====== GGA based surface science ======
GGA DFT calculations can be performed with CP2K relatively easily for many systems. While the CP2K {{ http://manual.cp2k.org/trunk/ | reference manual }} lists all of the various options, the initial setup of a system is easy, and few details about the internals needs to be known. The input files provide here form a good template to start.
Crucial to start are a reasonable initial structure, and for condensed phase systems the size of the simulation cell. Once these are known, copy&paste might be enough to start the simulation.
Among the important parameters of the simulations are:
* model (structure)
* Gaussian basis set
* Plane Waves (PW) cutoff
* Density functional
Assessing the influence of these parameters might be more challenging.
====== 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>Dye-sensitized_solar_cell|Dye-Sensitized Solar Cells]] as an anchoring moiety to bind light harvesting dyes to semi-conducting substrates. We will therefore use acetic acid as a model of the more complex dye molecules, as done in this paper: [[doi>10.1021/jp4117563]]. To speedup calculations, only the smallest slab model is employed.
{{ exercises:2015_ethz_mmm:dye2.png?600 |}}
===== 1. Task: Familiarize yourself with system and setup =====
* Use vmd to vizualize the geometries (provided below) named ''mode1.xyz'' and ''mode2.xyz''
* To edit the input files provided below, use an editor such as ''vi'' or ''nano''. While ''nano'' is simple to use, ''vi'' can be [[http://www.cp2k.org/tools| configured to colour-code cp2k inputs]].
* You will need files named ''BASIS_MOLOPT'' ''GTH_POTENTIALS'' ''dftd3.dat'' that are provided as part of CP2K in a directory ''cp2k/data'', unless the code has been compiled with the proper flag ('' -D__DATA_DIR'') so that these are found automatically.
* Use a job script to submit jobs on the cluster, an example job submission script might look like
#PBS -N mode1
#PBS -j oe
#PBS -q dist_small
#PBS -l nodes=4:ppn=16
#PBS -l walltime=10:00
#PBS -A cp2k2015
cd $PBS_O_WORKDIR
module purge
module load cp2k/2.6
prun cp2k.popt -i mode1.inp -o mode1.out
===== 2. Task: Binding induced density differences =====
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 ''mode1.inp''.
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.
cp2k.popt -i mode1.inp -o mode1.out
In addition to the output ''mode1.out'', other files are gerenated by CP2K named MODE1*
topics:
* General overiew
* OT output
* Various grid quantities
* Density cube output
* 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 ''mode1.xyz'')
- lone acetic acid molecule (just remove slab's coordinates from ''mode1.xyz''), name the file ''mode1_dye.xyz''
- lone TiO$_2$ slab (just remove the acid's coordinates from ''mode1.xyz''), name the file ''mode1_slab.xyz''
Create the .xyz files (check with vmd that they contain the right subsystems), and create mode1_dye.inp, mode1_slab.inp by changing both ''COORD_FILE_NAME'' and ''PROJECT'' accordingly.
After computing these input files, we analyze the results using a tool provided with cp2k ''cubecruncher.x'' that manipulates cube files (e.g. can compute difference).
~$ cubecruncher.x -i MODE1-ELECTRON_DENSITY-1_0.cube -subtract MODE1_dye-ELECTRON_DENSITY-1_0.cube -o tmp.cube
~$ cubecruncher.x -i tmp.cube -subtract MODE1_slab-ELECTRON_DENSITY-1_0.cube -center geo -o MODE1_delta.cube
You can visualize the resulting file ''MODE1_delta.cube'' with VMD.
What you get should look similar to this:
{{ exercises:2015_ethz_mmm:dye_tio_bonding_density.png?300 |}}
===== 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 (''&E_DENSITY_CUBE OFF'') in mode1.inp, change to ''RUN_TYPE GEO_OPT'' and adjust the project name. Create and run a similar input file for mode2.
input topics:
* BFGS vs LBFGS
* EPS_SCF, CUTOFF, MAX_DR, ..
output topics:
* ''Informations at step''
* Trajectory ''MODE1_GEO-pos-1.xyz''
Compare the final energies (''ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):''), and determine which mode is most stable. Does this agree with the values in table 1 of the manuscript cited ?
===== 4. Task: ab initio molecular dynamics =====
This task is optional, and can be done near the end if time is available. Ab initio MD will be briefly discussed in a next exercise.
