Program for calculating rotational constants from an xyz molecular geometry. Supports nonstandard isotopologues and will calculate internal rotation parameters for 1 internal rotor.
The program is self-contained in a single script: moments.py. On Mac/Linux, you can make the script executable and place in a directory contained in your PATH environment variable. The program requires only Python3, numpy, scipy, matplotlib, and pandas. It can also be imported and used as part of a python script; see moments-example.ipynb.
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Quick help
moments.py -h -
Basic usage
moments.py examples/acetaldehyde/acetaldehyde.xyz
- Nonstandard isotopes (change atom 0 to
$^{13}\text{C}$ and atom 2 to$^{18}\text{O}$ )
moments.py examples/acetaldehyde/acetaldehyde.xyz -i 0-13,2-18
- Compute parent and all singly-substituted
$^{2}\text{H}$ ,$^{13}\text{C}$ , and$^{18}\text{O}$ isotopologues
moments.py examples/acetaldehyde-subs/acetaldehyde.xyz -a H,C,O
- Compute all isotopologues with natural abundances greater than 1e-8:
moments.py examples/ocs/ocs.xyz -t 1e-8
- Calculate PAM and RAM Hamiltonian terms (methyl atoms are 1, 4, 5, and 6)
moments.py examples/acetaldehyde/acetaldehyde.xyz -r 1,4,5,6
- As above, but suppress output printing and specify names of output files
moments.py examples/acetaldehyde/acetaldehyde.xyz -r 1,4,5,6 -q -o output.csv -p coordinates.png
- Do not generate plots
moments.py examples/acetaldehyde/acetaldehyde.xyz -r 1,4,5,6 -q -o output.csv --no-plots
By using one of the options -t, -a, -m, -e, or -c, the program will run in a batch mode, performing the calculation for the parent and all selected isotopologues at once. By default, this mode does not generate plots or individual csv output files; instead, the spectroscopic parameters for all isotopologues are printed in one common csv file. The individual output files and/or plots may be generated using the -bf flag, in which the desired output directory should be provided. It will be created if it does not exist. Example commands and outputs are shown in the examples/aceteldehyde-subs/ and examples/ocs/ folders.
The modes provided are:
-t/--threshold-subs: Perform calculations for all isotopologues with natural abundances greater than a given fractional abundance threshold.-a/--auto-subs: Perform single isotopic subsitutions for all atoms of the elements listed, using the second most common isotope for each element.-m/--manual-subs: Perform single isotopic substitutions for each listed atom (by index) and mass number.-e/--explicit-subs: Perform arbitrary isotopic substitutions as provided in a list (which must be enclosed in quotes).-c/--combo-subs: Perform calculations for every possible combination of the listed subsitutions by index and mass number.
See below for further details about these options.
usage: Moments Calculator [-h] [-b] [-q] [-3d] [-s] [-d] [-n MOLNAME]
[-r ROTOR_ATOMS] [-o OUTFILE] [-p PLOTFILE]
[-bo BOUTFILE] [-bf BOUTFOLDER]
[-i ISOTOPES | -t THRESHOLDSUBS | -a AUTOSUBS | -m MANUALSUBS | -e EXPLICITSUBS | -c COMBOSUBS]
filename
Computes rotational constants and optionally internal rotation constants from
xyz coordinates.
positional arguments:
filename Name of xyz file (JMOLplot format)
optional arguments:
-h, --help show this help message and exit
-i ISOTOPES, --isotopes ISOTOPES
Use nonstandard isotopes. Specify as list of index-
massnumber (example: -i 0-18,1-2,2-2,3-13 for
^18O,D,D,^13C, if those are the first 4 atoms in the
file). Alternatively, add the mass number to the end
of the respective line in the input file. Isotopes
specified on the command line will supersede those
specified in the input file. An atom may only appear
once (if the same atom is indicated multiple times,
only the last entry will be used).
-t THRESHOLDSUBS, --threshold-subs THRESHOLDSUBS
Perform calculation for parent and every isotopologue
whose natural abundance is above the indicated
threshold. The threshold may be entered in either
floating point or scientific notation. Note that the
fractional abundance calculation is for the whole
molecule, not the individual nucleus. For instance,
for a hydrocarbon, a threshold of 0.01 will include
all single-13C substitutions, while for a Cl-
containing molecule it would not include any 13-C
substitutions owing to the abundances of the two
primary Cl isotopes. This mode implies --no-csv and
--no-plots; to override this behavior, provide the
--batch-folder option, and the results from each
calculation will be stored there. A single csv output
file will be generated (see --batch-outfile).
-a AUTOSUBS, --auto-single-subs AUTOSUBS
Perform calculation for parent and all singly-
subsituted isotopologues involving the listed
elements (case sensitive). The substitution will be
the second-most naturally abundant isotopologue. This
mode implies --no-csv and --no-plots; to override
this behavior, provide the --batch-folder option, and
the results from each calculation will be stored
there. A single csv output file will be generated
(see --batch-outfile). For example, to generate all D
and ^13C singly-substituted isotopologues, use -a
H,C.
