Introduction to the octopus code - TDDFT.org

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6 values they assumed in this run, which may be useful sometimes]. In the last one, you will see a file called info, where there is a summary of the final results. This is the file that contains the interesting information. You are now going to determine a reasonable grid spacing that ensures that your calculations are converged. To help you, a sample script is provided: look for xxx convergence.sh and edit it to suit your needs. Run the script and plot the total energy and some eigenvalues as a function of the grid spacing (use, e.g., xmgrace or gnuplot). Check also that the simulation box you use is of the convenient type and size. Can you answer the following questions Q1. What was the criterion for convergence of the SCF cycle Q2. How many SCF cycles were needed to meet this criterion Q3. Which grid spacing assures an error for the total energy smaller than 10 meV Q4. What can you say about the convergence of the eigenvalues differences Q5. Does your curve of the total energy as a function of the grid spacing look monotonous Why 2. Plot the density, potential and wave functions for the converged run Replace the grid spacing in the input file for the one you have just found. The input file as it is now will not output the wave functions or the density. In order to plot them you will have to add some variables to the input file. Try adding: Output = potential + density + wfs + geometry OutputHow = dx and run octopus with the new input file. This instructs the code to plot the KS potential, the density, the wavefunctions, and the molecular geometry, and to use for that purpose a format suitable to be opened with OpenDX, IBM’s Data Explorer visualization program. In thestatic directory you will now have some files with extension .dx. octopus provides an applet to ease the plotting of these files with Data Explorer: simply copy the mf.cfg and mf.net files in /usr/local/octopus/util to your current directory and type dx. Then, select Run Visual Programs... from the menu and open mf.net. Take a deep breath and start playing with the program. The applet instructions will appear as a separate window on your terminal if you select Application Comment from the Help menu (NOT the Help button on the initial window). Plot the density, the wave functions squared, and the Kohn- Sham potential. You can superimpose these plots on a ball and stick model of the molecule.... Note that you can also do simpler plots; take a look at the manual for some other possibilities for the OutputHow variable. 3. Calculate some unoccupied states Until now, you have just computed occupied states. This means that the number of Kohn-Sham wave functions used in the SCF cycle was exactly half the number of
section 2. First session 7 valence electrons (due to spin degeneracy). You could have added some extra wave functions to the static ground-state calculation by including, e.g., ExtraStates = 3 in the input file. This would instruct octopus to use three additional wave functions in the SCF cycle. Of course these wave functions would correspond to unoccupied states in the cases we are studying, but could be important if you had some degeneracy or quasi-degeneracy at the HOMO level. In that case you could also fix the occupation numbers and distribute the top-lying electrons among the degenerate orbitals. For example, to compute the ground-state of the carbon atom you could resort to: ExtraStates = 2 %Occupations 2 | 2/3 | 2/3 | 2/3 % These extra wave functions and eigenvalues would of course be updated during the SCF cycle and would contribute to the ground-state density. These “extra” states are not really unoccupied, but partially occupied. If the states that you want are really the empty states above the Fermi level (zero occupation) you can also, given some previously calculated ground-state density, determine those unoccupied states without including them in the SCF cycle. These states are calculated in a single run using a fixed density. This method of obtaining the unoccupied states is more adequate than using the previous one and setting some zeros in the %Occupations block. With these calculations one can get a first approximation to the excitation energies of the system by simply taking the differences between the eigenvalues. Although not justifiable, this approach does give a rough idea of the excitation spectrum. Now, you will calculate some unoccupied states of the system. This is done by replacing CalculationMode = gs with CalculationMode = unocc in the input file. The number of unoccupied Kohn-Sham states that is going to be calculated is decided with the variable NumberUnoccStates, e.g.: NumberUnoccStates = 10 Upon running the code with this input you will find the list of eigenvalues in static/eigenvalues. Please note that convergence can be very slow. There are some input variables that control the convergence of the process; note especially:
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Introduction to the octopus code - TDDFT.org

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