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--- exercises:2015_pitt:gga [2015/02/25 16:16] – vondele
+++ exercises:2015_pitt:gga [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====== 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.
+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.
@@ Line 15: / Line 15: @@
 ====== 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]]
+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  =====
+===== 1. Task: Familiarize yourself with system and setup =====
-The coordinate of the two binding modes are provided you as ''mode1.xyz'' and ''mode2.xyz''. Visualize the two geometries with VMD and familiarize yourself with the system.
-===== 2. Task: Bond induced density differences =====
+  * Use vmd to vizualize the geometries (provided below) named ''mode1.xyz'' and ''mode2.xyz''
-Compute the density difference induced by the bonding for the first binding mode.
+  * 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]].
-For this you will have to run three separate energy calculations:
+  * 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.
-  - combined system bound in the first mode (file ''mode1.xyz'')
+  * Use a job script to submit jobs on the cluster, an example job submission script might look like
-  - lone acetic acid molecule (just remove slab's coordinates from ''mode1.xyz'')
-  - lone TiO$_2$ slab (just remove the acid's coordinates from ''mode1.xyz'')
-In order to output the electronic densities as cube files, your input file has to contain the following snipped:
+<code - job>
-<code>
+#PBS -N mode1
-&DFT
+#PBS -j oe
-  &PRINT
+#PBS -q dist_small
-    &E_DENSITY_CUBE
+#PBS -l nodes=4:ppn=16
-    &END E_DENSITY_CUBE
+#PBS -l walltime=10:00
-  &END
+#PBS -A cp2k2015
-&END DFT
-</code>
-<note tip>
+cd $PBS_O_WORKDIR
-The calculations involving the large TiO$_2$ slab should be run on 16 nodes with ''bsub  -n 16''.
-</note>
-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 ''/cluster/home03/matl/schuetto/cubecruncher.x''. Before invoking the cubecruncher, you have to load the cp2k module. To simplify the following steps you should create a symbolic link to it in your working directory:
+module load cp2k/2.6
-<code>
-you@brutusX ~$ ln -s /cluster/home03/matl/schuetto/cubecruncher.x .
+prun cp2k.popt -i mode1.inp -o mode1.out
 </code>
-Now subtract the densities of the lone systems from the bonded system:
+===== 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.
 <code>
-you@brutusX ~$ ./cubecruncher.x -i mode1-ELECTRON_DENSITY-1_0.cube -subtract mode1_acid-ELECTRON_DENSITY-1_0.cube -o tmp.cube
+cp2k.popt -i mode1.inp -o mode1.out
-you@brutusX ~$ ./cubecruncher.x -i tmp.cube -subtract mode1_slab-ELECTRON_DENSITY-1_0.cube -o mode1_delta.cube
 </code>
+In addition to the output ''mode1.out'', other files are gerenated by CP2K named MODE1*
-The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool:
+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).
 <code>
-you@brutusX ~$ cubecruncher.x -center geo -i mode1_delta.cube -o mode1_delta-centered.cube
+~$ 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
 </code>
-You can visualize the resulting file ''mode1_delta-centered.cube'' with VMD. This has been covered in a [[mo_ethene| previous exercise]].
+You can visualize the resulting file ''MODE1_delta.cube'' with VMD.
 What you get should look similar to this:
-{{ dye_tio_bonding_density.png?300 |}}
+{{ exercises:2015_ethz_mmm:dye_tio_bonding_density.png?300 |}}
-===== 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 of four systems:
+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.
-  - lone acetic acid molecule (run geometry optimization, use energy of last step)
-  - lone TiO$_2$ slab  (you can use the already geometry optimized coordinates from ''relaxed_slab.xyz'' at the end of the exercise)
-  - combined system bound in the first mode (can be reused from previous task)
-  - combined system bound in the second mode (file ''mode2.xyz'')
-<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, ..
-</note>
+output topics:
+  * ''Informations at step''
+  * Trajectory ''MODE1_GEO-pos-1.xyz''
-===== Questions =====
+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 ?
-  * 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>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.</note>
-<note tip> When 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>
+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 :
-The provided [[wp>XYZ_file_format|XYZ-files]] can not be included into CP2K's input directly. You have to convert them to ''.coord'' files by removing the first line, which states the number of atoms, and the following empty comment line.
