pnictogen is both a library and a command-line tool that helps composing input files for computational chemistry packages. It is based on Jinja2, a modern and friendly templating language for Python:
$ cat new_template.ORCA.inp
# {{ molecules[0].title }}
! Opt
* xyz {{ molecules[0].charge }} {{ molecules[0].spin }}
{{ xyz(molecules[0]) }}
*
$ pnictogen new_template.ORCA.inp examples/water.xyz
examples/water.inp written
$ cat examples/water.inp
# A water molecule
! Opt
* xyz 0 1
O 0.05840 0.05840 0.00000
H 1.00961 -0.06802 0.00000
H -0.06802 1.00961 0.00000
*pnictogen is the big brother of nitrogen, hence the name.
pnictogen can currently create boilerplates for ADF, DALTON, GAMESS (US), GAMESS-UK, Gaussian, Jaguar, Molpro, MOPAC, MPQC, NWChem, ORCA, Psi, Q-Chem and ZINDO:
$ pnictogen -g new_template.MOPAC.mop
new_template.MOPAC.mop written
$ cat new_template.MOPAC.mop
CHARGE={{ molecules[0].charge }} MS={{ (molecules[0].spin - 1)/2 }}
{{ molecules[0].title }}
{{ xyz(molecules[0], style="MOPAC") }}(pnictogen -g new_template.inp creates a blank file.)
You can either create and edit a boilerplate template or start fresh. Once you have a template, generating inputs is easy:
$ pnictogen new_template.ORCA.inp examples/co.xyz examples/water.xyz
examples/co.inp written
examples/water.inp written(Wildcards are allowed, e.g., pnictogen new_template.ORCA.inp *.xyz works.)
Since pnictogen is built on top of Pybel, so it is able to read anything Open Babel reads. Check the list of all available file formats here.
You can use the full Jinja2 syntax within templates (check here its documentation for details).
Besides this, pnictogen also understands a special delimiter (--@) that allows one to generate many inputs from a single file:
$ cat examples/templates/opt.MOPAC.mop
{% for molecule in molecules %}
--@{{ loop.index }}
CHARGE={{ molecule.charge }} MS={{ (molecule.spin - 1)/2 }}
{{ molecule.title }}
{{ xyz(molecule, style="MOPAC") }}
{% endfor %}
$ pnictogen examples/templates/opt.MOPAC.mop examples/pentane_conformers.xyz
examples/pentane_conformers_1.mop written
examples/pentane_conformers_2.mop written
examples/pentane_conformers_3.mop written
examples/pentane_conformers_4.mop written
examples/pentane_conformers_5.mop written
examples/pentane_conformers_6.mop written
examples/pentane_conformers_7.mop writtenThe rest of the line after --@ is aways added to the name of the inputs after an underscore (_).
In the example above, examples/pentane_conformers.xyz contains seven conformers of pentane, so seven inputs were generated (the counting is provided by loop.index):
$ cat examples/pentane_conformers_5.mop
CHARGE=0 MS=0.0
C5H12
C 1.23923 1 1.46892 1 -1.23930 1
C 1.24920 1 0.57161 1 0.00000 1
C -0.00000 1 -0.31179 1 -0.00000 1
C -1.24920 1 0.57161 1 -0.00000 1
C -2.49842 1 -0.31168 1 0.01981 1
H 1.23217 1 0.84960 1 -2.13625 1
H 0.34926 1 2.09811 1 -1.22516 1
H 2.12917 1 2.09831 1 -1.23936 1
H 2.13917 1 -0.05758 1 -0.01415 1
H 1.25625 1 1.19094 1 0.89694 1
H -0.00000 1 -0.94109 1 -0.89000 1
H -0.00000 1 -0.94109 1 0.89000 1
H -1.24217 1 1.21085 1 0.88286 1
H -1.25629 1 1.19089 1 -0.89697 1
H -2.50545 1 -0.95092 1 -0.86305 1
H -2.49134 1 -0.93096 1 0.91678 1
H -3.38842 1 0.31762 1 0.01981 1pnictogen also has a helper conformers(), which makes it even easier to do the above.
Imagine we want to do energy decomposition analysis on the following water dimer:
$ cat water_dimer.xyz
6
O 0.12908 -0.26336 0.64798
H 0.89795 0.28805 0.85518
H 0.10833 -0.20468 -0.33302
O 0.31020 0.07569 -2.07524
H 0.64083 -0.57862 -2.71449
H -0.26065 0.64232 -2.62218The following template uses both fragment() and xyz() functions to generate ADF inputs in bulk:
$ cat EDA.ADF.in
{% set frags = fragment(molecules[0], [range(3), range(3, 6)]) %}
--@eda
ATOMS Cartesian
{% for frag in frags %}
{{ xyz(frag, "ADF", "frag{}".format(loop.index)) }}
{% endfor %}
End
Fragments
{% for frag in frags %}
frag{{ loop.index }} {{ input_prefix }}_frag{{ loop.index }}.t21
{% endfor %}
End
{% for frag in frags %}
--@frag{{ loop.index }}
ATOMS Cartesian
{{ xyz(frag) }}
End
{% endfor %}
$ pnictogen EDA.ADF.in examples/water_dimer.xyz
examples/water_dimer_eda.in written
examples/water_dimer_frag1.in written
examples/water_dimer_frag2.in writtenThe above creates inputs like the following:
$ cat water_dimer_eda.in
ATOMS Cartesian
O 0.12908 -0.26336 0.64798 f=frag1
H 0.89795 0.28805 0.85518 f=frag1
H 0.10833 -0.20468 -0.33302 f=frag1
O 0.31020 0.07569 -2.07524 f=frag2
H 0.64083 -0.57862 -2.71449 f=frag2
H -0.26065 0.64232 -2.62218 f=frag2
End
Fragments
frag1 examples/water_dimer_frag1.t21
frag2 examples/water_dimer_frag2.t21
End
$ cat water_dimer_frag1.in
ATOMS Cartesian
O 0.12908 -0.26336 0.64798
H 0.89795 0.28805 0.85518
H 0.10833 -0.20468 -0.33302
End