Running faps¶
Each job is uniquely identified by the $JOBNAME
. To run faps you will
usually just issue the command faps $JOBNAME
. A structure file is required,
and a configuration file is optional. By default, all calculation step will run
in sequence and $JOBNAME-$GUEST.csv
files with the adsoprtion data are
produced. A directory faps_$JOBNAME_properties
will contain output from
extra structure related analysis codes.
Structure files¶
Structures can be read from CIF
, PDB
, PQR
, VASP
, CSSR
SQL
or xyz
files. One file from this list is required. By default
the code will look for $JOBNAME.pdb
, other file formats may be set in the
config files or on the commandline with the initial_structure_format
option.
The charges can be specified with the structure for the CIF
, PQR
,
CSSR
and xyz
types. Details are given below.
-
$JOBNAME.cif
The Crystallogrphic Information File (CIF) is the preferred initial strcuture format and the default in faps. CIF is a very complex self describing format but the parser has been thoroughly tested and is capable of extracting atom positions, applying symmetry operations with a check made to remove duplicated atoms. The cell must be given and atom positions specified in fractional cooridinates.
The cif parser implements some non-standard fields; _atom_type_partial_charge will be read in as the atomic charge. _atom_site_description is used to determine the force-field atom type.
Bonding is also read in if specified and expanded according to the site labels. These are required for forec field optimisations.
Warning
Be careful with complex structures, symmetry rules and the duplicate atom check might not be perfect.
-
$JOBNAME.pdb
The structure from any standard Protein Data Bank (PDB) structure file,
$JOBNAME.pdb
, can be read by faps. These are fixed column formats and faps may not work if your pdb file is broken. The cell is taken from thecryst1
line. The position, in columns 31 to 54, and the atom type, at column 77, are required forATOM
orHETATM
records.If
pqr
input is requested then the extension.pqr
may be used and initial charges are also read in from the occupancy column in position 54. These will be replaced if a charge calulation is carried out.Warning
A .pdb file generated from a cif in Materials Studio can cause problems! In the lattice settings ensure that the cristal is re-orineted with ‘A along X and B in XY’, and in the peridicity make the crtystal P1 symmetry.
-
{$JOBNAME.{poscar|contcar}|{POSCAR|CONTCAR}}
Structures that are compatible with VASP 5 can be read by faps. The code will read a standard POSCAR type file provided the line with atom types is given (i.e. files written by VASP 4 with only the atom counts will not work).
-
$JOBNAME.xyz
Initial coordinates may be given to faps in plain xyz format. The file should be structured as one line containing only the number of atoms, a comment line (ignored), followed by
atom_type x.x y.y z.z
cartesian coordinates for each atom. As faps requires periodicity the structure is placed in the box defined by thedefault_cell
option.To specify charges in the
.xyz
put them in a fifth field on the atom line,atom_type x.x y.y z.z cha.rge
. Values that cannot be parsed as a number will fail silently and have an initial charge of 0.0.
Config files¶
Configuration files are optional. Faps will try to use sensible defaults for
everything, most installations will require customisation of the site.ini
.
-
$JOBNAME.fap
The per-job settings. This file should be placed in the running directory with the same basename as the structure file. This is not a conventional ‘input file’, as it is only required if non-defalut options are needed. Options are set in standard
.ini
format, as described in config files.
-
~/.faps/$JOB_TYPE.fap
Each user may have a directory with standard job types that are called with the –job-type commandline option. As with the
.fap
file, options are set in standard.ini
format, as described in config files. These options will override the defaults but be overridden by a per-job.fap
file.
-
site.ini
The
site.ini
is located in the code directory and can be used to override any of the options set in thedefault.ini
that is found in the same directory. Usually this file will be used to set all configuration for a particular machine (e.g. binary or pseudopotential locations), or a set of calaultions (desired state points for all high throughput structures).
Library files¶
-
guests.lib
Predefined guests are stored here. The library file is in standard
.ini
format. Faps will search for guests in the working directory first, then in the~/.faps/
directory and finally the standard guests library distributed with the code. Theguests.lib
provided with the code can be used as a template for new guests in a custom guests.lib but do not modify this file directly as it will be overwritten on updates.