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  • Introduction
    • Starting the GUI: start ADFjobs
      • UNIX (such as Linux) users
      • Windows users
      • Macintosh users
    • GUI modules
    • Keyboard shortcuts
  • GUI overview tutorials
    • Getting started: Geometry optimization of ethanol
      • Step 1: Preparations
        • Start ADFjobs
        • Make a directory for the tutorial
        • Start ADFinput
        • Undo
      • Step 2: Create your molecule
        • Create a molecule
        • Viewing the molecule
        • Molecular conformation
        • Getting and setting geometry parameters
        • Extending and changing your molecule
      • Step 3: Select calculation options
        • Task
        • XC functional
        • Basis set
        • Numerical quality
        • Geometry Convergence
        • Other input options
      • Step 4: Run your calculation
        • Save your input and create a job script
        • Run your calculation
      • Step 5: Results of your calculation
        • Logfile: ADFtail
        • Files
        • Geometry changes: ADFmovie
        • Orbital energy levels: ADFlevels
        • Electron density, potential and orbitals: ADFview
        • Browsing the Output: ADFoutput
    • Building Molecules
      • Step 1: Start ADFinput
      • Step 2: Search for ethanol
      • Step 3: Import XYZ for ethanol
      • Step 4: Import SMILES string
      • Step 5: Build ethanol using the structure tool
      • Step 6: Building a peptide chain using the structures tool
      • Step 7: Metal complexes and ligands
        • Predefined Metal Complex Geometries
        • Bidentate Ligands
        • Modifying the Plane Angle
      • Step 8: Your own structures library
        • Defining your structures
        • Using dummy atoms
      • Step 9: A sphere of Cu atoms, cut out of the crystal
      • Step 10: A carbon nanotube
    • Building Crystals and Slabs
      • The Crystal Structures Tool
      • The Crystal Structures Database
      • Crystal builder (from space group information)
      • Slicer: building slabs
      • Creating a supercell
    • Building Frameworks and Reticular Compounds
      • The Export Fragment tool
      • Framework builder : Build a pillared, functionalized MOF
  • ADF-GUI tutorials
    • Spectroscopy
      • Excitation energies and UV/Vis spectrum of ethene
        • Step 1: Start ADFinput
        • Step 2: Create your ethene molecule
        • Step 3: Optimize the geometry
        • Step 4: Calculate the excitation energies
        • Step 5: Results of your calculation
        • Step 6: Excited state geometry optimization and excited state density
      • Vibrational frequencies and IR spectrum of ethane
        • Step 1: Start ADFinput
        • Step 2: Create your ethane molecule
        • Step 3: Optimize the geometry
        • Step 4: Calculate the vibrational frequencies of ethane
        • Step 5: Results of your calculation
      • Analysis of the VCD spectrum of Oxirane with VCDtools
        • Step 1. Start ADFinput
        • Step 2: Create your oxirane molecule
        • Step 3: Optimize the geometry
        • Step 4: Calculate the VCD intensities
        • Step 5: Analyze the VCD Spectra
      • H-NMR spectrum with spin-spin coupling
        • Step 1: Start ADFinput
        • Step 2: Create the molecule
        • Step 3: Setting up the NMR calculation
        • Step 4: Results of your calculations
    • Analysis
      • Fragment Analysis
        • Step 1: Build Ni(CO)4
        • Step 2: Define fragments
        • Step 3: set up the fragment analysis run
        • Step 4: Run the fragment analysis and view the results
        • Step 5: Build PtCl4 H2 2-
        • Step 6: Define fragments
        • Step 7: Run the fragment analysis and view the results
      • QTAIM (Bader), (localized) orbitals and conceptual DFT
        • Step 1: QTAIM (Bader) analysis of Caffeine
        • Step 2: Benzene Bader charge analysis and NBOs
        • Step 3: Rationalizing a typical SN2 reaction using condensed Conceptual DFT descriptors
      • Visualization of densities, orbitals potentials, ...
        • Step 1: Get Single-Point calculation results with ADF on Anthracene
        • Step 2: Details: Divergent and Rainbow Colormap, scalar range of field on isosurface
        • Step 3: Multi Isosurface
        • Step 4: Combining visualization techniques
        • Step 5: Play with lights
        • Step 6: Special fields
      • Fukui Functions and the Dual Descriptor
        • Step 1: Setting up the calculation
        • Step 2: The output
        • Step 3: Visualizing the Fukui functions and Dual Descriptor
      • Interacting Quantum Atoms (IQA)
        • Step 1: Build H2O
        • Step 2: Calculate all inter-atomic interactions in H2O
        • Step 3: Analyze the results
        • Step 4: Build PF5
