exercises:2017_ethz_mmm:c2h2_pdga
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exercises:2017_ethz_mmm:c2h2_pdga [2017/05/05 07:07] – created dpasserone | exercises:2017_ethz_mmm:c2h2_pdga [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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====== Adsorption of C2H2 on PdGa(111) ====== | ====== Adsorption of C2H2 on PdGa(111) ====== | ||
In this exercise you will compute the adsorption energy of acetylene on a intermetallic catalyst. | In this exercise you will compute the adsorption energy of acetylene on a intermetallic catalyst. | ||
- | This process is important during the production of polyethylene, | + | This process is important during the production of polyethylene, |
+ | |||
+ | <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 total adsorption energy. | ||
+ | </ | ||
{{ : | {{ : | ||
- | <!-- | + | |
===== 1. Task: Familiarize yourself | ===== 1. Task: Familiarize yourself | ||
- | The coordinates of the two binding modes are provided to you as '' | + | The coordinates of the optimized configuration |
===== 2. Task: Bond induced density differences ===== | ===== 2. Task: Bond induced density differences ===== | ||
- | Compute the density difference induced by the bonding | + | Compute the density difference induced by the adsorption |
- | For this you will have to run three separate energy calculations: | + | For this you will have to run three separate energy calculations, using the *.ene.inp files. |
- | - combined system | + | - combined system |
- | - lone acetic acid molecule | + | - lone acetylene |
- | - lone TiO$_2$ | + | - lone slab (file '' |
In order to output the electronic densities as cube files, your input file has to contain the following snipped: | In order to output the electronic densities as cube files, your input file has to contain the following snipped: | ||
Line 28: | Line 33: | ||
<note tip> | <note tip> | ||
- | The calculations involving the large TiO$_2$ | + | 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: | + | To process the cube files we are going to use the [[tools: |
- | Therefore, you'll have to download | + | |
< | < | ||
- | you@eulerX ~$ svn checkout http:// | + | you@eulerX ~$ ./ |
- | you@eulerX ~$ cd cubecruncher | + | you@eulerX ~$ ./ |
- | you@eulerX ~$ make | + | |
- | you@eulerX ~$ ./ | + | |
- | </ | + | |
- | + | ||
- | Now subtract the densities of the lone systems from the bonded system: | + | |
- | < | + | |
- | you@eulerX ~$ ./ | + | |
- | you@eulerX ~$ ./ | + | |
</ | </ | ||
Line 49: | Line 45: | ||
The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool: | The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool: | ||
< | < | ||
- | you@eulerX ~$ ./ | + | you@eulerX ~$ ./ |
</ | </ | ||
- | You can visualize the resulting file '' | + | You can visualize the resulting file '' |
What you get should look similar to this: | What you get should look similar to this: | ||
Line 58: | Line 54: | ||
===== 3. Task: Bonding energies | ===== 3. Task: Bonding energies | ||
- | Compute the binding energy | + | Compute the binding energy: |
\[ E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants} \] | \[ E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants} \] | ||
- | For this you will need the energy values of four systems: | + | For this you will need the energy values of three systems: |
- | - lone acetic acid molecule (run geometry optimization, | + | - lone acetylene |
- | - lone TiO$_2$ | + | - lone slab (you can use the already geometry optimized coordinates from '' |
- | - combined system | + | - combined system |
- | - combined system bound in the second mode (file '' | + | |
<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. This has been covered in a | + | 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. |
- | [[geometry_optimization|previous exercise]]. | + | |
</ | </ | ||
===== Questions ===== | ===== Questions ===== | ||
- | * Sketch briefly the two binding modes. | + | * Sketch briefly the geometry of the molecule **when adsorbed** and **in the gas phase**. |
