def dipole(atomtype, coordinates, connectivity, ATOM, MPOLE, CHGPEN, POLARIZE, REPEL):
ATOMID = katom.returnatomid(atomtype, coordinates, connectivity, ATOM, MPOLE, CHGPEN, POLARIZE, REPEL)
config.rotmat(ATOMID)
em, eminter, nem = empole3.empole3a(ATOMID)
config.dfield0(ATOMID)
induce.induce0m(ATOMID)
dx, dy, dz, qdx, qdy, qdz = epolar3.compute_dipoles(ATOMID)
print(template.header)
print(template.analyze_m.format(dx, dy, dz, qdx, qdy, qdz))
def test_epolar3m(self):
kep = -0.96210636
knep = 27
tconfig.setup(key, xyz, dloop=True)
config.rotmat(tconfig.ATOMID)
config.dfield0(tconfig.ATOMID)
induce.induce0m(tconfig.ATOMID)
ep, einter, nep = epolar3.epolar3m(tconfig.ATOMID)
self.assertEqual(round(kep, 4), round(ep, 4))
self.assertEqual(knep, nep)
def test_epolar3a(self):
kep = -0.96210636
keinter = -0.96210636
knep = 9
tconfig.setup(key, xyz, dloop=True)
config.rotmat(tconfig.ATOMID)
config.dfield0(tconfig.ATOMID)
induce.induce0m(tconfig.ATOMID)
config.param_dict['epolar3a'] = True
ep, einter, nep = epolar3.epolar3(tconfig.ATOMID)
self.assertEqual(round(kep, 4), round(ep, 4))
self.assertEqual(round(keinter, 4), round(einter, 4))
self.assertEqual(knep, nep)
def energy(atomtype, coordinates, connectivity, ATOM, MPOLE, CHGPEN, POLARIZE, REPEL):
ATOMID = katom.returnatomid(atomtype, coordinates, connectivity, ATOM, MPOLE, CHGPEN, POLARIZE, REPEL)
config.rotmat(ATOMID)
em, eminter, nem = empole3.empole3a(ATOMID)
config.dfield0(ATOMID)
if len(ATOM) == len(REPEL):
config.rfield0(ATOMID)
if len(ATOM) == len(POLARIZE):
induce.induce0m(ATOMID)
ep, epinter, nep = epolar3.epolar3(ATOMID)
else:
ep, epinter, nep = 0,0,0
if len(ATOM) == len(REPEL):
er, erinter, ner = erepel3.erepel3a(ATOMID)
else:
er, erinter, ner = 0,0,0
exchind, exchind_inter, exchind_ne = erepel3.exchangeinduce(ATOMID)
e = em + ep + er + exchind
einter = eminter + epinter + erinter + exchind_inter
print(template.header)
print(template.analyze_e.format(einter, e, em, nem, er, ner, ep, nep, exchind, exchind_ne, ep+exchind))
def test_induce0m(self):
kuind = [[2.38082614e-02, -7.18338014e-20, 4.60949086e-03],
[3.35357882e-02, 6.41583027e-19, 8.46639724e-04],
[9.13084719e-03, 9.98402841e-20, -5.18881980e-03],
[4.11632270e-02, -1.59110481e-19, -8.14876329e-03],
[6.05978292e-03, 5.06831844e-03, -5.04490841e-03],
[6.05978292e-03, -5.06831844e-03, -5.04490841e-03]]
tconfig.setup(key, xyz, dloop=True)
config.rotmat(tconfig.ATOMID)
config.dfield0(tconfig.ATOMID)
induce.induce0m(tconfig.ATOMID)
n = len(tconfig.ATOMID)
for i in range(n):
self.assertListEqual(list(np.round(kuind[i], 3)),
list(np.round(tconfig.ATOMID[i].uind, 3)))