esta.surfReact package
Contents
Note
surfReact package: Surface reaction tool for finding various atomic structures created using different operations … more documentation will be added later.
esta.surfReact package#
Submodules#
esta.surfReact.conformer module#
- esta.surfReact.conformer.conf_surf(xlattice)#
find the conformers and store them in a specific place for further operation
Module contents#
Note
mlBag package: ML related algorithms are implemented such gaussian kernals, etc. Atomic and other descriptors creation is also possible provided DFT or low level calculation results are available. Also, various other algorithms are called from the well known package sklearn package.
esta.mlBag package#
Module contents#
Note
unit conversion: measure contains unit conversion tool from one units to another units. Also conversion from SI units to atomic units (Hartree units) and atomic Rydberg units is implemented.
esta.measure package#
Submodules#
esta.measure.atomic_units module#
In electronic structure calculations, we generally employ “atomic units” (a.u.): here three basic units are the fundamental constants i.e. electronic charge, electron mass, and hbar (reduced Planck’s constatn).
Here we do the conversion between atomic units (Hartree) and SI units, as well as conversion between Ryd atomic units and SI units.
Generally atomic units (au) means Hartree units, atomic Rydberg units (aru) means Rydberg units, and natural units means natural units.
Right now conversion between atomic units and Si units supported.
For details see: From: http://physics.nist.gov/constants Also see the pdf file in zot. for details.
Note
AU or au: Atomic units:
h_bar = me = e = 1 (The units in the electron’s world.)
ARU or aru: Atomic Rydberg Units:
Atomic Rydberg units (ARU) defined by: h_bar = 2me = e^2/2 = 1 (and 4*pi*epsiom = 1)
So the unit for angular momentum is h_bar, the unit for mass is 2m and the unit for charge is e/√2 … CTM sk!!
#————————————————————– 1 Hartree = 2 Ryd
! mass_e in au_ryd = 2 * mass_e in au-hartree unit, BUT energy in au_ryd = 1/2 * energy in au-hartree unit
=> mass in au-ryd is double than au-hartree
=> energy in au-ryd is half than in au-hartree #————————————————————–
#============================================================= All Q-E codes use atomic Rydberg units
# i.e. energy in Ry, lengths in Bohr radii (or hbar=1, e^2=2, electron mass m=1/2) => charge on e=sqrt(2); mass of e = 1/2 in rau
# with the exception of CP that uses atomic Hartree units
i.e. energy in Ha, lengths in Bohr radii (or hbar=1, e=1, electron mass m=1) #=============================================================
Tip
How it works:
This module converts SI units to atomic units i.e. Hartree units (SI to Ryd is on the same line)!!
e.g. how to convert 0.529 angstrom to au units?
>>In [7]: import esta.measure.atomic_units as atu
>>In [8]: 0.529e-10 * atu.length2au
>>Out[8]: 0.9996651248084494
>>In [8]: atu.ao2au *.529e-10
>>Out[8]: 0.9996651248084494
e.g. convert 82nN force to au units:
>>In [16]: 82e-9 * atu.force2au
>>Out[16]: 0.9953000213791756
author: skumar
email : sonukumar.physics@gmail.com
esta.measure.conversion_factors module#
library to get conversion factor to convert quantities from once to another
get commanly use physical constants in physical and chemical sciences
NOTE: ii —> means –> inverse
- WARNING: use scipy version >=1.4.1
otherwise you get inaccurate constants after 6-7 decimal places
# with scipy version 1.1.0 #bohr radius= 5.2917721067e-11 m ; less accurate #fac = cf.bohr2ang =0.529177210669 –< – less accuaret and # as a result atoms pos and cell param are wrong after 6 dec # places #In scipy version 1.4.1 #bohr radiun = 5.29177210903e-11 m; is same as given # in nist data ; https://physics.nist.gov/cgi-bin/cuu/Value?bohrrada0 #Numerical value 5.291 772 109 03 x 10-11 m #fac = 0.529177210903 # so take bohr2ang = 0.529177210903 if using lower version than required
Author: S. Kumar, email: sonukumar.physics@gmail.com
- esta.measure.conversion_factors.double(value)#