Introduction to Computational Quantum Chemistry Lesson 1: Molecular Builders & Single Point Calculations Martin Novák (NCBR) Builders and SPs September 22, 2015 1 /14 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 September 22, 2015 2/14 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 • Electron density, Electrostatic potential, Laplacian of el. density... • Generated from Gaussian wavefunction • Wavefunction files: • Gaussian: (Formatted) checkpoint • ADF: TAPEs • Turbomole: mos Martin Novák (NCBR) Builders and SPs September 22, 2015 3/14 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 Martin Novák (NCBR) Builders and SPs September 22, 2015 4/14 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 Martin Novák (NCBR) Builders and SPs September 22, 2015 5/14 Gaussian checkpoint • Stores wavefunction in binary • Convert into ASCII file: • formchk -3 file.chk • Can be read by gaussview • Analysis of orbitals, electron density • Export into cubefiles (ASCII grid files) Martin Novák (NCBR) Builders and SPs September 22, 2015 ^3 c\ 6/14 Practical task II: Turbomole • 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 September 22, 2015 7/14 Preparing the job: Define • 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 • * Proceed to next stage • Method • eht Perform initial guess from Extended Huckel Theory • Accept all defaults Martin Novák (NCBR) Builders and SPs September define - cont. • Method • dft Enter the DFT submenu • on Use DFT • 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 Builders and SPs September 22, 2015 9 /14 Turbomole job • For running TM in parallel mode use the parallel build • module add turbomole:6.05:x86.64:para • Infinity selects it by default if ncpu > 1 mnovak@wolf #!/bin/bash module add turbomole:6.05 jobex -ri -c 1024 > dft.out Martin Novák (NCBR) Builders and SPs September 22, 2015 10/14 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 September 22, 2015 11 /14 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 working only on wolf23 atm Martin Novák (NCBR) Builders and SPs September 22, 2015 12/14 • Using GUI (the easiest way) • Write from scratch • Keywords in blocks: ATOMS* definition of geometry in xyz SYMMETRY NOSYMM Switch off all symmetry XC* DFT functional BASIS* Basis set SAVE TAPE21 Save wavefunction NOPRINT LOGFILE 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 22, 2015 13/14 Running ADF • adf < input.adf > output.out Martin Novák (NCBR) Builders and SPs September 22, 2015 ^3 c\ 14/14