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.. QCEngine documentation master file, created by
sphinx-quickstart on Fri Aug 17 09:45:43 2018.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
=========
QCEngine
=========
*Quantum chemistry program executor and IO standardizer (QCSchema) for quantum chemistry.*
Program Execution
-----------------
A simple example of QCEngine's capabilities is as follows:
.. code:: python
>>> import qcengine as qcng
>>> import qcelemental as qcel
>>> mol = qcel.models.Molecule.from_data("""
>>> O 0.0 0.000 -0.129
>>> H 0.0 -1.494 1.027
>>> H 0.0 1.494 1.027
>>> """)
>>> model = qcel.models.AtomicInput(
>>> molecule=mol,
>>> driver="energy",
>>> model={"method": "SCF", "basis": "sto-3g"},
>>> keywords={"scf_type": "df"}
>>> )
These input specifications can be executed with the ``compute`` syntax along with a program specifier:
.. code:: python
>>> ret = qcng.compute(model, "psi4")
The results contain a complete record of the computation:
.. code:: python
>>> ret.return_result
-74.45994963230625
>>> ret.properties.scf_dipole_moment
[0.0, 0.0, 0.6635967188869244]
>>> ret.provenance.cpu
Intel(R) Core(TM) i7-7820HQ CPU @ 2.90GHz
Backends
--------
Currently available compute backends for single results are as follow:
- Quantum Chemistry:
- `adcc <https://adc-connect.org>`_
- `Entos <https://www.entos.info>`_
- `Molpro <https://www.molpro.net>`_
- `Psi4 <http://www.psicode.org>`_
- `Terachem <http://www.petachem.com>`_
- Semi-Emperical:
- `MOPAC <http://www.petachem.com>`_
- `xtb <https://xtb-docs.readthedocs.io>`_
- AI Potential:
- `TorchANI <https://github.com/aiqm/torchani>`_
- Molecular Mechanics:
- `RDKit <http://rdkit.org>`_
- Analytical Corrections:
- `DFTD3 <https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3/>`_
In addition, several procedures are available:
- Geometry Optimization:
- `geomeTRIC <https://github.com/leeping/geomeTRIC>`_
- `Pyberny <https://github.com/jhrmnn/pyberny>`_
Configuration Determination
---------------------------
In addition, QCEngine can automatically determine the following quantites:
- The number of physical cores on the system and to use.
- The amount of physical memory on the system and the amount to use.
- The provenance of a computation (hardware, software versions, and compute resources).
- Location of scratch disk space.
- Location of quantum chemistry programs binaries or Python modules.
Each of these options can be specified by the user as well.
.. code:: python
>>> qcng.get_config()
<JobConfig ncores=2 memory=2.506 scratch_directory=None>
>>> qcng.get_config(task_config={"scratch_directory": "/tmp"})
<JobConfig ncores=2 memory=2.506 scratch_directory='/tmp'>
>>> os.environ["SCRATCH"] = "/my_scratch"
>>> qcng.get_config(task_config={"scratch_directory": "$SCRATCH"})
<JobConfig ncores=2 memory=2.506 scratch_directory='/my_scratch'>
Program and Procedure Information
---------------------------------
Available programs and procedures may be printed using the :doc:`CLI <cli>`::
>>> qcengine info
>> Version information
QCEngine version: v0.11.0
QCElemental version: v0.11.0
>> Program information
Available programs:
mopac v2016
psi4 v1.3.2
rdkit v2019.03.4
Other supported programs:
cfour dftd3 entos gamess molpro mp2d nwchem terachem torchani
...
.. toctree::
:maxdepth: 2
:caption: Contents:
========
Index
-----
**Getting Started**
* :doc:`install`
.. toctree::
:maxdepth: 1
:hidden:
:caption: Getting Started
install
**User Interface**
* :doc:`single_compute`
* :doc:`environment`
* :doc:`cli`
.. toctree::
:maxdepth: 1
:hidden:
:caption: User Interface
single_compute
environment
cli
**Programs**
* :doc:`program_overview`
* :doc:`programs_molecular_mechanics`
.. toctree::
:maxdepth: 1
:hidden:
:caption: Programs
program_overview
programs_semiempirical
programs_molecular_mechanics
**Developer Documentation**
* :doc:`api`
* :doc:`changelog`
.. toctree::
:maxdepth: 1
:caption: Developer Documentation
api
changelog
dev_program_harness
|
