh    ::
+         :: -> isotropic ES            0.002035567940 Eh    ::
+         :: -> anisotropic ES          0.002321540923 Eh    ::
+         :: -> anisotropic XC          0.003585096725 Eh    ::
+         :: -> dispersion             -0.000661011606 Eh    ::
+         :: repulsion energy           0.072248782884 Eh    ::
+         :: add. restraining           0.000000000000 Eh    ::
+         :: total charge               0.000000000000 e     ::
+         :::::::::::::::::::::::::::::::::::::::::::::::::::::
+
+
+Property printout bound to 'properties.out'
+
+           -------------------------------------------------
+          | TOTAL ENERGY               -4.175218519976 Eh   |
+          | GRADIENT NORM               0.000006636122 Eh/α |
+          | HOMO-LUMO GAP              17.353314919929 eV   |
+           -------------------------------------------------
+
+------------------------------------------------------------------------
+ * finished run on 2022/07/22 at 20:01:44.835     
+------------------------------------------------------------------------
+ total:
+ * wall-time:     0 d,  0 h,  0 min,  0.032 sec
+ *  cpu-time:     0 d,  0 h,  0 min,  0.014 sec
+ * ratio c/w:     0.452 speedup
+ SCF:
+ * wall-time:     0 d,  0 h,  0 min,  0.021 sec
+ *  cpu-time:     0 d,  0 h,  0 min,  0.004 sec
+ * ratio c/w:     0.185 speedup
+
+
+-------------------------   --------------------
+FINAL SINGLE POINT ENERGY        -4.175218519980
+-------------------------   --------------------
+
+
+----------------------------------------------------------------------------
+                           ORCA NUMERICAL FREQUENCIES
+----------------------------------------------------------------------------
+
+Number of atoms                ... 5
+Central differences            ... used
+Number of displacements        ... 30
+Numerical increment            ... 5.000e-03 bohr
+IR-spectrum generation         ... on
+Raman-spectrum generation      ... off
+Surface Crossing Hessian       ... off
+
+The output will be reduced. Please look at the following files:
+SCF program output             ... >cmmd.lastscf
+Integral program output        ... >cmmd.lastint
+Gradient program output        ... >cmmd.lastgrad
+Dipole moment program output   ... >cmmd.lastmom
+AutoCI program output          ... >cmmd.lastautoci
+
+	<< Calculating on displaced geometry   1 (of  30) >>
+	<< Calculating on displaced geometry   2 (of  30) >>
+	<< Calculating on displaced geometry   3 (of  30) >>
+	<< Calculating on displaced geometry   4 (of  30) >>
+	<< Calculating on displaced geometry   5 (of  30) >>
+	<< Calculating on displaced geometry   6 (of  30) >>
+	<< Calculating on displaced geometry   7 (of  30) >>
+	<< Calculating on displaced geometry   8 (of  30) >>
+	<< Calculating on displaced geometry   9 (of  30) >>
+	<< Calculating on displaced geometry  10 (of  30) >>
+	<< Calculating on displaced geometry  11 (of  30) >>
+	<< Calculating on displaced geometry  12 (of  30) >>
+	<< Calculating on displaced geometry  13 (of  30) >>
+	<< Calculating on displaced geometry  14 (of  30) >>
+	<< Calculating on displaced geometry  15 (of  30) >>
+	<< Calculating on displaced geometry  16 (of  30) >>
+	<< Calculating on displaced geometry  17 (of  30) >>
+	<< Calculating on displaced geometry  18 (of  30) >>
+	<< Calculating on displaced geometry  19 (of  30) >>
+	<< Calculating on displaced geometry  20 (of  30) >>
+	<< Calculating on displaced geometry  21 (of  30) >>
+	<< Calculating on displaced geometry  22 (of  30) >>
+	<< Calculating on displaced geometry  23 (of  30) >>
+	<< Calculating on displaced geometry  24 (of  30) >>
+	<< Calculating on displaced geometry  25 (of  30) >>
+	<< Calculating on displaced geometry  26 (of  30) >>
+	<< Calculating on displaced geometry  27 (of  30) >>
+	<< Calculating on displaced geometry  28 (of  30) >>
+	<< Calculating on displaced geometry  29 (of  30) >>
+	<< Calculating on displaced geometry  30 (of  30) >>
+
+-----------------------
+VIBRATIONAL FREQUENCIES
+-----------------------
+
+Scaling factor for frequencies =  1.000000000 (already applied!)
+
+   0:         0.00 cm**-1
+   1:         0.00 cm**-1
+   2:         0.00 cm**-1
+   3:         0.00 cm**-1
+   4:         0.00 cm**-1
+   5:         0.00 cm**-1
+   6:      1385.80 cm**-1
+   7:      1385.81 cm**-1
+   8:      1385.82 cm**-1
+   9:      1557.27 cm**-1
+  10:      1557.28 cm**-1
+  11:      3090.01 cm**-1
+  12:      3103.92 cm**-1
+  13:      3103.94 cm**-1
+  14:      3103.96 cm**-1
+
+
+------------
+NORMAL MODES
+------------
+
+These modes are the cartesian displacements weighted by the diagonal matrix
+M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom
+Thus, these vectors are normalized but *not* orthogonal
+
+                  0          1          2          3          4          5    
