User Tools

Site Tools


exercises:2018_ethz_mmm:adsorption_2018

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision
Previous revision
exercises:2018_ethz_mmm:adsorption_2018 [2018/04/13 08:15] dpasseroneexercises:2018_ethz_mmm:adsorption_2018 [2020/08/21 10:15] (current) – external edit 127.0.0.1
Line 1: Line 1:
 ====== Adsorption of acetylene on an intermetallic surface ====== ====== Adsorption of acetylene on an intermetallic surface ======
-<!-- 
-The reaction is the following: 
-{{ :exercises:2017_ethz_mmm:screen_shot_2017-04-27_at_18.43.25.png?nolink&600 |}} 
-and this is the pictorial view in the gas phase: 
-{{ :exercises:2017_ethz_mmm:screen_shot_2017-04-27_at_18.50.10.png?nolink&600 |}} 
  
-In the supplementary material of the paper, which can be found [[http://www.rsc.org/suppdata/c6/ra/c6ra08509a/c6ra08509a1.pdf|here]], several calculation with different methods ranging from DFT to hybrid methods to high-level methods are described, together with the basis set dependence of the results.  +<note important>FILES CAN BE FOUND HERE: [[https://polybox.ethz.ch/index.php/s/QEjNuXEa4nHgrCV|tar file]]</note>
  
 +In this exercise you will compute the adsorption energy of acetylene on a intermetallic catalyst. 
 +This process is important during the production of polyethylene, and the system is described in this paper: [[doi>10.1021/ja505936b]].
  
-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 total adsorption energy. 
 +</note> 
  
-The input file structure is shown below: 
  
-<code cp2k> + {{ :exercises:2017_ethz_mmm:master.img-002.jpg?nolink&600 |}}
-&FORCE_EVAL                           ! This section defines method for calculating energy and forces+
  
-   METHOD Quickstep                   ! Electronic structure method (DFT,...) 
-   &DFT 
-      BASIS_SET_FILE_NAME ./BASIS_C_H_O  
-      &POISSON                        ! Solver requested for non periodic calculations 
-         PERIODIC NONE 
-         PSOLVER  WAVELET             ! Type of solver 
-      &END POISSON 
-      &QS                             ! Parameters needed to set up the Quickstep framework 
-         METHOD GAPW                  ! Method: gaussian and augmented plane waves  
-      &END QS 
-    
-# 
-# Include the exchange and correlation information 
-# 
-@INCLUDE './hf.inc' 
  
-   &END DFT+===== 1. Task: Familiarize yourself  ===== 
 +The coordinates of the optimized configuration are provided to you as ''S_M.opt.xyz'' (S stands for "Substrate", M for "Molecule", opt for "optimized"). Visualize the geometry with VMD and familiarize yourself with the system.
  
 +===== 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, using the *.ene.inp files. 
 +  - combined system  (file ''S_M.opt.xyz'')
 +  - lone acetylene (file ''M.S_M.xyz'')
 +  - lone slab (file ''S.S_M.xyz'')
  
-   &SUBSYS                            ! This section defines the system +In order to output the electronic densities as cube files, your input file has to contain the following snipped: 
-      &CELL                           ! Unit cell set up +<code> 
-         PERIODIC NONE                ! Non periodic calculation +&DFT 
-         ABC 10 10 10                 ! Lengths of the cell vectors A, B, and C +  &PRINT 
-      &END CELL +    &E_DENSITY_CUBE 
-      &COORD                          ! This section specify all the atoms and their coordinates +    &END E_DENSITY_CUBE 
-  H         2.5558925119        3.0          4.  +  &END 
-  O         4.00                3.5          4. +&END DFT 
-  H         5.4167134504        3.0669045998 4. +</code>
-      &END COORD +
-      &TOPOLOGY +
-          &CENTER_COORDINATES +
-          &END +
-      &END TOPOLOGY+
  