-</note>
+{{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.
 <code - mode1.inp>
 &GLOBAL
-  ! change name for each different run performed
+  ! the project name is made part of most output files... useful to keep order
-  PROJECT mode1
+  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
-       &E_DENSITY_CUBE        !  section to print the electronic density of the system (Task 2)
+       ! at the end of the SCF procedure generate cube files of the density
+       &E_DENSITY_CUBE ON
        &END E_DENSITY_CUBE
     &END
-    BASIS_SET_FILE_NAME BASIS_SETS
+    ! use the OT METHOD for robust and efficient SCF, suitable for all non-metallic systems.
-    ! This keyword refers the input to an external basis file, which has to be in the same directory as this input file
+    &SCF
-    POTENTIAL_FILE_NAME POTENTIALS
+      SCF_GUESS ATOMIC ! can be used to RESTART an interrupted calculation
-    ! This keyword refers the input to an external potential file, which has to be in the same directory as this input file
+      MAX_SCF 30
+      EPS_SCF 1.0E-6 ! accuracy of the SCF procedure typically 1.0E-6 - 1.0E-7
-    &SCF                                      ! Ensures convergence of SCF and simulations stability. This section should not be changed
-      MAX_SCF 50
       &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
+      &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
-      &XC_FUNCTIONAL PBE
+      ! 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
-      ABC 10.2270 11.3460 20.000
+      ! unit cells that are orthorhombic are more efficient with CP2K
+      ABC [angstrom] 10.2270 11.3460 20.000
     &END CELL
-    &COORD
+    ! atom coordinates can be in the &COORD section,
-! Here you either manually insert the coordinates of the system (as usual) OR use the @INCLUDE statement like this:
+    ! or provided as an external file.
-@INCLUDE 'mode1.coord'        ! The mode1.coord file must be present in the same directory as the input.
+    &TOPOLOGY
-                              ! The file should be similar to an *.xyz file but without the total number of atoms at the beginning
+      COORD_FILE_NAME mode1.xyz
+      COORD_FILE_FORMAT XYZ
-   &END COORD
+    &END
-    &KIND H                                 ! All basis sets and potentials are looked up in the external files specified above.
-      BASIS_SET DZVP-MOLOPT-GTH             ! search in the external basis file (specified above) the one named DZVP-MOLOPT-GTH for H.
+    ! MOLOPT basis sets are fairly costly,
-      POTENTIAL GTH-PBE-q1                  ! search in the external potential file (specified above) the one named GTH-PBE-q1 for H.
+    ! 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-GTH
+      BASIS_SET DZVP-MOLOPT-SR-GTH
       POTENTIAL GTH-PBE-q4
     &END KIND
     &KIND O
-      BASIS_SET DZVP-MOLOPT-GTH
+      BASIS_SET DZVP-MOLOPT-SR-GTH
       POTENTIAL GTH-PBE-q6
     &END KIND
@@ Line 167: / Line 244: @@
 &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
 </code>
-<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,
-#               Theor. Chem. Acc. 114, 145 (2005)
-#
-# Potential for the PBE functional
-#
-################################################################################
-#
-H GTH-PBE-q1
-.20000000    2    -4.17890044     0.72446331
-#
-C GTH-PBE-q4
-    2
-.33847124    2    -8.80367398     1.33921085
-.30257575    1     9.62248665
-.29150694    0
-#
-O GTH-PBE-q6
-    4
-.24455430    2   -16.66721480     2.48731132
-.22095592    1    18.33745811
-.21133247    0
-#
-Ti GTH-PBE-q12
-    6    2
-.38000000    2     8.71144218    -0.70028677
-.33777078    2     2.57526386     3.69297065
-                                       -4.76760461
-.24253135    2    -4.63054123     8.87087502
-                                      -10.49616087
