Contents
Table of Contents
Introduction
.. ADF-GUI modules
.. ADF installation
.. .. UNIX (such as Linux) users
.. .. Windows users
.. .. Macintosh users
Tutorials
.. Tutorial 1: ADF-GUI overview: 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
.. .. .. .. Create the first carbon atom
.. .. .. .. Create the second carbon atom
.. .. .. .. Create the oxygen atom
.. .. .. .. Add the hydrogens
.. .. .. .. Pre-optimize the geometry
.. .. .. Viewing the molecule
.. .. .. .. Rotate, translate, or zoom
.. .. .. .. Atom colors
.. .. .. .. Revert to default view options
.. .. .. .. Save picture
.. .. .. Molecular conformation
.. .. .. .. Rotate such that you look along the C-C axis
.. .. .. .. Select the top CH3 group
.. .. .. .. Rotate the selection
.. .. .. .. Back to Staggered Geometry
.. .. .. Getting and setting geometry parameters
.. .. .. .. Bond length
.. .. .. .. Bond angle
.. .. .. .. Dihedral angle
.. .. .. .. Coordinates
.. .. .. Extending and changing your molecule
.. .. .. .. Delete an atom
.. .. .. .. Change the type of an atom
.. .. .. .. Change the bond type of an existing bond
.. .. .. .. Add new (bonded) atoms
.. .. Step 3: Select calculation options
.. .. .. Preset
.. .. .. Title
.. .. .. XC functional
.. .. .. Basis set
.. .. .. Integration
.. .. .. 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
.. .. .. ADF Output: BOB
.. Tutorial 2: ADF-GUI overview: excitation energies of ethene
.. .. Step 1: Start ADFinput
.. .. Step 2: Create your ethene molecule
.. .. Step 3: Optimize the geometry
.. .. Step 4: Calculate the excitation energies
.. .. .. Select calculations options
.. .. .. Run the calculation
.. .. Step 5: Results of your calculation
.. .. .. Logfile: ADFtail
.. .. .. Energy levels: ADFlevels
.. .. .. Excitation spectrum: ADFspectra
.. .. .. Transition density: ADFview
.. .. .. ADF Output: BOB
.. .. .. Closing the ADF-GUI modules
.. Tutorial 3: ADF-GUI overview: vibrational frequencies 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
.. .. .. Logfile: ADFtail
.. .. .. IR-spectrum (vibrational spectrum): ADFspectra and ADFmovie
.. Tutorial 4: Structure Building
.. .. Step 1: Start ADFinput
.. .. Step 2: Building an ethanol molecule
.. .. .. Add a methyl group to the methane
.. .. .. Add the hydroxyl group
.. .. .. Add another 'solvent' ethanol
.. .. Step 3: Building a peptide chain
.. .. Step 4: Metal complexes and ligands
.. .. .. Predefined Metal Complex Geometries
.. .. .. Bidentate Ligands
.. .. .. Modifying the Plane Angle
.. .. Step 5: Your own structures library
.. .. .. Defining your structures
.. .. .. Using dummy atoms
.. .. Step 6: Internal Matrix and Linear Transit
.. .. .. Building a biphenyl for a linear transit run
.. .. .. Re-ordering atoms in the internal matrix
.. Tutorial 5: 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
.. Tutorial 6: TlH Spin-Orbit Coupling
.. .. Step 1. Prepare molecule
.. .. Step 2. Set calculation options
.. .. Step 3: Run your calculation
.. .. Step 4. Results of the calculation
.. .. .. TlH energy diagram
.. .. .. Visualization of spinors
.. .. Step 5. Calculate the atomization energy including spin-orbit coupling
.. .. .. The Tl atom
.. .. .. The H atom
.. .. .. TlH atomization energy
.. Tutorial 7: QM/MM using PDB file
.. .. Step 1. Use the visualization options
.. .. Step 2. Set up the QM/MM model system
.. .. Step 3. Set up the calculation details
.. .. Step 4. Save and view the protein in solvent
.. .. Step 5. Perform a trivial QM/MM calculation on a small system
.. Tutorial 8: ADF Fragment Analysis
.. .. Step 1. Build Ni(CO)
4
.. .. Step 2. Define fragments
.. .. Step 3. Run the fragment analysis and view the results
.. .. Step 4. Build PtCl
4
H
2
2-
.. .. Step 5. Define fragments
.. .. Step 6. Run the fragment analysis and view the results
Tutorials
Tutorial 1: ADF-GUI overview: geometry optimization of ethanol
Step 1: Preparations
Step 2: Create your molecule
Step 3: Select calculation options
Step 4: Run your calculation
Step 5: Results of your calculation
Tutorial 2: ADF-GUI overview: excitation energies 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
Tutorial 3: ADF-GUI overview: vibrational frequencies 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
Tutorial 4: Structure Building
Step 1: Start ADFinput
Step 2: Building an ethanol molecule
Step 3: Building a peptide chain
Step 4: Metal complexes and ligands
Step 5: Your own structures library
Step 6: Internal Matrix and Linear Transit
Tutorial 5: 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
Tutorial 6: TlH 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
Tutorial 7: QM/MM using PDB file
Step 1. Use the visualization options
Step 2. Set up the QM/MM model system
Step 3. Set up the calculation details
Step 4. Save and view the protein in solvent
Step 5. Perform a trivial QM/MM calculation on a small system
Tutorial 8: ADF Fragment Analysis
Step 1. Build Ni(CO)
4
Step 2. Define fragments
Step 3. Run the fragment analysis and view the results
Step 4. Build PtCl
4
H
2
2-
Step 5. Define fragments
Step 6. Run the fragment analysis and view the results
5.9.17.106
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