The PyRETIS library¶
This is the documentation for the PyRETIS library and usage of the application programming interface (API). An overview of the main classes and routines are given in the introduction to the library in the user guide. It might also be a good idea to have a look at the developer guide before making changes or reading through the API docs.
The PyRETIS package¶
The PyRETIS library contains methods and classes that handle the different parts of simulations. These are further grouped into sub-packages:
- pyretis.analysis for analysing the output from simulations.
- pyretis.core with the core functions for the different methods.
- pyretis.engines for integrating the equations of motion and for interfacing external MD software.
- pyretis.forcefield for defining force fields to use in simulations.
- pyretis.initiation with functions for initiation of path sampling simulations.
- pyretis.inout for handling the input and output to PyRETIS.
- pyretis.orderparameter for defining order parameters.
- pyretis.setup for creating the main objects.
- pyretis.simulation for running predefined simulations.
- pyretis.testing with functions which are used in connection with testing.
- pyretis.tools for performing some simple tasks useful for setting up simulations.
- pyretis.pyvisa for visualizing and analysing the simulation outputs.
The PyRETIS library can be imported by:
import pyretis
print(pyretis.__version__)
Or you can just import specific functions and classes from the sub-packages:
from pyretis.core import create_box
from pyretis.tools import generate_lattice
from pyretis.inout.formats.xyz import write_xyz_file
xyz, size = generate_lattice('diamond', [2, 2, 2], lcon=3.567)
write_xyz_file('diamond_small.xyz', xyz, names=['C']*len(xyz))
xyz, size = generate_lattice('diamond', [10, 10, 10], lcon=3.567)
write_xyz_file('diamond.xyz', xyz, names=['C']*len(xyz))
low = [i[0] for i in size]
high = [i[1] for i in size]
box = create_box(low=low, high=high)
print(box)
The usage of these sub-packages are described in the following:
Contents: The PyRETIS sub-packages¶
- pyretis.analysis package
- pyretis.core
- Package structure
- List of submodules
- pyretis.core.box module
- pyretis.core.common module
- pyretis.core.montecarlo module
- pyretis.core.particlefunctions module
- pyretis.core.particles module
- pyretis.core.path module
- pyretis.core.pathensemble module
- pyretis.core.properties module
- pyretis.core.random_gen module
- pyretis.core.retis module
- pyretis.core.system module
- pyretis.core.tis module
- pyretis.core.units module
- pyretis.engines package
- pyretis.forcefield package
- pyretis.inout package
- Package structure
- Modules
- Sub-packages
- Important classes defined in this package
- Important methods defined in this package
- Subpackages
- List of submodules
- pyretis.inout.archive module
- pyretis.inout.common module
- pyretis.inout.fileio module
- pyretis.inout.restart module
- pyretis.inout.screen module
- pyretis.inout.settings module
- pyretis.inout.simulationio module
- pyretis.inout.checker module
- pyretis.initiation package
- pyretis.orderparameter package
- pyretis.setup package
- pyretis.setup package
- pyretis.simulation package
- pyretis.simulation package
- pyretis.testing package
- pyretis.tools package
- pyretis.pyvisa package
- Package structure
- Modules
- Sub-packages
- Important classes defined in this package
- Important methods defined in this package
- List of submodules
- pyretis.pyvisa.inf module
- pyretis.pyvisa.common module
- pyretis.pyvisa.orderparam_density module
- pyretis.pyvisa.plotting module
- pyretis.pyvisa.resources_rc module
- pyretis.pyvisa.visualize module
- pyretis.pyvisa.statistical_methods module
In addition PyRETIS has the following submodules:
List of submodules¶
There are also some submodules with information about PyRETIS. These are:
pyretis.info module¶
This module just contains some info for PyRETIS.
Here we define the name of the program and some other relevant info.
This file is generated by PyRETIS (setup_version.py
)
pyretis.version module¶
Version information for PyRETIS.
This file is generated by PyRETIS (setup_version.py
)