+      0       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      1       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      2       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      3       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      4       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      5       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      6       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      7       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      8       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+      9       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+     10       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+     11       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+     12       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+     13       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+     14       0.000000   0.000000   0.000000   0.000000   0.000000   0.000000
+                  6          7          8          9         10         11    
+      0       0.096798   0.082365  -0.021256   0.000001  -0.000001   0.000098
+      1       0.084411  -0.089026   0.039430   0.000008  -0.000000   0.000065
+      2       0.010518  -0.043542  -0.120826   0.000003   0.000001  -0.000022
+      3       0.045040   0.038319  -0.009889   0.000004  -0.000001   0.499033
+      4      -0.396782   0.418488  -0.185363  -0.479370   0.142288   0.000034
+      5      -0.049440   0.204683   0.568001  -0.142299  -0.479333  -0.000010
+      6      -0.333231  -0.367059   0.284304   0.155352  -0.445070  -0.166911
+      7      -0.195392   0.451828   0.119524   0.350856   0.225673  -0.276043
+      8      -0.329034   0.158506   0.144889   0.320509  -0.031334   0.383124
+      9      -0.327694  -0.463680  -0.064905   0.307768   0.357083  -0.166753
+     10      -0.249018   0.329744  -0.376666   0.300713  -0.349484  -0.193551
+     11       0.279107   0.007359   0.142840  -0.254612   0.018810  -0.430254
+     12      -0.537524  -0.189019   0.043767  -0.463140   0.087997  -0.166531
+     13      -0.164623  -0.139255  -0.027336  -0.172300  -0.018473   0.468783
+     14      -0.025964   0.148290   0.583993   0.076373   0.491844   0.047399
+                 12         13         14    
+      0      -0.009344   0.020992  -0.084211
+      1      -0.030512   0.078496   0.022954
+      2       0.081248   0.031893  -0.001065
+      3       0.092484  -0.207489   0.830944
+      4      -0.014110   0.036300   0.010621
+      5       0.037575   0.014749  -0.000492
+      6       0.278034  -0.079154   0.011151
+      7       0.452776  -0.110634   0.093456
+      8      -0.610369   0.218675  -0.115458
+      9      -0.193492  -0.213085   0.030085
+     10      -0.233658  -0.222264   0.090733
+     11      -0.450372  -0.559929   0.177571
+     12      -0.065684   0.249590   0.131247
+     13       0.158564  -0.638735  -0.468319
+     14       0.055040  -0.053523  -0.048931
+
+
+-----------
+IR SPECTRUM
+-----------
+
+ Mode   freq       eps      Int      T**2         TX        TY        TZ
+       cm**-1   L/(mol*cm) km/mol    a.u.
+----------------------------------------------------------------------------
+  6:   1385.80   0.000189    0.95  0.000043  (-0.001721  0.006289  0.000000)
+  7:   1385.81   0.000135    0.68  0.000030  (-0.001464  0.005320  0.000000)
+  8:   1385.82   0.000005    0.03  0.000001  ( 0.000378  0.001044  0.000000)
+  9:   1557.27   0.000227    1.15  0.000046  (-0.000000  0.006748  0.000000)
+ 10:   1557.28   0.000003    0.01  0.000001  ( 0.000000  0.000724  0.000000)
+ 11:   3090.01   0.003589   18.14  0.000362  (-0.013875 -0.013034  0.000000)
+ 12:   3103.92   0.000238    1.20  0.000024  (-0.002465 -0.004227  0.000000)
+ 13:   3103.94   0.003188   16.11  0.000320  ( 0.005531  0.017026  0.000000)
+ 14:   3103.96   0.006430   32.49  0.000646  (-0.022149  0.012483  0.000000)
+
+* The epsilon (eps) is given for a Dirac delta lineshape.
+** The dipole moment derivative (T) already includes vibrational overlap.
+
+The first frequency considered to be a vibration is 6
+The total number of vibrations considered is 9
+
+
+--------------------------
+THERMOCHEMISTRY AT 298.15K
+--------------------------
+
+Temperature         ... 298.15 K
+Pressure            ... 1.00 atm
+Total Mass          ... 16.04 AMU
+
+Throughout the following assumptions are being made:
+  (1) The electronic state is orbitally nondegenerate
+  (2) There are no thermally accessible electronically excited states
+  (3) Hindered rotations indicated by low frequency modes are not
+      treated as such but are treated as vibrations and this may
+      cause some error
+  (4) All equations used are the standard statistical mechanics
+      equations for an ideal gas
+  (5) All vibrations are strictly harmonic
+
+freq.    1385.80  E(vib)   ...       0.00 
+freq.    1385.81  E(vib)   ...       0.00 
+freq.    1385.82  E(vib)   ...       0.00 
+freq.    1557.27  E(vib)   ...       0.00 
+freq.    1557.28  E(vib)   ...       0.00 
+freq.    3090.01  E(vib)   ...       0.00 
+freq.    3103.92  E(vib)   ...       0.00 
+freq.    3103.94  E(vib)   ...       0.00 
