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Python utilities for Molpro

License: MIT License

Shell 0.06% Python 99.94%

pymolpro's Introduction

Molpro python support

pymolpro is a Python library that provides support for working with the Molpro quantum chemistry package.

The principal feature is the Project class that provides access to a complete Molpro job, including input and output files together with metadata such as job status information. The project is stored as a bundle implemented as a directory in the file system. The class is a Python binding of the sjef library with additional Molpro-specific customisation, and the project bundle can be accessed also through a command-line interface and the gmolpro and iMolpro graphical user interfaces.

pymolpro is on conda forge and can be installed on most systems using conda install -c conda-forge pymolpro.

Documentation at https://molpro.github.io/pymolpro.

pymolpro's People

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pjknowles davidtvp nick-wilson andhessel chrinide

pymolpro's Issues

Ensure counterpoise is working correctly

Implement database subsets

Probably should be done at the level of reactions, then work out which molecules are needed.

database.run(...,subset=['HF','H2','F2'],...)
database.run(..., subset='large',...)

database.add_subset('large',['HF','H2','F2'])

import pymolpro
import pysjef
import os, shutil
pname = 'check_empty.molpro'
shutil.rmtree(pname)
os.mkdir(pname)
open(pname+'/Info.plist','w').write('')
try:
    p=pymolpro.Project(pname)
except:
    print("exception caught")

fails:

libc++abi: terminating due to uncaught exception of type sjef::runtime_error: error in loading /Users/sacpjk/current/PAPT/check_empty.molpro/Info.plist
No document element found

but is OK if pysjef.Project() is called instead.

% conda list |grep pymolpro
# packages in environment at /opt/homebrew/Caskroom/miniforge/base/envs/pymolpro-conda:
pymolpro                  0.1.2              pyhd8ed1ab_0    conda-forge

% python -c 'import pymolpro; print(pymolpro.__version__)'
0+untagged.24.g0d6a9fc.dirty

Project.energies() does not always return all energies

from pymolpro import Project
p=Project("Neon")
p.write_input("""
geometry={Ne}
rhf
uccsd
""")
p.run()
print(p.out)
p.energies()

I can see that the expected output is printed. However, p.energies() contains only a single entry and it’s the rhf energy. I was expecting uccsd and rhf.

XMLSyntaxError: Char 0x0 out of allowed range, line 16, column 46

line 16 is:

    <irreducibleRepresentation index="1" id="...." cartesian=""/>

Ensure that multiple-valued energy variable is handled correctly

database.load() is not helpful if a bad database reference or content is provided

>>> pymolpro.database.load('junk')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/Caskroom/miniconda/base/envs/pymolpro/lib/python3.10/site-packages/pymolpro/database.py", line 287, in load
    return Database().load(source)
  File "/usr/local/Caskroom/miniconda/base/envs/pymolpro/lib/python3.10/site-packages/pymolpro/database.py", line 208, in load
    __j = json.loads(source)
  File "/usr/local/Caskroom/miniconda/base/envs/pymolpro/lib/python3.10/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/local/Caskroom/miniconda/base/envs/pymolpro/lib/python3.10/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/local/Caskroom/miniconda/base/envs/pymolpro/lib/python3.10/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)