Graphic Interface

Parent Previous Next

Graphic Interface of Simulated Annealing

       The dialog window of Simulated Annealing procedure in EXPO is composed by 4 pages.
The first page 'SA conditions' contains the general settings of the Simulated Annealing algorithm:



Cost function: 2 cost functions can be selected: R weighted profile (default cost function), R-Bragg intensities.

Resolution: defines the maximum resolution used by Simulated Annealing procedure.

Random seed: selects the value determining the sequence of random numbers used from the algorithm. When is set to 0 the random seed will be calculated by the system clock.

Nr. of SA runs: select the number of Simulated Annealing runs. At the beginning of each run a new value of random seed is calculated.
Starting temperature: selects the starting temperature. Check on 'automatic' and the program automatically will find the starting temperature at the beginning of procedure.

Number of moves: the number of moves for each step of temperature is Np*N*20 where Np is the number of refined parameters and N is a number set by the user in the entry box.

Choosing 'automatic' the program automatically will determine the value of N by taking into account the external DOF, the internal DOF and the flexibility of molecule.
Cooling rate: the reduction factor applied to the temperature at each step in the annealing schedule. The default value is 0.90.
Solutions: browse the best solutions saved at the end of each run.

       The second page 'External DOF' contains information about the external degrees of freedom (DOFs):



Select fragment: selects the fragment and visualizes the corresponding structure information.
Atoms: list of the atoms in the selected fragment.
Parameter for fragment: list of the external DOFs for the selected fragment. Check the parameters to refine, enter the lower and upper bounds of the parameters.

       The third page 'Internal DOF' contains information about the internal degrees of freedom (DOFS):



Internal DOFs: list of the torsions associated to each refinable internal DOF. Check the parameters to refine, enter the lower and upper bounds of parameters.
Dynamical Occupancy Correction: automatic detection of atoms in special position and atoms that share the same position. If this option is not active all refined atoms are considered in general position (default). 

Press the button 'Atomic parameters' to access to the following dialog window:

X Y Z: check the buttons on column 'X Y Z' to refine the position of atoms, in this case the fragment is not rigid but the position of atoms are shifted respect to the barycenter. Click on label 'X Y Z' to select all checks in the column.

Thermal parameterscheck the buttons on column 'B[iso]' to refine the thermal parameters of atoms. Click on label 'B[iso]' to select all checks in the column. If the thermal parameters are non indicated in the imported fragment file, the program assigns the default values of B=3.0 for non-hydrogen atoms and B=6.0 for hydrogen atoms. These default values can be change editing the new values in the column. 

Maximum shift on position: enter the value of the maximum shift of the atomic positions. 0.020 is the suggested value. Increasing this value the space explored by the algorithm becomes wider and the probability of falling in a local minimum increases.

Pattern: check the button to detect preferred orientation effect.


A visual match between observed and calculated powder pattern is plotted when Simulated Annealing is running, the progress of structure solution is monitored and the user can examine:
1)graph of minimum values of the cost function (CF) vs. the number of moves;
2)visual match between observed and calculated pattern;
3)the crystal packing by using the button on the JAV viewer.

Use the buttons  to zoom on graph of CF.
During Simulated Annealing runs three buttons are active on the toolbar of the main window:
  open the JAV viewer for crystal structure visualization
  skip the current run
  stop the procedure

Created with the Personal Edition of HelpNDoc: Easily create Help documents