General Information for CLI
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PM has a collection of command line interfaces (CLI) for performing tasks. For the most part, a given CLI is associated with a class within PM, though there are CLI’s that rely on multiple classes. As outlined below, basic documentation about all commands can be obtained at the command line, and therefore this website only provides individualized attention to selected CLI’s which are nontrivial.
Each CLI starts with the prefix pm-, followed by some descriptive word,
such as pm-lattice, pm-crystal, etc. All PM CLI’s can be seen via
tab completion
$ pm-<TAB><TAB>
pm-abinitio-output pm-displaced-crystal pm-lattice-ftg
pm-cluster pm-disp-qrep pm-orbit-qrep
pm-convert-id-main-to-dev pm-file-hive pm-phonons-via-irr-derivatives
pm-crystal pm-get-variable-doc pm-point-group-viewer
pm-crystal-format pm-irr-rep-product pm-prototype-xtal
pm-crystal-ftg pm-irr-rep-symmetric-product pm-star-rep
pm-crystal-variables pm-kpoints-fsg pm-tensor-irr-rep
pm-crystal-viewer pm-lattice
Assuming that the python module
argcomplete has been installed and set up, all CLI options can be seen
by typing the command name followed by - and pressing tab twice.
$ pm-crystal -<TAB><TAB>
--basis-atoms --input-files --shift-atom
--convert-to-supercell --lattice-vectors --shift-into-cell
--degub --permute-atoms --shift-origin
-h --precision --strict-input
--help --print-attribute --use-cartesian-coordinates
-i --rotate-lattice-vectors
For flags that have restricted inputs, tab completion will show valid choices:
$ pm-crystal --print-attribute<TAB><TAB>
atom_names lattice_vectors_length reciprocal_vectors_angle
atoms_cartesian mass_vector reciprocal_vectors_length
atoms_species_map natoms reciprocal_volume
basis_atoms nspecies space_dim
center positions species
lattice_dimension positions_cartesian species_names
lattice_vectors precision species_to_elements
lattice_vectors_angle reciprocal_vectors volume
Executing -h will print out the command information
$ pm-crystal -h
usage: pm-crystal [-h] --basis-atoms ATOMS --lattice-vectors VEC [--shift-into-cell]
[--convert-to-supercell S] [--use-cartesian-coordinates] [--permute-atoms X]
[--shift-origin X] [--rotate-lattice-vectors O] [--shift-atom AMP]
[--precision N] [--degub] [--input-files FILE [FILE ...]] [--strict-input]
[--print-attribute ATTR [ATTR ...]]
Exposes the Crystal class, allowing the basic properties of a crystal to be constructed.
options:
-h, --help show this help message and exit
--basis-atoms ATOMS (required) Basis atoms of the crystal structure.
--lattice-vectors VEC
(required) Lattice vectors in three dimensions, stored in a
matrix \(\hat a\).
--shift-into-cell Shift atoms such that they are within the conventional unit cell.
Entering the command without any options will print out the missing required arguments:
$ pm-crystal
User Error: Must provide values for:
basis_atoms, lattice_vectors
Input tags can be provided on the command line, or they can be specified in yaml format
from standard input
or a file via the --input-file or -i tag.
Standard input is specified as - and an input file is given by name, such
as
$ pm-crystal -i -
$ pm-crystal -i input.yaml
Multiple input files can be specified, and can be mixed with standard input.
$ pm-crystal -i input1.yaml input2.yaml
$ pm-crystal -i - input1.yaml input2.yaml
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