Perform a short ab initio molecular dynamics simulation of the system (~1000 steps, ~0.5ps) by changing to ''RUN_TYPE MD''. After a couple of hours the job should be finished. Now analyze the OH distance in VMD. A possible outcome is :
{{exercises:2015_pitt:acetic_acid_mode1_md.png?600 |}}
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.
&GLOBAL
! the project name is made part of most output files... useful to keep order
PROJECT MODE1
! various runtypes (energy, geo_opt, etc.) available.
RUN_TYPE ENERGY
&END GLOBAL
&FORCE_EVAL
! the electronic structure part of CP2K is named Quickstep
METHOD Quickstep
&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, vibrational frequencies,
! NPT and cell optimizations, need higher cutoffs)
CUTOFF [Ry] 400
&END
&QS
! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme).
METHOD GPW
! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron,
! sets reasonable values for all other thresholds.
EPS_DEFAULT 1.0E-10
! used for MD, the method used to generate the initial guess.
EXTRAPOLATION ASPC
&END
&POISSON
PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and a wavelet solver
&END
&PRINT
! at the end of the SCF procedure generate cube files of the density
&E_DENSITY_CUBE ON
&END E_DENSITY_CUBE
&END
! use the OT METHOD for robust and efficient SCF, suitable for all non-metallic systems.
&SCF
SCF_GUESS ATOMIC ! can be used to RESTART an interrupted calculation
MAX_SCF 30
EPS_SCF 1.0E-6 ! accuracy of the SCF procedure typically 1.0E-6 - 1.0E-7
&OT
! an accurate preconditioner suitable also for larger systems
PRECONDITIONER FULL_SINGLE_INVERSE
! the most robust choice (DIIS might sometimes be faster, but not as stable).
MINIMIZER CG
&END OT
&OUTER_SCF ! repeat the inner SCF cycle 10 times
MAX_SCF 10
EPS_SCF 1.0E-6 ! must match the above
&END
&END SCF
! specify the exchange and correlation treatment
&XC
! use a PBE functional
&XC_FUNCTIONAL
&PBE
&END
&END XC_FUNCTIONAL
! adding Grimme's D3 correction (by default without C9 terms)
&VDW_POTENTIAL
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
PARAMETER_FILE_NAME dftd3.dat
TYPE DFTD3
REFERENCE_FUNCTIONAL PBE
R_CUTOFF [angstrom] 16
&END
&END VDW_POTENTIAL
&END XC
&END DFT
! description of the system
&SUBSYS
&CELL
! unit cells that are orthorhombic are more efficient with CP2K
ABC [angstrom] 10.2270 11.3460 20.000
&END CELL
! atom coordinates can be in the &COORD section,
! or provided as an external file.
&TOPOLOGY
COORD_FILE_NAME mode1.xyz
COORD_FILE_FORMAT XYZ
&END
! MOLOPT basis sets are fairly costly,
! but in the 'DZVP-MOLOPT-SR-GTH' available for all elements
! their contracted nature makes them suitable
! for condensed and gas phase systems alike.
&KIND H
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND C
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&KIND Ti
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q12
&END KIND
&END SUBSYS
&END FORCE_EVAL
! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section
&MOTION
&GEO_OPT
OPTIMIZER BFGS ! Good choice for 'small' systems (use LBFGS for large systems)
MAX_ITER 100
MAX_DR [bohr] 0.003 ! adjust target as needed
&BFGS
&END
&END
&MD
ENSEMBLE NVT ! sampling the canonical ensemble, accurate properties might need NVE
