exercises:2017_uzh_cp2k-tutorial:gapw
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exercises:2017_uzh_cp2k-tutorial:gapw [2017/07/06 00:03] – gtocci | exercises:2017_uzh_cp2k-tutorial:gapw [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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this tutorial we will just compute the XAS spectra of single snapshots for a small (1ps) trajectory | this tutorial we will just compute the XAS spectra of single snapshots for a small (1ps) trajectory | ||
of bulk water (32 H2Os). To start, extract the directories {{ : | of bulk water (32 H2Os). To start, extract the directories {{ : | ||
- | where you will be running the calculations. Also, besides | + | where you will be running the calculations. Also, load the CP2K module |
- | which you can load as explained in [[exercises: | + | as explained in [[exercises: |
Go to the directory '' | Go to the directory '' | ||
Line 104: | Line 104: | ||
! spin polarization required for the XAS calculation | ! spin polarization required for the XAS calculation | ||
LSD | LSD | ||
- | ! multigrid section here we use 5 different grid levels | ||
&MGRID | &MGRID | ||
NGRIDS 5 | NGRIDS 5 | ||
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&QS | &QS | ||
! Task: insert METHOD keyword to use gaussian and augmented plane wave method | ! Task: insert METHOD keyword to use gaussian and augmented plane wave method | ||
+ | !METHOD GAPW | ||
EXTRAPOLATION ASPC | EXTRAPOLATION ASPC | ||
EXTRAPOLATION_ORDER 3 | EXTRAPOLATION_ORDER 3 | ||
Line 120: | Line 119: | ||
QUADRATURE | QUADRATURE | ||
! parameters needed for the GAPW method, look at the manual for more details | ! parameters needed for the GAPW method, look at the manual for more details | ||
- | EPSFIT | + | EPSFIT |
EPSISO | EPSISO | ||
EPSRHO0 | EPSRHO0 | ||
LMAXN0 | LMAXN0 | ||
LMAXN1 | LMAXN1 | ||
- | ALPHA0_H | + | ALPHA0_H |
&END QS | &END QS | ||
&SCF | &SCF | ||
Line 165: | Line 164: | ||
&XAS | &XAS | ||
RESTART F | RESTART F | ||
- | ! Task: specify below the method | + | ! Task: specify below the METHOD |
- | ! half-core hole and the full core-hole are possible methods | + | ! half-core hole and the full core-hole are possible methods, choose |
+ | ! METHOD TP_HH | ||
| | ||
- | |||
DIPOLE_FORM | DIPOLE_FORM | ||
- | ! Task: include the STATE_TYPE | + | ! Task: include the STATE_TYPE |
- | ! in NEXAFS experiments one looks at the excitation of the inner-core shell | + | ! in NEXAFS experiments one looks at the excitation of the innermost-core shell |
- | + | | |
- | ! Task: include the ATOMS_LIST | + | ! Task: include the ATOMS_LIST |
! you can look at the list of atoms to include in the .xyz file for the snapshot | ! you can look at the list of atoms to include in the .xyz file for the snapshot | ||
! In order to include atoms from X to Y use the syntax X..Y | ! In order to include atoms from X to Y use the syntax X..Y | ||
- | + | ! ATOMS_LIST 1..32 | |
- | ! This tag indicates the number of virtual KS orbitals | + | ! This keyword |
! to compute the XAS | ! to compute the XAS | ||
ADDED_MOS | ADDED_MOS | ||
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! for both O and H we want to use the all-electron 6-31G* basis set | ! for both O and H we want to use the all-electron 6-31G* basis set | ||
&KIND H | &KIND H | ||
- | + | ! BASIS_SET 6-31G* | |
+ | ! POTENTIAL ALL | ||
! number of points for the angular part of the grid, needed for GAPW | ! number of points for the angular part of the grid, needed for GAPW | ||
LEBEDEV_GRID 80 | LEBEDEV_GRID 80 | ||
Line 237: | Line 236: | ||
&END KIND | &END KIND | ||
&KIND O | &KIND O | ||
- | + | ! BASIS_SET 6-31G* | |
+ | ! POTENTIAL ALL | ||
LEBEDEV_GRID 80 | LEBEDEV_GRID 80 | ||
RADIAL_GRID 200 | RADIAL_GRID 200 | ||
Line 257: | Line 256: | ||
mpirun -n 4 cp2k.popt | mpirun -n 4 cp2k.popt | ||
</ | </ | ||
- | It should take about half an hour to run this job so while waiting | + | Check the output file as it's being written. You should notice that after the first SCF cycle, where the wavefunction is optimized, |
- | this, let us calculate the XAS spectra for ice. At the end of the tutorial we | + | there are a number of SCF loops where CP2K is performing the XAS simulation, see for instance in the output |
+ | '' | ||
+ | It should take about half an hour to run this job so while waiting, | ||
+ | let us calculate the XAS spectra for ice. At the end of the tutorial we | ||