-      +<note tip> 
-      &KIND O                                      ! potential and basis for O  +The calculations involving the slab should be run with a reduced model with the serial cp2k ''cp2k.ssmp -i file.inp > file.out''. </note>
-         BASIS_SET _MYBASIS_ +
-         POTENTIAL ALL +
-         &POTENTIAL +
-        4    0 +
-     0.24762086    0 +
-         &END  +
-      &END KIND +
-      &KIND H                                      ! potential and basis for H  +
-         BASIS_SET _MYBASIS_ +
-         POTENTIAL ALL +
-         &POTENTIAL +
-          1    0    0 +
-          0.20000000    0 +
-         &END  +
-      &END KIND +
-      &KIND C                         ! potential and basis for C +
-         BASIS_SET _MYBASIS_ +
-         POTENTIAL ALL +
-         &POTENTIAL +
-            4    2    0 +
-            0.34883045    0 +
-         &END +
-      &END KIND +
-   &END SUBSYS +
-&END FORCE_EVAL                     ! This section defines method for calculating energy and forces+
  
-&GLOBAL                             ! Section with general information regarding which kind of simulation to perform an parameters for the whole PROGRAM +To process the cube files we are going to use the [[tools:cubecruncher | cubecruncher]] toolIt is part of CP2K and is in your exercise directory. 
-   PRINT_LEVEL LOW                  ! Global print level +<code> 
-   PROJECT h2o                      ! Name of the projectThis word will appear as part of a name of all ouput files (except main ouput file, specified with -o option) +(aiida) max@qmobile:~/exercise_6$ ./cubecruncher.x -i S_M-ELECTRON_DENSITY-1_0.cube -subtract S.S_M-ELECTRON_DENSITY-1_0.cube -o tmp.cube 
-   RUN_TYPE GEO_OPT                 ! Geometry optimization +(aiida) max@qmobile:~/exercise_6$ ./cubecruncher.x -i tmp.cube -subtract M.S_M-ELECTRON_DENSITY-1_0.cube -o Delta_ads.cube
-&END GLOBAL +
-                                                                                  +
 </code> </code>
  
-The exercise is executed on the virtual machine cluster. After creating a directory as usual, you can download the file from here: 
-[[https://polybox.ethz.ch/index.php/s/wtxgaO9IEPM7FXs|(tar file)]] 
  
-Copy the file to the created directory in the ''EXERCISES'' path, and execute+The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool:
 <code> <code>
-tar xvf exercise_5.tar+(aiida) max@qmobile:~/exercise_6$ ./cubecruncher.x -center geo -i Delta_ads.cube -o Delta_ads-centered.cube
 </code> </code>
-<note tip> 
-In the directory you will find the following files: 
-  * ''h2o_template.inp'' for the geometry optimization of water 
-  * ''ethanol_template.inp'' for the geometry optimization of ethanol 
-  * ''ethylene_template.inp'' for the geometry optimization of ethylene (ethene) 
-  * ''hf.inc'' file describing the level of theory (exchange and/or correlation functional), in this case Hartree Fock 
-  * ''BASIS_H_C_O'' a repository file for basis sets. 
-</note> 
  
-First you have to modify the input files in order to prescribe certain basis setYou have, from the simplest to the most advanced:+You can visualize the resulting file ''delta_ads-centered.cube'' with VMD. This has been covered in a [[https://www.cp2k.org/exercises:2017_ethz_mmm:reaction_energy_2017|previous exercise]].
  
-  3-21G* +<!-- What you get should look similar to this:  
-  - 6-31G* +{{ dye_tio_bonding_density.png?300 |}} 
-  - 6-31Gxx +  
-  6-31++Gxx +--> 
-  - 6-311Gxx +===== 3. Task: Bonding energies  ===== 
-  - 6-311++Gxx+Compute the binding energy:
  
-For example,  +\[ E_\text{binding}=\sum E_\text{products} \sum E_\text{reactants} \]
-<code> +
-m_replace _MYBASIS_ '6-31G*' < h2o_template.inp > h2o_BASIS1.inp +
-</code> +
-(note: **use the quote, because the star is a bash special character!!!**) +
-The command to launch the job is +
-<note important> cp2k.ssmp -i h2o_BASIS1.inp > h2o_BASIS1.out </note> +
-In the ''*.out'' files you can look for the final energies by the following command: +
-<note important>> grep 'ENERGY|' myoutput.out </note>.+
  
