exercises:2017_ethz_mmm:qmmm
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exercises:2017_ethz_mmm:qmmm [2017/06/02 02:28] – dpasserone | exercises:2017_ethz_mmm:qmmm [2017/06/02 03:43] – dpasserone | ||
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=== (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> | |
- | ===== 2. Task: Bond induced density differences ===== | + | * Make three copies of **input.inp** and call them **qm_1l.inp**, **qm_2l.inp** and **qm.inp**. |
- | Compute the density difference induced by the adsorption bonding. | + | * **qm_1l.inp** should have '' |
- | For this you will have to run three separate energy calculations, using the *.ene.inp files. | + | * **qm_2l.inp** should have '' |
- | - combined system | + | * **qm.inp** should have '' |
- | - lone acetylene (file '' | + | |
- | - lone slab (file '' | + | |
- | + | ||
- | In order to output | + | |
- | < | + | |
- | &DFT | + | |
- | & | + | |
- | & | + | |
- | &END E_DENSITY_CUBE | + | |
- | &END | + | |
- | &END DFT | + | |
- | </ | + | |
- | + | ||
- | <note tip> | + | |
- | The calculations involving the slab should be run on at least 16 cores with '' | + | |
</ | </ | ||
- | To process the cube files we are going to use the [[tools: | + | ===== 2. Task: Run the jobs ===== |
- | < | + | |
- | you@eulerX ~$ ./ | + | |
- | you@eulerX ~$ ./ | + | |
- | </ | + | |
- | + | ||
- | + | ||
- | The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool: | + | |
- | < | + | |
- | you@eulerX ~$ ./ | + | |
- | </ | + | |
- | + | ||
- | 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> | <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. | + | * Run the jobs by giving |
+ | * You will also get cube files for hartree potential and electronic density. They can be examined with vmd. | ||
+ | * For each job, a '' | ||
</ | </ | ||
+ | |||
===== Questions ===== | ===== Questions ===== | ||
- | | + | |
- | * 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 75: | ||
#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