====== Guests ====== Faps is distributed with a number of standard guests available in the :file:`guests.lib` file in the faps directory. It is also possible to add custom guests for your simulation either in :file:`~/.faps/guests.lib` that is queried for all simulations or a :file:`$JOBDIR/guests.lib` that is queried for all jobs running in that directory. ---------------- Available guests ---------------- These guests are available as standard with the identifier with the :envvar:`guests` option. ============ =========================================================== Identifier Guest ============ =========================================================== CO2 Carbon Dioxide for Adsorption in Zeolites :cite:`Garcia-Sanchez2009` CO2-TraPPE TraPPE Carbon Dioxide :cite:`Potoff2001` CO-MOF Carbon Monoxide Optimised for CuBTC MIL-47 and IRMOF1 :cite:`Martin-Calvo2012` CO-UFF Carbon Monoxide with UFF Parameters and Mulliken Charges CO-Graphite Carbon Monoxide Adsorbed on Graphite CO-Ligand Carbon Monoxide in Myoglobin TIP5P TIP5P Water TIP5P-Ew TIP5P-Ew Water for Ewald sums TIP4P-Ew TIP4P-Ew Four-Site Water Model for Biomolecular Simulations CH4-TraPPE TraPPE Methane; Single Site CH4-5s Methane 5 Site N2 Three Site Nitrogen Based on TraPPE N2-2site Two Site, Chargeless Nitrogen N2-Etters Nitrogen Based on Etters Potential H2S Hydrogen Sulphide for Vapor-Liquid Equilibria N2O-PE Nitrous Oxide for Phase Equilibria with Oxygen N2O-Sol Nitrous Oxide for Solubility in Fluorinated Liquids NO2 Nitrogen Dioxide N2O4 Dinitrogen Tetroxide NO Nitric Oxide for Diffusion in Water O2-TraPPE Oxygen for Liquid Vapour Phase Equilibria O2-PE Oxygen for Phase Equilibria with Nitrous Oxide SO2 Sulphur Dioxide for Vapor-Liquid Equilibria H2 Anisotropic Hydrogen Diatom for Condensed Phase I2 Iodine Diatom with UFF parameters ============ =========================================================== .. _custom-guests: ------------------ Customising guests ------------------ To use custom guests create a ``guests.lib`` in the job working directory to add your own. The file follows standard ``.ini`` syntax. The following example is explained below. .. code-block:: ini [CO2-GS] name = Carbon Dioxide (Garcia Sanchez) source = http://dx.doi.org/10.1021/jp810871f atoms = Cx 12.0107 0.65120 0.0 0.0 0.0 Ox 15.9994 -0.32560 1.149 0.0 0.0 Ox 15.9994 -0.32560 -1.149 0.0 0.0 potentials = Cx 2.745 0.05948 Ox 3.017 0.17023 probability = 0 2 3 probe radius = 1.71 The name in square brackets ``[CO2-GS]`` is the identifier to use in the ``guests`` option in your ``.fap`` file. Try to be short but descriptive, but this must be unique. ``name`` is the full name and should differentiate it from similar guests. Include a reference in ``source`` so that the results are always traceable. The ``atoms`` block has the molecule's structure. The block **must be indented** so that all the atoms are read in. Each line must follow: ``atom_name atom_mass atom_charge atom_x atom_y atom_z``. If ``atom_name`` is the element then standard UFF parameters will be used, use unique identifiers, like ``Cx``, with the ``potentials`` to use custom potential parameters. The ``potentials`` block specifies custom potentials to use when running simulations with this molecule, in the form ``atom_name atom_sigma atom_epsilon``. The vdW parameters are standard sigma and epsilon values for Lorentz-Berthelot mixing. Any number of atom types can be specified here; If you set parameters for standard element names, like ``C``, they will be used instead of the standard UFF values. Unspecified atoms will be set to 0. Goups of atoms can be chosen for probability plotting in the ``probability`` block. Each line is the atom identifiers for a single group (1 is the first atom), 0 is the centre of mass. In this case the second plot is for the oxygen atoms. .. bibliography:: library.bib