def test_dsp(self):
mycosmo = cosmo.Cosmo()
mycosmo.load(filename)
mol = mycosmo.mol
disp_eps, disp_type = mol.get_dispersion_type()
self.assertAlmostEqual(disp_eps, 97.15234615384617, 9)
self.assertEqual(disp_type, "COOH")
import os
import unittest
import numpy as np
from pycosmosac.cosmo import cosmo
from pycosmosac.utils import misc
here = os.path.abspath(os.path.dirname(__file__))
filename = here + "/h2o.cosmo"
mycosmo = cosmo.Cosmo()
class KnownValues(unittest.TestCase):
def test_load(self):
mycosmo.load(filename)
mol = mycosmo.mol
xyz = mol.geometry["xyz"]
atom = mol.geometry["atom"]
self.assertAlmostEqual(misc.fp(xyz), -1.3049969366762706, 8)
self.assertEqual(atom, ['O', 'H', 'H'])
cavity = mol.cavity
total_area = cavity.area
self.assertAlmostEqual(total_area, 43.223568, 8)
total_volume = cavity.volume
self.assertAlmostEqual(total_volume, 25.661981, 8)
segments = cavity.segments
charge = segments["charge"]
area = segments["area"]
self.assertAlmostEqual(np.sum(area), total_area, 6)
sigma = charge / area
sigma0 = segments["sigma"]
self.assertTrue(np.allclose(sigma, sigma0) == True)
from pycosmosac.cosmo import cosmo 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
lngamma += lngamma_r(self.mols, self.sigmas, self.x, self.T, self.parameters.parameters, self.solve_gamma_thresh, self.solve_gamma_maxiter)
else:
lngamma += lngamma_r3(self.mols, self.sigmas, self.x, self.T, self.parameters.parameters, self.solve_gamma_thresh, self.solve_gamma_maxiter)
if self.dispersion:
lngamma += lngamma_dsp(self.mols, self.sigmas, self.x, self.parameters.parameters)
return lngamma
if __name__ == "__main__":
from pycosmosac.param import parameters, data
from pycosmosac.cosmo import cosmo
from pycosmosac.sigma import sigma
myparam = parameters.Parameters()
mol1 = cosmo.Cosmo().load("./test/butane.cosmo")
sigma1 = sigma.Sigma(mol1, myparam)
sigma1.write_sigma_file = False
sigma1.kernel()
mol2 = cosmo.Cosmo().load("./test/h2o.cosmo")
sigma2 = sigma.Sigma(mol2, myparam)
sigma2.write_sigma_file = False
sigma2.kernel()
x = [0., 1.]
T = 298.15
myac = AC([mol1,mol2], x, T, [sigma1,sigma2], myparam)
print(myac.kernel() - np.asarray([10.05271196, 0.0]))
myparam = parameters.Parameters(data.Hsieh_2010)
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.ac import ac
here = os.path.abspath(os.path.dirname(__file__))
mol1 = cosmo.Cosmo().load(here + "/butane.cosmo")
mol2 = cosmo.Cosmo().load(here + "/h2o.cosmo")
x = [0., 1.]
T = 298.15
class KnownValues(unittest.TestCase):
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])))