Reference Manual

• Note that Fox can store some preferences between sessions.

Command-line options

(how to launch optimizations from the command-line, without a graphical interface - useful for scripts or using a cluster) It is possible to use command-line arguments for Fox (use Fox --help to get all options), e.g.:

• Fox silicon.xml : will load the silicon.xml file and launch the GUI.

• Fox silicon.cif : will load the silicon.cif CIF file, try to extract any crystal structure or powder pattern data from that CIF file and will launch the GUI. See this page on Fox support for CIF import.

• Fox silicon.xml --nogui -n 10000 -o out.xml --nbrun 10 : will load the silicon.xml file, and run the optimization without GUI for 10000 trials, for 10 runs, then output the best solution to out.xml.

• Fox example/pbso4-joint.xml --nogui --randomize -n 100000 --nbrun 10 --finalcost 1000 -o test.xml : will run Fox (without GUI) on the PbSO4 example for at most 100000 trials after first randomizing the structure (useful for tests), and stop the optimization when the overall cost falls below 1000; this is repeated for the 10 runs then the best solution is stored in test.xml . You can run that one from the main Fox directory.

• Fox alumina.xml --loadfouriergrd alumina.grd will load the alumina.xml file, and display the first crystal structure in 3D, and load the fourier map as well. The .grd fourier map can be generated by expgui, gsas, and the forgrid package which you can get from ftp://ftp.ncnr.nist.gov/pub/cryst/gsas/ (precompiled binaries in the exe_{linux|sgi|win} directories).

• Fox alumina.xml --loadfourierdsn6 alumina.DN6 : will load a DSN6 fourier map and display it with the first crystal structure in the xml file. The DSN6 fourier map can be created using the 'O' command in GSAS forplot ("Convert map to DSN6 format"). You must use a z-sliced fourier map, and the fourier map must go from 0.0 to 1.0 along all 3 directions, as Fox does not take care of filling the remaining of the Fourier map by symmetry.

• Fox --speedtest : Do a speedtest of Fox (takes about 2mn).

Graphical Interface (GUI) reference

Note About Parameters

• All the parameters that can be optimized in Fox have two checkboxes between the name and the field where you can read and enter the value for the parameter. The left checkbox (R) can trigger the refinable status of the parameter (unchecked= not optimized), and the right one (L) enables the limits for that parameter.

• For some parameters (e.g. the atomic positions in a Molecule), you may not have access to these fix/limit buttons, because the functionality to restrain the evolution parameters is provided at a higher level (e.g. in the Molecule object, atomic positions are limited relatively to each other through intelligent restraints, not individual limits).

• Also, some parameters which do have R/L checkboxes cannot be optimized by Fox, because it does not make sense to refine some parameters using a global optimization algorithms. See the FAQ for a few more details.

Main Menus

• The File menu allows to save or load a "project" file in which are saved Crystal structures, diffraction data and algorithms... Everything which can be seen in the Fox main window is saved. It is stored using an XML format specific to Fox/!ObjCryst++ (note that the xml file is easily readable, so you can edit it if necessary), and support for CIF (Crystallographic Information File) is now included. Note that starting with Fox 1.7, the xml files are compressed by default using gzip, with the full extension being .xml.gz - they can be gunzip'ed if you wish to edit them manually. If you prefer to save files in an uncompressed manner, you can toggle this behaviour through the Preferences menu. You can also exit through this menu.

• The Objects menu can be used to create new Crystal, PowderPattern, DiffractionDataSingleCrystal and algorithms objects. Remember that you can create several of these objects simultaneously (limited only by memory !).

• The Preferences menu

• The Help menu gives you access to the "about box" of Fox, and you can toggle the use of tooltips.

Below the menus you have 4 tabs, where you can respectively find the Crystal, Powder Pattern, Single Crystal and optimization algorithms.

Crystal structure description

• See the Crystal page

Powder Pattern description

• See the Powder Pattern page

Single Crystal Diffraction Data description

• See the single crystal page

Global Optimization algorithms setup

• See the algorithms page