def test_initialise(self):
x = ut.read_nist(test_data)
a, b, c, d = p_vs_t.inititalise(x, -10.0, 1000, -13, 5.5)
assert_almost_equal(d[0], -10.000, decimal=3)
assert_almost_equal(d[1], -10.000, decimal=3)
assert_almost_equal(d[-1], -10.103, decimal=3)
assert_almost_equal(d[-2], -10.103, decimal=3)
def test_calculate(self):
stoich = DataSet(cation=24,
x=48,
y=0,
area=60.22,
energy=-530.0,
label="Stoich")
H2O = DataSet(cation=24,
x=48,
y=2,
area=60.22,
energy=-620.0,
label="Stoich")
H2O_2 = DataSet(cation=24,
x=48,
y=4,
area=60.22,
energy=-677.0,
label="Stoich")
data = [H2O, H2O_2]
SE = 1.0
adsorbant = -10.0
thermochem = ut.read_nist(test_data)
system = p_vs_t.calculate(stoich, data, SE, adsorbant, thermochem)
expectedx = np.arange(2, 1000)
expectedy = np.arange(-13, 5.5, 0.1)
expectedz = np.zeros(((expectedy.size), (expectedx.size)))
assert_almost_equal(system.x, expectedx)
assert_almost_equal(system.y, expectedy)
assert_almost_equal(system.z, expectedz)
def test_wulff_calculate(self):
stoich = data.DataSet(cation=20,
x=50,
y=0,
area=60.00,
energy=-500.00,
label="One")
H2O = data.DataSet(cation=20,
x=50,
y=2,
area=60.00,
energy=-600.00,
label="Two")
dataset = [H2O]
x = ut.read_nist(test_data)
y = wulff.calculate_surface_energy(stoich, dataset, 1.0, -10.0, x, 100,
2)
assert_almost_equal(y[0], 1.0)
assert_almost_equal(y[1], -9.6914, decimal=4)
def temperature_correction(nist_file, temperature):
"""Use experimental data to correct the DFT free energy of an adsorbing
species to a specific temperature.
Parameters
----------
nist_file : array like
numpy array containing experiemntal data from NIST_JANAF
temperature : int
Temperature to correct to
Returns
-------
gibbs : float
correct free energy
"""
nist_data = ut.read_nist(nist_file)
h0 = nist_data[0, 4]
fitted_s = ut.fit(nist_data[:, 0], nist_data[:, 2], np.arange(1, 1000))
fitted_h = ut.fit(nist_data[:, 0], nist_data[:, 4], np.arange(1, 1000))
fitted_h = fitted_h + h0
gibbs = ut.calculate_gibbs(np.arange(1, 1000), fitted_s, fitted_h)
return gibbs[(temperature - 1)]
def test_calculate(self):
stoich = {
'M': 24,
'X': 48,
'Y': 0,
'Area': 60.22,
'Energy': -530.0,
'Label': '0'
}
H2O = {
'M': 24,
'X': 48,
'Y': 2,
'Area': 60.22,
'Energy': -620.0,
'Label': '1'
}
H2O_2 = {
'M': 24,
'X': 48,
'Y': 4,
'Area': 60.22,
'Energy': -670.0,
'Label': '2'
}
data = [H2O, H2O_2]
SE = 1.0
adsorbant = -10.0
thermochem = ut.read_nist(test_data)
system, SE = p_vs_t.calculate(stoich, data, SE, adsorbant, thermochem)
expectedx = np.arange(2, 1000)
expectedy = np.arange(-13, 5.5, 0.1)
expectedz = np.zeros(((expectedy.size), (expectedx.size)))
assert_almost_equal(system.x, expectedx)
assert_almost_equal(system.y, expectedy)
assert_almost_equal(system.z, expectedz)
def test_read_nist(self):
x = ut.read_nist(test_data)
assert x[1, 0] == 100
assert x[10, 0] == 1000
assert x[1, 1] == 1
def test_temperature_correction(self):
x = ut.read_nist(test_data)
adsorbant = wulff.temperature_correction(100, x, -10.0)
assert_almost_equal(adsorbant, -10.0010467948, decimal=3)
import numpy as np
from surfinpy import p_vs_t as pt
from surfinpy import wulff
from surfinpy import utils as ut
from pymatgen.core.surface import SlabGenerator, generate_all_slabs, Structure, Lattice
from pymatgen.analysis.wulff import WulffShape
adsorbant = -14.22
thermochem = ut.read_nist('H2O.txt')
SE = 1.44
stoich = {
'M': 24,
'X': 48,
'Y': 0,
'Area': 60.22,
'Energy': -575.66,
'Label': 'Stoich'
}
Adsorbant_1 = {
'M': 24,
'X': 48,
'Y': 2,
'Area': 60.22,
'Energy': -609.23,
'Label': '1 Species'
}
data = [Adsorbant_1]
Surface_100_1 = wulff.calculate_surface_energy(stoich, data, SE, adsorbant,
thermochem, 298, 0)
from surfinpy import utils as ut
from surfinpy import p_vs_t
adsorbant = -14.00
SE = 1.40
stoich = {'Cation': 24, 'X': 48, 'Y': 0, 'Area': 60.22, 'Energy': -575.00, 'Label': 'Bare'}
H2O = {'Cation': 24, 'X': 48, 'Y': 2, 'Area': 60.22, 'Energy': -605.00, 'Label': '1 Water'}
H2O_2 = {'Cation': 24, 'X': 48, 'Y': 8, 'Area': 60.22, 'Energy': -695.00, 'Label': '2 Water'}
data = [H2O, H2O_2]
coverage = ut.calculate_coverage(data)
thermochem = ut.read_nist("H2O.txt")
system = p_vs_t.calculate(stoich, data, SE, adsorbant, thermochem, coverage)
system.plot(output="Example_4.png",)