        • Step 5: Select two atoms (P and equatorial F) and calculate this specific interaction
        • Step 6: Analyze the results (a single P-Feq bond in PF5 )
        • Step 7: Compare equatorial and axial P-F bonds
      • Analysis of NMR parameters with Localized Molecular Orbitals
        • Introduction
        • Step 1: Preparations
        • Step 2: Calculation Settings
        • Step 3: Running the Calculations
        • NMR Results
        • NLMO/NBO Analysis
        • Inspecting NLMOs
        • Further Reading
    • Relativistic Effects
      • TlH (thallium hydride) Spin-Orbit Coupling
        • Step 1: Prepare molecule
        • Step 2: Set calculation options
        • Step 3: Run your calculation
        • Step 4: Results of the calculation
        • Step 5: Calculate the atomization energy including spin-orbit coupling
    • Multiple Jobs, Multi-Level, Multiple Compounds
      • Generating a batch of jobs and collecting results: Basis Set Effects for NH3 Geometry
        • Step 1: Create and pre-optimize your molecule
        • Step 2: Set up a single ADF calculation
        • Step 3: Set up a batch of ADF jobs
        • Step 4: Run your set of ADF jobs
        • Step 5: Analyze results of several calculations at once
      • Multi-Level principles: Regions, QUILD, QMMM, Quality per region
        • Step 1: Regions for multi-level calculations, visualization and grouping
        • Step 2: QUILD
        • Step 3: QMMM
        • Step 4: DRF
        • Step 5: Quality per region
      • Multiple molecules, conformers, multiple methods
        • Multiple molecules
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    • Structure and Reactivity
      • Spin Coupling in Fe4S4 Cluster
        • Step 1: Create and pre-optimize the Fe4 S4 cubane model
        • Step 2: Optimize the structure with ADF
        • Step 3: Obtain the solution for the high-spin (HS) state of the cubane
        • Step 4: Couple the spins in Fe4 S4 using the SpinFlip option
        • Step 5: Coupling the spins using the ModifyStartPotential option, use ARH SCF convergence method
        • Step 6: View the spin density of the broken symmetry (BS) solutions
      • HCN Isomerization Reaction
        • Step 1: Prepare the HCN molecule
        • Step 2: Create a rough approximation for the transition state geometry
        • Step 3: Finding the transition state: prepare approximate Hessian
        • Step 4: Search for the transition state
        • Step 5: Calculating frequencies at the transition state
        • Step 6: Following the reaction coordinate
        • Step 7: Following orbitals along the IRC: reporting from .t21 files
        • Step 8: Following orbitals for the LT afterwards: generating jobs for many geometries
      • Transition State Search with ASE using the Nudged Elastic Band method
        • Step 1: Import the initial and final molecule
        • Step 2: Set the calculation details
        • Step 3: Viewing the Results
  • AMS-GUI tutorials
    • Diamond Lattice Optimization and Phonons
      • Set up the calculation
      • Run the calculation
      • Visualize the Phonons
    • PES scan and transition state search
      • PES Scan
      • Frequencies calculation
      • Transition state search
  • BAND-GUI tutorials
    • Getting started with BAND
      • Create a work directory and start up ADFInput
      • Set up the NaCl crystal calculation
      • Run the calculation
      • Examine the band structure and DOS
      • Visualize results with ADFView
    • Bonding Analysis
      • Periodic Energy Decomposition Analysis - PEDA
        • Step 1: Start ADFinput
        • Step 2: Set up the system - CO@MgO(sqrt(2)xsqrt(2))
        • Step 3: Running the PEDA calculation
        • Step 4: Checking the results
      • PEDA-NOCV - decomposing the orbital relaxation term
        • Step 1: Setting up the System and the Calculation
        • Step 2: Checking the results
        • Step 3: Plotting NOCV orbitals and deformation densities
      • PEDA-NOCV for Spin Unrestricted Calculations
        • Step 1: Start ADFinput
        • Step 2: Set up the system - Ethane
        • Step 3: Running the PEDA-NOCV calculation
        • Step 4: Checking the results
        • Step 5: Plotting NOCV orbitals and deformation densities
    • TD-CDFT and Linear Response Properties
      • TD-CDFT Response Properties For Crystals (OldResponse)
        • Step 1: Create the system
        • Step 2: Run a Single Point Calculation (LDA)
        • Step 3: Run an OldResponse Calculation (ALDA)
      • TD-CDFT Response properties for a 2D periodic system (NewResponse)
        • Step 1: Create the system
        • Step 2: Run a Singlepoint Calculations (LDA)
        • Step 3: Run an NewResponse Calculation (ALDA)
    • Model Hamiltonians
      • NiO and DFT+U
        • Step 1: adfinput
        • Step 2: Setup the system - NiO
        • Step 3: BP86 without Hubbard
