orcagabedit manual

Dr. Michael Patzschke I Institute for Resource Ecology I www.hzdr.de

CSC Spring School 2015

Quantum Chemistry Workshop Basics

Orca & Gabedit

Michael Patzschke Institute for Resource Ecology

HZDR

11.03.2015

Member of the Helmholtz Association Page 2 Dr. Michael Patzschke I Institute for Resource Ecology I www.hzdr.de

The Codes

Orca general purpose QC code Free (download from http://cec.mpg.de/forum/) Developed by F.Neese et al. in C++ Precompiled binaries (no sources)

Gabedit Free (download from https://sites.google.com/site/allouchear/Home/gabedit/download) Developed by A.-R. Allouche Sources and Binaries available

Both codes available for Mac, Linux & Windows Good combination for research & teaching


Learning Outcome

Draw and import molecular structure Pre-optimization Creating input files using the GUI Writing simple input files Comparing QC methods (quality and timing) Running constraint optimizations Relativistic effect

An example follows on Friday Visualizing results

Much more on Thursday using VMD


Gabedit

Assuming you have the gabedit executable in your $PATH Please open a terminal:

mkdir qc_lab cd qc_lab gabedit

Have a look around Open the structure

editor


Editing Structures

Press the pen tool to add atoms Press the periodic-table button

to change the atom (C is standard) Press the button below that to

toggle adding hydrogens Pre-optimizing self-drawn structures

Important for speedup of real calculations Avoid for transition metals, lanthanides & actinides Two methods available: MM or semiempirical calculations

Press M button or right-click in drawing window Choose Molecular Mechanics

Optimization


Editing Structures Further Points

Fragments can be used to draw structures Parts of the molecule can be selected Atoms and parts of the molecule can be removed And moved

Structural parameters can be measured and changed Measurements can be shown or removed

For Semiempirical methods:

Interface to Mopac, Orca & Firefly


Drawing Formaldehyde

Please try to draw formaldehyde Menu-Edit-Delete Molecule Add Carbon Choose Oxygen from periodic table Replace one hydrogen Click on the bond to make double bond Pre optimize using MM

The result should look like this

Close the drawing window (Menu-Close)

(saving possible not necessary here)


Setting up an Orca calculation

Gabedit generates input for different QC codes Choose Orca from the top menu

The pop-up menu lets you set up the

calculation Change Job Type to

Equilibrium Structure Search Change Type of method to

Meta-GGA and hybrid meta GGA's Change Method to

TPSS Change Type to

def2 Ahlrichs basis sets


Setting up an Orca calculation

Basis will change, leave that choice

Press Ok


Orca Input Files

Inspect the generated input file # Lines are comments ! Lines contain keywords % Lines start key blocks end lines end key blocks * starts and ends the geometry block

Comments can be inserted like this: ! Opt # this will be ignored # TPSS

The output block is added by gabedit for visualisation, but not necessary

The geom block is wrong (more later) Please remove it!


Running Orca

Input files can be saved (File menu)

QC codes can be run by Gabedit Set up run commands in

Settings-Preferences on the Commands tab

Press cogwheels to start a job Choose Orca Press Ok Click on NoName.out tab

to see the output


Interlude

Congratulations, you have hopefully just run your Orca calculation A few considerations:

Gabedit is useful for drawing simple structures many alternatives exist (have a look at Avogadro)

Good to remember basic input file structure Excellent for visualizing results The input file can be changed in gabedit A simple text editor might be easier to use ...

We will visualize the results Then an editor will be used to set up some more advanced calculations


Looking at Results

During a run you can Look at the output file Update it Look at geometry convergence Visualize MO's & Densities

from the first step of the calculation Get data from remote calculations

After the calculation has finished, press the

visualize button


Visualizing Orbitals

In the visualization window click M or right-click

Choose Orbitals from the menu

Choose Orca output file Read the NoName.out file An MO selection should appear

Select an orbital The right part shows its

participating AOs Change cut-off value here Click Ok


Visualising Orbitals

Orbitals are calculated in a cube Select position here Select size here Select quality here Standard choices are ok Press Ok

After the calculation is finished you can

Change the iso-value 0.1 should be a good choice Get a proposition for a certain size Press Ok


Other Things to Visualise

Take a few moments to look around the menu (M or right-click)

Geometry optimizations can be visualized from the .trj files

Choose Animation and load the .trj file Press Play

A movie can be made for presentation

purposes (using ImageMagick)


Orca Input Help

Have the orca manual ready (532 pages including theory...) Actually a rather useful textbook as well

Have a look at https://sites.google.com/site/orcainputlibrary/home a very good input library

Under http://cec.mpg.de/forum/ you can join the forum Very active, fast help Please read the manual and consult the forum before complaining!