will try to compare the water and ice spectra. | will try to compare the water and ice spectra. | ||
===== 2. Task: compute the XAS spectrum of ice-1h ===== | ===== 2. Task: compute the XAS spectrum of ice-1h ===== | ||
- | Go to the directory '' | + | Go to the directory '' |
- | Run the XAS simulation using only 2 cores (there | + | Run the XAS simulation using only 2 cores. There is no need to edit the input file this time. |
The spectrum calculation for ice should be quicker because there is no need to average it over | The spectrum calculation for ice should be quicker because there is no need to average it over | ||
- | many different molecules. After finishing | + | many different molecules. After this calculation is finished |
contain the bare XAS spectra. In the first column there is the index of the virtual KS state, the second column is | contain the bare XAS spectra. In the first column there is the index of the virtual KS state, the second column is | ||
the transition energy, the third, fourth and fifth column are the transition probabilities projected onto | the transition energy, the third, fourth and fifth column are the transition probabilities projected onto | ||
Line 285: | Line 287: | ||
</ | </ | ||
- | Now run the execute | + | Now run the following command to convolute the spectrum |
- | previous | + | previously published |
< | < | ||
- | ../../ | + | ../ |
</ | </ | ||
Line 295: | Line 297: | ||
plot " | plot " | ||
</ | </ | ||
+ | |||
+ | **Question: | ||
How do your results for the convoluted spectrum compare with previous experiments and simulations? | How do your results for the convoluted spectrum compare with previous experiments and simulations? | ||
- | Look for instance at the Bottom | + | Look for instance at the bottom |
- | or Fig 2 of [[doi>http:// | + | or Fig 2 of [[doi> 10.1063/ |
There should be several things that do not match with our calculations. | There should be several things that do not match with our calculations. | ||
Apart from a shift towards larger binding energies compared with the two papers, | Apart from a shift towards larger binding energies compared with the two papers, | ||
it looks like not all the states of the conduction band are present. | it looks like not all the states of the conduction band are present. | ||
- | Now the task is to correct this by editing a tag in the '' | + | Now the task is to correct this by editing a tag in the '' |
- | remove the '' | + | So remove the '' |
- | and repeat the tasks shown. How does the spectrum compare now? There should still be | + | and repeat the tasks just described. How does the spectrum compare now? There should still be |
- | apparent | + | clear differences, |
The presence of a broad band corresponding to the conduction band of ice | The presence of a broad band corresponding to the conduction band of ice | ||
should be visible, as well as an apparent shoulder (the main edge) just to the left of | should be visible, as well as an apparent shoulder (the main edge) just to the left of | ||
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Now the calculation of the water spectra should be finished. So from the directory | Now the calculation of the water spectra should be finished. So from the directory | ||
- | '' | + | '' |
for water averaged over the 32 molecules and plot it in '' | for water averaged over the 32 molecules and plot it in '' | ||
together with the ice spectrum | together with the ice spectrum | ||
Line 322: | Line 326: | ||
</ | </ | ||
- | * Compare the spectra between each other and with the paper [[doi>http:// | + | * Compare the spectra between each other and with the paper [[doi> |
- | + | * Fig.5 of this review [[doi> | |
- | * Fig.5 of this review [[doi> | + | |
- | * Can you now clearly identify the pre-, main- and post-edge features in the bulk water spectra and in ice? | + | |
* What is the main reason for the different shapes between water and ice? | * What is the main reason for the different shapes between water and ice? | ||
* If our results do not match well with previously published experimental or the simulation data, could you think of possible reasons for the discrepancy? | * If our results do not match well with previously published experimental or the simulation data, could you think of possible reasons for the discrepancy? |
exercises/2017_uzh_cp2k-tutorial/gapw.1499299438.txt.gz · Last modified: 2020/08/21 10:15 (external edit)