def test_load(self):
myparam = parameters.Parameters() #default
self.assertEqual(myparam.parameters["a_eff"], 6.22, 9)
myparam = parameters.Parameters(parameters=data.Mullins_2006)
self.assertEqual(myparam.parameters["a_eff"], 7.5, 9)
myparam = parameters.Parameters(parameters=here + "/Hsieh_2010.json")
self.assertEqual(myparam.parameters["a_eff"], 7.25, 9)
def test_dump(self):
myparam = parameters.Parameters()
s = myparam.dump_to_string()
param = json.loads(s)
self.assertEqual(param["a_eff"], 6.22, 9)
myparam.dump_to_json("/tmp/tmp.json")
with open("/tmp/tmp.json", 'r') as f:
param = json.load(f)
self.assertEqual(param["a_eff"], 6.22, 9)
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.])))
import os import numpy as np from pycosmosac.param import data, parameters 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)
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)
lngamma = lngamma_c(self.mols, self.x, self.parameters.parameters)
if not self.split_sigma:
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]))
ac.AC.__init__(self, mols, x, T, sigmas, parameters)
self.comb = True
def kernel(self):
mu = mu_s(self.mols, self.sigmas, self.x, self.T, self.parameters.parameters)
if self.comb:
mu += mu_c(self.mols, self.x, self.T, self.parameters.parameters)
return mu
if __name__ == "__main__":
from pycosmosac.param import parameters, data
from pycosmosac.cosmo import cosmo
from pycosmosac.sigma import sigma
myparam = parameters.Parameters(data.COSMORS)
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
myrs = RS([mol1,mol2], x, T, [sigma1,sigma2], myparam)
print(myrs.kernel())