update

Molecular_Ensembles.rst

@@ -157,8 +157,70 @@ For liquids containing multiple compounds quite diverse situations
 may be encountered: 
 
 *  the liquids are miscible (mixture)
+
+.. code-block:: none
+
+   # get the structure of acetonitrile and tetrahydrofuran
+   # have the file one.smi contain the lines 
+   acetonitril:CC#N:OB+MOPAC:0:1
+   tetrahydrofuran:C1CCOC1:OB+MOPAC:0:1
+   # run structure generation
+   apptainer run  -c --bind $PWD:/data --app getstructure SGTk.sif one.smi
+   # PM6 equilibrium structure in acetonitril/acetonitril.opt_pm6.moldenin
+   # PM6 equilibrium structure in tetrahydrofuran/tetrahydrofuran.opt_pm6.moldenin
+   #packmol.inp: THF 0.887 g/ml (7.4 molecules/nm\ :sub:`3`) AN: 0.776 g/ml (11.4 molecules/nm\ :sub:`3`) 
+   # 1:1 molecular mixture
+   tolerance 2.0 
+   output ANTHF_md.xyz
+   filetype xyz  
+   structure acetonitril/acetonitril.opt_pm6.moldenin
+     number 45
+     inside cube 0.2 0.2 0.2 19.6
+   end structure 
+   structure tetrahydrofuran/tetrahydrofuran.opt_pm6.moldenin
+     number 30
+     inside cube 0.2 0.2 0.2 19.6
+   end structure 
+
+   apptainer run  -c --bind $PWD:/data --app packmol SGTk.sif packmol.inp 
+   # box is found in ANTHF_md.xyz
+   apptainer run  -c --bind $PWD:/data --app cp2k_md SGTk.sif \
+              ANTHF_md.xyz  gopt=30  
+
+
 *  the liquids do not mix, so that a variety of
    interfaces with a boundary surface can be constructed
+
+.. code-block:: none
+
+   # get the structure of toluene and water 
+   # have the file one.smi contain the lines 
+   toluene:c1cccc(C)c1:OB+MOPAC:0:1
+   water:O[H2]:OB+MOPAC:0:1
+   # run structure generation
+   apptainer run  -c --bind $PWD:/data --app getstructure SGTk.sif one.smi
+   # PM6 equilibrium structure in toluene/toluene.opt_pm6.moldenin
+   # PM6 equilibrium structure in water/water.opt_pm6.moldenin
+   #packmol.inp: toluene 0.867 g/ml (5.8 molecules/nm\ :sub:`3`) AN: 1.000 g/ml (33.4 molecules/nm\ :sub:`3`) 
+   # lower half water, upper half toluene 
+   tolerance 2.0 
+   output tolwat_md.xyz
+   filetype xyz  
+   structure toluene/toluene.opt_pm6.moldenin
+     number 23 
+     inside box 10.0 10.0 10.0 19.6 19.6 19.6
+   end structure 
+   structure water/water.opt_pm6.moldenin
+     number 134 
+     inside cube 0.2 0.2 0.2 10.0 10.0 10.0
+   end structure 
+
+   apptainer run  -c --bind $PWD:/data --app packmol SGTk.sif packmol.inp 
+   # box is found in tolwat_md.xyz
+   apptainer run  -c --bind $PWD:/data --app cp2k_md SGTk.sif \
+              tolwat_md.xyz  gopt=30  
+
+
 *  one compound (solute) is dissolved in another (solution)
    forming solvation shells (model for micro solvation)