More Advanced Calculations

Close gabedit (Press File-Exit from the main window) Open your input file using your favourite editor Edit it to look like this: Change the functional

For a list see next page Change the basis set

For a list see further down Save the input file under a new name Start orca by issuing at the prompt: orca filename.inp > filename.out &

!Opt TPSS Def2-SV(P) * xyz 0 1 C -1.182146 -0.191818 -11.887076 H -1.567738 0.546391 -12.590258 H -1.864597 -0.714867 -11.217165 O 0.022990 -0.429026 -11.844415 *


Orca List of DFT functionals

Available functionals Double hybrids are available

(MP2 calculation will be performed!) DFT tries to use the RI approach

automatically (NORI to witch of) Dispersion correction with

keywords vdw10 or vdw10bj


Basis Sets in Orca

Many different basis sets available some examples: Ahlrich's good for DFT Dunning's good for CC Basis set can be changed for an element:

%basis newgto Element "def2-TZVPP # Specifying the basis set on "Element end

Or for a specific atom in the geometry section: H 0.0 0.0 1.0 newgto "def2-TZVP" end

To try MP2 use the following line: !Opt RI-MP2 def2-TZVPP def2-TZVPP/J def2-TZVPP/C TightSCF RIJCOSX

For test purposes here you might want to replace TZVPP by SVP


Your Task Just an Idea Make a small table for the C-O bond length of formaldehyde

and computational timings using two or three different methods and two or three different basis sets

Run calculations, fill in the table and compare with experimental data SVP TZVPP QZVPP Exp

BP86 r(CO) = r(CO) = r(CO) =

r(CO) = 120.5 pm

t = t = t =

TPSS r(CO) = r(CO) = r(CO) = t = t = t =

PBE0 r(CO) = r(CO) = r(CO) = t = t = t =

HF r(CO) = r(CO) = r(CO) = t = t = t =

MP2 r(CO) = r(CO) = r(CO) = t = t = t =


Remarks on the Task The table is a suggestion only To run HF simply do:

! Opt def2-SVP

MP2 TZVPP took 30 s on my laptop MP2 QZVPP should be feasible If you want to have fun, try:

!Opt def2-TZVPP def2-TZVPP/J def2-TZVPP/C TightSCF RIJCOSX !DLPNO-CCSD(T) NumGrad %maxcore 2000 This does a numerical CCSD(T) optimisation Needs a lot of memory Useful for optimising certain structural parameters


Further Remarks Defining charge and multiplicity first line of geometry block:

* int 0 1 first word = form of geometry data (xyz or int) first number = charge, second number = multiplicity (1 for singlet, 2 for doublet)

or reading an external file with: * xyzle 1 2 lename.xyz

One can add dummies (DA), ghosts (Mg:), point charges (Qn.nn) and many more

Orca does not use symmetry to speed up calculations Symmetry can be used to classify MOs To do this, add the keyword UseSym

To run orca in parallel add the keyword PalN where N

is the number of cores Alternatively use the block:

%pal nprocs 4 # any number (posidve integer) end

Do not use more than 16 cores


Properties Vibrational frequencies are available for HF, MP2, GGA and hybrid GGA

functionals through: !Opt Freq

Speedup through much memory, give per core with the extra line: %maxcore 1000

For all other methods numerical frequencies possible: !Opt NumFreq

Using at least TightSCF is recommended for frequency runs Thermochemistry for different temperatures with:

%freq Temp 290, 295, 300 end

Many other properties available (electronic absorption, NMR, ESR (!)) Not part of the basic tutorial


Solvent Effects

Solvent effects on structures and frequencies through COSMO Treatment differs for MP2 from Turbomole, different results possible Two ways to specify,

in command line: ! COSMO(solvent) As input block: ! COSMO

%cosmo epsilon 78 end

The more recent SMD (solvent model density) is also available: %cosmo smd true solvent DMF end


Relativity Two ways to include scalar relativistic effects (no SO!):

For elements heavier than Kr one can include ECPs with: ! BP def2-SVP def2-SVP/J ECP{def2-SVP,def2-SVP/J} printbasis where printbasis prints the basis, in order to check that ECP and basis set fit

Manually define ECPs for certain elements: ! ECP{TZVP=Hf-Hg} ! ECP{TZVP=[Ag,Pt,Au]}

All electron ZORA or DKH2 calculations: ! BP86 ZORA def2-SVP def2-SVP/J TIGHTSCF printbasis ! BP86 DKH2 def2-SVP def2-SVP/J TIGHTSCF printbasis

Very important: ZORA/DKH2 and basis set definitions have to be on the same line!

