# Open SourceMolecular Dynamics

### Site Tools

exercises:2019_conexs_newcastle:ex3

# Differences

This shows you the differences between two versions of the page.

 exercises:2019_conexs_newcastle:ex3 [2019/09/10 16:43]abussy [MgO] exercises:2019_conexs_newcastle:ex3 [2019/09/12 09:30]abussy [Part 2: XAS calculations] Both sides previous revision Previous revision 2019/09/13 10:57 abussy [Part 2: XAS calculations] 2019/09/12 09:30 abussy [Part 2: XAS calculations] 2019/09/12 06:21 abussy [Part 4: Changing basis set] 2019/09/10 16:49 abussy 2019/09/10 16:43 abussy [MgO] 2019/09/10 14:50 abussy [MgO] 2019/09/10 14:26 abussy [MgS] 2019/09/10 12:34 abussy [MgS and MgO: Periodic systems and XAS] 2019/09/10 12:33 abussy [MgS and MgO: Periodic systems and XAS] 2019/09/09 08:12 abussy [Part 4: Changing basis-set] 2019/09/09 08:11 abussy 2019/09/09 07:56 abussy 2019/09/09 07:53 abussy [MgO] 2019/09/09 07:48 abussy [MgS and MgO: Periodic systems and XAS] 2019/09/09 07:44 abussy [Part 4: Changing basis-set] 2019/09/09 07:43 abussy 2019/09/08 07:17 abussy [Part 3: $\Delta$SCF calculations] 2019/09/07 12:06 abussy [MgS and MgO: Periodic systems and XAS] 2019/09/07 11:59 abussy [Part 3: $\Delta$SCF calculations] 2019/09/07 11:55 abussy 2019/09/07 11:54 abussy [Part 2: XAS calculations] 2019/09/07 11:51 abussy [Part 3: $\Delta$SCF calculations] 2019/09/07 11:51 abussy [Part 2: XAS calculations] 2019/09/07 11:40 abussy [Part 3: $\Delta$SCF calculations] 2019/09/07 11:39 abussy 2019/09/07 09:35 abussy 2019/09/07 07:34 abussy created Next revision Previous revision 2019/09/13 10:57 abussy [Part 2: XAS calculations] 2019/09/12 09:30 abussy [Part 2: XAS calculations] 2019/09/12 06:21 abussy [Part 4: Changing basis set] 2019/09/10 16:49 abussy 2019/09/10 16:43 abussy [MgO] 2019/09/10 14:50 abussy [MgO] 2019/09/10 14:26 abussy [MgS] 2019/09/10 12:34 abussy [MgS and MgO: Periodic systems and XAS] 2019/09/10 12:33 abussy [MgS and MgO: Periodic systems and XAS] 2019/09/09 08:12 abussy [Part 4: Changing basis-set] 2019/09/09 08:11 abussy 2019/09/09 07:56 abussy 2019/09/09 07:53 abussy [MgO] 2019/09/09 07:48 abussy [MgS and MgO: Periodic systems and XAS] 2019/09/09 07:44 abussy [Part 4: Changing basis-set] 2019/09/09 07:43 abussy 2019/09/08 07:17 abussy [Part 3: $\Delta$SCF calculations] 2019/09/07 12:06 abussy [MgS and MgO: Periodic systems and XAS] 2019/09/07 11:59 abussy [Part 3: $\Delta$SCF calculations] 2019/09/07 11:55 abussy 2019/09/07 11:54 abussy [Part 2: XAS calculations] 2019/09/07 11:51 abussy [Part 3: $\Delta$SCF calculations] 2019/09/07 11:51 abussy [Part 2: XAS calculations] 2019/09/07 11:40 abussy [Part 3: $\Delta$SCF calculations] 2019/09/07 11:39 abussy 2019/09/07 09:35 abussy 2019/09/07 07:34 abussy created Last revision Both sides next revision Line 161: Line 161: ​Even though we are not changing the name of the basis set or pseupotential used, cp2k will use the parameters for the sulfur atom now, since the ''​ELEMENT''​ type is different. However, it is important to check in the ''​GTH_BASIS_SET''​ and ''​GTH_POTENTIALS''​ files whether the names are the same for different atoms.​Even though we are not changing the name of the basis set or pseupotential used, cp2k will use the parameters for the sulfur atom now, since the ''​ELEMENT''​ type is different. However, it is important to check in the ''​GTH_BASIS_SET''​ and ''​GTH_POTENTIALS''​ files whether the names are the same for different atoms.