def test_dampmut(self):
tconfig.setup(key, xyz, dloop=True)
n = len(tconfig.r_list)
index = [2, 4]
for i in range(n):
dmpik = damping.dampmut(tconfig.r_list[i], tconfig.alphai_list[i],
tconfig.alphak_list[i])
for j in index:
self.assertEqual(round(kdmpik[i][j], 5), round(dmpik[j], 5))
def test_atomid(self):
key = f'{path}/testitems/water21test.key'
xyz = f'{path}/testitems/waterwater.xyz'
tconfig.setup(key, xyz)
for i in tconfig.ATOMID:
i.rotmat(tconfig.ATOMID)
i.rotsite()
n = len(tconfig.atomtype[0])
rotmat = [np.array([[-0.85607447, 0., 0.5168525 ],
[ 0., -1., 0. ],
[ 0.5168525, 0., 0.85607447]]),
np.array([[-0.11350188, 0., -0.99353778],
[ 0., 1., 0. ],
[ 0.99353778, 0., -0.11350188]]),
np.array([[ 0.93207075, 0., 0.36227631],
[ 0., -1., 0. ],
[ 0.36227631, 0., -0.93207075]]),
np.array([[ 0., -0.86273158, 0.50566216],
[-1., -0., 0. ],
[ 0., -0.50566216, -0.86273158]]),
np.array([[ 4.00153410e-01, 8.62731581e-01, -3.09146353e-01],
[-6.11369365e-01, 2.77555756e-17, -7.91345373e-01],
[-6.82718645e-01, 5.05662159e-01, 5.27447659e-01]]),
np.array([[ 4.00153410e-01, -8.62731581e-01, -3.09146353e-01],
[ 6.11369365e-01, 2.77555756e-17, 7.91345373e-01],
[-6.82718645e-01, -5.05662159e-01, 5.27447659e-01]])]
pole = [np.array([-0.374842, 0.0, 0.0, 0.02863695393261772, 0.06349786711892166, 0.0, 0.0, 0.0, -0.057043769783220545, 0.0, 0.0, 0.0, -0.006454097335701115]),
np.array([0.187421, 0.0, 0.0, -0.10589682669043772, 0.006247996344765849, 0.0, 0.0006849497606354099, 0.0, 0.004089723196031596, 0.0, 0.0006849497606354099, 0.0, -0.010337719540797445]),
np.array([0.187421, 0.0, 0.0, -0.10589682669043772, 0.006247996344765849, 0.0, 0.0006849497606354099, 0.0, 0.004089723196031596, 0.0, 0.0006849497606354099, 0.0, -0.010337719540797445]),
np.array([-0.374842, 0.0, 0.0, 0.02863695393261772, 0.06349786711892166, 0.0, 0.0, 0.0, -0.057043769783220545, 0.0, 0.0, 0.0, -0.006454097335701115]),
np.array([0.187421, 0.0, 0.0, -0.10589682669043772, 0.006247996344765849, 0.0, 0.0006849497606354099, 0.0, 0.004089723196031596, 0.0, 0.0006849497606354099, 0.0, -0.010337719540797445]),
np.array([0.187421, 0.0, 0.0, -0.10589682669043772, 0.006247996344765849, 0.0, 0.0006849497606354099, 0.0, 0.004089723196031596, 0.0, 0.0006849497606354099, 0.0, -0.010337719540797445])]
rpole = [np.array([-0.374842, 0.014801081257770974, 0.0, 0.024515365062338562, 0.04481114362986063, 0.0, -0.030951242019077944, 0.0, -0.057043769783220545, 0.0, -0.030951242019077944, 0.0, 0.01223262615335991]),
np.array([0.187421, 0.10521249821235, 0.0, 0.012019489299502403, -0.009969569720161681, 0.0, -0.002537646589370999, 0.0, 0.004089723196031596, 0.0, -0.002537646589370999, 0.0, 0.005879846524130083]),
np.array([0.187421, -0.03836391140936379, 0.0, 0.0987033343128746, 0.004533788668292257, 0.0, 0.005095292897111618, 0.0, 0.004089723196031596, 0.0, 0.005095292897111618, 0.0, -0.008623511864323854]),
np.array([-0.374842, 0.01448062395724662, 0.0, -0.024706004540347774, -0.04410828298700111, 0.0, -0.022069780726477247, 0.0, 0.06349786711892166, 0.0, -0.022069780726477247, 0.0, -0.019389584131920556]),
np.array([0.187421, 0.03273761779816242, 0.08380096380258448, -0.05585503334314615, 0.002886995206979475, -0.004144993603861457, 0.002052025054034695, -0.004144993603861457, -0.003475671731847581, 0.007071948770927506, 0.002052025054034695, 0.007071948770927506, 0.0005886765248681071]),
np.array([0.187421, 0.03273761779816242, -0.08380096380258448, -0.05585503334314615, 0.002886995206979475, 0.004144993603861457, 0.002052025054034695, 0.004144993603861457, -0.003475671731847581, -0.007071948770927506, 0.002052025054034695, -0.007071948770927506, 0.0005886765248681071])]
self.assertEqual(tconfig.atomtype[0], [i.atomtype for i in tconfig.ATOMID])
self.assertEqual([i.tolist() for i in tconfig.coordinates[0]], [i.coordinates.tolist() for i in tconfig.ATOMID])
self.assertEqual(tconfig.connectivity[0], [i.connectivity for i in tconfig.ATOMID])
self.assertEqual([np.round(i,6).tolist() for i in rotmat], [np.round(i.a,6).tolist() for i in tconfig.ATOMID])