TEMPERATURE [K] 300
TIMESTEP [fs] 0.5
STEPS 1000
# GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md
# GLE provides an effective NVT sampling.
&THERMOSTAT
REGION MASSIVE
TYPE GLE
&GLE
NDIM 5
A_SCALE [ps^-1] 1.00
A_LIST 1.859575861256e+2 2.726385349840e-1 1.152610045461e+1 -3.641457826260e+1 2.317337581602e+2
A_LIST -2.780952471206e-1 8.595159180871e-5 7.218904801765e-1 -1.984453934386e-1 4.240925758342e-1
A_LIST -1.482580813121e+1 -7.218904801765e-1 1.359090212128e+0 5.149889628035e+0 -9.994926845099e+0
A_LIST -1.037218912688e+1 1.984453934386e-1 -5.149889628035e+0 2.666191089117e+1 1.150771549531e+1
A_LIST 2.180134636042e+2 -4.240925758342e-1 9.994926845099e+0 -1.150771549531e+1 3.095839456559e+2
&END GLE
&END THERMOSTAT
&END
&END
116
Ti -0.0179479198 -0.0078042700 -0.0922850421
O 0.4497915479 0.0007412647 1.9321232563
Ti -1.4316444492 -0.0089893346 2.8221490912
O -1.7887110897 0.0007867236 0.7998892697
O -3.2081345298 0.0411605531 3.6695321087
O -1.8010755493 -1.8874663742 2.8216777686
Ti -3.7269830403 -1.9006613639 3.6517557753
O 0.3830863054 -1.8910765741 -0.0700021876
Ti 3.7557586944 -1.8917451634 2.9143676586
O 3.3146470921 -0.0011081937 2.8729289358
O -4.6680663094 -1.8855446073 2.0338712494
O -5.4086768695 -1.8843459443 4.3991860126
Ti -0.0282285127 -3.7757033787 -0.0787156736
O 0.4462623263 -3.7813137083 1.9359917441
Ti -1.3999537875 -3.7707056149 2.8874421519
O -1.7903153040 -3.7850263943 0.8021001791
O -3.2390175951 -3.7978185279 3.6716494047
O -1.7864035184 -5.6734792481 2.8627360747
Ti -3.7357623244 -5.6788609282 3.4482649850
O 0.3837694100 -5.6723382681 -0.0690470865
Ti 3.7205660980 -5.6668034549 2.9114784222
O 3.3236114384 -3.7787921003 2.8721776992
O -4.6689995455 -5.6807480198 1.9358553242
O -5.3525041570 -5.6742752842 4.3359372112
Ti -0.0314402214 3.7828933451 -0.0777664638
O 0.4518754735 3.7839662632 1.9399715530
Ti -1.3792280628 3.7857276911 2.9025413153
O -1.7909627210 3.7866794195 0.8027290293
O -3.2026665631 3.7827561658 3.7306777258
O -1.7857471998 1.9013100770 2.8154049594
Ti -3.7307612355 1.9120465523 3.4387577457
O 0.3836352141 1.8909325251 -0.0691199251
Ti 3.7223424203 1.8887162901 2.9133081650
O 3.3250830331 3.7807500488 2.8687333178
O -4.6728325926 1.9008997868 1.9326739591
O -5.3457700344 1.8899459254 4.3344454640
Ti -1.4852085406 -0.0011927086 -3.7100466053
O -1.0850586016 -0.0008795951 -1.6147031707
Ti -2.8526945884 -0.0039467894 -0.7412906371
O -3.3269327110 -0.0004491456 -2.7420242486
O -4.7289708978 -0.0017641392 -0.0618098107
O -3.2591453480 -1.8898583454 -0.7264179834
Ti -5.1372070666 -1.8918692243 -0.0012386637
O -1.0878410276 -1.8908975100 -3.6681494905
Ti 2.2953566326 -1.8945802968 -0.7324918911
O 1.8572641703 -0.0016921856 -0.7344045642
O 4.0371444331 -1.8910414726 -1.5881377025
O 3.3210868792 -1.8907741455 0.8191885244
Ti -1.4878179598 -3.7811586802 -3.7059227721
O -1.0853532342 -3.7809408508 -1.6116052274
Ti -2.8450252555 -3.7788195849 -0.7274776599
O -3.3267379004 -3.7812381637 -2.7423527944
O -4.7300872942 -3.7790968457 -0.0598090260
O -3.2604741093 -5.6718710426 -0.7338292499
Ti -5.1447866872 -5.6729502955 -0.0741564861
