def test_printed_potential_match(self):
p = Potential.from_file('m2p2.pot')
with open('printed_potential.pot', 'w') as f:
f.write(str(p))
p2 = Potential.from_file('printed_potential.pot')
self.assertEqual(p == p2, True)
delete_file('printed_potential.pot')
def test_potential_charge(self):
""" tests the total charge """
p = Potential.from_file('m0.pot')
self.assertEqual(p.charge, 0)
p = Potential.from_file('nomul.pot')
self.assertEqual(p.charge, 0)
def test_potential_charge(self):
""" tests the total charge """
p = Potential.from_file('m0.pot')
self.assertEqual(p.charge, 0)
p = Potential.from_file('nomul.pot')
self.assertEqual(p.charge, 0)
def test_printed_potential_match(self):
p = Potential.from_file('m2p2.pot')
with open('printed_potential.pot', 'w') as f:
f.write(str(p))
p2 = Potential.from_file('printed_potential.pot')
self.assertEqual(p == p2, True)
delete_file('printed_potential.pot')
def test_add_potentials_with_multipoles_mixed(self):
""" Adds potentials with mixed multipole moments """
m2p2 = Potential.from_file('m2p2.pot')
m0 = Potential.from_file('m0.pot')
# check we can add both ways
p2 = m0 + m2p2
self.assertEqual(p2.nsites, 15)
self.assertEqual(len(p2.polarizabilities), 15)
self.assertEqual(max(p2.multipoles.keys()), 2)
p1 = m2p2 + m0
self.assertEqual(p1.nsites, 15)
self.assertEqual(len(p1.polarizabilities), 15)
self.assertEqual(max(p1.multipoles.keys()), 2)
def test_add_potentials_with_multipoles_mixed(self):
""" Adds potentials with mixed multipole moments """
m2p2 = Potential.from_file('m2p2.pot')
m0 = Potential.from_file('m0.pot')
# check we can add both ways
p2 = m0 + m2p2
self.assertEqual(p2.nsites, 15)
self.assertEqual(len(p2.polarizabilities), 15)
self.assertEqual(max(p2.multipoles.keys()), 2)
p1 = m2p2 + m0
self.assertEqual(p1.nsites, 15)
self.assertEqual(len(p1.polarizabilities), 15)
self.assertEqual(max(p1.multipoles.keys()), 2)
def test_get_pol_matrix(self):
""" polarization matrix """
p = Potential.from_file('nomul.pot')
pol = p.polarizabilities[0]
mat = util.get_polarization_matrix(p)
self.assertEqual(pol[0], mat[0,0])
self.assertEqual(pol[3], mat[1,1])
self.assertEqual(pol[5], mat[2,2])
def setUp(self):
c1 = [[0.0, 0.0, 0.0]]
q1 = [[1.0]]
self.p1 = Potential.from_multipoles( c1, q1 )
c2 = [[5.4, 0.0, 0.0]]
d2 = [[1.0, 1.0, 0.0]]
self.p2 = Potential.from_multipoles( c2, d2 )
# a potential from a file
self.pfile = Potential.from_file('pehf_iter.pot')
def setUp(self):
c1 = [[0.0, 0.0, 0.0]]
q1 = [[1.0]]
self.p1 = Potential.from_multipoles(c1, q1)
c2 = [[5.4, 0.0, 0.0]]
d2 = [[1.0, 1.0, 0.0]]
self.p2 = Potential.from_multipoles(c2, d2)
# a potential from a file
self.pfile = Potential.from_file('pehf_iter.pot')
def test_add_potentials_with_only_polarization(self):
""" Potential addition with only polarization """
p = Potential.from_file('nomul.pot')
p2 = p + p
self.assertEqual(p2.nsites, 2)
self.assertEqual(p2.npols, 2)
def test_nopol_potential_fails(self):
""" testing that potential without polarizibility correctly loads """
p = Potential.from_file('nopol.pot')
self.assertEqual(p.nsites, 3)
self.assertEqual(p.npols, 0)
def test_potential_equal(self):
""" tests equality of potentials """
p = Potential.from_file('m0.pot')
self.assertEqual(p == p, True)
def test_add_potentials_with_only_polarization(self):
""" Potential addition with only polarization """
p = Potential.from_file('nomul.pot')
p2 = p + p
self.assertEqual(p2.nsites, 2)
self.assertEqual(p2.npols, 2)
def test_potential_equal(self):
""" tests equality of potentials """
p = Potential.from_file('m0.pot')
self.assertEqual(p == p, True)
def test_nopol_potential_fails(self):
""" testing that potential without polarizibility correctly loads """
p = Potential.from_file('nopol.pot')
self.assertEqual(p.nsites, 3)
self.assertEqual(p.npols, 0)
# linear combination of all the stored guesses so far
new_guess = numpy.zeros(numpy.shape(self.guess_storage[0]))
for i in range(n):
new_guess += coeff[i] * self.guess_storage[i]
# remove unwanted (non-contributing) solutions from the
# DIIS space
selection = list(numpy.where(numpy.abs(coeff) < self.diis_vector_threshold)[0])
selection.reverse()
for i in selection:
self.guess_storage.pop(i)
self.diff_storage.pop(i)
return new_guess
if __name__ == '__main__':
import sys
from fields import get_static_field
from potential import Potential
from util import get_interaction_matrix, get_polarization_matrix
filename = sys.argv[1]
p = Potential.from_file(filename)
polmat = get_polarization_matrix(p)
intmat = get_interaction_matrix(p, induced_damping=True)
field = get_static_field(p)
s = IterativeDIISSolver(polmat, intmat, field, verbose = True, threshold = 1.0e-5)
result = s.Solve()
# DIIS space
selection = list(
numpy.where(numpy.abs(coeff) < self.diis_vector_threshold)[0])
selection.reverse()
for i in selection:
self.guess_storage.pop(i)
self.diff_storage.pop(i)
return new_guess
if __name__ == '__main__':
import sys
from fields import get_static_field
from potential import Potential
from util import get_interaction_matrix, get_polarization_matrix
filename = sys.argv[1]
p = Potential.from_file(filename)
polmat = get_polarization_matrix(p)
intmat = get_interaction_matrix(p, induced_damping=True)
field = get_static_field(p)
s = IterativeDIISSolver(polmat,
intmat,
field,
verbose=True,
threshold=1.0e-5)
result = s.Solve()