        • Step 4: Run the calculation - BP86+U
      • Benzene molecule in a magnetic field
        • Step 1: adfinput
        • Step 2: Setup the system - benzene
    • Electronic Transport with NEGF
      • Carbon nanotube
        • Setting up the system
        • Running the calculation
        • Visualizing the results
      • CO on 1D gold chain
        • Introduction
        • Creating the lead file
        • Gold chain transport calculation
        • CO on gold chain transport calculation
      • Au-(4,4’-bipyridine)-Au molecular junction
        • Using tips
      • Spin transport in Chromium wire
      • Gate and Bias potentials
  • DFTB-GUI tutorials
    • DFTB charges, frequencies and dynamics (MD)
      • Step 1: DFTB: Pre-optimization and Charges
      • Step 2: Frequency evaluation
      • Step 3: Molecular dynamics
    • Proton affinities with DFTB3
      • Step 1: Optimization of the neutral molecule
      • Step 2: Optimization of the acetate and the hydrogen ions
    • UV/Vis spectrum of Ir(ppy)3
    • Electronic transport with DFTB-NEGF
      • Carbon nanotube
        • Setting up the system
        • Running the calculation
        • Visualizing the results
      • CO on 1D gold chain
        • Introduction
        • Creating the lead file
        • Gold chain transport calculation
        • CO on gold chain transport calculation
      • Au-(4,4’-bipyridine)-Au molecular junction
        • Using tips
        • Gate potential
  • MOPAC-GUI tutorial
    • Toluene charges, movies, frequencies and normal modes
      • Set up Toluene in MOPACinput
      • Run interactively
      • Save job and results: charges, movies, IR spectrum and normal modes
  • Quantum ESPRESSO GUI tutorials
    • Geometry and Lattice Optimization
      • Step 1: Start ADFinput
      • Step 2: Set up the system - Silicon
      • Step 3: Setting up the calculation
      • Step 4: Running your job
      • Step 5: Checking the results
    • Magnetism, Band Structure and pDOS
      • Step 1: Start ADFinput
      • Step 2: Set up the system - Iron supercell
      • Step 3: Set up the anti-ferromagnetic iron calculation
      • Step 4: Set up the ferromagnetic iron calculation
      • Step 5: Run the calculations
      • Step 6: Examine the results
        • KFBrowser
        • BANDstructure
        • ADFview
  • ReaxFF-GUI tutorials
    • Burning methane
      • Step 1: Start ReaxFFinput
      • Step 2: Create a methane / oxygen mixture
      • Step 3: Prepare for burning: set up the simulation
      • Step 4: Burn it: run the simulation
      • Step 5: Analyze it: Create a reaction network
      • Step 6: Analyze it: Browse a reaction network
      • Step 7: Analyze it: Filter a reaction network
    • Water on an aluminum surface
      • Step 1: Start ReaxFFinput
      • Step 2: Creating the surface
      • Step 3: Add solvent
      • Step 4: Set up the simulation, including a temperature regime
      • Step 5: Run the simulation
    • The Molecule Gun
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        • Setting up the system
        • Setting up the calculation
        • Running the calculation and visualizing the results
  • COSMO-RS GUI Tutorials
    • COSMO result files
      • Step 1: Start ADFinput
      • Step 2: Create the molecule
      • Step 3: ADF COSMO result file
      • Step 4: MOPAC COSMO result file
      • Step 5: Fast Sigma: QSPR COSMO result file
    • Overview: parameters and analysis
      • Step 1: Start ADFcrs
      • Step 2: Add Compounds
      • Step 3: Set pure compound parameters
      • Step 4: COSMO-RS, COSMO-SAC, and UNIFAC parameters
      • Step 5: Visualize the COSMO surface: ADFview
      • Step 6: Analysis: The sigma profile
      • Step 7: Analysis: The sigma potential
    • Overview: properties
      • Step 1: Start ADFcrs
      • Step 2: Vapor pressure
      • Step 3: Boiling point
      • Step 4: Flash point
      • Step 5: Activity coefficients, Henry coefficients, Solvation free energies
      • Step 6: Partition coefficients (log P)
      • Step 7: Solubility
        • Solubility liquid in a solvent
        • Solubility solid in a solvent
        • Solubility gas in a solvent
      • Step 8: Binary mixtures VLE/LLE
        • Isothermal
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      • Step 9: Ternary mixtures VLE/LLE
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      • Step 10: A composition line between solvents s1 and s2
      • Step 11: Pure Compound Properties
      • Step 12: Solvent Optimizations: Optimize Solubility
      • Step 13: Solvent Optimizations: Optimize Liquid-Liquid Extraction
    • The COSMO-RS compound database
      • 4.1: Install and use the COSMO-RS compound database
        • Step 1: Install database
        • Step 2: Add or search compounds
        • Step 3: Set pure compound data
        • References
