janash

def generate_cubic_lattice(num_atoms, density):
  """
  Generate points on a cubic lattice using a desired final density.

  Parameters
  ----------
  num_atoms: int
    The number of atoms to place on the lattice.
  density: float
    The desired system density.

janash

"""
Stats functions
"""


def mean(my_list):

    my_sum = sum(my_list)

    my_average = my_sum / len(my_list)

janash

import os
import numpy as np
import matplotlib.pyplot as plt

from mpl_toolkits.mplot3d import Axes3D

%matplotlib notebook

def calculate_distance(rA, rB):
    # This function calculates the distance between two points given as numpy arrays.

janash

janash

"AtomicNumber","Symbol","Name","AtomicMass","CPKHexColor","ElectronConfiguration","Electronegativity","AtomicRadius","IonizationEnergy","ElectronAffinity","OxidationStates","StandardState","MeltingPoint","BoilingPoint","Density","GroupBlock","YearDiscovered"
1,"H","Hydrogen",1.0080,"FFFFFF","1s1",2.2,120,13.598,0.754,"+1, -1","Gas",13.81,20.28,0.00008988,"Nonmetal",1766
2,"He","Helium",4.00260,"D9FFFF","1s2","",140,24.587,"","0","Gas",0.95,4.22,0.0001785,"Noble gas",1868
3,"Li","Lithium",7.0,"CC80FF","[He]2s1",0.98,182,5.392,0.618,"+1","Solid",453.65,1615,0.534,"Alkali metal",1817
4,"Be","Beryllium",9.012183,"C2FF00","[He]2s2",1.57,153,9.323,"","+2","Solid",1560,2744,1.85,"Alkaline earth metal",1798
5,"B","Boron",10.81,"FFB5B5","[He]2s2 2p1",2.04,192,8.298,0.277,"+3","Solid",2348,4273,2.37,"Metalloid",1808
6,"C","Carbon",12.011,"909090","[He]2s2 2p2",2.55,170,11.260,1.263,"+4, +2, -4","Solid",3823,4098,2.2670,"Nonmetal","Ancient"
7,"N","Nitrogen",14.007,"3050F8","[He] 2s2 2p3",3.04,155,14.534,"","+5, +4, +3, 

janash

import numpy
import os

def calculate_distance(coords1, coords2):
    x_distance = coords1[0] - coords2[0]
    y_distance = coords1[1] - coords2[1]
    z_distance = coords1[2] - coords2[2]
    distance = numpy.sqrt(x_distance**2 + y_distance**2 + z_distance**2)
    return distance

janash

r = abs(5)

def abs(values):
    """Extend abs function to work on lists"""
    
    import builtins

    if type(values) == list:
        for i in range(len(values)):
            values[i] = builtins.abs(values[i])

janash

name: pySCF-env
channels:
  - defaults
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=4.5=1_gnu
  - ca-certificates=2021.7.5=h06a4308_1
  - certifi=2021.5.30=py38h06a4308_0
  - ld_impl_linux-64=2.35.1=h7274673_9
  - libffi=3.3=he6710b0_2

janash

"""
deltaG and deltaH of formation for various substances. 

Obtained from 
https://www.engineeringtoolbox.com/standard-state-enthalpy-formation-definition-value-Gibbs-free-energy-entropy-molar-heat-capacity-d_1978.html
"""

deltaG = [
    2.4600e02,
    0.0000e00,

janash

mkdir hello_world
cd hello_world
echo "HELLO WORLD" > hello.txt
rm hello.txt
cd ..
rm -r hello_world
git clone https://github.com/msse-2021-bootcamp/lessons.git
cd lessons
git checkout -b my-new-branch
echo "This line will be at the end of the readme" >> README.md