lmmentel / chemtools Goto Github PK

Python tools for quantum chemical calculations

License: MIT License

Python 99.89% Batchfile 0.06% Shell 0.05%

python quantum-chemistry molpro gamessus basis-set optimization molecular-simulation gaussian chemistry computational-chemistry

chemtools's Introduction

chemtools: Python toolbox for Computational Chemistry

Chemtools is a set of modules that is intended to help with more advanced computations using common electronic structure programs.

The main to goal was to enable convenient basis set manipulations, including designing and optimizing exponents of basis sets. To achieve that there are several modules abstracting various functionalities.

Currently there is support optimizing basis set (or doing general computations) with:

Getting Started
- Installation
- Documentation
Contributing
Contact
Citing
Funding
License

Getting Started

The best way to get started is to go over the tutorials illustrating the functionalities and giving examples of basis set optimization tasks.

Installation

Most convenient way to install the package is with pip

pip install chemtools

Documentation

The documentation in hosted at Read The Docs.

Contributing

Contact

Łukasz Mentel

github: lmmentel
email: lmmentel <at> gmail.com

Citing

If you use chemtools in a scientific publication, please consider citing the software as

Łukasz Mentel, chemtools -- A Python toolbox for computational chemistry, 2014-- . Available at: https://github.com/lmmentel/chemtools.

Here's the reference in the BibLaTeX format

 @software{chemtools2014,
    author = {Mentel, Łukasz},
    title = {{chemtools} -- A Python toolbox for computational chemistry},
    url = {https://github.com/lmmentel/chemtools},
    version = {0.9.2},
    date = {2014--},
}

or the older BibTeX format

@misc{chemtools2014,
   auhor = {Mentel, Łukasz},
   title = {{chemtools} -- A Python toolbox for computational chemistry, ver. 0.9.2},
   howpublished = {\url{https://github.com/lmmentel/chemtools}},
   year  = {2014--},
}

Funding

This project was realized through the support from the National Science Center (Poland) grant number UMO-2012/07/B/ST4/01347.

License

The project is distributed under the MIT License. See LICENSE for more information.

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chemtools's Issues

Problem because exponents are sorted

Hi!

I installed chemtools with pip:
chemtools 0.9.2

I have a GAMESS-US file which looks like this:

$DATA
CARBON
S 9
  1 0.051344      0.013991
  2 0.102619      0.169852
  3 0.205100      0.397529
  4 0.409924      0.380369
  5 0.819297      0.180113
  6 1.637494      -0.033512
  7 3.272791      -0.121499
  8 6.541187      0.015176
  9 13.073594      -0.000705
P 9
  1 0.029281      0.001787
  2 0.058547      0.050426
  3 0.117063      0.191634
  4 0.234064      0.302667
  5 0.468003      0.289868
  6 0.935757      0.210979
  7 1.871016      0.112024
  8 3.741035      0.054425
  9 7.480076      0.021931

BORON
S 9
  1 0.040569      0.032031
  2 0.081044      0.243317
  3 0.161898      0.434636
  4 0.323418      0.329581
  5 0.646080      0.111875
  6 1.290648      -0.078699
  7 2.578276      -0.098781
  8 5.150520      0.016164
  9 10.288990      -0.000016
S 1
  1 0.082968      1.000000
S 1
  1 0.305133      1.000000
S 1
  1 0.422217      1.000000
P 9
  1 0.029207      0.019909
  2 0.058408      0.141775
  3 0.116803      0.294463
  4 0.233582      0.309028
  5 0.467115      0.236378
  6 0.934132      0.131317
  7 1.868068      0.066454
  8 3.735743      0.021248
  9 7.470701      0.002837

$END

when I run

from chemtools.basisset import BasisSet
print(basis["B"])

I get the list of exponents reversed, but not the coefficients:

Name                 = test_file
Element              = B
Family               = None
Kind                 = None
Functions:

================s shell=================
Contracted:
    1       10.2889900000     0.03203100
    2        5.1505200000     0.24331700
    3        2.5782760000     0.43463600
    4        1.2906480000     0.32958100
    5        0.6460800000     0.11187500
    6        0.3234180000    -0.07869900
    7        0.1618980000    -0.09878100
    8        0.0810440000     0.01616400
    9        0.0405690000    -0.00001600
Uncontracted:
   10        0.0829680000     1.00000000
   11        0.3051330000     1.00000000
   12        0.4222170000     1.00000000

================p shell=================
Contracted:
    1        0.0292070000     0.01990900
    2        0.0584080000     0.14177500
    3        0.1168030000     0.29446300
    4        0.2335820000     0.30902800
    5        0.4671150000     0.23637800
    6        0.9341320000     0.13131700
    7        1.8680680000     0.06645400
    8        3.7357430000     0.02124800
    9        7.4707010000     0.00283700

It could be related to a sort that happens in the list of exponents...

Cannot locate DDI on Linux

Use of Gamess wrapper impossible on Linux machines due to chemtools providing an invalid command to the shell resulting in a DDI error and failed computation. Could you rework get_command module to provide a proper command as in pygamess:
exec_string = "{0} {1} {2} -ddi {3} {3} {4} -scr {5} > {6}".format(ddikick, gamess, self.jobname, self.num_cores, hostname, self.tempdir, self.gamout)
where ddikick is a path to DDI, gamess is a path to executable, self.jobname is an input file, num_cores is a number of cores, self.tempdir is a scratch folder, and self.gamout is an output file.

Some questions about your chemtools programes

Hi, Dr. Mentel. I have used 'pip' to install your chemtools and the program to read two-electrons integrals from Gamess-us. I have followed your tutorial, but there are some questions. Firstly, the modules 'gamessreader' and 'gamessus' are in the calculators floder, but there are 'from chemtools.gamessreader' and 'from chemtools.gamessus'. So, I have changed my python program based on your tutorial. When I run my python program, it will get '.F' files, however, it will be a new error which says name 'twoe' is not defined. The 'twoe' is in the module gamessreader.py.I have put my python program which I wrote following your tutorial, bash script and error.out in the appendix. Please find them attached. It will be appreciated to hear from you asap.
run.sh.txt
twoint.py.txt

Parsing Gaussian basis sets with more than 9 exponents/coefficients fails (skips function)

I've noticed that in parse_gaussian_basis the regular expression has an issue.

shellre = re.compile(r'^\s*(?P[SPDFGHILspdfghil]+)\s*(?P[1-9]+)\s*(?P-?\d+.\d+)')
I think should be
shellre = re.compile(r'^\s*(?P[SPDFGHILspdfghil]+)\s*(?P[0-9]+)\s*(?P-?\d+.\d+)')

That fixes the problem for me. Basis sets with 10 exponents are now accepted.

I was trying to branch and pull request but I'm new to git and can't seem to figure it out.

Tobias