+freq.    3103.96  E(vib)   ...       0.00 
+
+------------
+INNER ENERGY
+------------
+
+The inner energy is: U= E(el) + E(ZPE) + E(vib) + E(rot) + E(trans)
+    E(el)   - is the total energy from the electronic structure calculation
+              = E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc)
+    E(ZPE)  - the the zero temperature vibrational energy from the frequency calculation
+    E(vib)  - the the finite temperature correction to E(ZPE) due to population
+              of excited vibrational states
+    E(rot)  - is the rotational thermal energy
+    E(trans)- is the translational thermal energy
+
+Summary of contributions to the inner energy U:
+Electronic energy                ...     -4.17521852 Eh
+Zero point energy                ...      0.04482019 Eh      28.13 kcal/mol
+Thermal vibrational correction   ...      0.00003140 Eh       0.02 kcal/mol
+Thermal rotational correction    ...      0.00141627 Eh       0.89 kcal/mol
+Thermal translational correction ...      0.00141627 Eh       0.89 kcal/mol
+-----------------------------------------------------------------------
+Total thermal energy                     -4.12753439 Eh
+
+
+Summary of corrections to the electronic energy:
+(perhaps to be used in another calculation)
+Total thermal correction                  0.00286394 Eh       1.80 kcal/mol
+Non-thermal (ZPE) correction              0.04482019 Eh      28.13 kcal/mol
+-----------------------------------------------------------------------
+Total correction                          0.04768413 Eh      29.92 kcal/mol
+
+
+--------
+ENTHALPY
+--------
+
+The enthalpy is H = U + kB*T
+                kB is Boltzmann's constant
+Total free energy                 ...     -4.12753439 Eh 
+Thermal Enthalpy correction       ...      0.00094421 Eh       0.59 kcal/mol
+-----------------------------------------------------------------------
+Total Enthalpy                    ...     -4.12659018 Eh
+
+
+Note: Rotational entropy computed according to Herzberg 
+Infrared and Raman Spectra, Chapter V,1, Van Nostrand Reinhold, 1945 
+Point Group:  Td, Symmetry Number:  12  
+Rotational constants in cm-1:     5.355312     5.355310     5.355304 
+
+Vibrational entropy computed according to the QRRHO of S. Grimme
+Chem.Eur.J. 2012 18 9955
+
+
+-------
+ENTROPY
+-------
+
+The entropy contributions are T*S = T*(S(el)+S(vib)+S(rot)+S(trans))
+     S(el)   - electronic entropy
+     S(vib)  - vibrational entropy
+     S(rot)  - rotational entropy
+     S(trans)- translational entropy
+The entropies will be listed as multiplied by the temperature to get
+units of energy
+
+Electronic entropy                ...      0.00000000 Eh      0.00 kcal/mol
+Vibrational entropy               ...      0.00003597 Eh      0.02 kcal/mol
+Rotational entropy                ...      0.00478798 Eh      3.00 kcal/mol
+Translational entropy             ...      0.01627961 Eh     10.22 kcal/mol
+-----------------------------------------------------------------------
+Final entropy term                ...      0.02110356 Eh     13.24 kcal/mol
+
+In case the symmetry of your molecule has not been determined correctly
+or in case you have a reason to use a different symmetry number we print 
+out the resulting rotational entropy values for sn=1,12 :
+ --------------------------------------------------------
+|  sn= 1 | S(rot)=       0.00713418 Eh      4.48 kcal/mol|
+|  sn= 2 | S(rot)=       0.00647973 Eh      4.07 kcal/mol|
+|  sn= 3 | S(rot)=       0.00609689 Eh      3.83 kcal/mol|
+|  sn= 4 | S(rot)=       0.00582527 Eh      3.66 kcal/mol|
+|  sn= 5 | S(rot)=       0.00561458 Eh      3.52 kcal/mol|
+|  sn= 6 | S(rot)=       0.00544244 Eh      3.42 kcal/mol|
+|  sn= 7 | S(rot)=       0.00529689 Eh      3.32 kcal/mol|
+|  sn= 8 | S(rot)=       0.00517081 Eh      3.24 kcal/mol|
+|  sn= 9 | S(rot)=       0.00505960 Eh      3.17 kcal/mol|
+|  sn=10 | S(rot)=       0.00496012 Eh      3.11 kcal/mol|
+|  sn=11 | S(rot)=       0.00487013 Eh      3.06 kcal/mol|
+|  sn=12 | S(rot)=       0.00478798 Eh      3.00 kcal/mol|
+ --------------------------------------------------------
+
+
+-------------------
+GIBBS FREE ENERGY
+-------------------
+
+The Gibbs free energy is G = H - T*S
+
+Total enthalpy                    ...     -4.12659018 Eh 
+Total entropy correction          ...     -0.02110356 Eh    -13.24 kcal/mol
+-----------------------------------------------------------------------
+Final Gibbs free energy         ...     -4.14769375 Eh
+
+For completeness - the Gibbs free energy minus the electronic energy
+G-E(el)                           ...      0.02752477 Eh     17.27 kcal/mol
+
+
+
+Timings for individual modules:
+
+Sum of individual times         ...       51.025 sec (=   0.850 min)
+Numerical frequency calculation ...       50.947 sec (=   0.849 min)  99.8 %
+XTB module                      ...        0.078 sec (=   0.001 min)   0.2 %
+                             ****ORCA TERMINATED NORMALLY****
+TOTAL RUN TIME: 0 days 0 hours 0 minutes 51 seconds 56 msec

