Electronic structure code for molecules and clusters
TO-DO - Associated with
Run MATLAB and then RSDFT inside the RSDFT/ directory for a GUI. Running
main will instead run without any GUI, and should be
considered a fall back method. The included help assumes use of the GUI.
Use the drop-down menu at the top left to select the element of the next atom. Input the xyz coordinates of the atom in the 3 text boxes to the right. Click 'Add Atom'. The atom will be added to the list of atoms and will also be shown in the molecule visualization. The molecule visualization can be rotated for a better view by left clicking and dragging. If a mistake is made, select the offending atoms from the list and click the 'Delete Selected Atom(s)' button.
Once the molecule is done, it can be saved by clicking the 'Save' button or selecting 'Save' from the file menu. Give the molecule a name and choose the file extension to use. '.mat' is binary and can only be read by MATLAB, '.dat' is a text format and can be viewed by any text editor.
Click the button marked 'Load' or select 'Load' from the file menu. Choose either '.mat' or '.dat' extension and select a previously created molecule. The atoms that make up the molecule will be added to the list and visualization.
Once the 'Start' button has been clicked, the Progress Window will open. This window will show the current progress being made on the calculations in two ways. At the bottom of the window will be a progress bar. NOTE: the progress bar determines the percentage completed by using the SCF error. Because the SCF error can increase, the progress bar can go backwards.
The second method provides more information. The text shows at what step the calculations are at. It also shows the current diagonalization method and the subsequent error. Once the calculations are finished, the eigenvalues and energy statistics will be printed.
The most recent modifications to RSDFT
have the purpose of decreasing the
time it takes to run the calculations. Some of the
optimizations used may not be compatible with all
computers, may not speed up the program much, or in
the worst case, may slow down execution. This is why
a flag is made available to the user, allowing the
user to decide which optimizations to use. Level 0
optimization only uses MATLAB code. This level should
be compatible with all recent versions of MATLAB.
The next step up is level 1 and this level allows the
use of mex files. Mex files are binary files that have
been compiled from C code. These mex files will
execute faster than their m file counterparts. The
downside is that compatibility is not guaranteed.
MEX Files are currently unsupported
The values set in RSDFTsettings.m are the values that these settings will use when RSDFT is first started up.
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Enable Charge Density Visualization: Controls whether a visualization of the molecule's charge density is shown after execution is completed.
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useIsosurface: {1 | [0]} - determines whether visualization uses isosurface rendering methods or contour rendering.
Explaination of Charge Density Visualization
If the check box enabling the visualization is
checked, once the calculations are finished, a
new window showing a visualization of the charge density
of the current molecule will open. The way to interpret
the graph is that the graph is showing a slice through the
volume that is parallel to the xy plane. The z axis and colors
of the graph represent charge density values. By using the
scroll bar on the right, different slices can be viewed.
The scroll bar on the bottom changes the y axis and color scale.
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Precondition CG: Control whether or not preconditioning is used.
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Use Adpative Scheme: Controls whether or not certain perameters are changed during execution. This is mainly used to speedup execution, but this speed up has two potential downsides. The first is that the final eigenvalues are slightly different and that under the wrong conditions, execution might take longer so use this option with care.
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Diagonalization Method: Use drop-down menu to select which diagonalization method(s) are used. 0 --> Lanczos 1st step and chebyshev filtering thereafter 1 --> Lanczos all the time 2 --> Full-Chebyshev subspace iteration first step chebyshev filtering thereafter.
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Polynomial Degree for Chebyshev filtering: Used to specify the degree of the Chebyshev polynomial. 10 is a good mix of speed and accuracy.
The one potential problem is the lack of a MATLAB compatible compiler. The first time the user attempts to compile the mex files, if MATLAB has not been setup, the user will be prompted to choose a compiler that is installed on the current computer. If a compatible compiler cannot be found, the compiling cannot continue. RSDFT is shipped with precompiled mex files, but if these do not execute properly, then the optimization level must be set to 0.
There are two main reasons that a mex file might have compatibility problems.The first is that the mex file was compiled for a different operating systemor architecture. The second problem is that mex files are not guaranteed to be compatible on a different version of MATLAB than the version it was compiled on. The only solution to these two problems is to recompile the mex files. This can be done two ways. Either run the script, compileMexFiles.m, or from the first graphical user interface window, click the 'compile C code' button.
The user has two ways to control the optimization level. If the graphical user interface is being used, on the first window, use the drop down menu near the bottom center of the window. If the text based interface is in use, go into the file, settings.m, and near the bottom should be a statement, OPTIMIZATIONLEVEL= #. Replace the number with the desired optimization level. Note that the value used set to the variable OPTIMIZATIONLEVEL in settings.m is used as the default value in the graphical user interface. Progress Window Information