self.assertEqual([np.round(i,6).tolist() for i in pole], [np.round(i.pole,6).tolist() for i in tconfig.ATOMID])
self.assertEqual([np.round(i,6).tolist() for i in rpole], [np.round(i.rpole,6).tolist() for i in tconfig.ATOMID])
def test_damprep(self):
tconfig.setup(key, xyz, dloop=True)
n = len(tconfig.r_list)
for i in range(n):
dmpikr = damping.damprep(tconfig.r_list[i], tconfig.r2_list[i],
tconfig.rr1_list[i], tconfig.rr3_list[i],
tconfig.rr5_list[i], tconfig.rr7_list[i],
tconfig.rr9_list[i], 9,
tconfig.dmppri_list[i],
tconfig.dmpprk_list[i])
self.assertListEqual(list(np.round(kdmpikr[i], 5)),
list(np.round(list(dmpikr), 5)))
def test_damppole(self):
tconfig.setup(key, xyz, dloop=True)
n = len(tconfig.r_list)
for i in range(n):
dmpi, dmpk, dmpik = damping.damppole(tconfig.r_list[i], 9,
tconfig.alphai_list[i],
tconfig.alphak_list[i])
self.assertListEqual(list(np.round(kdmpi[i], 5)),
list(np.round(list(dmpi), 5)))
self.assertListEqual(list(np.round(kdmpk[i], 5)),
list(np.round(list(dmpk), 5)))
self.assertListEqual(list(np.round(kdmpik[i], 5)),
list(np.round(list(dmpik), 5)))
def test_empole3a(self):
key = f'{path}/testitems/water21test.key'
xyz = f'{path}/testitems/waterwater.xyz'
tconfig.setup(key, xyz)
kem = -8.503511879615823
keinter = -8.503511879615823
knem = 9
config.rotmat(tconfig.ATOMID)
em, einter, nem = empole3.empole3a(tconfig.ATOMID)
self.assertEqual(np.round(kem, 6), np.round(em, 6))
self.assertEqual(np.round(keinter, 6), np.round(einter, 6))
self.assertEqual(knem, nem)
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_dampmutm(self):
tconfig.setup(key, xyz, dloop=True)
n = len(tconfig.r_list)
indexi = [2]
indexk = [2]
indexik = [2, 4, 6]
for i in range(n):
dmpi, dmpk, dmpik = damping.dampmutm(tconfig.r_list[i],
tconfig.alphai_list[i],
tconfig.alphak_list[i])
for j in indexi:
self.assertEqual(round(kdmpi[i][j], 5), round(dmpi[j], 5))
for j in indexk:
self.assertEqual(round(kdmpk[i][j], 5), round(dmpk[j], 5))
for j in indexik:
self.assertEqual(round(kdmpik[i][j], 5), round(dmpik[j], 5))
def test_dfield0m(self):
kfieldp = [[
0.02379644, 0.0335467, 0.01730396, 0.05066768, 0.01820036,
0.01820036
], [0., 0., 0., 0., 0.01092463, -0.01092463],
[
0.00623291, 0.00776782, -0.0017124, -0.00968786,
-0.01237913, -0.01237913
]]
tconfig.setup(key, xyz, dloop=True)
config.rotmat(tconfig.ATOMID)
field, fieldp = induce.dfield0m(tconfig.ATOMID)
for i in range(3):
self.assertListEqual(list(np.round(kfieldp[i], 5)),
list(np.round(fieldp[i], 5)))
def test_dfield0a(self):
kfieldp = [[
0.02619577, 0.07496387, 0.01744932, 0.04682931, 0.01790609,
0.01790609
], [0., 0., 0., 0., 0.01083918, -0.01083918],
[
0.00620645, 0.0047009, -0.00175382, -0.00948837,
-0.01230889, -0.01230889
]]
tconfig.setup(key, xyz, dloop=True)
config.rotmat(tconfig.ATOMID)
field, fieldp = induce.dfield0a(tconfig.ATOMID)
for i in range(3):
self.assertListEqual(list(np.round(kfieldp[i], 5)),
list(np.round(fieldp[i], 5)))
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 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)))
def test_katom(self):
key = f'{path}/testitems/water21test.key'
xyz = f'{path}/testitems/waterwater.xyz'
tconfig.setup(key, xyz)
for k in tconfig.atom_dict.keys():
self.assertEqual(tconfig.atom_dict[k], tconfig.ATOM[k].returnlist())
for k in tconfig.bond_dict.keys():
self.assertEqual(tconfig.bond_dict[k], tconfig.BOND[k].returnlist())
for k in tconfig.angle_dict.keys():
self.assertEqual(tconfig.angle_dict[k], tconfig.ANGLE[k].returnlist())
for k in tconfig.repel_dict.keys():
self.assertEqual(tconfig.repel_dict[k], tconfig.REPEL[k].returnlist())
for k in tconfig.disp_dict.keys():
self.assertEqual(tconfig.disp_dict[k], tconfig.DISP[k].returnlist())
for k in tconfig.mpole_dict.keys():
self.assertTrue(set(tconfig.mpole_dict[k]).issubset(set(tconfig.MPOLE[k].returnlist())))
for k in tconfig.chgpen_dict.keys():
self.assertEqual(tconfig.chgpen_dict[k], tconfig.CHGPEN[k].returnlist())
for k in tconfig.polarize_dict.keys():
self.assertEqual(tconfig.polarize_dict[k], tconfig.POLARIZE[k].returnlist())
for k in tconfig.chgtrn_dict.keys():
self.assertEqual(tconfig.chgtrn_dict[k], tconfig.CHGTRN[k].returnlist())
