exercises:2015_pitt:gga
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====== GGA based surface science ====== | ====== GGA based surface science ====== | ||
- | GGA DFT calculations can be performed with CP2K relatively easily for many systems. While the CP2K {{ http:// | + | GGA DFT calculations can be performed with CP2K relatively easily for many systems. While the CP2K {{ http:// |
Crucial to start are a reasonable initial structure, and for condensed phase systems the size of the simulation cell. Once these are known, copy& | Crucial to start are a reasonable initial structure, and for condensed phase systems the size of the simulation cell. Once these are known, copy& | ||
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====== Dye anchoring to TiO$_2$ ====== | ====== Dye anchoring to TiO$_2$ ====== | ||
- | In this exercise you will compare two possible binding modes of acetic acid to anatase TiO$_2$. Acetic acid contains the carboxylic group. It is commonly used in [[wp> | + | In this exercise you will compare two possible binding modes of acetic acid to anatase TiO$_2$. Acetic acid contains the carboxylic group. It is commonly used in [[wp> |
{{ exercises: | {{ exercises: | ||
- | ===== 1. Task: Familiarize yourself | + | ===== 1. Task: Familiarize yourself |
- | The coordinate of the two binding modes are provided you as '' | + | |
- | ===== 2. Task: Bond induced density differences ===== | + | * Use vmd to vizualize |
- | Compute the density difference induced by the bonding for the first binding mode. | + | |
- | For this you will have to run three separate energy calculations: | + | |
- | - combined system bound in the first mode (file '' | + | * Use a job script to submit jobs on the cluster, an example job submission script might look like |
- | | + | |
- | | + | |
- | In order to output the electronic densities as cube files, your input file has to contain the following snipped: | + | < |
- | < | + | #PBS -N mode1 |
- | &DFT | + | #PBS -j oe |
- | & | + | #PBS -q dist_small |
- | & | + | #PBS -l nodes=4: |
- | & | + | #PBS -l walltime=10: |
- | & | + | #PBS -A cp2k2015 |
- | &END DFT | + | |
- | </ | + | |
- | <note tip> | + | cd $PBS_O_WORKDIR |
- | The calculations involving the large TiO$_2$ slab should be run on 16 nodes with '' | + | |
- | </ | + | |
- | To process the cube files we are going to use the cubecruncher tool. It is part of CP2K, but not installed on brutus. | + | module purge |
- | Therefore, a compiled binary of the tool is provided at ''/ | + | module |
- | < | + | |
- | you@brutusX ~$ ln -s / | + | prun cp2k.popt |
</ | </ | ||
- | Now subtract | + | ===== 2. Task: Binding induced density differences ===== |
+ | |||
+ | We start with single point energy calculations on binding mode 1, to visualize | ||
+ | |||
+ | \[ \rho_\text{induced}= \rho_\text{slab-dye-complex} - \rho_\text{dye} - \rho_\text{slab} \] | ||
+ | |||
+ | First, we'll discuss in detail | ||
+ | |||
+ | topics: | ||
+ | * Project name | ||
+ | * Runtype | ||
+ | * Gaussian Basis, pseudopotentials | ||
+ | * PW Cutoff | ||
+ | * thresholds | ||
+ | * SCF: OT | ||
+ | * XC and -D3 correction | ||