        • Step 4: Visualize the COSMO surface: ADFview
      • 4.2: Octanol-Water partition coefficients (log POW )
        • References
      • 4.3: Henry’s law constants
        • References
      • 4.4: Solubility of Vanillin in organic solvents
        • References
      • 4.5: Binary mixture of Methanol and Hexane
        • References
      • 4.6: Large infinite dilution activity coefficients in Water
        • References
      • 4.7: Parametrization of ADF COSMO-RS: solvation energies, vapor pressures, partition coefficients
        • Table: Parametrization of COSMO-RS
        • References
      • 4.8: COSMO-SAC 2013-ADF
        • References
      • 4.9: Optimize solvents for LLE of Acetic acid and Water
    • pKa values
      • 5.1: Empirical pKa calculation method
      • 5.2: Relative pKa calculation method
    • Ionic Liquids
      • 6.1: Using the ADF COSMO-RS ionic liquid database
        • Reparameterization of COSMO-RS for ionic liquids
        • References
      • 6.2: Ionic liquid volumes and densities
        • References
      • 6.3: Activity coefficient calculation
        • References
      • 6.4: Henry’s law constants
        • References
      • 6.5: Gas solubility and selectivity in ionic liquids
        • References
      • 6.6: VLE for systems containing ionic liquids
    • Using the UNIFAC program
      • Selecting/inputting compounds
      • Inputting property values
      • Calculations with the UNIFAC program
        • Vapor Pressure Mixture
        • Activity Coefficients
        • Partition Coefficients (LogP)
        • Solubility in Pure Solvents
        • Solubility in Mixture
        • Binary Mixture VLE/LLE
        • Ternary Mixture VLE/LLE
      • Common issues
  • Scripting tutorials
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  • Advanced tutorials
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        • Overview
        • The System
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        • Calculating the chemical potential for Li
        • Setting up the GCMC calculation
        • GCMC Troubleshoot
        • Results
      • Li-Ion Diffusion Coefficients in cathode materials
      • Polymer structures with the bond boost acceleration method
        • Overview
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        • Description of the workflow
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        • The System
        • Preparation
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        • Improving the CV using the Bias Deposition Plot
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        • Analyzing the System Composition
        • Discussion
        • Summary
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        • Overview
        • Setting up
        • Setting up the strain rate
        • Results
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        • Co.ff
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        • Overview of the workflow
        • Generating reference data
        • Preparing the training data
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        • How to monitor a running optimization
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        • How to cross-validate a fitted force field
        • Running the optimizer
    • ADF advanced tutorials
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        • Computational Description of TADF 1: Electronic Structure
        • Computational Description of TADF 2: Spin-Orbit Coupling
        • Computational Description of TADF 3: Vibrations
        • Computational Description of TADF 4: Solvent Effects
      • TDDFT Study of 3 different Dihydroxyanthraquinones
        • Scientific Questions
        • Model Questions
        • Pre-requisities
        • Overview
        • 0. What functional, What basis set?
        • 1. Geometry Optimization
        • 2. TDDFT Calculations
        • 3. Analyzing TDDFT Calculations
        • 4. Faster TDDFT variant: sTDDFT
        • 5. Analyzing the Orbitals
        • 6. Analyzing the NTOs
        • 7. Localized Analysis of Canonical Molecular Orbitals (CMO) with NBO6
      • 13 C - NMR chemical shifts in substituted benzenes w. ADF & NBO
      • Plasmon Enhanced Two Photon Absorption
        • Model and Methods
        • Workflow and Calculation Script
        • Calculation and Results
    • BAND advanced tutorials
      • Calculation of Band Structure and COOP of CsPbBr3 with BAND
        • Step 1: Preparations
        • Step 2: Calculations
        • Step 3: Inspecting the Band Structure
        • Interpretation of Results
      • Periodic Energy Decomposition of the Tetrahydrofuran/Si(001) System
        • Model
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        • NOCV Orbitals
Tutorials
  • Documentation/
  • Tutorials/
  • AMS-GUI tutorials/
  • PES scan and transition state search

