fox (1)

fox [options][file.xml]

The fox (Free Objects for Crystallography) program was made for the ab initio crystal structure solution from diffraction data. Its most interesting features for ab initio structure determination are:

* versatile description of the crystal contents;

* automatic correction for special positions and shared atoms between polyhedra;

* the ability to use simultaneously multiple powder patterns;

* smart global optimization algorithms;

* a graphical interface with a 3D crystal structure view and live updates during the optimization process.

This program my be executed with or without command line options or input file (file.xml). It follows the usual GNU command line syntax, with long options starting with two dashes (`-'). A summary of options is included below. For a complete description, see the fox wiki http://objcryst.sourceforge.net/Fox/Manual

--help

Show summary of options.

--loadfouriergrd map.grd

Load and display 'map.grd' fourier map with (first) crystal structure

--loadfourierdsn6 map.DN6

Load and display a DSN6 fourier map with (first) crystal structure

--nogui

Run without GUI, automatically launches optimization --nogui may be accompanied by the following options:

-n 10000

Run for 10000 trials at most (default: 1000000)

--nbrun 5

Do 5 runs, randomizing before each run (default: 1), use -1 to run indefinitely

-o out.xml

Output in 'out.xml'

--randomize

Randomize initial configuration

--silent

Produce (almost) no text output

--finalcost 0.15

Run optimization until cost < 0.15

--cif2pattern 1.5406 170 5000 .1

Simulate pattern for input crystal, wavelength=1.5406 up to 170° with 500 points anda peak width of 0.1°

Fox silicon.xml

Load file 'silicon.xml' and launch GUI.

Fox Cimetidine-powder.xml --nogui --randomize -n 1000000 -o best.xml

Load file 'ktartrate.xml', randomize, then make 1 optimization of 1 million trials, and save the best structure in 'best.xml'.

Fox Cimetidine-powder.xml --nogui --randomize -n 10000000 --nbrun 10 -o best.xml

Load file 'Cimetidine-powder.xml', then make 10 runs (starting from a random structure) of 10 million trials (each run saves one xml file), and save the best structure in 'best.xml'.

Fox Cimetidine-powder.xml --nogui --silent --randomize -n 10000000 --nbrun 10 --finalcost 200000 -o best.xml

Load file 'Cimetidine-powder.xml', then make 10 silent runs of 10 million trials (each run saves one xml file), and save the best structure in 'best.xml'. For each run, the optimization stops if the cost goes below 200000.

fox was written by Vincent Favre-Nicolin <[email protected]>.

This manual page was written by Carlo Segre <[email protected]>, for the Debian project (but may be used by others).