ABINIT TUTORIAL EBOOK
ABINIT is a software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials. Starting from the quantum equations of . The examples in this tutorial will use these shell variables so that one can easily . This is described in the abinit help file, see the input variable prtkpt, and the. >30 tutorial lessons (each hours) 6. ABINIT tutorial: layout + dependencies Jollet, Torrent, Holzwarth, Computer Physics Comm.
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ABINIT, first lesson of the tutorial: The H2 molecule, without convergence studies. This lesson aims at showing how to get the following physical properties. This lesson aims at showing you how to get the following physical properties, for an The file ~ABINIT/Tutorial/yazik.info lists the file names and root names. Elastic properties / Specific heat / ABINIT Computer program. Abstract. A brief introduction .. Beyond the tutorial, the documentation provided in the package is .
Here, we follow the prescription for bulk silicon. After modifying the following section, one might need to regenerate the pickle database with runtests. The message that you get a few dozen of lines before the end of the log file is: !
However, note that it might be due to the user, if nkpt is explicitely defined in the input file. In this case, please check your input file. This is a typical abinit error message. It states what is the problem that causes the stop of the code, then suggests that it might be due to an error in the input file, namely, an erroneous value of nkpt. The expected value, nkpt 10 is mentioned before the notice that the input file might be erroneous. Then, the file at which the problem occurred is mentioned, as well as the number of the line in that file.
As the computation of nkpt for specific grids of k-points is not an easy task, while the even more important selection of specific economical grids the best ratio between the accuracy of the integration in the Brillouin zone and the number of k-points is more difficult, some help to the user is provided by ABINIT. The code is able to examine automatically different k-point grids, and to propose the best grids for integration.
Langreth, Phys. Fiolhais, J. Perdew, S. Armster, J. MacLaren, and M. Brajczewska, Phys. B 51, , E ibid.
ABINIT, third lesson of the tutorial:
Nogueira, C. He, J. Perdew, and A.
Rubio, J. Matter 8, Fiolhais, F. Nogueira, and C. Henriques, Prog. Pollack, J. Perdew, J. He, M. Marques, F. Fiolhais, Phys.
B 55, Fiolhais, and J. Perdew, Phys. B 59, Perdew, F. Fiolhais, Theochem 9, Shaw, Jr. Rev , Callaway and P. Laghos, Phys.
Topp and J. Hopfield, Phys. Heine, Solid State Phys. CrossRef Google Scholar Harrison, Pseudopotentials in the Theory of Metals W. Benjamin, New York, Heine and D. Weaire, Solid State Phys.
Hafner and V. Heine, J. F: Met. Starkloff and J. Joannopoulos, Phys. Zunger and M. B 18, Troullier and J. Martins, Phys. B 43, Hamann, M. Chiang, Phys.
Bachelet, D. Hamann, and M. B 40, Martins, Solid State Commun. Kerker, J. Shirley, D.
Allan, R. Martin, and J.
The Fragment Molecular Orbital Method
Rappe, K. Rabe, E.
Kaxiras, and J. B 41, Kresse, J. Hafner, and R. Needs, J. Matter 4, Rappe and J. Meyer and V. You should likely have a look at the section that describes the " irdwfk " and " getwfk " input variables: in particular, look at the meaning of getwfk -1 Also, define explicitely the number of states or supercell "bands" to be one, using the input variables " nband ".
So, you run the code with your input file this might take one or two minutes , examine the output file quickly there are many repetition of sections, for the different datasets , and get the output energies gathered in the final echo of variables : etotal1 The minimum of energy in the above list is clearly between dataset 11 and 12, that is : xcart11 The forces vanish also between 1. Note that the number of SCF cycles drops from 7 to 5 when the wavefunctions are read from the previous dataset.
There are different algorithms to do that. See the input variable " ionmov ", with values 2, 3 and 7. In the present case, with only one degree of freedom to be optimized, the best choice is ionmov 3.
You have also to define the maximal number of timesteps for this optimization.
Set the input variable " ntime " to 10, it will be largely enough. For the stopping criterion " tolmxf ", use the reasonable value of 5. This defines the force treshhold to consider that the geometry is converged. The code will stop if the residual forces are below that value before reaching " ntime ". It is also worth to change the stopping criterion for the SCF cycle, in order to be sure that the forces generated for each trial interatomic distance are sufficiently converged.
So, change " toldfe " in " toldff ", and set the latter input variable to ten times smaller than " tolmxf ". If you decide to use these files, do not forget to change the file names in the t1x. So, you run the code with your input file it should take less than one minute , examine quietly this file which is much smaller than the t If you have time this is to be done at home , you might try to change the stopping criteria, and redo the calculation, to see the level of convergence of the interatomic distance.
Note that the final value of fcart in your run might differ slightly from the one shown above less than one percent change. Such a fluctuation is quite often observed for a value converging to zero remember, we ask the code to determine the equilibrium geometry, that is, forces should be zero when the same computation is done on different platforms.
Computation of the charge density. We start from the optimized interatomic distance 1. The input variable " prtden " must be set to 1.
If you decide to use this file, do not forget to change the file names in t1x. The run will take a few seconds. Try to edit it No luck! It contains first a header, then the density numbers.
The description of the header is presented in section 6. It is the appropriate time to read also the description of the potential files and wavefunctions files, as these files contain the same header as the density file, see sections 6.
You might try to use it now, to generate two-dimensional cuts in the density, and visualize the charge density contours. Read the corresponding Cut3D help file. You should first try to translate the unformatted density data to indexed formatted data, by using option 6 in the adequate menu.
For further treatment, you might choose to select another option than 6. Another option might be to use the XCrysDen software, for which you need to use option 9.Set the input variable " ntime " to 10, it will be largely enough. We offer a free ebook reader to download with our books where users can freely make notes, highlight texts and do citations and save them in their accounts. Providing a unique and accessible approach, The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems is for those researchers eager to obtain useful information from electronic structure calculations of large systems, and for those who wish to know what can be elucidated with the calculations at present and in the near future.
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Cohen and V. Froyen, and M. Baldridge, J. B 59, Heine, Solid State Phys. It can happen that the highest or two highest band s , if not separated by a gap from non-treated bands, can exhibit a very slow convergence rate.