PES scan and transition state search¶

In this tutorial we will locate the transition state for Pyrithione tautomerization:

../_images/PES-scan_TS_skeletal.png

Specifically, we will use AMS in combination with the DFTB Engine to:

  • Perform a 1D Potential Energy Surface (PES) scan, a.k.a. linear transit, to locate the initial guess for the subsequent Transition State (TS) search
  • Compute the Hessian and normal modes by performing a Frequencies calculation
  • Perform a transition state search using the Hessian computed in the previous step

More informations on these features can be found in the AMS User manual:

  • PES scan section of the AMS manual
  • Properties section of the AMS manual
  • Transition State search section of the AMS manual

PES Scan¶

Let us begin by starting up the ADFInput GUI module:

1. Start ADFjobs
2. Click on SCM → New Input. This will open ADFInput
3. In ADFInput, select the DFTB panel: ADF → DFTB

To create the Pyrithione molecule:

Copy-paste the following coordinates in the Molecule Editing Area of ADFInput
13

C      -2.30800400      -0.33458354      -0.03944688
C      -3.55161726      -0.98161691      -0.01806157
C      -3.59405760      -2.37377447       0.06998894
N      -2.43475599      -3.05706858       0.13215278
C      -1.19114674      -2.47716286       0.11543345
C      -1.13146988      -1.07344958       0.02678424
H      -4.47776711      -0.41946857      -0.06866615
H      -4.51286388      -2.95462913       0.09224655
O      -2.42829502      -4.40191846       0.21755293
S       0.09533105      -3.63607352       0.21049529
H      -0.16385857      -0.58321314       0.01095504
H      -2.26672769       0.74932834      -0.10794508
H      -1.26310602      -4.50300286       0.24347732

We now need to select the task and the DFTB parameter set:

1. In the main panel, select Task → PES Scan
2. Click on the folder next to Parameter directory and select DFTB.org/3ob-3-1

Your ADFInput window should look like this:

../_images/PES-scan_TS_pes_main.png

Now switch to the “Geometry Constraints and PES Scan” input panel:

In the menu bar, select Model → Geometry Constraints and PES Scan

We will now set up the coordinate along which to scan the potential energy surface:

In the Pyrithione tautomerization, the hydrogen atom bonded to oxygen will cross a small energy barrier and bond to the sulfur atom next to it. We will therefore scan the energy as a function of the H-S distance:

1. Select the H atom attached to O
2. Holding down Shift, select the S atom
3. Click on + next to H(13) S(10) (distance)

This will add the H-S distance as a scan coordinate.