+ | * Unit cell choice | ||
+ | |||
+ | Second, we run the cp2k input and store the output for analysis and discussion. | ||
< | < | ||
- | you@brutusX ~$ ./ | + | cp2k.popt -i mode1.inp -o mode1.out |
- | you@brutusX ~$ ./ | + | |
</ | </ | ||
+ | In addition to the output '' | ||
- | The generated | + | topics: |
+ | * General overiew | ||
+ | * OT output | ||
+ | * Various grid quantities | ||
+ | * Density | ||
+ | * Timing report | ||
+ | |||
+ | Third, we compute the changes in density induced by the binding. For this you will have to run three separate energy calculations: | ||
+ | - combined system bound in the first mode (file '' | ||
+ | - lone acetic acid molecule (just remove slab's coordinates from '' | ||
+ | - lone TiO$_2$ slab (just remove the acid's coordinates from '' | ||
+ | |||
+ | Create the .xyz files (check | ||
+ | |||
+ | After computing these input files, we analyze the results using a tool provided with cp2k '' | ||
< | < | ||
- | you@brutusX | + | ~$ cubecruncher.x -i MODE1-ELECTRON_DENSITY-1_0.cube -subtract MODE1_dye-ELECTRON_DENSITY-1_0.cube -o tmp.cube |
+ | ~$ cubecruncher.x | ||
</ | </ | ||
- | 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: | ||
- | {{ dye_tio_bonding_density.png? | + | {{ exercises: |
- | ===== 3. Task: Bonding energies | + | ===== 3. Task: relative stabilities |
- | Compute the binding energy for both binding modes: | + | |
- | \[ E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants} \] | + | In order to compute the relative stability of mode1 and mode2, both configurations need to be geometry optimized. |
- | For this you will need the energy values | + | To do so, turn off the generation |
- | - lone acetic acid molecule | + | |
- | - lone TiO$_2$ slab (you can use the already geometry optimized coordinates from '' | + | |
- | - combined system bound in the first mode (can be reused from previous task) | + | |
- | - combined system bound in the second mode (file '' | + | |
- | <note important> | + | input topics: |
- | 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 | + | * BFGS vs LBFGS |
- | [[geometry_optimization|previous exercise]]. | + | * EPS_SCF, CUTOFF, MAX_DR, .. |
- | </ | + | |
+ | output topics: | ||
+ | * '' | ||
+ | * Trajectory '' | ||
- | ===== Questions | + | Compare the final energies ('' |
- | * Sketch briefly the two binding modes. | + | ===== 4. Task: ab initio molecular dynamics |
- | * Report the system energy for the two binding modes, lone slab, and lone acid molecule. | + | |
- | * Which binding mode is more stable? | + | |
- | * Briefly report the bond induced density difference on the system. | + | |
- | ===== Required Files ===== | + | < |
- | < | + | |
- | <note warning> | + | Perform a short ab initio molecular dynamics simulation of the system (~1000 steps, ~0.5ps) by changing |
- | The provided [[wp> | + | |
- | </ | + | |
+ | {{exercises: | ||
+ | |||
+ | What can you say about the hydrogen bond to the surface, relative acidity of the two oxygens ? | ||
+ | Note that, in order to be statistically relevant, longer trajectories should be employed, and surface slab thickness will play an important role. Also compare to Fig. 7 of the paper referenced. | ||