cmmde_gui/test/metana3/freq/cmmd_property.txt

@@ -0,0 +1,48 @@
+-------------------------------------------------------------
+----------------------- !PROPERTIES! ------------------------
+-------------------------------------------------------------
+# -----------------------------------------------------------
+$ THERMOCHEMISTRY_Energies
+   description: The Thermochemistry energies
+   geom. index: 0
+   prop. index: 1
+        Temperature (Kelvin)           :        298.1500000000
+        Pressure (atm)                 :          1.0000000000
+        Total Mass (AMU)               :         16.0430000000
+        Spin Degeneracy                :          1.0000000000
+        Electronic Energy (Hartree)    :         -4.1752185200
+        Translational Energy (Hartree) :          0.0014162714
+        Rotational Energy (Hartree)    :          0.0014162714
+        Vibrational Energy (Hartree)   :          0.0000314005
+        Number of frequencies          :     15      
+        Scaling Factor for frequencies :          1.0000000000
+        Vibrational frequencies        :     
+                  0    
+      0       0.000000
+      1       0.000000
+      2       0.000000
+      3       0.000000
+      4       0.000000
+      5       0.000000
+      6     1385.801243
+      7     1385.807833
+      8     1385.817738
+      9     1557.267071
+     10     1557.277517
+     11     3090.006354
+     12     3103.916950
+     13     3103.935349
+     14     3103.957551
+        Zero Point Energy (Hartree)    :          0.0448201861
+        Inner Energy (Hartree)         :         -4.1275343905
+        Enthalpy (Hartree)             :         -4.1265901815
+        Electronic entropy             :          0.0000000000
+        Rotational entropy             :          0.0047879801
+        Vibrational entropy            :          0.0000359731
+        Translational entropy          :          0.0047879801
+        Entropy                        :          0.0211035637
+        Gibbs Energy (Hartree)         :         -4.1476937451
+        Is Linear                      :                 false
+# -------------------------------------------------------------
+----------------------- !GEOMETRIES! ------------------------
+# -------------------------------------------------------------