O -1.0884608345 -5.6727912820 -3.6676316873
Ti 2.2684209803 -5.6717142765 -0.7217304029
O 1.8574125893 -3.7804564443 -0.7330818756
O 4.0285990372 -5.6721054737 -1.6077890803
O 3.3201243312 -5.6722897918 0.8087243331
Ti -1.4884820434 3.7822906244 -3.7073217712
O -1.0847762013 3.7818636329 -1.6113017246
Ti -2.8439453199 3.7841411650 -0.7265400935
O -3.3267270296 3.7819066970 -2.7433025606
O -4.7312054524 3.7823723470 -0.0697069103
O -3.2595288817 1.8897668415 -0.7334187674
Ti -5.1446141745 1.8933189943 -0.0754881482
O -1.0885182339 1.8906776867 -3.6679434552
Ti 2.2687722606 1.8941648243 -0.7213872473
O 1.8555780589 3.7824519637 -0.7335160805
O 4.0283551896 1.8906904137 -1.6083035670
O 3.3194888527 1.8901215845 0.8082989311
Ti 1.3702533850 -0.0107406935 3.4478828397
O -2.6375196242 -0.0002691731 -5.1384544425
Ti -4.2555253076 -0.0004346746 -4.2635860836
O -0.2706997157 -0.0070914550 4.3327078320
O 4.0252034756 -0.0000815787 -3.6655962284
O -4.7789243271 -1.8904283625 -4.5262265362
Ti 3.6276350884 -1.8913012322 -3.6941431294
O 1.8693336769 -1.8883429262 3.7243207414
Ti 0.8648978359 -1.8921733057 -4.2643698117
O 0.3356892769 -0.0005951329 -4.5283168344
O 2.4831990038 -1.8910320844 -5.1341360953
O 1.7891597814 -1.8911498456 -2.7417208102
Ti 1.3675607179 -3.7714249561 3.4584460387
O -2.6361368408 -3.7817733748 -5.1377491017
Ti -4.2537976019 -3.7816703567 -4.2621660812
O -0.2527486810 -3.7773208994 4.3296691681
O 4.0251551834 -3.7817133665 -3.6656274881
O -4.7792586102 -5.6728660382 -4.5273909859
Ti 3.6247553952 -5.6729206250 -3.7048960624
O 1.9006169442 -5.6721819263 3.7282320026
Ti 0.8602204280 -5.6728510136 -4.2616392365
O 0.3358111887 -3.7815283986 -4.5276229355
O 2.4785034911 -5.6729185089 -5.1373985723
O 1.7869078663 -5.6728807589 -2.7423620036
Ti 1.3817457800 3.7823928879 3.4589497419
O -2.6363646230 3.7820140473 -5.1385122329
Ti -4.2543090361 3.7822671573 -4.2626609244
O -0.2374835922 3.7781640807 4.3379058406
O 4.0248222240 3.7818879520 -3.6667895479
O -4.7794862202 1.8903770813 -4.5277962247
Ti 3.6243254290 1.8913422637 -3.7051707738
O 1.8974839341 1.8882474143 3.7289879155
Ti 0.8600377417 1.8920214690 -4.2620560393
O 0.3346421543 3.7821159876 -4.5275899679
O 2.4782941685 1.8909856222 -5.1376874872
O 1.7866749487 1.8910410218 -2.7427494459
H -3.2770955004 -2.4268873548 8.1687296457
C -3.1978647566 -1.3575831172 7.9359146369
H -4.2239524320 -0.9733256879 7.8414028480
H -2.6752907472 -0.8249390527 8.7355765151
C -2.5132448898 -1.1924834089 6.6141051521
O -2.8755597850 -1.8460118394 5.6163779603
O -1.5275649623 -0.3212592281 6.6009413157
H -1.0670534373 -0.2549619720 5.6840567874
116
Ti 0.0150786099 -0.0030604155 -0.2374201259
O 0.4515580466 -0.0646282100 1.8001155831
Ti -1.5073356783 -0.0021026124 2.5525864818
O -1.7759961007 -0.0002275800 0.6680111337
O -3.3291162152 -0.0023490698 3.0696212715
O -1.7197127142 -1.8809866556 2.8642842575
Ti -3.6978004404 -1.8661667177 3.6084326925
O 0.3785074831 -1.8945596770 -0.1980298452
Ti 3.7996574045 -1.9219539316 2.8301270999
O 3.3305054330 -0.0058364403 2.7942261562
O -4.6900333011 -1.9659285303 1.9448925419
O -5.3925681292 -1.8976344334 4.3248895668