Defining a special basis set requires: U 0.0 0.0 1.0 newgto "ZORA-def2-TZVP" end


Constraints

Useful for optimisations Freeze parts of the molecule

during optimisation:

Wildcards to freeze all bonds/angles/torsions to certain atoms Giving no value takes that value from the geometry section

Just optimize hydrogens (useful for crystal structures):

%geom Constraints { B 0 1 1.25 C } { A 2 0 3 120.0 C }

end end

Constraining bond distances : { B N1 N2 value C } Constraining bond angles : { A N1 N2 N1 value C } Constraining dihedral angles : { D N1 N2 N3 N4 value C } Constraining cartesian coordinates : { C N1 C }

%geom opdmizehydrogens true end


Hydrogen Optimisation

A simple example One hydrogen is moved

! TPSS KeepDens PrintBasis Def2-SV(P) Opt %geom opdmizehydrogens true end * xyz 0 1 C -1.137634 0.702379 0.000000 C -1.137634 -0.702379 0.000000 N 0.000002 -1.415106 0.000000 C 1.137633 -0.702378 0.000000 C 1.137633 0.702380 0.000000 N -0.000001 1.415106 0.000000 H -2.180421 1.269265 0.000000 H -2.080418 -1.269269 0.000000 H 2.080422 -1.269260 0.000000 H 2.080419 1.269264 0.000000 *


Constrained Scans

Scan energy along bond expansion, optimise all steps:

Took 1,5 min on my laptop File filename.allxyz contains optimized geometries for all steps File filename.relaxscanact.dat contains energy data

(visualize with e.g. gnuplot)

! RKS BP SV(P) TightSCF Opt %geom Scan B 0 1 = 1.35, 1.10, 12 # scan C-O distance end end * int 0 1 C 0 0 0 0.0000 0.000 0.00 O 1 0 0 1.3500 0.000 0.00 H 1 2 0 1.1075 122.016 0.00 H 1 2 3 1.1075 122.016 180.00 *


An Advanced Example

Reminder: static vs. dynamic correlation For static correlation Orca offers CASSCF or MRCI calculations Try this example, rotation of the double bond in ethylene:

! RHF SV(P) SV/C SmallPrint NoPop NoMOPrint%casscf nel = 2 norb = 2 mult = 1,3 nroots = 2,1 TrafoStep RI switchstep nr end%paras R= 1.3385 Alpha=0,180,37 end* int 0 1C 0 0 0 0 0 0C 1 0 0 {R} 0 0H 1 2 0 1.07 120 0H 1 2 3 1.07 120 180H 2 1 3 1.07 120 {Alpha}H 2 1 3 1.07 120 {Alpha+180}*


An Advanced Example

With UHF the lowest singlet and triplet look like this:

Things to note around 0: Singlet energy too high Triplet energy too low

Around 90: Singlet convergence issues Orca reuses orbitals from

previous runs


Energy extrapolation We would like to know energies at the basis set limit

Computationally not feasible Extrapolation procedures exist for e.g. Dunning's and ANO basis sets

Orca uses for HF:

And for the correlation part:

Look at a simple example: ! RHF MP2 CCSD(T) Extrapolate(2/3,cc) TightSCF Conv Bohrs * int 0 1 O 0 0 0 0 0 0 H 1 0 0 1.81975 0 0 H 1 2 0 1.81975 105.237 0 *


Visualising Without Gabedit Orca can produce molden input files After the calculation is finished,

write at the prompt: orca_2mkl basename molden

Orca has an interactive program to produce cube files Orbitals and densities are

available Excited state density

differences possible Different formats available

Start at the prompt with: orca_plot lename.gbw -i


Calculating other Properties

Different programs can be interfaced Common file format molden Molden input files can be converted to .wfn files for AIM, MultiWFN,

NCIplot More on Friday


The End

Have fun with Orca Thank you for your attention!

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