Gparse.m

From Spinach Documentation Wiki
Jump to: navigation, search

A parser for Gaussian03 and Gaussian09 calculation logs.

Syntax

    props=gparse(filename,options)

Description

The function extracts all potentially useful information from the Gaussian log. The following sections must be added to the route section of the Gaussian03/9 input file to produce a useful log:

    #p nmr=(giao,spinspin,susceptibility) output=pickett

Examples of complete Gaussian input files that perform geometry optimisation followed by magnetic properties calculations may be downloaded here, here, and here. Some real-life Gaussian logs that may be used for practice with data import are given in examples/standard_systems directory.

Arguments

    filename - the name of the file to be parsed, a character string

    options  - a cell array of character strongs, the following:

               'g_nosymm'   - turns off g-tensor symmetrisation

               'cst_nosymm' - turns off shielding tensor symmetrisation

               'hfc_nosymm' - turns off hyperfine tensor symmetrisation 

Returns

The following output fields are returned, if the corresponding information is present in the log file:

    props.inp_geom         - input geometry, natoms x 3 array, Angstrom

    props.std_geom         - standard geometry, natoms x 3 array, Angstrom

    props.natoms           - number of atoms, an integer

    props.method           - model chemistry Gaussian had used, e.g. 'B3LYP'

    props.energy           - SCF energy, Hartree

    props.hfc.iso          - isotropic hyperfine couplings, natoms x 1 array, Gauss

    props.hfc.full.eigvals - HFC eigenvalues, natoms x 1 cell array of 3-vectors, Gauss

    props.hfc.full.eigvecs - HFC eigenvectors, natoms x 1 cell array of 3x3 matrices

    props.hfc.full.matrix  - HFC tensors, natoms x 1 cell array of 3x3 matrices, Gauss

    props.g_tensor.eigvecs - g-tensor eigenvectors, 3x3 matrix

    props.g_tensor.eigvals - g-tensor eigenvalues, 3-vector, Bohr magneton units

    props.g_tensor.matrix  - g-tensor, 3x3 matrix, Bohr magneton units

    props.cst              - absolute shielding tensors, natoms x 1 cell array of 3x3 matrices, ppm relative to bare nucleus in vacuum

    props.j_couplings      - isotropic J-couplings, nspins x nspins matrix, Hz

    props.srt              - spin-rotation tensor, nspins x 1 cell array of 3x3 matrices, Hz

    props.nqi              - nuclear quadrupole interaction tensors, nspins x 1 cell array of 3x3 matrices, Hz

    props.chi              - magnetic susceptibility tensor, 3x3 matrix, cubic Angstroms

    props.gibbs            - Gibbs free energy, Hartree

    props.symbols          - atomic symbols, nspins x 1 cell array of character strings

    props.atomic_numbers   - atomic numbers, nspins x 1 array of integers

    props.filename         - log file name, a character string

    props.error            - set to 1 if the log contains an error message

Examples

A typical example of a Spinach input that uses data import from a Gaussian log appears below.

    % Read the spin system properties (vacuum DFT calculation)
    options.min_j=1.0;
    [sys,inter]=g2spinach(gparse('../standard_systems/sucrose.log'),{ {'H','1H'} },31.8,options);
    
    % Magnet field
    sys.magnet=14.1;
    
    % Basis set
    bas.formalism='sphten-liouv';
    bas.approximation='IK-2';
    bas.connectivity='scalar_couplings';
    bas.space_level=2;
    
    % Relaxation theory parameters
    inter.relaxation={'redfield'};
    inter.rlx_keep='secular';
    inter.tau_c=1e-9;
    
    % Spinach housekeeping
    spin_system=create(sys,inter);
    spin_system=basis(spin_system,bas);
    
    % Sequence parameters
    parameters.spins={'1H'};
    parameters.rho0=state(spin_system,'L+','1H','cheap');
    parameters.coil=state(spin_system,'L+','1H','cheap');
    parameters.decouple={};
    parameters.offset=1800;
    parameters.sweep=5000;
    parameters.npoints=8192;
    parameters.zerofill=65536;
    parameters.axis_units='ppm';
    parameters.invert_axis=1;
    
    % Simulation
    fid=liquid(spin_system,@acquire,parameters,'nmr');
    
    % Apodization
    fid=apodization(fid,'crisp-1d');
    
    % Fourier transform
    spectrum=fftshift(fft(fid,parameters.zerofill));
    
    % Plotting
    plot_1d(spin_system,real(spectrum),parameters);

Notes

  1. Gaussian prints all anisotropic quantities relative to what it calls "standard geometry".
  2. Chemical shielding is not the same as chemical shift.
  3. Spin-rotation tensors are imported, but not used anywhere in Spinach at the moment.
  4. This function parses Gaussian logs. Use g2spinach.m to convert that information into Spinach input structures.
  5. The parser is a bit old-school. If you are proficient with regular expressoins, we would really appreciate a hand.

See also

oparse.m, g2spinach.m


Version 1.9, authors: Ilya Kuprov, Gareth Charnock, Jennifer Handsel