- | * Report the system energy for the two binding modes, lone slab, and lone acid molecule. | + | * Report the system energy for the bonded system, lone slab, and lone molecule. |
- | * Which binding mode is more stable? | + | * Can you estimate the contribution due to the geometry relaxation? |
* Briefly report the bond induced density difference on the system. | * Briefly report the bond induced density difference on the system. | ||
Line 84: | Line 78: | ||
<note warning> | <note warning> | ||
- | The provided | + | The provided files are all in the directory |
</ | </ | ||
- | <code - mode1.inp> | + | <code - S_M.inp> |
- | & | + | |
- | ! change name for each different run performed | + | |
- | PROJECT mode1 | + | |
- | RUN_TYPE ENERGY | + | |
- | &END GLOBAL | + | |
& | & | ||
METHOD Quickstep | METHOD Quickstep | ||
&DFT | &DFT | ||
- | + | ||
- | + | &E_DENSITY_CUBE | |
- | | + | &END E_DENSITY_CUBE |
- | | + | &END |
+ | | ||
+ | POTENTIAL_FILE_NAME ./GR | ||
+ | &QS | ||
+ | EPS_DEFAULT 1.0E-10 | ||
+ | METHOD GPW | ||
+ | EXTRAPOLATION ASPC | ||
+ | EXTRAPOLATION_ORDER 3 | ||
+ | | ||
+ | & | ||
+ | CUTOFF 400 | ||
+ | NGRIDS 5 | ||
&END | &END | ||
- | + | | |
- | BASIS_SET_FILE_NAME BASIS_SETS | + | MAX_SCF |
- | ! This keyword refers the input to an external basis file, which has to be in the same directory as this input file | + | SCF_GUESS RESTART |
- | POTENTIAL_FILE_NAME POTENTIALS | + | EPS_SCF 1.0E-5 |
- | ! This keyword refers the input to an external potential file, which has to be in the same directory as this input file | + | |
- | + | ||
- | | + | |
- | MAX_SCF | + | |
&OT | &OT | ||
- | PRECONDITIONER FULL_SINGLE_INVERSE | + | PRECONDITIONER |
- | & | + | MINIMIZER |
+ | &END | ||
& | & | ||
- | MAX_SCF | + | MAX_SCF |
+ | EPS_SCF 1.0E-5 | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | &EACH | ||
+ | GEO_OPT 2 | ||
+ | &END | ||
+ | ADD_LAST NUMERIC | ||
+ | FILENAME RESTART | ||
+ | &END | ||
+ | & | ||
+ | &END | ||
&END | &END | ||
&END SCF | &END SCF | ||
- | |||
&XC | &XC | ||
& | & | ||
&END XC_FUNCTIONAL | &END XC_FUNCTIONAL | ||
&END XC | &END XC | ||
- | |||
- | |||
&END DFT | &END DFT | ||
- | | ||
&SUBSYS | &SUBSYS | ||
&CELL | &CELL | ||
- | ABC 10.2270 11.3460 20.000 | + | A [angstrom] 14.08557 0 0 |
+ | B [angstrom] 0 12.1985 0 | ||
+ | C [angstrom] 0.000000 | ||
&END CELL | &END CELL | ||
- | &COORD | + | &TOPOLOGY |
- | + | COORD_FILE_NAME | |
- | ! Here you either manually insert the coordinates of the system (as usual) OR use the @INCLUDE statement like this: | + | COORDINATE |
- | @INCLUDE 'mode1.coord' | + | &END |
- | ! The file should be similar to an *.xyz file but without the total number of atoms at the beginning | + | & |
- | + | BASIS_SET DZVP-MOLOPT-SR-GTH-q18 | |
- | | + | POTENTIAL GTH-PBE-q18 |
- | & | + | &END KIND |
- | BASIS_SET DZVP-MOLOPT-GTH | + | &KIND Ga |
- | POTENTIAL GTH-PBE-q1 ! search in the external potential file (specified above) the one named GTH-PBE-q1 for H. | + | BASIS_SET |
+ | POTENTIAL GTH-PBE-q13 | ||
&END KIND | &END KIND | ||
&KIND C | &KIND C | ||
- | BASIS_SET | + | BASIS_SET |
POTENTIAL GTH-PBE-q4 | POTENTIAL GTH-PBE-q4 | ||
&END KIND | &END KIND | ||
- | & | + | & |
- | BASIS_SET | + | BASIS_SET |
- | POTENTIAL GTH-PBE-q6 | + | POTENTIAL GTH-PBE-q1 |
- | &END KIND | + | |
- | &KIND Ti | + | |
- | BASIS_SET DZVP-MOLOPT-SR-GTH | + | |
- | POTENTIAL GTH-PBE-q12 | + | |
&END KIND | &END KIND | ||
&END SUBSYS | &END SUBSYS | ||
&END FORCE_EVAL | &END FORCE_EVAL | ||
+ | & | ||
+ | PRINT_LEVEL LOW | ||
+ | PROJECT S_M | ||
+ | RUN_TYPE ENERGY | ||
+ | &END GLOBAL | ||
</ | </ | ||
+ | <!-- | ||
<code - POTENTIALS> | <code - POTENTIALS> | ||
################################################################################ | ################################################################################ |
exercises/2017_ethz_mmm/c2h2_pdga.1493968048.txt.gz · Last modified: 2020/08/21 10:15 (external edit)