exercises:2015_pitt:gga
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exercises:2015_pitt:gga [2015/02/26 12:56] – vondele | exercises:2015_pitt:gga [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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* Use vmd to vizualize the geometries (provided below) named '' | * Use vmd to vizualize the geometries (provided below) named '' | ||
* To edit the input files provided below, use an editor such as '' | * To edit the input files provided below, use an editor such as '' | ||
- | * You will need files named '' | + | * You will need files named '' |
- | * Use a job script to submit jobs on the cluster, an example job submission script might look like (TODO: adjust for environment) | + | * Use a job script to submit jobs on the cluster, an example job submission script might look like |
<code - job> | <code - job> | ||
- | #!/ | + | #PBS -N mode1 |
- | #SBATCH | + | #PBS -j oe |
- | #SBATCH --nodes=6 | + | #PBS -q dist_small |
- | #SBATCH | + | #PBS -l nodes=4:ppn=16 |
- | #SBATCH | + | #PBS -l walltime=10:00 |
- | aprun -n 144 -N 24 -d 1 ../ | + | #PBS -A cp2k2015 |
- | </ | + | |
+ | cd $PBS_O_WORKDIR | ||
- | ===== 2. Task: Bond induced density differences ===== | + | module purge |
- | Compute the density difference induced by the bonding for the first binding mode. | + | module load cp2k/2.6 |
- | For this you will have to run three separate energy calculations: | + | |
- | - combined system bound in the first mode (file '' | + | |
- | - lone acetic acid molecule (just remove slab's coordinates from '' | + | |
- | - lone TiO$_2$ slab (just remove the acid's coordinates from '' | + | |
- | In order to output the electronic densities as cube files, your input file has to contain the following snipped: | + | prun cp2k.popt -i mode1.inp -o mode1.out |
- | < | + | |
- | &DFT | + | |
- | & | + | |
- | & | + | |
- | &END E_DENSITY_CUBE | + | |
- | &END | + | |
- | &END DFT | + | |
</ | </ | ||
- | <note tip> | ||
- | 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. | + | ===== 2. Task: Binding induced density differences ===== |
- | Therefore, a compiled binary of the tool is provided at ''/ | + | |
- | < | + | |
- | you@brutusX ~$ ln -s / | + | |
- | </ | + | |
+ | We start with single point energy calculations on binding mode 1, to visualize the interaction between molecule and surface. The goal is to compute the binding induced density difference: | ||
+ | |||
+ | \[ \rho_\text{induced}= \rho_\text{slab-dye-complex} - \rho_\text{dye} - \rho_\text{slab} \] | ||
+ | |||
+ | First, we'll discuss in detail the structure and the choices made in the sample input file '' | ||
+ | |||
+ | 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. | ||
- | Now subtract the densities of the lone systems from the bonded system: | ||
< | < | ||
- | 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: relative stabilities | ||
+ | |||
+ | In order to compute the relative stability of mode1 and mode2, both configurations need to be geometry optimized. | ||
+ | |||
+ | To do so, turn off the generation of cubes (''& | ||
+ | |||
+ | input topics: | ||
+ | * BFGS vs LBFGS | ||
+ | * EPS_SCF, CUTOFF, MAX_DR, .. | ||
+ | |||
+ | output topics: | ||
+ | * '' | ||
+ | * Trajectory '' | ||
+ | |||
+ | Compare the final energies ('' | ||
+ | ===== 4. Task: ab initio molecular dynamics | ||
- | ===== 3. Task: Bonding energies | + | < |
- | Compute | + | |
- | \[ E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants} \] | + | Perform a short ab initio molecular dynamics simulation of the system (~1000 steps, ~0.5ps) by changing to '' |
- | For this you will need the energy values of four systems: | + | {{exercises:2015_pitt: |
- | - lone acetic acid molecule (run geometry optimization, | + | |
- | - 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> | + | What can you say about the hydrogen bond to the surface, relative acidity of the two oxygens ? |
- | 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 | + | 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. |
- | [[geometry_optimization|previous exercise]]. | + | ====== Required Files ====== |
- | </ | + | |
+ | (right) click on the filename to download to your local machine. | ||
- | ===== Required Files ===== | ||
<code - mode1.inp> | <code - mode1.inp> | ||
&GLOBAL | &GLOBAL | ||
Line 121: | Line 145: | ||
&MGRID | &MGRID | ||
! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect. | ! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect. | ||
- | ! certain calculations (e.g. geometry optimization, | + | ! certain calculations (e.g. geometry optimization, |
+ | | ||
| | ||
&END | &END | ||
&QS | &QS | ||
- | METHOD GPW | + | ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme). |
- | EPS_DEFAULT 1.0E-10 | + | METHOD GPW |
- | EXTRAPOLATION ASPC ! used for MD, the method used to generate the initial guess. | + | ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron, |
+ | | ||
+ | | ||
+ | ! used for MD, the method used to generate the initial guess. | ||
+ | | ||
&END | &END | ||
Line 185: | Line 214: | ||
&END CELL | &END CELL | ||
- | ! atom coordinates can be in the &COORD section, or provided as an external file. | + | ! atom coordinates can be in the &COORD section, |
+ | ! or provided as an external file. | ||
& | & | ||
COORD_FILE_NAME mode1.xyz | COORD_FILE_NAME mode1.xyz | ||
Line 191: | Line 221: | ||
&END | &END | ||
- | ! MOLOPT basis sets are fairly costly, but in the ' | + | ! MOLOPT basis sets are fairly costly, |
- | ! their contracted nature makes them suitable for condensed and gas phase systems alike. | + | ! but in the ' |
+ | ! their contracted nature makes them suitable | ||
+ | ! for condensed and gas phase systems alike. | ||
&KIND H | &KIND H | ||
BASIS_SET DZVP-MOLOPT-SR-GTH | BASIS_SET DZVP-MOLOPT-SR-GTH | ||
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| | ||
| | ||
- | | + | |
# GLE thermostat as generated at http:// | # GLE thermostat as generated at http:// | ||
# GLE provides an effective NVT sampling. | # GLE provides an effective NVT sampling. |
exercises/2015_pitt/gga.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1