+ | ====== Required Files ====== | ||
+ | |||
+ | (right) click on the filename to download to your local machine. | ||
<code - mode1.inp> | <code - mode1.inp> | ||
&GLOBAL | &GLOBAL | ||
- | ! change | + | ! the project |
- | PROJECT | + | PROJECT |
+ | ! various runtypes (energy, geo_opt, etc.) available. | ||
RUN_TYPE ENERGY | RUN_TYPE ENERGY | ||
&END GLOBAL | &END GLOBAL | ||
& | & | ||
+ | ! the electronic structure part of CP2K is named Quickstep | ||
METHOD Quickstep | METHOD Quickstep | ||
&DFT | &DFT | ||
+ | ! basis sets and pseudopotential files can be found in cp2k/data | ||
+ | BASIS_SET_FILE_NAME BASIS_MOLOPT | ||
+ | POTENTIAL_FILE_NAME GTH_POTENTIALS | ||
+ | |||
+ | ! Charge and multiplicity | ||
+ | CHARGE 0 | ||
+ | MULTIPLICITY 1 | ||
+ | |||
+ | &MGRID | ||
+ | ! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect. | ||
+ | ! certain calculations (e.g. geometry optimization, | ||
+ | ! NPT and cell optimizations, | ||
+ | | ||
+ | &END | ||
+ | |||
+ | &QS | ||
+ | ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme). | ||
+ | | ||
+ | ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron, | ||
+ | ! sets reasonable values for all other thresholds. | ||
+ | | ||
+ | ! used for MD, the method used to generate the initial guess. | ||
+ | | ||
+ | &END | ||
+ | |||
+ | & | ||
+ | | ||
+ | &END | ||
- | & | + | |
+ | & | ||
& | & | ||
&END | &END | ||
- | | + | ! use the OT METHOD for robust and efficient SCF, suitable for all non-metallic systems. |
- | | + | |
- | | + | |
- | ! This keyword refers the input to an external potential file, which has to be in the same directory as this input file | + | |
- | + | | |
- | & | + | |
- | MAX_SCF 50 | + | |
&OT | &OT | ||
+ | ! an accurate preconditioner suitable also for larger systems | ||
PRECONDITIONER FULL_SINGLE_INVERSE | PRECONDITIONER FULL_SINGLE_INVERSE | ||
+ | ! the most robust choice (DIIS might sometimes be faster, but not as stable). | ||
+ | MINIMIZER CG | ||
&END OT | &END OT | ||
- | & | + | & |
MAX_SCF 10 | MAX_SCF 10 | ||
+ | EPS_SCF 1.0E-6 ! must match the above | ||
&END | &END | ||
&END SCF | &END SCF | ||
+ | ! specify the exchange and correlation treatment | ||
&XC | &XC | ||
- | & | + | |
+ | | ||
+ | &PBE | ||
+ | & | ||
&END XC_FUNCTIONAL | &END XC_FUNCTIONAL | ||
+ | ! adding Grimme' | ||
+ | & | ||
+ | | ||
+ | & | ||
+ | PARAMETER_FILE_NAME dftd3.dat | ||
+ | TYPE DFTD3 | ||
+ | REFERENCE_FUNCTIONAL PBE | ||
+ | R_CUTOFF [angstrom] 16 | ||
+ | & | ||
+ | &END VDW_POTENTIAL | ||
&END XC | &END XC | ||
- | |||
- | |||
&END DFT | &END DFT | ||
- | | + | |
+ | ! description of the system | ||
&SUBSYS | &SUBSYS | ||
- | &CELL | + | & |
- | ABC 10.2270 11.3460 20.000 | + | ! unit cells that are orthorhombic are more efficient with CP2K |
+ | ABC [angstrom] | ||
&END CELL | &END CELL | ||
- | &COORD | + | |
- | | + | ! atom coordinates |
- | ! Here you either manually insert the coordinates | + | ! or provided as an external file. |
- | @INCLUDE ' | + | & |
- | ! The file should be similar to an *.xyz file but without the total number of atoms at the beginning | + | COORD_FILE_NAME mode1.xyz |
