diff --git a/Molecular_Ensembles.rst b/Molecular_Ensembles.rst index 8dae07a0ed8e334763268f01eea339a5ad5ede0d..91a0455ea7805c4346534b32aec4ec315dd34db8 100644 --- a/Molecular_Ensembles.rst +++ b/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) @@ -224,7 +286,7 @@ The range of methods is not limited to DFT, but supports HF, semi-empirical models such as PM6, MNDO, tight-binding models xtb, MP2 and more. Nowadays also excited states are available via Bethe-Salpeter Equation and TDDFT. Both all-electron as well as pseudo-potential calculations - as well as metadynamics are supported. +as well as metadynamics are supported. * `XTB/GFNx (extended Tight-Binding) <https://xtb-docs.readthedocs.io>`_ `<https://github.com/grimme-lab/xtb>`_