../_images/PES-scan_TS_constraints_1.png

We now need to set the initial value, final value and number of intermediate steps for the H-S distance:

1. Set initial distance to 1.612
2. Set final distance to 1.4
3. Set the number of scan points for coordinate SC-1 to 8
../_images/PES-scan_TS_constraints_2.png

We are now ready to run the calculation:

1. Click on File → Save As... and give it the name “PES_scan”
2. Click on File → Run . This will bring the ADFJobs window to the front
3. Wait for the calculation to finish...

After the calculation is completed, we can visualize the results:

In ADFJobs, select the job “PES_scan” then click on SCM → Movie

This will open the ADFMovie program and show the energy profile of the PES scan.

../_images/PES-scan_TS_adfmovie_pes.png
With ADFMovie into focus, use the the right and left arrow keys to go through the frames

As initial guess for the TS search, we pick the geometry corresponding to the highest energy in the PES scan, i.e. frame number 3.

1. In ADFMovie, using either arrow keys or the slider, select Frame number 3
2. Click on File → Update Geometry in Input

This will bring ADFInput to the front update the geometry of the Pyrithione molecule.

Frequencies calculation¶

It is important to have a good starting Hessian with one imaginary frequency when performing a TS search.

Here we calculate the Hessian matrix that will be used in the subsequent TS search.

In ADFInput:

1. In ADFInput, go to the Main panel
2. Select Task → Single Point
3. Select Followed by → Frequencies
../_images/PES-scan_TS_freq_main.png

We can now run the Frequency calcualtion, which will compute the Hessian and the normal modes:

1. Click on File → Save As... and give it the name “Frequencies”
2. Click on File → Run . This will bring the ADFJobs window to the front
3. Wait for the calculation to finish...

When the calculation is finished, we can visualize the normal modes using ADFSpectra:

In ADFJobs select the job “Frequencies” then click on SCM → Spectra

This will open ADFSpectra:

../_images/PES-scan_TS_adfspectra.png

The first mode should have an imaginary frequency (which in the table is shown as a negative frequency). Click on the line in the table corresponding to the imaginary frequency to visualize the mode.

We are now ready to perform the TS search.

Transition state search¶

1. Open the ADFInput window of the job “Frequencies”
2. Select Task → Transition State
3. Make sure that Followed by is set to Frequencies

The main panel should look like this:

../_images/PES-scan_TS_ts_main.png
1. Go to the panel Details → Geometry Optimization
2. Select Initial Hessian → From File
3. click on the folder next to Initial Hessian From:
4. Select the file dftb.rkf in the folder Frequencies.results

Note that ADFInput still carries the geometry constraint from the previous PES scan calculation, which has to be removed before starting the new calculation:

1. Go to the panel Model → Geometry Constraints and PES Scan
2. Remove the H(13) S(10) constraint by clicking on - in front of it

We can now run the TS search calculation:

1. Click on File → Save As... and give it the name “TS”
2. Click on File → Run . This will bring the ADFJobs window to the front
3. Wait for the calculation to finish...

You can now visualize the TS search using ADFMovie:

In ADFJobs select the job TS and select SCM → Movie
../_images/PES-scan_TS_adfmovie_ts.png

And confirm that the there is exactely one imaginary (negative) frequency by inspecting the IR spectra with ADFSpectra:

In ADFJobs select the job TS and select SCM → Spectra
../_images/PES-scan_TS_adfspectra_ts.png

This concludes the PES scan and transition state search tutorial.

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