- | + | | |
- | | + | &END |
- | | + | |
- | BASIS_SET | + | ! MOLOPT |
- | POTENTIAL GTH-PBE-q1 | + | ! but in the 'DZVP-MOLOPT-SR-GTH' available for all elements |
+ | | ||
+ | ! for condensed and gas phase systems alike. | ||
+ | &KIND H | ||
+ | BASIS_SET | ||
+ | POTENTIAL GTH-PBE-q1 | ||
&END KIND | &END KIND | ||
&KIND C | &KIND C | ||
- | BASIS_SET DZVP-MOLOPT-GTH | + | BASIS_SET DZVP-MOLOPT-SR-GTH |
POTENTIAL GTH-PBE-q4 | POTENTIAL GTH-PBE-q4 | ||
&END KIND | &END KIND | ||
&KIND O | &KIND O | ||
- | BASIS_SET DZVP-MOLOPT-GTH | + | BASIS_SET DZVP-MOLOPT-SR-GTH |
POTENTIAL GTH-PBE-q6 | POTENTIAL GTH-PBE-q6 | ||
&END KIND | &END KIND | ||
Line 167: | Line 244: | ||
&END FORCE_EVAL | &END FORCE_EVAL | ||
+ | ! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section | ||
+ | &MOTION | ||
+ | & | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | | ||
+ | | ||
+ | STEPS 1000 | ||
+ | # GLE thermostat as generated at http:// | ||
+ | # GLE provides an effective NVT sampling. | ||
+ | & | ||
+ | | ||
+ | TYPE GLE | ||
+ | & | ||
+ | NDIM 5 | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | &END | ||
</ | </ | ||
- | |||
- | <code - POTENTIALS> | ||
- | ################################################################################ | ||
- | # | ||
- | # Potential data base file for CP2K (Quickstep) | ||
- | # | ||
- | ################################################################################ | ||
- | # ----------------------------------------------------- | ||
- | # | ||
- | # Literature: - S. Goedecker, M. Teter, and J. Hutter, | ||
- | # Phys. Rev. B 54, 1703 (1996) | ||
- | # - C. Hartwigsen, S. Goedecker, and J. Hutter, | ||
- | # Phys. Rev. B 58, 3641 (1998) | ||
- | # - M. Krack, | ||
- | # | ||
- | # | ||
- | # Potential for the PBE functional | ||
- | # | ||
- | ################################################################################ | ||
- | # | ||
- | H GTH-PBE-q1 | ||
- | 1 | ||
- | | ||
- | 0 | ||
- | # | ||
- | C GTH-PBE-q4 | ||
- | 2 2 | ||
- | | ||
- | 2 | ||
- | | ||
- | | ||
- | # | ||
- | O GTH-PBE-q6 | ||
- | 2 4 | ||
- | | ||
- | 2 | ||
- | | ||
- | | ||
- | # | ||
- | Ti GTH-PBE-q12 | ||
- | 4 6 2 | ||
- | | ||
- | 3 | ||
- | | ||
- | | ||
- | | ||
- | -10.49616087 | ||
- | | ||
- | |||
- | </ | ||
- | |||
- | <code - BASIS_SETS> | ||
- | ######################################################################### | ||
- | # | ||
- | # This is a library of molecularly optimised basis functions as described in the paper: | ||
- | # | ||
- | # Gaussian basis sets for accurate calculations on molecular systems | ||
- | # in gas and condensed phases | ||
- | # | ||
- | # Joost VandeVondele and Juerg Hutter | ||
- | # J. Chem. Phys. 127, 114105 (2007) | ||
- | # | ||
- | # URL: http:// | ||
- | # DOI: 10.1063/ | ||
- | # | ||
- | ########################################### | ||
- | | ||
- | 1 | ||
- | 2 0 1 7 2 1 | ||
- | | ||
- | 3.700758562763 | ||
- | 1.446884268432 | ||
- | 0.716814589696 | ||
- | 0.247918564176 | ||
- | 0.066918004004 | ||
- | 0.021708243634 -0.001125195500 -0.059693171300 | ||
- | | ||
- | 1 | ||
