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Manual For GUINEA

Overview:

GUINEA evaluates vibrational energies and properties using explicitly summed Rayleigh-Schroedinger type perturbation theory. Vibrational energies, transition intensities, dipole moment corrections and harmonic derivatives may all be calculated at the VPT2 (second-order) and VPT4 (fourth-order) levels of perturbation theory. The numerical sums are written in such a way as to minimize the number of unnecessary intermediate states generated. This formulation is quite efficient, even for large numbers of modes (up to 24 modes have been tested and such calculations may be run in real-time). GUINEA may also explicitly form and diagonalize an effective Hamiltonian, followed by a transformation of other quantities such as transition moments, which may be useful for resonant systems. GUINEA uses for defining the necessary operators the files generated by the xcubic program of CFOUR, e.g. "quadratic", "cubic", "rota", "coriolis", etc. The files defining the elecronic potential must be present, while the rotational files and dipole moment files are optional, as are the main job archive files JOBARC/JAINDX. GUINEA will optionally use the additional "didq" file for third- and fourth-order Coriolis terms.

Input:

GUINEA accepts user input either from a file, such as with the syntax "guinea < input_file", or interactively from the terminal. By default, interactive sessions prefix input lines with a prompt, ">", for clarity, while input from a file does not. Keywords are given one to a line, with any extra input for that keyword on one or more additional lines. Blank lines are ignored.

Keywords are grouped into two categories: "state commands" and "action commands". State commands add to, remove from, or otherwise modify the groups of states, called "sets", upon which the action commands act. A set may have any number of states, although only 100 sets may exist at any one time. Each set has its own settings for diagonalization, while the reference state and temperature (used in the Boltzmann factor for hot bands) are shared among all sets. Action commands then run the various calculations, or specify which calculations to run later, on the states in the selected set.

Units:

  • All energies are in wavenumber units (cm-1).
  • Intensities are in km/mol.
  • Dipole moment corrections are in milli-Debye (mD).
  • First harmonic derivatives are unitless, and second harmonic derivatives are in reciprocal wavenumber units (cm).

Memory Management:

Unlike ACES2, GUINEA uses its own memory management in which segments are allocated dynamically rather than from a common block. Total memory usage is limited by a user-defined limit (default is unlimited). The current version may have a few memory leaks and/or inconsistencies in the reported memory usage. However, these should be slight enough as to not affect normal usage (unless perhaps a huge number of states are shuffled in and out or the number of modes is very very large).

Keywords:

This is a summary of all of the available keywords. If a keyword accepts additional input, the syntax will be given. Note that when the summary for a calculation is printed, states are listed in order of increasing energy, not the order in which they were added to the set, and that states are sorted by symmetry as they are added to a set. For diagonalized sets, the state printed for each level is the dominant contribution the that level's eigenvector.

I. Global commands


print
Sets the print verbosity level: 1 = display < 2 = interactive < 3 = full; interactive is the default for terminal input, and display is the default for input from a file.
    print
    [1,2,3]

    OR

    print
    [display,interactive,full]
?print
Lists the current print verbosity level.
relative
Sets that printed energies should be relative to ground (i.e ZPVE is not included).
!relative
Sets that printed energies should be absolute (i.e ZPVE is included).
?relative
Lists whether printed energies are relative to ground.
freqformat
Sets the format for printed frequencies.
    freqformat
    width.precision
intformat
Sets the format for printed intensities.
    intformat
    width.precision
dipformat
Sets the format for printed dipole moment corrections.
    dipformat
    width.precision
inttype
Sets the type of transition intensities to print.
    inttype
    [total,cartesian,both]
diptype
Sets the type of dipole moment corrections to print.
    diptype
    [total,cartesian,both]
memory
Sets the maximum amount of memory to use, initially unlimited. The amount must be integer for byte amounts but may be floating point for larger units.
    memory
    n    [in bytes, 0=unlimited]