-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, use energy of last step) 
 +  - lone  slab  (you can use the already geometry optimized coordinates from ''S.opt.xyz'' at the end of the exercise) 
 +  - 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 energy [$E_h$] ^ +<note important> 
-| BASIS 1(Name)              | ....             | ....              | ....            | ....                       | ....                      | +You can not reuse the energy values for the lone sub-systems from the previous taskSince the unbound subsystems might relax into a different geometry, they have to be geometry optimized first.  
-| BASIS 2(Name)| ....             | ....              | ....            | ....                       | ....                      | +</note>
-| BASIS 3(Name)| ....             | ....              | ....            | ....                       | ....                      | +
-| BASIS 4(Name)| ....             | ....              | ....            | ....                       | ....                      | +
-| BASIS 5(Name)| ....             | ....              | ....            | ....                       | ....                      | +
-| BASIS 6(Name)| ....             | ....              | ....            | ....                       | ....                      |+
  
  
-<note important>The binding energy is only significant if all terms were calculated with the same basis-set.</note> +===== 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 tipWhen 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, the basis-sets, and the pseudo-potentials. All these files should reside in the same directory as the main input file.</note> 
 <note warning> <note warning>
-Assignments: +The provided files are all in the directory of the exercisesChange the name of the xyz file accordingly in the input files.
-  - Compute the reaction energy for the dehydration reaction of ethanol +
-  - Prepare a table with rows and columns: on the rows the basis set, on the columns different quantities (see above). +
-  - Compare the results with the published ones (note the conversion factorsYou can use the tool at [[http://www.colby.edu/chemistry/PChem/Hartree.html|Energy converter]] +
-  - Comment on the dependence on the basis set  +
-  - Is this information enough to determine the rates of reaction? Why?+
 </note> </note>
  
  
-=== BONUS TRACK ===+<code - S_M.ene.inp>
  
-<note tip>We may be interested in the visualisation of the electronic density. Copy the ''ethanol_BASIS1.inp'' into ''ethanol_dens_BASIS1.inp''.</note> +&FORCE_EVAL 
- +  METHOD Quickstep 
-Add the following sections: +  &DFT 
-**under &DFT** +  &PRINT 
-<code cp2k> +    &E_DENSITY_CUBE 
-       &PRINT  +    &END E_DENSITY_CUBE 
-          &E_DENSITY_CUBE +  &END 
-          &END +    BASIS_SET_FILE_NAME ./BR 
-       &END       +    POTENTIAL_FILE_NAME ./GR 
-       &SCF +    &QS 
-          SCF_GUESS RESTART +      EPS_DEFAULT 1.0E-10 
-       &END +      METHOD GPW 
-</code> +      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: +    &MGRID 
-<code cp2k> +      CUTOFF 400 
-&EXT_RESTART +      NGRIDS 5 
-     RESTART_FILE_NAME ./c2h6o-1.restart+    &END 
 +    &SCF 
 +      MAX_SCF 20 
 +      SCF_GUESS RESTART 
 +      EPS_SCF 1.0E-5 
 +      &OT 
 +        PRECONDITIONER  FULL_SINGLE_INVERSE 
 +        MINIMIZER  CG 
 +      &END 
 +      &OUTER_SCF 
 +        MAX_SCF 50 
 +        EPS_SCF 1.0E-5 
 +      &END 
 +      &PRINT 
 +      &END 
 +    &END SCF 
 +    &XC 
 +      &XC_FUNCTIONAL PBE 
 +      &END XC_FUNCTIONAL 
 +    &END XC 
 +    &POISSON 
 +       PERIODIC XY 
 +       POISSON_SOLVER ANALYTIC 
 +    &END 
 +  &END DFT 
 +  &SUBSYS 
 +    &CELL 
 +A [angstrom] 7.042785 0 0 
 +B [angstrom] 0  6.09925  0. 
 +C [angstrom] 0.000000   0.   15. 
 +       PERIODIC XY 
 +    &END CELL 
 +    &TOPOLOGY 
 +     COORD_FILE_NAME ./S_M.opt.xyz 
 +     COORDINATE xyz 
 +    &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 
 +&GLOBAL 
 +  PRINT_LEVEL LOW 
 +  PROJECT S_M 
 +  RUN_TYPE ENERGY 
 +  WALLTIME 860000 
 +&END GLOBAL
 &END &END
-</code> 
  
-Then, change ''RUN_TYPE GEO_OPT'' to ''RUN_TYPE ENERGY'' to only run a single point calculation. It will generate a cubefile with the density which you may visualize with VMD.+</code> 
  
--->+<
exercises/2018_ethz_mmm/adsorption_2018.1523607304.txt.gz · Last modified: 2020/08/21 10:15 (external edit)