pyscf / semiempirical

Semi-empirical methods for PySCF

Python-based Simulations of Chemistry Framework

2024-09-23

• Stable release 2.7.0
• Changelog
• Documentation
• Installation
• Features

Installation

• Install stable release:

    pip install pyscf
  

• New features developed in recent years are available in the pyscf-forge package:

    pip install pyscf-forge
  

• Certain modules are maintained as extensions of PySCF, such as dispersion, dmrgscf, fciqmc, icmpspt, properties, semiempirical, shciscf ... (more on https://github.com/pyscf) can be installed using pip:

    pip install pyscf[all]
  

  An individual extension can be installed:

    pip install pyscf[dispersion]
  

• More details of custom installation can be found in installation manual

Citing PySCF

Base PySCF

The following paper should be cited in publications utilizing the PySCF program package:

Recent developments in the PySCF program package, Qiming Sun, Xing Zhang, Samragni Banerjee, Peng Bao, Marc Barbry, Nick S. Blunt, Nikolay A. Bogdanov, George H. Booth, Jia Chen, Zhi-Hao Cui, Janus J. Eriksen, Yang Gao, Sheng Guo, Jan Hermann, Matthew R. Hermes, Kevin Koh, Peter Koval, Susi Lehtola, Zhendong Li, Junzi Liu, Narbe Mardirossian, James D. McClain, Mario Motta, Bastien Mussard, Hung Q. Pham, Artem Pulkin, Wirawan Purwanto, Paul J. Robinson, Enrico Ronca, Elvira R. Sayfutyarova, Maximilian Scheurer, Henry F. Schurkus, James E. T. Smith, Chong Sun, Shi-Ning Sun, Shiv Upadhyay, Lucas K. Wagner, Xiao Wang, Alec White, James Daniel Whitfield, Mark J. Williamson, Sebastian Wouters, Jun Yang, Jason M. Yu, Tianyu Zhu, Timothy C. Berkelbach, Sandeep Sharma, Alexander Yu. Sokolov, and Garnet Kin-Lic Chan, J. Chem. Phys., 153, 024109 (2020). doi:10.1063/5.0006074

Density functional calculations

As PySCF does not implement density functionals, instead employing external libraries to handle their evaluation, these libraries should also be cited in publications employing PySCF for density functional calculations.

If your calculation employed Libxc, cite

Recent developments in libxc — A comprehensive library of functionals for density functional theory, Susi Lehtola, Conrad Steigemann, Micael J.T. Oliveira, and Miguel A.L. Marques, SoftwareX 7, 1 (2018). doi:10.1016/j.softx.2017.11.002

If your calculation employed XCFun, cite

Arbitrary-order density functional response theory from automatic differentiation, Ulf Ekström, Lucas Visscher, Radovan Bast, Andreas J. Thorvaldsen, and Kenneth Ruud, J. Chem. Theory Comput. 6, 1971 (2010). doi:10.1021/ct100117s

Bug reports and feature requests

Please submit tickets on the issues page.

semiempirical's Issues

'libsemiempirical' error when importing am1?

Hello,

I am new to trying PySCF, so I apologise if I did some stupid mistake. I installed the semiempirical plugin, and it seems to work. Except I cannot import the am1 module because the program fails at loading libsemiempirical. Any hint on what I should do to be able to use AM1? Thanks in advance!

Here's an example

In [1]: from pyscf.semiempirical import MINDO3

In [2]: from pyscf.semiempirical import am1
/home/dpadula/Data/software/anaconda3/envs/working/lib/python3.7/site-packages/pyscf/semiempirical/am1.py:24: UserWarning: AM1 model is under testing
  warnings.warn('AM1 model is under testing')
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-2-5a7da9c66551> in <module>
----> 1 from pyscf.semiempirical import am1

~/Data/software/anaconda3/envs/working/lib/python3.7/site-packages/pyscf/semiempirical/am1.py in <module>
     24 warnings.warn('AM1 model is under testing')
     25 
---> 26 libsemiempirical = lib.load_library('libsemiempirical')
     27 ndpointer = numpy.ctypeslib.ndpointer
     28 libsemiempirical.MOPAC_rotate.argtypes = [

