exercises:2017_ethz_mmm:c2h2_pdga
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exercises:2017_ethz_mmm:c2h2_pdga [2017/05/05 07:14] – dpasserone | exercises:2017_ethz_mmm:c2h2_pdga [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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{{ : | {{ : | ||
- | <!-- | + | |
===== 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: | ||
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<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 ~$ ./ | + | |
</ | </ | ||
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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: | ||
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===== 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. | ||
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<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.1493968442.txt.gz · Last modified: 2020/08/21 10:15 (external edit)