    OR

    memory
    n[KB,MB,GB]
?memory
Lists the current memory limit and use.
polyad
Define a polyad from a set of states given as a list of integers, one for each normal mode. Defined polyads can be included in subsequent definitions of states as if they were additional normal modes (listed in the order defined). A polyad definition may include previously defined polyads. Polyads may be used in any set.
    polyad
    n
    p_1,1 p_1,2 ... p_1,m
    p_2,1 p_2,2 ... p_2,m
    ...
    p_n,1 p_n,2 ... p_n,m
!polyad
Remove the specified polyad by index.
    !polyad
    i
?polyad
List all currently defined polyads and their order.
reference
Set the reference for hot bands.
    reference
    r_1 r_2 ... r_m
?reference
List the reference for hot bands.
temp
Sets the temperature for hot bands.
?temp
Prints the temperature for hot bands.
adjfreq
Adjusts a harmonic frequency empirically.
    adjfreq
    i
    frequency
load
Runs all of the commands in the given file.
    load
    filename
save
Write a file containing all of the commands necessary to reproduce the current program state (excluding the output of any calculations or queries).
    save
    filename
done
Bye-bye! (also "quit", "exit", "bye")

II. State commands


states
Add all of the specified states to the current set. States are given as a list of integers, one for each normal mode (and optionally, each polyad).
    states
    n
    s_1,1 s_1,2 ... s_1,m
    s_2,1 s_2,2 ... s_2,m
    ...
    s_n,1 s_n,2 ... s_n,m
!states
Remove all of the specified states from the current set.
    !states
    n
    s_1,1 s_1,2 ... s_1,m
    s_2,1 s_2,2 ... s_2,m
    ...
    s_n,1 s_n,2 ... s_n,m
?states
List all of the states in the current set.
!indices
Remove the states with the given indices from the current set.
    !indices
    n
    i_1
    i_2
    ...
    i_n
combination
Add all of the states from the given combination to the current set. This is all states with total number of quanta m in modes q_1 q_2 ... q_n. n=0 selects states with total number of quanta m in any mode
    combination
    m n
    q_1 q_2 ... q_n

    OR

    combination
    m 0
!combination
Remove all of the states from the given combination from the current set. Same syntax as 'combination'.
    !combination
    m n
    q_1 q_2 ... q_n

    OR

    !combination
    m 0
copyset
Add all states from the given set to the current set.
    copyset
    i
fermi
Enables Fermi resonance terms in the effective Hamiltonian for the current set.
!fermi
Disables Fermi resonance terms in the effective Hamiltonian for the current set.
?fermi
Lists whether the current set includes Fermi resonance terms or not.
dd
Enables Darling-Dennison resonance terms in the effective Hamiltonian for the current set.
!dd
Disables Darling-Dennison resonance terms in the effective Hamiltonian for the current set.
?dd
Lists whether the current set includes Darling-Dennison resonance terms or not.
diagonalize
Enables diagonalization of the effective Hamiltonian for the current.
!diagonalize
Disables diagonalization of the effective Hamiltonian for the current.
?diagonalize
List whether the current set is diagonalized.
set
Creates a new set.
setset
Sets the current set.
    setset
    i
?set
Lists basic information about all of the sets (does not list states).
!set
Removes the given set, 0 for current set.
    !set
    i
copyset
Copies all states from the specified set to the current set.
    copyset
    i

III. Action commands


vibration
Set the calculation level for vibrational energies (default vpt2).
    vibration
    [harmonic,vpt2,vpt4]
?vibration
List the current calculation level for vibrational energies.
intensity
Set the calculation level for intensities (default off).
    intensity
    [off,harmonic,vpt2]
?intensity
List the current calculation level for intensities.
dipole
Set the calculation level for dipole moment corrections (default off).
    dipole
    [off,harmonic,vpt2]
?dipole
List the current calculation level for dipole moment corrections.
harmderiv
Runs a harmonic derivative calculation.
calc
Runs the specified calculations on the current set.
?calc
Lists which calculations are turned on.

Examples

Example 1 Input Example 1 Output
(this example uses a quartic force field of water)

See Also

Calculation Of Anharmonic Force Fields

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Page last modified on January 16, 2020, at 09:12 PM
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CFOUR is partially supported by the U.S. National Science Foundation.