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https://github.com/aspuru-guzik-group/DiffiQult
A fully autodifferentiable and variational HF
https://github.com/aspuru-guzik-group/DiffiQult
Last synced: 3 months ago
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A fully autodifferentiable and variational HF
- Host: GitHub
- URL: https://github.com/aspuru-guzik-group/DiffiQult
- Owner: aspuru-guzik-group
- License: mit
- Created: 2017-09-29T19:30:30.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2020-06-18T17:37:59.000Z (over 4 years ago)
- Last Synced: 2024-06-29T12:33:00.830Z (5 months ago)
- Language: Python
- Homepage: https://aspuru-guzik-group.github.io/DiffiQult
- Size: 9.83 MB
- Stars: 40
- Watchers: 5
- Forks: 6
- Open Issues: 1
-
Metadata Files:
- Readme: README.rst
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README
.. _intro:
DiffiQult
===========
*DiffiQult* is an open source autodifferentiable quantum chemistry package.
.. figure:: docs/h2o_3g_MO_1.gif
Method:
* RHF
Features:
* Single point calculations
* Energy gradients with respect to any parameter of the one-particle basis functions.
* Energy optimization with respect of any parameter of the Gaussian basis functions.
===============
Getting started with DiffiQult
===============
Requirements
______________________________
* Numpy
* Algopy
* Official releases and installation:
Available at: http://pypi.python.org/pypi/algopy
``pip install algopy``
* Python 2.7 (so far tested).
Installation
______________________________
* From source:
``git clone https://github.com/ttamayo/DiffiQult.git``
``python setup.py install``
===============
Usage
===============
Molecular system
______________________________
We define the parameters of a molecular systems with an ``System_mol`` object:
* molecular geometry in xyz format and atomic units
* basis sets (data base so far sto_3G
* number of electrons
For example:
.. code-block:: python
# Basis set is sto_3G
from diffiqult.Basis import basis_set_3G_STO as basis
# Our molecule H_2
d = -1.64601435
mol = [(1,(0.0,0.0,0.20165898)),(1,(0.0,0.0,d))]
# Number of electrons
ne = 2
system = System_mol(mol, ## Geometry
basis, ## Basis set (if shifted it should have the coordinates too)
ne, ## Number of electrons
shifted=False, ## If the basis is going to be on the atoms coordinates
mol_name='agua') ## Units -> Bohr
Tasks
______________________________
The jobs in *Diffiqult* are managed by a ``Tasks`` object,
.. code-block:: python
manager = Tasks(system,
name='h2_sto_3g', ## Prefix for all optput files
verbose=True) ## If there is going to be an output
where we defined the molecular system to
optimize with the object ``system``, and output options with ``verbose``.
The class ``Task`` contains the method ``Tasks.runtask``, it computes one the following options:
+----------------------+--------------+-------------------------------------------------------------------+
| Task | Key | Description |
+======================+==============+===================================================================+
| Single point energies| ``Energy`` | It calculates the RHF energy and updates some attibute in system |
+----------------------+--------------+-------------------------------------------------------------------+
| Optimization | ``Opt`` | It optimizes a given parameter and updates the basis set in system|
+----------------------+--------------+-------------------------------------------------------------------+
Single point calculation
`````````````
.. code-block:: python
manager.runtask('Energy',
max_scf=50, # Maximum number of SCF cycles
printcoef=True, # This will produce a npy file with the molecular coefficients
name='Output.molden', # Name of the output file (Compatible with molden)
output=True)
**Notes:**
* We currently don't have convergence options for the SCF.
* The molden file also contains an input section that can be used as input for system with the option ``shifted``
* The geometry and MOs can be vizualized with *molden*,and the molden file.
Optimization
`````````````
To optimize one or many input parameters, we use the option ``Opt``. After a succesful optimization or
If the optimization reaches the maximum number of steps or convergence, it updates
the attributes of the ``system_mol`` object.
.. code-block:: python
manager.runtask('Opt',
max_scf=50,
printcoef=False,
argnum=[2], # Optimization of centers
output=True) # We optimized all the steps
print(manager.syste.energy)
where ``argnum`` recieves a list with the parameters to optimize with the following convention:
+--------------------------+------------+
| Parameter | ``argnum`` |
+==========================+============+
| Widths | 0 |
+--------------------------+------------+
| Contraction coefficients | 1 |
+--------------------------+------------+
| Gaussian centers | 2 |
+--------------------------+------------+
for example, we can optimize the atomic centered basis function with respect of their widths and contraction
coefficients in the following way.
.. code-block:: python
manager.runtask('Opt',
max_scf=50,
printcoef=False,
argnum=[0,1], # Optimization of centers
output=True) # We print a molden file of all steps
Additionally, if ``output`` is set to ``True``, a molden file of each optimization step is printed.