The directives in Simulated Annealing

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The directives in Simulated Annealing

       Usually you don't need to read this paragraph unless you are interested to run Simulated Annealing without interaction  with graphic interface. In this case use the command %sannel to run Simulated Annealing from the input file (*.exp).  Use command %automatic to skip the interaction with the graphical interface and the program will perform the Simulated Annealing using the default values. An example of input file with command %automatic and %sannel:

%automatic
%Structure paracetamol
%Initialize
%Job paracetamol
%Data
Cell  7.100  9.380  11.708  90.0  97.42  90.0
SpaceGroup p 21/n
Content    c 32  o 8 n 4 h 36
Pattern   paracetamol.pow
filetype xy
Wavelength 1.54056
Range      10   65.00 0.0145
%fragment paracetamol.mol
%sannel
%continue

To modify the default value some directives can be used after the command %sannel.

An example of application of directive NRUN

%automatic
%Structure paracetamol
%Initialize
%Job paracetamol
%Data
Cell  7.100  9.380  11.708  90.0  97.42  90.0
SpaceGroup p 21/n
Content    c 32  o 8 n 4 h 36
Pattern   paracetamol.pow
filetype xy
Wavelength 1.54056
Range      10   65.00 0.0145
%fragment paracetamol.mol
%sannel
nrun 20
%end

Directives in Simulated Annealing command

The following directives must be added after the command '%sannel' in the input file to activate some specific features of the Simulated Annealing procedure

Abbreviations for directives name at least 4 character are permissible, i.e. "cost 2" instead of  "cost_function 2".

NRUN n
To modify the number of Simulated Annealing runs. The default is 10 runs

NITER n
To modify the number of moves for each temperature step. In default the number of moves is automatically calculated.

RESMAX val
To define the maximum resolution used by Simulated Annealing. The default value is 2.0 Å.

TEMPER temp
To modify the initial temperature. In default the initial temperature is automatically calculated.

TFACTOR val
Val ranges between 0 and 1 and determines the cooling rate. The default value is 0.90.

FIXROTATION n1 n2
To fix the internal DOF. n1 and n2 are the atoms associated to the DOF. This directive is useful when relying on the prior chemical knowledge of the structure to fix some of its internal DOFs. For example, double bonds in conjugated acyclic systems, triple bonds, nitrilic triple bonds, etc.

FFTRANSLATION n
To fix the translation of fragment containing n atom, where n is the order number of any atom in the fragment. This directive is repeated in case of fixing the translation of different fragments.

FFROTATION n
To fix the rotation of fragment containing n atom, where n is the order number of any atom in the fragment. This directive is repeated in case of fixing the rotation of different fragments.

REFINETF
To refine the thermal parameters.

SHIFT_ATOM val or SHIFT_ATOM val n1 n2 n3 ….
To refine the atomic parameters by applying shifts (up to val) on the atoms with respect to the center of gravity of the fragment. The suggested val is 0.02. Add n1,n2,n3,… to refine only some specific atoms.

COST_FUNCTION n
To choose the cost function: 1 for Rw-profile, 2 for RF, 3 for RI. The default is 1.
RANDOMIZE n
To randomize the internal and external DOFs and the atomic parameters (if refined). n is an optional parameters used as seed of random generator. The randomized structural model appears in the output as shown below. 

ROTAT n1 n2
To specify the internal DOF using the input file. 

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