-.24331694    1    -9.40665268
-</code>
-<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://link.aip.org/link/?JCP/127/114105
-# DOI: 10.1063/1.2770708
-#
-###########################################
- H  DZVP-MOLOPT-GTH DZVP-MOLOPT-GTH-q1
-0 1 7 2 1
-.478000339908  0.024916243200 -0.012512421400  0.024510918200
-.700758562763  0.079825490000 -0.056449071100  0.058140794100
-.446884268432  0.128862675300  0.011242684700  0.444709498500
-.716814589696  0.379448894600 -0.418587548300  0.646207973100
-.247918564176  0.324552432600  0.590363216700  0.803385018200
-.066918004004  0.037148121400  0.438703133000  0.892971208700
-.021708243634 -0.001125195500 -0.059693171300  0.120101316500
- C  DZVP-MOLOPT-GTH DZVP-MOLOPT-GTH-q4
-0 2 7 2 2 1
-.132624767898 -0.105576563700  0.024850587600  0.035098108400 -0.056712999000  0.037469425800
-.625196064782 -0.174866621100  0.147440856000  0.114197930900 -0.076743951500  0.071047574800
-.045456957247  0.064464981400 -0.421418379200  0.215908137300 -0.528056757000  0.619330561200
-.478316330874  0.830447035300  0.823051336800  0.355929151000  0.394594045700  0.710730857000
-.178617414302  0.371911373800  0.184880712100  0.271541842000  0.721247475800  0.389148235000
-.075144725465  0.006174464000 -0.742086051600  0.056256557700  0.733902531700  0.346374124100
-.030286753006  0.008966477300  0.083382192000  0.004998059700  0.248172175500 -0.005142430900
- O  DZVP-MOLOPT-GTH DZVP-MOLOPT-GTH-q6
-0 2 7 2 2 1
-.015954705512 -0.060190841200  0.065738617900  0.036543638800 -0.034210557400  0.014807054400
-.108150287385 -0.129597923300  0.110885902200  0.120927648700 -0.120619770900  0.068186159300
-.048398039874  0.118175889400 -0.053732406400  0.251093670300 -0.213719464600  0.290576499200
-.832381575582  0.462964485000 -0.572670666200  0.352639910300 -0.473674858400  1.063344189500
-.352316246455  0.450353782600  0.186760006700  0.294708645200  0.484848376400  0.307656114200
-.142977330880  0.092715833600  0.387201458600  0.173039869300  0.717465919700  0.318346834400
-.046760918300 -0.000255945800  0.003825849600  0.009726110600  0.032498979400 -0.005771736600
- Ti DZVP-MOLOPT-SR-GTH DZVP-MOLOPT-SR-GTH-q12
-0 3 6 3 2 2 1
-.884569925997  0.004750577412 -0.002690702837  0.075105591562 -0.108736525246  0.023185061556  0.052842407451 -0.038307431199 -0.002442658125
-.894698463070  0.499503858222  0.103956524568  0.048602853477  0.100912855636 -0.027189036213  0.195986532018 -0.076880250937  0.013119020987
-.513588828959 -0.664995883766 -0.256641947580  0.079732563787  0.527328996047 -0.230044390357  0.330343722079 -0.242486488988 -0.206817889885
-.596768079836 -0.726044574739 -0.451591547817  1.660896378972  0.468197803110 -0.126795185046  0.396808432313 -0.118369379707 -0.546596492823
-.222222125842 -0.029011079755  0.165167622946 -2.748651632733  0.077640626075  0.343517279356  0.347092399871  0.038099375809 -0.279145975103
-.077078461321  0.075171747143  0.993127316430  1.368227638651 -0.007523238420  0.946960702315  0.132320900948  1.046553050597  0.934394052863
-</code>
 <code - mode1.xyz>
@@ Line 395: / Line 396: @@
 O        -1.5275649623       -0.3212592281        6.6009413157
 H        -1.0670534373       -0.2549619720        5.6840567874
 </code>
@@ Line 517: / Line 517: @@
 O        -2.9500441444        1.1398319329        5.4010622063
 H        -0.3897742635        1.0153182782        4.6757696096
-</code>
-<code - relaxed_slab.xyz>
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-Ti        3.5972989622        1.8909274430       -3.7515400005
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-O         0.2999353645        3.7820068984       -4.5423256737
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-O         1.7900926030        1.8909706946       -2.7855892400
 </code>