Guests

Faps is distributed with a number of standard guests available in the guests.lib file in the faps directory. It is also possible to add custom guests for your simulation either in ~/.faps/guests.lib that is queried for all simulations or a $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 guests option.

Identifier	Guest
CO2	Carbon Dioxide for Adsorption in Zeolites [GSAP+09]
CO2-TraPPE	TraPPE Carbon Dioxide [PS01]
CO-MOF	Carbon Monoxide Optimised for CuBTC MIL-47 and IRMOF1 [MartnCLMartnC12]
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

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.

[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.

[GSAP+09]

Almudena Garcia-Sanchez, Conchi O. Ania, Jose B. Parra, David Dubbeldam, Thijs J. H. Vlugt, Rajamani Krishna, and Sofia Calero. Transferable Force Field for Carbon Dioxide Adsorption in Zeolites. The Journal of Physical Chemistry C, 113(20):8814–8820, May 2009. URL: http://pubs.acs.org/doi/abs/10.1021/jp810871f, doi:10.1021/jp810871f.

[MartnCLMartnC12]

Ana Mart\’ın-Calvo, Francisco D. Lahoz-Mart\’ın, and Sof\’ıa Calero. Understanding Carbon Monoxide Capture Using Metal-Organic Frameworks. The Journal of Physical Chemistry C, 116(11):6655–6663, March 2012. URL: http://pubs.acs.org/doi/abs/10.1021/jp211563e, doi:10.1021/jp211563e.

[PS01]

Jeffrey J. Potoff and J. Ilja Siepmann. Vapor-liquid equilibria of mixtures containing alkanes, carbon dioxide, and nitrogen. AIChE Journal, 47(7):1676–1682, July 2001. URL: http://doi.wiley.com/10.1002/aic.690470719, doi:10.1002/aic.690470719.