Introduction to Computational Quantum Chemistry
Practical Lesson 1: Molecular Builders & Single Point Calculations
Martin Novák (NCBR)
Builders and SPs
September 26, 2017      1 /1
Available builders on Wolf cluster
• Avogadro
• + fast
• + free
• + forcefield preoptimization
• Gabedit
• + aligning structures in coordinate system
• - relatively slow
• Gaussview
• + generating specific distances/angles/dihedrals
• + aligning molecules
• - commercial
• Nemesis
• No idea
Martin Novák (NCBR)
Builders and SPs
□       SP        -        =        5 -Oc\o September 26, 2017 2/1
Structure files
• The most widely used in QM are XYZ and Z-matrices
• Cube files:
• Grid of points with specific values of a given quality
o Electron density Electrostatic potential, Laplacian of el. density
• Generated from Gaussian wavefunction
• Wavefunction files:
• Gaussian: (Formatted) checkpoint o ADF: TAPEs
• Turbomole: mos
Martin Novák (NCBR)
Builders and SPs
September 26, 2017 3/1
Practical task I: Gaussian
• Prepare input file for calculations:
Most builders can generate the file for you (usually has to be edited)
• You can write it yourself from scratch General suffix is either ".com" or ".gjf"
• Use:
• 2 cores
• 3 GB of memory
• Save the wavefunction
• Gaussian manual:
http://www.gaussian.com/g_tech/gO 9ur.htm
• Add gaussian module
• g09 input.com
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Builders and SPs
September 26, 2017
4/1
Gaussian logfile
• Read the logfile, see the structure, extract information
* qmutil: nifty module to extract data from gaussian output:
• extract-gopt-ene logfile
• extract-gopt-xyz logfile
• extract-gdrv-ene logfile
• extract-gdrv-xyz logfile
• extract-xyz-str xyzfile framenumber © extract-xyz-numstr xyzfile
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Martin Novák (NCBR)
Builders and SPs
September 26, 2017
Gaussian checkpoint
• Stores wavefunction in binary
• Convert into ASCII file:
• formchk -3 file.chk
• Can be read by gaussview 1
• Analysis of orbitals, electron density
• Export into cubefiles (ASCII grid files)
1A bug in Gaussview: Change word "independent" to "independant".    =    i <o<K<y
Builders and SPs September 26, 2017 6/1
Martin Novák (NCBR)
Practical task I: furbomole
• Turbomole is probably the fastest code available here (for Gaussian-type basis functions)
• Tmolex as GUI (licence not available)
• Rl-J approximation of coulombic term - extremely fast (meta)GGA SCF convergence
• Interactive preparation of the input using define
• Turbomole manual: http:
//www.turbomole-gmbh.com/turbomole-manuals.html
Martin Novák (NCBR)
Builders and SPs
□       SP        -        =        5 -Oc\o September 26, 2017 7/1
Preparing the job: Define
o First two items can be skipped
• Molecular geometry:
• a coord Reads in the geometry
• ired Generates internal coordinates
• * Proceed to next stage
• Basis set:
• b all def2-SVP Assign this basis set to all atoms 9 * Proceed to next stage
• Method
• eht Perform initial guess from Extended Huckel Theory
• Accept all defaults
Martin Novák (NCBR)
Builders and SPs
□       SP        -        =        5 -Oc\o September 26, 2017 8/1
define - cont.
• Method
• dft Enter the DFT submenu
• on Use DFT
9 tunc b-lyp Select the functional
• grid m5 Increase the gridsize to m5
• * Exit the submenu
• ri Enter the Rl submenu
• m Assign memory for Rl
• 2000 As much as possible
• on Use Rl
• * Exit the submenu
• dsp Use dispersion correction
• on Use Grimme D3 correction
• * Exit the submenu
• marij Multipole-Accelerated Rl-J
• * End the define session
Martin Novák (NCBR)
Builders and SPs
□       SP        -        =        5 -Oc\o September 26, 2017 9/1
Turbomole job
For running TM in parallel mode use the parallel build module add turbomole:7.00:x86.64:para Infinity selects it by default if ncpu > 1
mnovak@wolf
#!/bin/bash
module add turbomole:7.00 jobex -ri -c 1024 > dft.out
Martin Novák (NCBR)
Builders and SPs
September 26, 2017 10/1
Turbomole output
File Contens
dft.out Optimization procedure
energy Energies of steps
gradient Gradients of steps
mos Molecular orbitals
freq.out Output from aoforce program
Martin Novák (NCBR)
Builders and SPs
□       SP        -        =        5 -Oc\o September 26, 2017      11 /1
Practical task III: ADF
• Only software using Slater-type orbitals
• Up to 2-component relativistic effects (ZORA+SpinOrbit)
• Awful output file structure
• Extremely fast and efficient
• ADF GUI: adfview
• Very bad memory handling
Martin Novák (NCBR)
Builders and SPs
□       SP        -        =        5 -Oc\o September 26, 2017 12/1
Preparing ADF input
• Using GUI (the easiest way)
• Write from scratch
• Keywords in blocks:
ATOMS*
SYMMETRY NOSYMM
XC*
BASIS*
SAVE TAPE21
NOPRINT LOGFILE
definition of geometry in xyz Switch off all symmetry DFT functional Basis set
Save wavef unction
Do not print input into logfile
Section terminated by END keyword
Manual pages: http : //www. scm.com/Doc/Doc2014/ADF/ ADFUsersGuide/pagel.html
Martin Novák (NCBR)
Builders and SPs
September 26, 2017 13/1
Running ADF
• adf < input.adf > output.out
Martin Novák (NCBR)
Builders and SPs
September 26, 2017 14/1