PyMoments

This is a Python library for calculating rotational constants from some standard forms of input, for example XYZ and Z-matrix representations. Additionally, there is some high-level functionality that will help streamline certain workflows involving rotational constants; the most useful probably is the ability to automatically compute isotopic shifts for common isotopologues.

Instructions

Installation should be relatively straightforward, either clone this repository followed by pip, or directly:

pip install git+https://github.com/laserkelvin/PyMoments

If you use PyMoments for your work, consider citing the Zenodo DOI (provided in the badge above).

Usage

After installing, you should have access to pymoments as both a library and a command-line call accessible simply by running pymoments:

➜ pymoments --help
Usage: pymoments [OPTIONS] INPUT_FILE

  Read in internal coordinates from an input file, and print out the
  rotational constants, etc. formatted for reading.

  Takes the path to the file as input, as well as `format` argument that
  specifies which parser to use. Currently, three formats are supported:

  1. Legacy internal coordinate format

  2. Z-matrix/internal coordinate format

  3. XYZ format

  For the latter two formats, there is additional support for automatic
  generation of isotopologues for a molecule. The options `iso` and
  `abundance` control whether these routines are used, and in the latter
  case, what the minimum fractional abundance to consider. For example, the
  default value is 1e-4, which is sufficiently low to account for deuterium.

  Parameters ---------- filepath : str     Path to the legacy ZMAT file

  format : str     Format of the input file; this determines the parser
  used to create the `Molecule` object.

Options:
  --format [legacy|zmat|xyz]  Specifies the file format to parse.
  --iso                       Controls whether isotopologues are generated.
  --abundance FLOAT           Decimal natural abundance threshold for rare
                              isotopes.

  --help                      Show this message and exit.

The minimum input for this command is the filepath to an input file. Additional options are available, which support different file formats. The preferred way for pymoments is to use the --format=zmat, which uses the internal coordinate representation that looks something like this:

O
H 1 0.79
H 1 0.79 2 108.0

Cartesian coordinates are also supported:

O 0.030541 0.042037 -0.000000
H -0.759459 0.042037 -0.000000
H 0.274665 -0.709298 0.000000

You can find these in the tests folder. As an example of how to run the command line too, you can run pymoments tests/h2o.xyz --format=xyz --iso in the root directory. This is the kind of output you can expect:

===================== Primary input
Formula: OHH
Masses (AMU): [15.99491462  1.00782503  1.00782503]
Short masses (AMU): [16.  1.  1.]
===================== Parameters
Rotational constants (MHz): [1309350.48351127  613808.06588457  417901.00358681]
Inertial axis vectors:
[[ 8.09016994e-01 -5.87785252e-01  0.00000000e+00]
 [-5.87785252e-01 -8.09016994e-01 -6.12323400e-17]
 [-3.59914664e-17 -4.95380036e-17  1.00000000e+00]]
===================== Derived values
Asymmetry parameter: -0.5605
Inertial defect (amu A**2): 0.0000
Scaling factor: 1.0

Rare isotopologues

When using the command line tool, you can specify the flag --iso, which will automatically generate all isotopologues with natural abundance above a certain value specified with --abundance=1e-4. This value is set by default, and includes deuterium isotopologues. Symmetry is taken into account in a dumb way: before handing you the isotopologue data, we check that the rotational constants are unique. In an ideal world, you can probably do a better job with internal coordinate or cartesian coordinate transforms, but that is left to the reader.

pymoments as a library

The command line tool provides a very quick way to calculate isotopologues, or just to do sanity checks with the rotational constants and structure. There is additional functionality provided, however, if you use pymoments as a library instead. For example, you can manipulate Molecule objects with math operations and comparisons:

water = Molecule.from_zmat_str("""O
    H 1 0.79
    H 1 0.79 2 108.0"""
    )
com, rotational_constants, pmm = water.orient()

isotopologues = water.generate_isotopologues()

# scalar scaling factor; can also be a NumPy array
scaling = 0.9729
# returns a new list of scaled values
scaled_isotopologues = [isotopologue * scaling for isotopologue in isotopologues]

# another way to obtain scaling factors
d2o = isotopologues[-1]
# this sets the scaling attribute of water; can access through water.scaling
water / d2o
# returns a new list of scaled values
scaled_isotopologues = [isotopologue * water for isotopologue in isotopologues]

Contributing

Open to pull requests and contributions.