pyscf / semiempirical Goto Github PK

7.0 8.0 7.0 34 KB

Semi-empirical methods for PySCF

License: Apache License 2.0

Python 64.31% C 35.69%

semiempirical's Issues

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

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.

Extension modules need re-link

I clicked 'Extension modules'

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

'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

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>

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?

pyscf / semiempirical Goto Github PK

semiempirical's Issues

Release version

Errors when running Geometry optimizations

Extension modules need re-link

'libsemiempirical' error when importing am1?

NameErrors when running RMINDO3 for Mac OS pyscf 2.0.1

PyPI release does not contains C extensions files

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