Introduction to the octopus code - TDDFT.org

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4 • The choice of the mesh In octopus the Kohn-Sham equations are discretized on a finite mesh in real space. This means that derivatives are evaluated using a finite differences method (octopus uses by default a 9-point rule for the laplacian, although other rules can be chosen) and integrals are weighted sums over the grid points. The mesh is by default uniform, but the code allows for curvilinear meshes that adapt better to the problem geometry. The grid points play the role of the ‘basis functions’ of the methods where an expansion of the Kohn-Sham wave functions in some bases is employed (e.g., plane-waves or Gaussian wave functions). But, contrary to, e.g., plane-waves, this ‘basis set’ is not variational. Care must be taken to ensure that the calculations are converged with respect to these basis fuctions. This implies performing calculations with different grid spacings. As the combination of pseudopotentials and the LDA will always introduce a ∼0.1 eV error, the convergence with grid spacing is good enough when energy differences vary by less than 0.1 eV. 2 First session Objectives Tasks • Get a working knowledge of the octopus input file; • Calculate the ground state for some small molecules (Na 2 , C 2 H 2 , and SiH 4 ) using different exchange and correlation functionals (LDA, GGA, and EXX); • Study the convergence of the calculations; • Plot the density, potential, and wave functions; • Calculate some unoccupied states; • Start a linear response calculation. 1. Convergence of the total energy with respect to the grid spacing Move to the directory ∼/molecules/. There you will find three input files (c2h2.inp, na2.inp, and sih4.inp), for three different systems. Pick the file corresponding to the system assigned to you and take a look at the input variables. ✎ Information on the input variables is available on the file: /usr/local/doc/octopus.pdf or else at the code online manual:
section 2. First session 5 http://www.tddft.org/programs/octopus/wiki/index.php/Manual. You will notice that the input file is rather short. This means that all the missing input variables will be given some reasonable default values. In particular, you will not find in the input files any information neither on the exchange and correlation functional to be used nor on the pseudopotentials. If you were assigned an exchange and correlation functional different from the default Perdew-Zunger LDA you will have to add some variables to the input file. Find out which variables to add and type them in. Fill in the following table. ✌ Molecule being studied: Geometry Box type Box size Grid spacing XC functional Pseudopotentials Do a test run of octopus by copying xxx.inp to inp and typing, e.g.: prompt$ octopus > xxx.out xxx represents the system you will be studying. The code prints out some information to standard output, and that is why it is good to redirect standard output to some file like xxx.out. If you want to see the output as it progresses, you can do: prompt$ octopus | tee xxx.out The run should take a few minutes. This way it is not necessary to put it in the background. For long runs, it is better to hide it, so that a terminal crash will not stop the run: prompt$ octopus > xxx.out 2>&1 & At the end of the run you will see three new directories: tmp, status and static. The first two hold information that is normally only useful for the internal work of the code, and in general you do not have to worry about them. [Nevertheless, the file status/out.oct is the list of ALL the input variables of octopus and the
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