Computational chemistry with GAMESS: a very brief overview with examples
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1 Computational chemistry with GAMESS: a very brief overview with examples PHY-6120 Molecular Physics (Spring 2015), UConn Phys. Dept. Feb 17 th 2015
2 H = ħ2 2μ i Intro: V(R) for diatomic molecules + k Z A Z B e2 R AB i 2 ħ2 2 I I,i 1 2 M I + I i> j k Z I e 2 Born-Oppenheimer approximation: separate electronic and nuclear motion k e 2 fix R = R AB, solve for the electronic motion, then solve for the slower nuclear motion higher-order electronic correlations (core-valence) neglected Energies and total wavefunctions r ij r A, i R AB r Ii +... A B M I m e i E = E elec + G (v)+ F ( J ) ψ i, v BO elec. = Φ i, Λ, S, Σ (r, R)χ nucl. v ( R) Non-trivial (14 terms total, different bases sets) plus non-born-oppenheimer terms, perturbations,...
3 LiNa molecule, 2 lowest electronic states V ex R = ±A R exp R V lr R = C 6 R C 8 6 R C 10 8 R 10
4 Quantum chemistry ab-initio codes Popular: GAMESS (free, opensource) NWCHEM (mostly commercial) GAUSSIAN (commercial) MOLPRO (commercial) Common methods: Hartree-Fock (HF) post-hartree-fock CC, CCSD, CCSD(T) MP2 CI and variants Density Functional Theory (DFT)
5 GAMESS on out machines our machines: hex.phys.uconn.edu (16 CPUs, 32 GB RAM) octane.phys.uconn.edu (8 CPUs, 8 GB RAM) pauli.phys.uconn.edu, fermi.phys.uconn.edu (Côté group research) on hex.phys.uconn.edu: /scratch/gacesa/gamess -> GAMESS installation /scratch/gacesa/gamess-class/_sample-input.zip -> sample inputs create folder corresponding to your username in /scratch/gacesa/gamess-class/ : e.g. mkdir /scratch/gacesa/gamess-class/gacesa
6 GAMESS input Main input groups: $CONTRL - (type of wavefunction, method, things to calculate) $SYSTEM - system parameters (memory, directories,...) $BASIS - the basis is specified here $DATA (required) - molecular composition and geometry selected optional groups $ZMAT (if NZVAR>0 in $CNTRL), $SCF (if $SCFTYP = RHF, UHF, or ROHF; required for GVB) $DFT, $TDDFT,..., $CIS (excited states), $MP2, $CP(MC)HF (solution of response HF equations), $MASS (isotopes),...
7 $CONTRL group SCFTYP = { RHF, UHF, ROHF, GVB, MCSCF, none } elec. correlation: MPLEVL, CITYP, CCTYP, DFTTYP, VBTYP,... RUNTYP = { ENERGY (def), GRADIENT, HESSIAN, OPTIMIZE, SADPOINT, OPTFMO, PROP, NACME, TRANSITN,... } ICHARG = molecular charge (default = 0) MULT = 1 (singlet = default), 2 (doublet), 3 (triplet),... Geometry: COORD (mol. coord.), UNITS, NZVAR Pseudopotentials: PP = { NONE, READ ($ECP), MCP,... } LOCAL = {NONE, BOYS, SVD,... } - orbital localization ($LOCAL)
8 $BASIS group Three ways to specify a basis (GBASIS, BASNAM, EXTFIL); or in $DATA GBASIS = MINI, DZV, TZV (good for start; ) ECP, MCP, empirical... check page of input.pdf custom: support.scinet.utoronto.ca/wiki/index.php/user_codes#tips_from_the_fekl_lab
9 $DATA group TITLE GROUP, NAXIS specified as a symmetry group (en.wikipedia.org/wiki/schoenflies_notation) e.g. Cnv 2 = C2v ; note: C1 = no symmetry; see e.g. Cotton "Group Theory" skip Lines 3 and 4 (for our purposes) and replace with a blank line for COORD=UNIQUE in ($CONTRL): (other formats possible) NAME (10 chars), ZNUC (nucl. charge), X, Y, Z (coordinates) Example for H-H molecule: $DATA hydrogen molecule, no symmetry C1 H H $END
10 A very simple input file for H 2 (X 1 Σ + ) H2-rhf.inp $CONTRL SCFTYP=RHF RUNTYP=ENERGY $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 $END $DATA hydrogen molecule with 6-G31 C1 H H $END Pople notation for the basis: 6 Gaussians for the inner elec, 4 (3+1) for valence Polarized orbitals included in the basis set demonstration: run GAMESS for H2-rhf.inp (on hex):./rungms H2-rhf.inp >& H2-rhf.log
11 GAMESS output /scratch/gamess-class/$user/h2-rhf.log check for these: number of SCF cycles needed for convergence (section "RHF SCF CALCULATION") the HF energy (section "ENERGY COMPONENTS") the dipole moment (section "ELECTROSTATIC MOMENTS") (optional) visualization (using VMD or similar)
12 Example: LiH potential energy curve (PES) click on constants of diatomic molecules r e = Bohr (ground state) demonstration #1: run GAMESS for LiH-rhf.inp edit/create the file -> replace '???' with correct values./rungms lih-rhf.inp >& lih-rhf.log demonstration #2: lih-rhf-scan.inp edit/create the file lih-rhf-scan.inp./rungms lih-rhf-scan.inp >& lih-rhf-scan.log./scanlog2dat.sh./xmgrace -free lih-rhf-scan_pes.dat
13 Excited states simplest: Equation-of-motion (EOM) methods works with RHF, CCSD(T), and some higher level methods pay attention to the symmetry / electron multiplicity! parsing output becomes more complicated add CCTYP into $CONTRL, and $CCINP & $EOMINP groups $CONTRL SCFTYP=RHF CCTYP=EOM-CCSD RUNTYP=ENERGY $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 $END $CCINP MULT=1 $END $DATA H2 with 6-G31 + first excited state C1 H H $END
14 Details about basis sets
15
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