~/Data/software/anaconda3/envs/working/lib/python3.7/site-packages/pyscf/lib/misc.py in load_library(libname)
     52     try:
     53         _loaderpath = os.path.dirname(__file__)
---> 54         return numpy.ctypeslib.load_library(libname, _loaderpath)
     55     except OSError:
     56         from pyscf import __path__ as ext_modules

~/Data/software/anaconda3/envs/working/lib/python3.7/site-packages/numpy/ctypeslib.py in load_library(libname, loader_path)
    151                     raise
    152         ## if no successful return in the libname_ext loop:
--> 153         raise OSError("no file with expected extension")
    154 
    155 

PyPI release does not contains C extensions files

The sdist on PyPI is missing some files versus the github repository : https://pypi.org/project/pyscf-semiempirical/#files
Namely, the c extensions files:

$ tar --list -f pyscf-semiempirical-0.1.0.tar.gz | fgrep -e '*.c'
$ 

This results in a universal wheel without the library.

Can the PyPi release be yanked in favor of one that contains the c files?

Errors when running Geometry optimizations

Hi there! I have been trying to perform geometry optimizations with the semiempirical approach and I have discovered that there is a misspelling in the following lines:

Class RMINDO3 line 175 from pyscf import semiemprical -> from pyscf import semiempirical
Class UMINDO3 line 253 from pyscf import semiemprical -> from pyscf import semiempirical

Once these two misspellings are corrected the geometry optimization is performed. I hope this error is corrected in the repo since
for the moment I need to clone the code, correct it myself in order to be able to use it. Thanks in advance.

Release version

Hello,

Please tag or make a release for this repository.
A tag or release let us distribute software in a reproductible manner.

Thanks

Extension modules need re-link

I clicked 'Extension modules'

Then,
https://pyscf.org/pyscf/install.html#extension-modules
seems broken

NameErrors when running RMINDO3 for Mac OS pyscf 2.0.1

Steps to reproduce

>>> import pyscf
>>> mol_h2o = pyscf.gto.M(atom = 'O 0 0 0; H 0 1 0; H 0 0 1', basis = 'ccpvdz')
>>> from pyscf.semiempirical import mindo3
>>> solver = mindo3.RMINDO3(mol_h2o)
>>> solver.run()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/jamesbrown/Documents/Coding/environments/pyscftest/lib/python3.9/site-packages/pyscf/lib/misc.py", line 512, in run
    self.kernel(*args)
  File "/Users/jamesbrown/Documents/Coding/environments/pyscftest/lib/python3.9/site-packages/pyscf/lib/misc.py", line 631, in aliased_fn
    return getattr(self, fname)(*args, **kwargs)
  File "/Users/jamesbrown/Documents/Coding/environments/pyscftest/lib/python3.9/site-packages/pyscf/scf/hf.py", line 1642, in scf
    self.dump_flags()
  File "/Users/jamesbrown/Documents/Coding/environments/pyscftest/lib/python3.9/site-packages/pyscf/semiempirical/mindo3.py", line 173, in dump_flags
    log = logger.new_logger(mol, verbose)
NameError: name 'mol' is not defined

If you change mol in line 173 to self.mol or self._mindo_mol. I don't know which is correct, then it fails again at line 181

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/jamesbrown/Documents/Coding/environments/pyscftest/lib/python3.9/site-packages/pyscf/lib/misc.py", line 512, in run
    self.kernel(*args)
  File "/Users/jamesbrown/Documents/Coding/environments/pyscftest/lib/python3.9/site-packages/pyscf/lib/misc.py", line 631, in aliased_fn
    return getattr(self, fname)(*args, **kwargs)
  File "/Users/jamesbrown/Documents/Coding/environments/pyscftest/lib/python3.9/site-packages/pyscf/scf/hf.py", line 1642, in scf
    self.dump_flags()
  File "/Users/jamesbrown/Documents/Coding/environments/pyscftest/lib/python3.9/site-packages/pyscf/semiempirical/mindo3.py", line 181, in dump_flags
    return hf.RHF.dump_flags(self, log)
NameError: name 'hf' is not defined

Changing line 181
return hf.RHF.dump_flags(self, log) to return scf.hf.RHF.dump_flags(self, log) allows the calculation to finish.

converged SCF energy = -12.5424908345999
Heat of formation = -48.8262064549162 kcal/mol, -0.07780798779448 Eh
<pyscf.semiempirical.mindo3.RMINDO3 object at 0x10f6ffc40>