cmmde_gui/test/metana3/freq/freq/cmmd.in

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

cmmde_gui/test/metana3/freq/freq/cmmd.out

@@ -0,0 +1,142 @@
+
+                                 *****************
+                                 * O   R   C   A *
+                                 *****************
+
+                                            #,                                       
+                                            ###                                      
+                                            ####                                     
+                                            #####                                    
+                                            ######                                   
+                                           ########,                                 
+                                     ,,################,,,,,                         
+                               ,,#################################,,                 
+                          ,,##########################################,,             
+                       ,#########################################, ''#####,          
+                    ,#############################################,,   '####,        
+                  ,##################################################,,,,####,       
+                ,###########''''           ''''###############################       
+              ,#####''   ,,,,##########,,,,          '''####'''          '####       
+            ,##' ,,,,###########################,,,                        '##       
+           ' ,,###''''                  '''############,,,                           
+         ,,##''                                '''############,,,,        ,,,,,,###''
+      ,#''                                            '''#######################'''  
+     '                                                          ''''####''''         
+             ,#######,   #######,   ,#######,      ##                                
+            ,#'     '#,  ##    ##  ,#'     '#,    #''#        ######   ,####,        
+            ##       ##  ##   ,#'  ##            #'  '#       #        #'  '#        
+            ##       ##  #######   ##           ,######,      #####,   #    #        
+            '#,     ,#'  ##    ##  '#,     ,#' ,#      #,         ##   #,  ,#        
+             '#######'   ##     ##  '#######'  #'      '#     #####' # '####'        
+
+
+
+                  #######################################################
+                  #                        -***-                        #
+                  #          Department of theory and spectroscopy      #
+                  #    Directorship and core code : Frank Neese         #
+                  #        Max Planck Institute fuer Kohlenforschung    #
+                  #                Kaiser Wilhelm Platz 1               #
+                  #                 D-45470 Muelheim/Ruhr               #
+                  #                      Germany                        #
+                  #                                                     #
+                  #                  All rights reserved                #
+                  #                        -***-                        #
+                  #######################################################
+
+
+                         Program Version 5.0.2 -  RELEASE  -
+
+
+ With contributions from (in alphabetic order):
+   Daniel Aravena         : Magnetic Suceptibility
+   Michael Atanasov       : Ab Initio Ligand Field Theory (pilot matlab implementation)
+   Alexander A. Auer      : GIAO ZORA, VPT2 properties, NMR spectrum
+   Ute Becker             : Parallelization
+   Giovanni Bistoni       : ED, misc. LED, open-shell LED, HFLD
+   Martin Brehm           : Molecular dynamics
+   Dmytro Bykov           : SCF Hessian
+   Vijay G. Chilkuri      : MRCI spin determinant printing, contributions to CSF-ICE
+   Dipayan Datta          : RHF DLPNO-CCSD density
+   Achintya Kumar Dutta   : EOM-CC, STEOM-CC
+   Dmitry Ganyushin       : Spin-Orbit,Spin-Spin,Magnetic field MRCI
+   Miquel Garcia          : C-PCM and meta-GGA Hessian, CC/C-PCM, Gaussian charge scheme
+   Yang Guo               : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization
+   Andreas Hansen         : Spin unrestricted coupled pair/coupled cluster methods
+   Benjamin Helmich-Paris : MC-RPA, TRAH-SCF, COSX integrals
+   Lee Huntington         : MR-EOM, pCC
+   Robert Izsak           : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM
+   Marcus Kettner         : VPT2
+   Christian Kollmar      : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K
+   Simone Kossmann        : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian
+   Martin Krupicka        : Initial AUTO-CI
+   Lucas Lang             : DCDCAS
+   Marvin Lechner         : AUTO-CI (C++ implementation), FIC-MRCC
