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https://github.com/ben-albrecht/qcl

Quantum Chemistry Laboratory package
https://github.com/ben-albrecht/qcl

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Quantum Chemistry Laboratory package

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README 

        
# qcl



qcl is a python package for managing the workflow and automating tasks that

many computational chemists face on a daily basis. The package serves as both a

command line tool, `qcl`, and a Python module that could be used in other Python

programs.



Here are some features currently available:



    figs                Quick plots of convergence criteria given an outputfile

    conformers          Naive conformer generation in Python

    obconformers        Open Babel conformer generation wrapper

    stretch             Stretch product at bond-forming atoms for transition state initial guess.

    templates           Template file management

    minima              Find minimum energy among many outputfiles

    zmatrix             Generate Z-Matrix from xyzfile

    rmsd                Align geometry and compute rmsd between 2 xyzfiles



## Installation



Install release from PyPI:



`pip install qcl`



Install from master:



```bash

# Clone the source

>git clone https://github.com/ben-albrecht/qcl

>cd qcl



# Install dependencies and package (in a virtualenv if you prefer)

>pip install -r requirement.txt

>python setup.py install # (or `make install`)



# qcl command line tool should now be in your $PATH

>qcl --help



usage: qcl [-h]

           {figs,conformers,obconformers,stretch,templates,minima,zmatrix,rmsd,job}

           ...



positional arguments:

  {figs,conformers,obconformers,stretch,templates,minima,zmatrix,rmsd,job}

                        sub-commands

    figs                Figure generation on the fly

    conformers          Conformer generation on the fly

    obconformers        Conformer generation on the fly with Open Babel

    stretch             TS search from product of combination reactions.

    templates           Template file management

    minima              Find global minimum of many outputs

    zmatrix             Generate Z-Matrix

    rmsd                Compute rmsd between 2 xyzfiles

    job                 Extract ccdata from files and write new inputs



optional arguments:

  -h, --help            show this help message and exit



# and your $PYTHONPATH

>python

Python 3.5.2 (default, Nov  5 2016, 21:37:10)

[GCC 4.2.1 Compatible Apple LLVM 7.3.0 (clang-703.0.31)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import qcl

>>> print(qcl.parse.xyzfile.__doc__)

Parse xyzfile to ccData or ccData_xyz object

>>>



```



## Usage



### Command line tool



Usage information for a specific subcommand is printed when throwing `--help`

like so:



```bash

>qcl conformers --help



usage: qcl conformers [-h] [--interval INTERVAL]

                      [--templatefiles TEMPLATEFILES [TEMPLATEFILES ...]]

                      xyzfile



positional arguments:

  xyzfile               xyz file, with charge and multiplicity as comments



optional arguments:

  -h, --help            show this help message and exit

  --interval INTERVAL   Angle interval to rotate dihedral angle by

  --templatefiles TEMPLATEFILES [TEMPLATEFILES ...], -t TEMPLATEFILES [TEMPLATEFILES ...]

                        Single template file or list of template files.

                        Necessary to generate inputs for conformers

```



### Conformers Example



The conformers subcommand will generate all conformers of a molecule provided

as an xyzfile using a naive algorithm. The default interval of rotation is 60

degrees, but this can be changed with the --interval flag. The resulting

conformers will be written to a multixyzfile named `all.xyz` in the current

working directory.



```bash

>qcl conformers test/test.xyz

Total number of rotatable bonds          : 3

interval (degrees) of dihedral rotation : 60.0

Total intervals per rotatable bond      : 6

Total number of systematical conformers  : 216

216 conformers generated



>head all.xyz

13



  C 0.00000000 0.00000000 0.00000000

  O 1.35990413 0.00000000 0.00000000

  O -0.58772319 0.00000000 -1.07001980

  C -0.80335693 0.07246293 1.27324932

  Si -0.87463131 -1.59912105 2.12493402

  H 0.44123291 -2.12448304 2.50700950

  H -1.51109961 -2.56720463 1.21939819

  H -1.69316219 -1.47832678 3.34026474

```

### Terminology and Formats



qcl uses the excellent computational chemistry parsing and algorithms module,

[cclib](https://github.com/cclib/cclib).

The qcl chemical data structures are represented as [cclib

objects](http://cclib.github.io/data.html), which this package consistently

refers to as `ccdata`.



In qcl, `xyzfile` refers to the

[xyz file format](https://en.wikipedia.org/wiki/XYZ_file_format), and

`multixyzfile` refers to multiple xyzfiles concatenated, which is supported by

most xyzfile file viewers, e.g. [Avogadro](https://avogadro.cc/).



`zmatrix` refers to the

[Z-Matrix](https://en.wikipedia.org/wiki/Z-matrix_(chemistry)) of a system.



`qcheminput` refers to [Q-Chem input files](http://www.q-chem.com/), and

`mopacinput` refers to [MOPAC input files](http://openmopac.net/).