def test_infinity_dilution(self):
myparam = parameters.Parameters()
sigma1 = sigma.Sigma(mol1, myparam)
sigma1.write_sigma_file = False
sigma1.kernel()
sigma2 = sigma.Sigma(mol2, myparam)
sigma2.write_sigma_file = False
sigma2.kernel()
myac = ac.AC([mol1, mol2], x, T, [sigma1, sigma2], myparam)
myac.solve_gamma_thresh = 1e-6
myac.solve_gamma_maxiter = 500
self.assertTrue(
np.allclose(myac.kernel(), np.asarray([10.05122252, 0.0])))
def test_infinity_dilution3(self):
myparam = parameters.Parameters(data.Hsieh_2010)
sigma1 = sigma.Sigma(mol1, myparam)
sigma1.write_sigma_file = False
sigma1.split_sigma = True
sigma1.kernel()
sigma2 = sigma.Sigma(mol2, myparam)
sigma2.write_sigma_file = False
sigma2.split_sigma = True
sigma2.kernel()
myac = ac.AC([mol1, mol2], x, T, [sigma1, sigma2], myparam)
myac.solve_gamma_thresh = 1e-6
myac.solve_gamma_maxiter = 500
self.assertTrue(
np.allclose(myac.kernel(), np.asarray([8.81631154, 0.0])))
def test_dispersion(self):
myparam = parameters.Parameters(data.Hsieh_2010)
sigma1 = sigma.Sigma(mol1, myparam)
sigma1.write_sigma_file = False
sigma1.split_sigma = True
sigma1.kernel()
sigma2 = sigma.Sigma(mol2, myparam)
sigma2.write_sigma_file = False
sigma2.split_sigma = True
sigma2.kernel()
myac = ac.AC([mol1, mol2], x, T, [sigma1, sigma2], myparam)
myac.solve_gamma_thresh = 1e-6
myac.solve_gamma_maxiter = 500
myac.dispersion = True
self.assertTrue(
np.allclose(myac.kernel(), np.asarray([9.55918891, 0.])))
from pycosmosac.sigma import sigma from pycosmosac.ac import ac from pycosmosac.utils import thermo ''' An example to compute hydration free energy of carbofuran ''' path = os.path.abspath(os.path.dirname(__file__)) + "/" #load parameters myparam = parameters.Parameters(parameters=data.BIOSAC_SVP_GEPOL) #compute sigma profile for solute solute = "carbofuran" mol1 = cosmo.Cosmo().load(path + solute + ".cosmo") sigma1 = sigma.Sigma(mol1, myparam) #whether or not to write the sigma file sigma1.write_sigma_file = False sigma1.sigma_filename = solute + ".sigma" #default bounds for the grid; if "bounds too narrow" error occures, increase the numbers sigma1.bounds = [-0.025, 0.025] sigma1.kernel() #compute sigma profile for solvent solvent = "h2o" mol2 = cosmo.Cosmo().load(path + solvent + ".cosmo") sigma2 = sigma.Sigma(mol2, myparam) sigma2.write_sigma_file = False sigma2.sigma_filename = solvent + ".sigma" #bounds should be consistent for every component in the solution sigma2.bounds = [-0.025, 0.025]
import os
import unittest
import numpy as np
from pycosmosac.param import parameters, data
from pycosmosac.cosmo import cosmo
from pycosmosac.sigma import sigma
from pycosmosac.utils import misc
here = os.path.abspath(os.path.dirname(__file__))
mycosmo = cosmo.Cosmo()
mol = mycosmo.load(here+"/h2o.cosmo")
param1 = parameters.Parameters()
sigma1 = sigma.Sigma(mol, param1)
sigma1.write_sigma_file = False
sigma1.kernel()
param3 = parameters.Parameters(data.Hsieh_2010)
sigma3 = sigma.Sigma(mol, param3)
sigma3.split_sigma = True
sigma3.write_sigma_file = False
sigma3.kernel()
class KnownValues(unittest.TestCase):
def test_sigma(self):
self.assertAlmostEqual(misc.fp(sigma1.pA), -1.917622937152116, 8)
def test_sigma3(self):
self.assertTrue(np.allclose(sigma3.pA, sigma3.pA_nhb + sigma3.pA_oh + sigma3.pA_ot))
self.assertAlmostEqual(misc.fp(sigma3.pA_nhb), 0.049856600131970685, 8)