Ti -0.0283064667 -3.7737024590 -0.1507446117
O 0.4475870469 -3.7803762159 1.8621586431
Ti -1.3713031978 -3.7725215345 2.8511642577
O -1.7912822225 -3.7729870345 0.7436262925
O -3.1963784791 -3.7804631987 3.6648868231
O -1.7705984874 -5.6752809020 2.8039139185
Ti -3.7092032911 -5.6725438342 3.3897938268
O 0.3841910583 -5.6739517448 -0.1381224421
Ti 3.7513121067 -5.6747221635 2.8551954028
O 3.3367138059 -3.7840186471 2.8127851513
O -4.6560725160 -5.6733549533 1.8776383238
O -5.3204369054 -5.6669271369 4.2778026483
Ti -0.0266777619 3.7696389407 -0.1491534163
O 0.4524897086 3.7857220830 1.8631418152
Ti -1.3730627656 3.7742135603 2.8371003388
O -1.7905256319 3.7786525562 0.7422177730
O -3.1948630000 3.7795989881 3.6670918260
O -1.7343662633 1.8899845272 2.8090040137
Ti -3.6974632076 1.8668219133 3.5884163764
O 0.3822543310 1.8874843004 -0.1432095900
Ti 3.7864567490 1.9054527096 2.8508016360
O 3.3675002865 3.7799021368 2.8626057027
O -4.6840457398 1.9746044749 1.9466850498
O -5.3729095331 1.8414022655 4.3320391075
Ti -1.5079668291 -0.0008456767 -3.7989215478
O -1.0951317039 0.0022938033 -1.7345576883
Ti -2.8929121223 -0.0000735048 -0.8782772455
O -3.3736661811 0.0005357865 -2.8128806833
O -4.7193863680 0.0001570116 -0.0748056115
O -3.2632860440 -1.8860154449 -0.7956216654
Ti -5.1307996411 -1.8978086035 -0.0398179095
O -1.1320787396 -1.8909803808 -3.7440163178
Ti 2.3133857413 -1.9061341614 -0.8099170994
O 1.8786839357 0.0011314062 -0.8069543100
O 4.0385009963 -1.8895616393 -1.6570045786
O 3.3115055560 -1.8920970172 0.7501369741
Ti -1.5256127358 -3.7819843403 -3.7701763163
O -1.0940683369 -3.7869847697 -1.6789541127
Ti -2.8425313294 -3.7819322313 -0.7839726892
O -3.3422315516 -3.7760564219 -2.8030699366
O -4.7315665522 -3.7831312336 -0.1321164185
O -3.2580399316 -5.6728032840 -0.7985618810
Ti -5.1462151180 -5.6726106968 -0.1400092932
O -1.1340144859 -5.6732616791 -3.7388880843
Ti 2.2670101177 -5.6749205566 -0.7762329495
O 1.8631140907 -3.7853073574 -0.7974118985
O 4.0263575475 -5.6730177766 -1.6715945206
O 3.3250517248 -5.6784227751 0.7515944134
Ti -1.5248867442 3.7818848512 -3.7712820230
O -1.0907299886 3.7812336768 -1.6778258037
Ti -2.8428177895 3.7841675976 -0.7861032158
O -3.3397902383 3.7762483047 -2.8026235400
O -4.7304156316 3.7842200412 -0.1318958639
O -3.2645051173 1.8869138058 -0.7933488063
Ti -5.1241443302 1.8993249071 -0.0252297449
O -1.1314283131 1.8906347021 -3.7440419862
Ti 2.3185671036 1.9017475834 -0.7833845676
O 1.8597419566 3.7800089897 -0.7974665372
O 4.0344536794 1.8895028649 -1.6315658326
O 3.3098310076 1.8936248995 0.7823280807
Ti 1.4537853090 -0.0347286638 3.2604875735
O -2.6845024000 0.0000746592 -5.2147510734
Ti -4.2967571219 0.0018586454 -4.3442818967
O -0.2511143909 0.1328085915 4.2720687411
O 3.9819696258 0.0012627538 -3.7355131655
O -4.8038476957 -1.8889916108 -4.5923792314
Ti 3.5953547314 -1.8907810205 -3.7642624098
O 1.8553660493 -1.8815919187 3.6062633048
Ti 0.8351449362 -1.8959349617 -4.3196742869
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O 2.4377532123 -1.8915585194 -5.2027330310
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