exercises:2018_ethz_mmm:adsorption_2018
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exercises:2018_ethz_mmm:adsorption_2018 [2018/04/13 08:14] – created dpasserone | exercises:2018_ethz_mmm:adsorption_2018 [2018/04/13 14:56] – dpasserone | ||
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====== Adsorption of acetylene on an intermetallic surface ====== | ====== Adsorption of acetylene on an intermetallic surface ====== | ||
- | << | ||
- | The reaction is the following: | ||
- | {{ : | ||
- | and this is the pictorial view in the gas phase: | ||
- | {{ : | ||
- | In the supplementary material of the paper, which can be found [[http://www.rsc.org/suppdata/c6/ra/ | + | <note important> |
+ | In this exercise you will compute the adsorption energy of acetylene on a intermetallic catalyst. | ||
+ | This process is important during the production of polyethylene, | ||
- | We will compare our results with the published ones. | + | <note tip> |
+ | * In the first part of the exercise you will consider the optimized configuration (already in the directory) and study the pure electronic adsorption energy, namely the difference between the total energy of the surface-molecule system and the energy of the molecule alone and surface alone **in the same geometry as the surface-molecule system minimum structure**. This will allow to show the binding pattern of the electronic density. | ||
+ | * In the second part, you will optimize the surface and the molecule separately; this will allow to compute | ||
+ | </ | ||
- | The input file structure is shown below: | ||
- | <code cp2k> | + | {{ : |
- | &FORCE_EVAL | + | |
- | | ||
- | & | ||
- | BASIS_SET_FILE_NAME ./ | ||
- | & | ||
- | | ||
- | | ||
- | &END POISSON | ||
- | & | ||
- | | ||
- | &END QS | ||
- | |||
- | # | ||
- | # Include the exchange and correlation information | ||
- | # | ||
- | @INCLUDE ' | ||
- | & | + | ===== 1. Task: Familiarize yourself |
+ | The coordinates of the optimized configuration are provided to you as '' | ||
+ | ===== 2. Task: Bond induced density differences ===== | ||
+ | Compute the density difference induced by the adsorption bonding. | ||
+ | For this you will have to run three separate energy calculations, | ||
+ | - combined system | ||
+ | - lone acetylene (file '' | ||
+ | - lone slab (file '' | ||
- | & | + | In order to output |
- | & | + | < |
- | | + | &DFT |
- | ABC 10 10 10 ! Lengths of the cell vectors A, B, and C | + | |
- | & | + | &E_DENSITY_CUBE |
- | &COORD ! This section specify all the atoms and their coordinates | + | &END E_DENSITY_CUBE |
- | | + | &END |
- | O | + | & |
- | H | + | </ |
- | | + | |
- | &TOPOLOGY | + | |
- | &CENTER_COORDINATES | + | |
- | &END | + | |
- | & | + | |
- | + | <note tip> | |
- | & | + | The calculations involving the slab should be run with a reduced model with the serial cp2k '' |
- | | + | |
- | | + | |
- | & | + | |
- | | + | |
- | 0.24762086 | + | |
- | & | + | |
- | &END KIND | + | |
- | &KIND H ! potential and basis for H | + | |
- | | + | |
- | | + | |
- | & | + | |
- | 1 0 0 | + | |
- | 0.20000000 | + | |
- | & | + | |
- | &END KIND | + | |
- | &KIND C ! potential and basis for C | + | |
- | | + | |
- | | + | |
- | & | + | |
- | 4 2 0 | + | |
- | 0.34883045 | + | |
- | & | + | |
- | &END KIND | + | |
- | & | + | |
- | &END FORCE_EVAL | + | |
- | & | + | To process the cube files we are going to use the [[tools: |
- | | + | < |
- | | + | (aiida) max@qmobile: |
- | RUN_TYPE GEO_OPT | + | (aiida) max@qmobile: |
- | &END GLOBAL | + | |
- | | + | |
</ | </ | ||
- | The exercise is executed on the virtual machine cluster. After creating a directory as usual, you can download the file from here: | ||
- | [[https:// | ||
- | Copy the file to the created directory in the '' | + | The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool: |
< | < | ||
- | tar xvf exercise_5.tar | + | (aiida) max@qmobile: |
</ | </ | ||
- | <note tip> | ||
- | In the directory you will find the following files: | ||
- | * '' | ||
- | * '' | ||
- | * '' | ||
- | * '' | ||
- | * '' | ||
- | </ | ||
