sebagodoy / stegoplot

Ab-initio thermodynamics and Reaction Energy Profiles

Stego(reaction) plot, a DFT analysis tool

A python package that helps with organizing and analyzing DFT results, computing thermodynamic properties, analyzing DOS and more things to come.

Requirements

• Python 3.6 or later
• NumPy
• matplotlib
• scipy (optional, for curvy reaction profiles)

Installation

Install the Numpy and matplotlib if you dont have these already. Install the distribution uploaded to TestPy with

python3 -m pip install --index-url https://test.pypi.org/simple/ --no-deps stegoplot

Installation in virtual environment

While testing, is recomended to install stego in a separate virtual environment, so it does not interfere with anything else. Following this, this and this guides (in Ubuntu 20.04 with python3 and pip):

# select a location, open a terminal there, 
# create a folder for the virtual environment and move in
mkdir sandbox
cd sandbox 

# create virtual environment
python3 -m venv ./
source ./bin/activate

# install stego and other packages
python3 -m pip install --index-url https://test.pypi.org/simple/ --no-deps stegoplot
pip install numpy
pip install matplotlib

or use pip3 is needed for you will be using python3. If you want to plot smooth reaction profiles be sure to also install the scipy package with pip3 install scipy.

While in this virtual environment, python3 can import stegoplot, numpy and matplotlib, give it a test entering with python3 and checking the value of the Boltzmann constant (in m2 kg / s2 K) with import stegoplot.parameters as stg; stg.kb (spoiler: 1.3806488e-23). To use jupyter notebooks with this virtual environment you need to create and add a new kernel using:

# create and add kernel for jupyter notebooks
pip install ipykernel
python -m ipykernel install --user --name=sandbox

now you can call jupyter notebook from any terminal and select the kernel > sandbox to use stego and check the test examples included in the test folder.

Basic examples

1. Properties for some species

Loading and adding a molecule

import stegoplot.item_types as stg
H2O = stg.Gas(Name='H2O',
              G_ID='ads', E0=-14.14745554,
              F_ID='McQuarrie', FreqR=[3833.413608, 3721.047191, 1597.447164],
              Geometry='Poliatomic', Mass=18.00,
              RotT=[40.1, 20.9, 13.4], RotSymNum=2)

Computing some properties

H2O.E0                        # electronic energy
H2O.ZPVE                      # Zero Point Vibrational Energy
H2O.E0ZPVE()                  # electronic energy + ZPVE
H2O.Enthalpy(T=298.15, P=1)   # enthalpy
H2O.Entrop(T=298.15, P=1)     # entropy
H2O.Gibbs(T=298.15, P=1)      # Gibbs free energy

2. Basic plot

Let's plot CO(g) + * -> *CO, *CO + * -> *C + *O. Start by adding the species

# load species
import stegoplot.item_types as Model

# CO in empty cubic box: CO(g)
COg = Model.GasItem(Name="CO(g)", 
                    E0=-14.42576166, # DFT energy, eV
                    FreqR=[2104.300781], # Real frequencies, cm-1
                    Geometry='Diatomic heteronuclear', 
                    Mass=28.01, # Atomic mass, g/mol
                    RotT=2.77, # Rotational temperature, K
                    RotSymNum=1 # Rotational symmetry number = 1 (diatomic heteronuclear)
                   )
# Clean Ni(100) surface
N100 = Model.CleanSurf(Name='Ni100', E0=-291.86035891)

# Adsorbed CO/Ni(100)
N100_CO = Model.AdsItem(Name='N10/R17i CO.h', E0=-307.82811536,
                        FreqR=[1597.286883, 238.05862, 229.727279, 199.589309, 147.878114, 117.974835])
# Transition state CO -> C + O /Ni(100)
N100_CO_TS = Model.AdsItem(Name='N10/R17d CO.h -> C.h + O.h', E0=-305.94631980, 
                           FreqR=[593.036612, 551.302284, 450.144514, 344.84786, 250.855827], 
                           FreqI=[367.384136] # Imaginary frequency, cm-1 (not used, may be omited)
                          )
# Co-Adsorbed C+O/Ni(100) 
N100_C_O = Model.AdsItem(Name='N10/R17f C.h + O.h', E0=-307.69629330, 
                         FreqR=[672.032831, 640.703844, 400.586463, 342.050762, 328.190997, 259.747561])

Create the plot and add the steps

# plot base
import matplotlib.pyplot as plt
import stegoplot.Plot as stgplt

fig, axs = plt.subplots(1, 1, figsize=(8., 3.))
MyRef = stgplt.RxRef(1.5, 0.)

# Adding to plot
stgplt.RxStepTS([ [N100,COg], N100_CO ], Ref=MyRef, ThermoType='Gibbs', T = 265 + 273.15, P=1.,
    Name='CO adsorption', Hover=True, Color='r', AlphaLines=1.)
stgplt.RxStepTS([ N100_CO, N100_CO_TS, N100_CO ], Ref=MyRef, ThermoType='Gibbs', T = 265 + 273.15, 
    Name='CO disociation', Hover=True, Color='b', AlphaLines=1., PlotShape='Spline')

Remove PlotShape='Spline' if you don't have the scipy package. Add a couple things to get a nicer plot

# Make it nicer
plt.ylabel("Gibbs free energy (kJ/mol)", fontweight='bold', fontsize='9')
plt.tick_params(axis="y", direction="inout", length=12.)
plt.axhline(y=0., color="k", alpha=.5, linewidth=.4)
axs.set_xticks([i[0] for i in MyRef.log])
axs.set_xticklabels(['CO + Ni(100)', 'C/Ni(100)', 'C+O/Ni(100)'])
plt.grid(which='major', color='k', linestyle='dashed', linewidth=.5, alpha=.3)
plt.show()

3. Analysis of Density of States files (DOSCAR)

Loading a VASP-DOS file

import stegoplot.dedos as ds

N100 = ds.DOS("./DOSCAR_direction", Name="Ni(111), polarized, spd partition, no ml partition, 64 atoms and 656 electrons", 
              Pol=True, Orb="spd", ml=False, Nelect=656)

Ploting DOS

import matplotlib.pyplot as plt
fig, axs = plt.subplots(1, 1)

# plot total DOS
N100.Plot(("total", "+"), Filled=True) 
N100.Plot(("total", "-"), Filled=True, PlotDown=True)

# plot d dos atom 32, amplified for better visibility
N100.Plot(("32", "+"), AmplifyFactor=10, Color='r') 
N100.Plot(("32", "-"), PlotDown=True, AmplifyFactor=10, Color='r')

# create curve summing d-DOS atoms 30-35 and plot it
N100.SumDOS(("d30-35",'d+'),[(str(i), 'd+') for i in range(30,36)])
N100.SumDOS(("d30-35",'d-'),[(str(i), 'd-') for i in range(30,36)])

N100.Plot(("d30-35", "d+"), AmplifyFactor=5, Color='g') 
N100.Plot(("d30-35", "d-"), PlotDown=True, AmplifyFactor=5, Color='g')

FAQ: Why "stego"?

I like dinosaurs 🦖 🦕.