​ - Now the input is ready, and can be run in the same way as before, just changing ​the input and output files names. + Now the input is ready and it can be run in the same way as before, just remember to change ​the file ''​cp2k.sh''​. - + - <​code>​ + - ./cp2k.sopt -i MgS_opt.inp -o MgS_opt.out & + -  ​ + After the calculation is finished, open the output file ''​MgS_opt.out''​ and look for the same banner as before. The optimized atomic positions are written in the file ''​MgS-pos-1.xyz''​. After the calculation is finished, open the output file ''​MgS_opt.out''​ and look for the same banner as before. The optimized atomic positions are written in the file ''​MgS-pos-1.xyz''​. Line 185: Line 181: &DFT &DFT - ​BASIS_SET_FILE_NAME ​ EMSL_BASIS_SETS ​! basis set file with all-electron basis set + !where to find all-electron basis sets and potentials - POTENTIAL_FILE_NAME ​ POTENTIAL ​! file with parameters for all-electron calculations + BASIS_SET_FILE_NAME ​ EMSL_BASIS_SETS + POTENTIAL_FILE_NAME ​ POTENTIAL ​ UKS UKS Line 342: Line 339: ​At this time we are using cartesian coordinates to indicate the position of the atoms, so the keyword ''​SCALED''​ should be removed.​At this time we are using cartesian coordinates to indicate the position of the atoms, so the keyword ''​SCALED''​ should be removed.​ - To run this calculation ​type in terminal: + To run this calculation ​proceed as you did before. - + - <​code>​ + - ./cp2k.sopt -i MgS_xas.inp -o MgS_xas.out & + - ​ + This calculation should take longer than the geometry optimization to run. Once it is finished, check the number of warnings and if the calculation converged. Sometimes it does not converge within the maximum number of iterations we set in the input file. If this is the case, you can increase the number using the keyword ''​MAX_SCF''​. This calculation should take longer than the geometry optimization to run. Once it is finished, check the number of warnings and if the calculation converged. Sometimes it does not converge within the maximum number of iterations we set in the input file. If this is the case, you can increase the number using the keyword ''​MAX_SCF''​. Line 388: Line 381: ​ - For the MgS system, for example, run the calculation ​typing ​ + instead of ''​TP_HH''​, and you can run the calculation ​in the same way as you did before. - <​code>​ + After the calculation ​is done, look for the message - ./cp2k.sopt -i MgS_dscf.inp -o MgS_dscf.out & + - ​ + - + - After the calculation ​ran, look for the message + <​code>​ <​code>​ Line 413: Line 402: <​note>​ In this exercise we have obtained absorption spectra using a simple basis set, in order to performed the calculations on small machines and using a limited time. Therefore, careful tests on basis set size, XC functional etc have to be carried out for production runs to get more reliable spectra.  ​ <​note>​ In this exercise we have obtained absorption spectra using a simple basis set, in order to performed the calculations on small machines and using a limited time. Therefore, careful tests on basis set size, XC functional etc have to be carried out for production runs to get more reliable spectra.  ​ + + You can check the tutorial [[exercises:​2017_uzh_cp2k-tutorial:​gapw|Gaussian and Augmented Plane Wave Method]] in case you want to compute more absorption spectra.
exercises/2019_conexs_newcastle/ex3.txt · Last modified: 2019/09/13 10:57 by abussy