- | 2 0 2 7 2 2 1 | ||
- | 6.132624767898 -0.105576563700 | ||
- | 2.625196064782 -0.174866621100 | ||
- | 1.045456957247 | ||
- | 0.478316330874 | ||
- | 0.178617414302 | ||
- | 0.075144725465 | ||
- | 0.030286753006 | ||
- | | ||
- | 1 | ||
- | 2 0 2 7 2 2 1 | ||
- | | ||
- | 5.108150287385 -0.129597923300 | ||
- | 2.048398039874 | ||
- | 0.832381575582 | ||
- | 0.352316246455 | ||
- | 0.142977330880 | ||
- | | ||
- | Ti DZVP-MOLOPT-SR-GTH DZVP-MOLOPT-SR-GTH-q12 | ||
- | 1 | ||
- | 2 0 3 6 3 2 2 1 | ||
- | 7.884569925997 | ||
- | 3.894698463070 | ||
- | 1.513588828959 -0.664995883766 -0.256641947580 | ||
- | 0.596768079836 -0.726044574739 -0.451591547817 | ||
- | 0.222222125842 -0.029011079755 | ||
- | 0.077078461321 | ||
- | |||
- | </ | ||
<code - mode1.xyz> | <code - mode1.xyz> | ||
Line 395: | Line 396: | ||
O -1.5275649623 | O -1.5275649623 | ||
H -1.0670534373 | H -1.0670534373 | ||
- | |||
</ | </ | ||
Line 517: | Line 517: | ||
O -2.9500441444 | O -2.9500441444 | ||
H -0.3897742635 | H -0.3897742635 | ||
- | </ | ||
- | |||
- | <code - relaxed_slab.xyz> | ||
- | 108 | ||
- | |||
- | Ti | ||
- | O | ||
- | Ti | ||
- | O -1.7917634261 | ||
- | O -3.2061730694 | ||
- | O -1.7223354624 | ||
- | Ti | ||
- | O | ||
- | Ti 3.7576915752 | ||
- | O | ||
- | O -4.6411313870 | ||
- | O -5.3047652050 | ||
- | Ti | ||
- | O | ||
- | Ti | ||
- | O -1.7918422000 | ||
- | O -3.2061826485 | ||
- | O -1.7223161680 | ||
- | Ti | ||
- | O | ||
- | Ti 3.7576114879 | ||
- | O | ||
- | O -4.6411391763 | ||
- | O -5.3047626840 | ||
- | Ti | ||
- | O | ||
- | Ti | ||
- | O -1.7918406363 | ||
- | O -3.2061760961 | ||
- | O -1.7223390903 | ||
- | Ti | ||
- | O | ||
- | Ti 3.7576703685 | ||
- | O | ||
- | O -4.6411291967 | ||
- | O -5.3047626859 | ||
- | Ti | ||
- | O -1.0530794682 | ||
- | Ti | ||
- | O -3.3233955054 | ||
- | O -4.7234020378 | ||
- | O -3.2337827875 | ||
- | Ti | ||
- | O -1.1292018546 | ||
- | Ti 2.2748016978 | ||
- | O | ||
- | O | ||
- | O | ||
- | Ti | ||
- | O -1.0531792321 | ||
- | Ti | ||
- | O -3.3234176494 | ||
- | O -4.7234014156 | ||
- | O -3.2338808261 | ||
- | Ti | ||
- | O -1.1292133652 | ||
- | Ti 2.2753347025 | ||
- | O | ||
- | O | ||
- | O | ||
- | Ti | ||
- | O -1.0531788180 | ||
- | Ti | ||
- | O -3.3234140545 | ||
- | O -4.7234083483 | ||
- | O -3.2338028141 | ||
- | Ti | ||
- | O -1.1292026624 | ||
- | Ti 2.2752985947 | ||
- | O | ||
- | O | ||
- | O | ||
- | Ti 1.4062179326 | ||
- | O -2.6647908793 | ||
- | Ti | ||
- | O -0.1912654580 | ||
- | O | ||
- | O -4.8135555127 | ||
- | Ti 3.5973231742 | ||
- | O | ||
- | Ti 0.8351562937 | ||
- | O | ||
- | O | ||
- | O | ||
- | Ti 1.4062978231 | ||
- | O -2.6648159269 | ||
- | Ti | ||
- | O -0.1912655926 | ||
- | O | ||
- | O -4.8135568089 | ||
- | Ti 3.5973007930 | ||
- | O | ||
- | Ti 0.8351415277 | ||
- | O | ||
- | O | ||
- | O | ||
- | Ti 1.4062636238 | ||
- | O -2.6648052713 | ||
- | Ti | ||
- | O -0.1912672794 | ||
- | O | ||
- | O -4.8135603835 | ||
- | Ti 3.5972989622 | ||
- | O | ||
- | Ti 0.8351502243 | ||
- | O | ||
- | O | ||
- | O | ||
</ | </ |
exercises/2015_pitt/gga.1424880963.txt.gz · Last modified: 2020/08/21 10:14 (external edit)