+   Dagmar Lenk            : GEPOL surface, SMD
+   Dimitrios Liakos       : Extrapolation schemes; Compound Job, initial MDCI parallelization
+   Dimitrios Manganas     : Further ROCIS development; embedding schemes
+   Dimitrios Pantazis     : SARC Basis sets
+   Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients
+   Taras Petrenko         : DFT Hessian,TD-DFT gradient, ASA, ECA, R-Raman, ABS, FL, XAS/XES, NRVS
+   Peter Pinski           : DLPNO-MP2, DLPNO-MP2 Gradient
+   Christoph Reimann      : Effective Core Potentials
+   Marius Retegan         : Local ZFS, SOC
+   Christoph Riplinger    : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples
+   Tobias Risthaus        : Range-separated hybrids, TD-DFT gradient, RPA, STAB
+   Michael Roemelt        : Original ROCIS implementation
+   Masaaki Saitow         : Open-shell DLPNO-CCSD energy and density
+   Barbara Sandhoefer     : DKH picture change effects
+   Avijit Sen             : IP-ROCIS
+   Kantharuban Sivalingam : CASSCF convergence, NEVPT2, FIC-MRCI
+   Bernardo de Souza      : ESD, SOC TD-DFT
+   Georgi Stoychev        : AutoAux, RI-MP2 NMR, DLPNO-MP2 response
+   Willem Van den Heuvel  : Paramagnetic NMR
+   Boris Wezisla          : Elementary symmetry handling
+   Frank Wennmohs         : Technical directorship
+
+
+ We gratefully acknowledge several colleagues who have allowed us to
+ interface, adapt or use parts of their codes:
+   Stefan Grimme, W. Hujo, H. Kruse, P. Pracht,  : VdW corrections, initial TS optimization,
+                  C. Bannwarth, S. Ehlert          DFT functionals, gCP, sTDA/sTD-DF
+   Ed Valeev, F. Pavosevic, A. Kumar             : LibInt (2-el integral package), F12 methods
+   Garnet Chan, S. Sharma, J. Yang, R. Olivares  : DMRG
+   Ulf Ekstrom                                   : XCFun DFT Library
+   Mihaly Kallay                                 : mrcc  (arbitrary order and MRCC methods)
+   Jiri Pittner, Ondrej Demel                    : Mk-CCSD
+   Frank Weinhold                                : gennbo (NPA and NBO analysis)
+   Christopher J. Cramer and Donald G. Truhlar   : smd solvation model
+   Lars Goerigk                                  : TD-DFT with DH, B97 family of functionals
+   V. Asgeirsson, H. Jonsson                     : NEB implementation
+   FAccTs GmbH                                   : IRC, NEB, NEB-TS, DLPNO-Multilevel, CI-OPT
+                                                   MM, QMMM, 2- and 3-layer-ONIOM, Crystal-QMMM,
+                                                   LR-CPCM, SF, NACMEs, symmetry and pop. for TD-DFT,
+                                                   nearIR, NL-DFT gradient (VV10), updates on ESD,
+                                                   ML-optimized integration grids
+   S Lehtola, MJT Oliveira, MAL Marques          : LibXC Library
+   Liviu Ungur et al                             : ANISO software
+
+
+ Your calculation uses the libint2 library for the computation of 2-el integrals
+ For citations please refer to: http://libint.valeyev.net
+
+ Your ORCA version has been built with support for libXC version: 5.1.0
+ For citations please refer to: https://tddft.org/programs/libxc/
+
+ This ORCA versions uses:
+   CBLAS   interface :  Fast vector & matrix operations
+   LAPACKE interface :  Fast linear algebra routines
+   SCALAPACK package :  Parallel linear algebra routines
+   Shared memory     :  Shared parallel matrices
+   BLAS/LAPACK       :  OpenBLAS 0.3.15  USE64BITINT DYNAMIC_ARCH NO_AFFINITY SkylakeX SINGLE_THREADED
+        Core in use  :  SkylakeX
+   Copyright (c) 2011-2014, The OpenBLAS Project
+
+
+
+
+***************************************
+The coordinates will be read from file: ../cmmd.xyz
+***************************************
+
+

cmmde_gui/test/metana3/freq/freq/run.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
+export PATH=/home/adit/opt/openmpi411/bin:$PATH
+export OMP_NUM_THREADS=1
+cd $PWD
+$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

cmmde_gui/test/metana3/freq/freq/slurm-2909.out

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

cmmde_gui/test/metana3/freq/run.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
+export PATH=/home/adit/opt/openmpi411/bin:$PATH
+export OMP_NUM_THREADS=1
+cd $PWD
+$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

cmmde_gui/test/metana3/geom.smi

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

cmmde_gui/test/metana3/geom.xyz

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

cmmde_gui/test/metana3/run.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
+export PATH=/home/adit/opt/openmpi411/bin:$PATH
+export OMP_NUM_THREADS=1
+cd $PWD
+$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe

cmmde_gui/test/metana3/run_babel.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=168:0:0
+export OMP_NUM_THREADS=1
+cd $PWD
+obabel geom.smi -O geom.xyz --gen3d