exercises:2017_ethz_mmm:qmmm
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
exercises:2017_ethz_mmm:qmmm [2017/06/02 02:28] – dpasserone | exercises:2017_ethz_mmm:qmmm [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
Line 2: | Line 2: | ||
=== (exercise by Matthew Watkins, University college, London) === | === (exercise by Matthew Watkins, University college, London) === | ||
In this exercise you will validate the mixed quamtum/ | In this exercise you will validate the mixed quamtum/ | ||
- | Hte : [[doi> | + | The present exercise is referring to the following paper: [[doi> |
<note tip> | <note tip> | ||
- | * In the first part of the exercise you will consider | + | * You will optimize |
- | * In the second part, you will optimize | + | {{ : |
+ | | ||
+ | | ||
+ | * In particular | ||
</ | </ | ||
- | {{ : | ||
- | ===== 1. Task: Familiarize yourself | + | ===== 1. Task: Prepare the input files |
- | The coordinates | + | The file input.inp contains the partition |
+ | <note important> | ||
+ | | ||
+ | * **qm_1l.inp** should have '' | ||
+ | * **qm_2l.inp** should have '' | ||
+ | * **qm.inp** should have '' | ||
+ | </ | ||
- | ===== 2. Task: Bond induced density differences | + | ===== 2. Task: Run the jobs |
- | Compute | + | <note important> |
- | For this you will have to run three separate energy calculations, | + | * Run the jobs by giving |
- | | + | |
- | | + | |
- | - lone slab (file '' | + | </ |
- | In order to output | + | ===== 3. Task: Checking |
- | < | + | < |
- | &DFT | + | By direct inspection of the last configuration in each file '' |
- | & | + | |
- | & | + | |
- | &END E_DENSITY_CUBE | + | |
- | &END | + | |
- | &END DFT | + | |
- | </ | + | |
- | + | ||
- | < | + | |
- | The calculations involving | + | |
</ | </ | ||
- | To process the cube files we are going to use the [[tools: | ||
- | < | ||
- | you@eulerX ~$ ./ | ||
- | you@eulerX ~$ ./ | ||
- | </ | ||
+ | ===== 4. Task: Electronic properties | ||
- | The generated cube file is not aligned with the simulation cell. Center | + | <note important> |
- | < | + | Extract a smeared dos from the '' |
- | you@eulerX ~$ ./ | + | < |
+ | > python get-smearing-pdos.py KCl_1-PDOS-QMMM-k1-1.pdos | ||
+ | > mv smeared.dat KCl_1.K.dat | ||
+ | > python get-smearing-pdos.py KCl_1-PDOS-QMMM-k2-1.pdos | ||
+ | > mv smeared.dat KCl_1.Cl.dat | ||
+ | > paste KCl_1.K.dat KCl_1.Cl.dat > KCl_1.KCl.dat # all in the same file. The columns are '' | ||
</ | </ | ||
+ | Plot the '' | ||
+ | <code bash> | ||
+ | > gnuplot | ||
+ | gnuplot> set xrange [-5:10] | ||
+ | gnuplot> plot ' | ||
+ | </ | ||
+ | * **Note the differences you observe** | ||
+ | * Find the value of the band gap in the '' | ||
+ | </ | ||
- | You can visualize the resulting file '' | ||
- | What you get should look similar to this: | ||
- | {{ dye_tio_bonding_density.png? | ||
- | ===== 3. Task: Bonding energies | + | |
- | Compute the binding energy: | + | |
- | + | ||
- | \[ E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants} \] | + | |
- | + | ||
- | For this you will need the energy values of three systems: | + | |
- | - lone acetylene molecule (run geometry optimization, | + | |
- | - lone slab (you can use the already geometry optimized coordinates from '' | + | |
- | - combined system adsorbed (can be reused from previous task) | + | |
- | + | ||
- | <note important> | + | |
- | You can not reuse the energy values for the lone sub-systems from the previous task. Since the unbound subsystems might relax into a different geometry, they have to be geometry optimized first. | + | |
- | </ | + | |
- | + | ||
- | + | ||
- | ===== Questions ===== | + | |
- | * Sketch briefly the geometry of the molecule **when adsorbed** and **in the gas phase**. | + | |
- | * Report the system energy for the bonded system, lone slab, and lone molecule. | + | |
- | * Can you estimate the contribution due to the geometry relaxation? | + | |
- | * Briefly report the bond induced density difference on the system. | + | |
===== Required Files ===== | ===== Required Files ===== | ||
- | <note tip> When you are dealing with big systems and multiple atomic species, the input can be simplified by splitting it into multiple files. We are going to use separate files for the coordinates, | + | <note tip> When you are dealing with complex job structure, the input can be simplified by splitting it into multiple files. We are going to use separate files for the coordinates, |
<note warning> | <note warning> | ||
- | The provided files are all in the directory ''/ | + | The provided files are all in the directory ''/ |
</ | </ | ||
Line 114: | Line 101: | ||
#but should be treated as parameters in general | #but should be treated as parameters in general | ||
#fit to some physical property | #fit to some physical property | ||
- | & | + | |
- | RADIUS 1.52 | + | |
- | &END MM_KIND | + | |
& | & | ||
- | RADIUS 1.67 | ||
- | &END MM_KIND | ||
- | #define the model | ||
- | & | ||
- | MM_INDEX 25..32 41..48 | ||
- | &END QM_KIND | ||
- | & | ||
RADIUS 1.67 | RADIUS 1.67 | ||
&END MM_KIND | &END MM_KIND |
exercises/2017_ethz_mmm/qmmm.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1