ChemIITools
================
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Documentation can be found at https://kgrewal1.github.io/ChemIITools/
## Install
``` sh
pip install ChemIITools
```
## How to use
### Solve the Huckel Equation
Easily solve the Huckel equation for complex systems
``` python
mol = Huckel("c1cc2ccc3ccc4ccc5ccc6ccc1c7c2c3c4c5c67")
print(mol)
mol.molecule
```
Huckel Energies (degeneracy) for c1cc2ccc3ccc4ccc5ccc6ccc1c7c2c3c4c5c67: [-2.675 (1)] [-2.214 (2)] [-1.675 (2)] [-1.539 (1)] [-1.214 (1)] [-1.000 (3)] [-0.539 (2)] [0.539 (2)] [1.000 (3)] [1.214 (1)] [1.539 (1)] [1.675 (2)] [2.214 (2)] [2.675 (1)]
``` python
mol.plot()
```
### Parse .out files and plot energy surfaces
Plot potential energy surfaces of symmetric triatomics and find the
vibrational frequencies
``` python
surface_plot(h2o_vals)
```
``` python
r_opt, theta_opt, nu_r, nu_theta = vib_calc(h2o_vals)
print('the optimum bond length of water is ', r_opt, ' angstroms with angle ', theta_opt, ' degrees' )
print('the stretching frequency ', round(nu_r), ' cm-1 and bending frequency ', round(nu_theta), ' cm-1' )
```
the optimum bond length of water is 0.95 angstroms with angle 105.0 degrees
the stretching frequency 3113 cm-1 and bending frequency 1665 cm-1
### Calculate steady state concentrations
Find the steady state concentration for chemical systems of the form
$$D \xrightleftharpoons[k_{u}^{R15}]{k_{f}^{R15}} I \xrightleftharpoons[k_{u}^{R16}]{k_{f}^{R16}} N$$
``` python
kf1 = 26000
kr1 = 0.06
kf2 = 730
kr2 = 0.00075
urea_conc = np.linspace(0, 8, num=1000)
ss_conc = np.array([steady_state_calc(kf1*np.exp(-1.68*conc), kr1*np.exp(0.95*conc), kf2*np.exp(-1.72*conc), kr2*np.exp(1.20*conc)) for conc in urea_conc])
plt.plot(urea_conc,ss_conc[:, 0],label='D')
plt.plot(urea_conc,ss_conc[:, 1],label='I')
plt.plot(urea_conc,ss_conc[:, 2],label='N')
plt.xlabel('[Urea]/ M')
plt.ylabel('Fraction of Species')
plt.legend()
plt.show()
```
### Caclualte time evolution of a chemical system
``` python
A, B, X, Y, Z, P, Q = 0.06, 0.06, 10**(-9.8),10**(-6.52), 10**(-7.32), 0, 0
concs = [A, B, X, Y, Z, P, Q]
t, conc_t= oreg_calc(concs)
As, Bs, Xs, Ys, Zs, Ps, Qs = conc_t
```
``` python
plt.plot(t[::10000],Xs[::10000],label='X')
plt.plot(t[::10000],Ys[::10000],label='Y')
plt.plot(t[::10000],Zs[::10000],label='Z')
plt.yscale('log')
plt.xlabel('time/ s')
plt.ylabel('Concentration/ M')
plt.legend(bbox_to_anchor =(1.15, 0.6))
plt.show()
```
### Optimise Cluster Geometry
``` python
lj7 = System(7, '(4*((1/r)**12 -(1/r)**6))')
lj7.optimise()
print(lj7)
lj7.plot()
```
Energy -16.505384, for 7 points