- | First you have to modify | + | You can visualize |
- | | + | <!-- What you get should look similar to this: |
- | - 6-31G* | + | {{ dye_tio_bonding_density.png? |
- | - 6-31Gxx | + | |
- | - 6-31++Gxx | + | --> |
- | | + | ===== 3. Task: Bonding energies |
- | - 6-311++Gxx | + | Compute the binding energy: |
- | For example, | + | \[ E_\text{binding}=\sum E_\text{products} |
- | < | + | |
- | m_replace _MYBASIS_ '6-31G*' < h2o_template.inp > h2o_BASIS1.inp | + | |
- | </ | + | |
- | (note: **use the quote, because the star is a bash special character!!!**) | + | |
- | The command to launch the job is | + | |
- | <note important> | + | |
- | In the '' | + | |
- | <note important>> | + | |
- | This will list all the energies. Then you can redo the exercise with different basis set, reusing the command **m_replace**. | + | 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) | ||
- | ^ Basis set ^ Energy H2O [$E_h$] ^ Energy Ethylene [$E_h$] ^ Energy Ethanol [$E_h$]^ Distance CC Ethanol [$Å$] ^ Reaction | + | <note important> |
- | | BASIS 1(Name) | + | You can not reuse the energy |
- | | BASIS 2(Name)| .... | .... | .... | .... | .... | | + | </ |
- | | BASIS 3(Name)| .... | .... | .... | .... | .... | | + | |
- | | BASIS 4(Name)| .... | .... | .... | .... | .... | | + | |
- | | BASIS 5(Name)| .... | .... | .... | .... | .... | | + | |
- | | BASIS 6(Name)| .... | .... | .... | .... | .... | | + | |
- | < | + | ===== 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 ===== | ||
+ | < | ||
<note warning> | <note warning> | ||
- | Assignments: | + | The provided files are all in the directory |
- | - Compute | + | |
- | - Prepare a table with rows and columns: on the rows the basis set, on the columns different quantities (see above). | + | |
- | - Compare | + | |
- | - Comment on the dependence on the basis set | + | |
- | - Is this information enough to determine the rates of reaction? Why? | + | |
</ | </ | ||
- | === BONUS TRACK === | + | <code - S_M.ene.inp> |
- | <note tip>We may be interested in the visualisation of the electronic density. Copy the '' | + | & |
- | + | | |
- | Add the following sections: | + | &DFT |
- | **under | + | & |
- | <code cp2k> | + | & |
- | + | & | |
- | & | + | &END |
- | &END | + | BASIS_SET_FILE_NAME ./BR |
- | | + | POTENTIAL_FILE_NAME ./GR |
- | | + | &QS |
- | SCF_GUESS RESTART | + | EPS_DEFAULT 1.0E-10 |
- | & | + | |
- | </ | + | EXTRAPOLATION ASPC |
- | This tells to read the old wavefunction and to print the cubefile of the density. | + | EXTRAPOLATION_ORDER 3 |
- | + | &END QS | |
- | At the end of the input file: | + | & |
- | <code cp2k> | + | CUTOFF 400 |
- | &EXT_RESTART | + | NGRIDS 5 |
- | RESTART_FILE_NAME | + | &END |
+ | | ||
+ | | ||
+ | | ||
+ | EPS_SCF 1.0E-5 | ||
+ | &OT | ||
+ | PRECONDITIONER | ||
+ | MINIMIZER | ||
+ | &END | ||
+ | & | ||
+ | MAX_SCF 50 | ||
+ | EPS_SCF 1.0E-5 | ||
+ | &END | ||
+ | & | ||
+ | &END | ||
+ | &END SCF | ||
+ | &XC | ||
+ | & | ||
+ | &END XC_FUNCTIONAL | ||
+ | &END XC | ||
+ | & | ||
+ | PERIODIC XY | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | &CELL | ||
+ | A [angstrom] 7.042785 0 0 | ||
+ | B [angstrom] 0 6.09925 | ||
+ | C [angstrom] 0.000000 | ||
+ | PERIODIC XY | ||
+ | &END CELL | ||
+ | & | ||
+ | COORD_FILE_NAME | ||
+ | | ||
+ | &END | ||
+ | &KIND Pd | ||
+ | BASIS_SET DZVP-MOLOPT-SR-GTH-q18 | ||
+ | POTENTIAL GTH-PBE-q18 | ||
+ | &END KIND | ||
+ | &KIND Ga | ||
+ | BASIS_SET DZVP-MOLOPT-SR-GTH-q13 | ||
+ | POTENTIAL GTH-PBE-q13 | ||
+ | &END KIND | ||
+ | &KIND C | ||
+ | BASIS_SET TZV2P-MOLOPT-GTH | ||
+ | POTENTIAL GTH-PBE-q4 | ||
+ | &END KIND | ||
+ | &KIND H | ||
+ | BASIS_SET TZV2P-MOLOPT-GTH | ||
+ | POTENTIAL GTH-PBE-q1 | ||
+ | &END KIND | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | & | ||
+ | PRINT_LEVEL LOW | ||
+ | PROJECT S_M | ||
+ | RUN_TYPE ENERGY | ||
+ | WALLTIME 860000 | ||
+ | &END GLOBAL | ||
&END | &END | ||
- | </ | ||
- | Then, change '' | + | </ |
- | -> | + | < |
exercises/2018_ethz_mmm/adsorption_2018.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1