-m MANUALSUBS, --manual-single-subs MANUALSUBS
Perform calculation for parent and the specified
single isotope substitutions. The format is the same
as for --isotopes, with the exception that the same
atom may apper multiple times. This mode implies
--no-csv and --no-plots; to override this behavior,
provide the --batch-folder option, and the results
from each calculation will be stored there. A single
csv output file will be generated (see --batch-
outfile). For example, assume atom 10 is S; to
compute the parent (32S) as well as 33S and 34S, use
-m 10-33,10-34.
-e EXPLICITSUBS, --explicit-subs EXPLICITSUBS
Perform calculation for parent and the specified
substitutions. The format is similar to --isotopes,
with each set of substitutions separated by
semicolons. The list must be contained in quotes.
This mode implies --no-csv and --no-plots; to
override this behavior, provide the --batch-folder
option, and the results from each calculation will be
stored there. A single csv output file will be
generated (see --batch-outfile). For example, assume
atoms 1 and 3 are C and atom 2 is O. Passing -e
"1-13;3-13;1-13,3-13;2-18;1-13,2-18" would perform
the following sets of calculations: 12-16-12,
13-16-12, 13-16-13, 12-16-13, 12-18-12, and 13-18-12.
-c COMBOSUBS, --combo-subs COMBOSUBS
Perform calculation for parent and every combination
of the indicated substitutions. The format is the
same as for --isotopes, with the exception that the
same atom may apper multiple times. This mode implies
--no-csv and --no-plots; to override this behavior,
provide the --batch-folder option, and the results
from each calculation will be stored there. A single
csv output file will be generated (see --batch-
outfile). For example, assume atom 0 is C, atom 1 is
D, and atom 2 is S. Passing -c 0-13,1-2,2-33,2-34
will perform the calculations 12-1-32, 13-1-32,
12-2-32, 12-1-33, 12-1-34, 13-2-32, 13-1-33, 13-1-34,
13-2-33, and 13-2-34.
Input/output options:
-b, --bohr Atomic coordinates in the input file are in Bohr
-q, --quiet Do not print text; only write output files
-3d, --3d-plots Generate 3D plots instead of 2D. WARNING: 3D plotting
is very slow!
-s, --no-plots Do not generate atomic coordinate plots
-d, --no-csv Do not generate output csv file
-n MOLNAME, --name MOLNAME
Molecule name (optional, if omitted it is read from
line 2 of the input file or the input filename)
-r ROTOR_ATOMS, --rotor ROTOR_ATOMS
Indices of atoms in rotor. Atoms are indexed from 0.
(optional, example -r 0,2,3,4)
-o OUTFILE, --outfile OUTFILE
Name of output file. If not specified, will use
{input_filebase}-moments.csv
-p PLOTFILE, --plotfile PLOTFILE
Base filename for atomic coordindate plots. If not
specified, will use {input_filebase}-ab.png, etc
-bo BOUTFILE, --batch-outfile BOUTFILE
Name of output file for a batch calculation. If not
specified, will use {input_filebase}-all.csv. This
argument has no effect if only a single isotopologue
is calculated
-bf BOUTFOLDER, --batch-folder BOUTFOLDER
If provided, output files for each individual
calculation in a batch will be generated and stored
in the indidated folder. The folder will be created
if it does not exist
From a command line, run the script and pass the name of a file containing the molecular geometry in xyz format. As an example:
moments.py examples/acetaldehyde/acetaldyhyde.xyz
The script will print information to standard output (see below for examples) and will generate 2 output files: a csv file containing the spectrosscopic constants and atomic masses, and an image file showing the molecular geometry in principal axis coordinates.
The input file should be in JMOLplot-like format. For example, the examples/acetaldehyde/acetaldehyde.txt file contains:
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C 0.2318720 0.4020210 -0.0000010
C -1.1692990 -0.1492850 -0.0000010
O 1.2348180 -0.2777630 0.0000010
H 0.3048290 1.5072150 -0.0000040
H -1.1484750 -1.2375600 -0.0001760
H -1.7051140 0.2178780 0.8795140
H -1.7052250 0.2181590 -0.8793310
The first line is ignored. The second line may optionally contain the molecule's name, and the remaining lines contain the atoms and their coordinates. By default, the program assumes the coordinates are in units of Angstrom, but this can be modified by passing the -b or --bohr flag. Any whitespace characters may be used to separate the columns. Atom labels are case-sensitive. The script will remove any dummy atoms (indicated by x or X), but any ghost atoms will need to be removed manually.
By default, the program will use the mass corresponding to the most abundant isotopologue for the indicated atom. To perform computations for other isotopologues, pass the desired mass numbers for particular atoms using the -i/--isotopes flag. Atoms are specified by their index, starting from 0, followed by a dash and finally the mass number. For example, to change the first carbon atom (0) to moments.py examples/acetaldehyde/acetaldehyde.xyz -i 0-13,2-18,4-2,5-2,6-2
Several batch modes are available for performing sets of substitutions at once; these are described in the help documentation above, and examples can be found in the examples/acetaldehyde-subs and examples/ocs folders.
If the molecule contains an internal rotor, the program can be used to additional compute internal rotation parameters relevant for the RAM Hamiltonian (e.g., -r/--rotor flag and pass the indices of the rotor in a comma-delimited list. For example,
moments.py examples/acetaldehyde/acetaldehyde.xyz -r 1,4,5,6
Note that the atom numbering starts at 0. For molecules which possess multiple rotors, the script can be run separately for each rotor. See examples/ac-ala-ome.
For additional use cases, see the examples folder.