本文整理汇总了Python中yaff.pes.test.common.check_vtens_part函数的典型用法代码示例。如果您正苦于以下问题：Python check_vtens_part函数的具体用法？Python check_vtens_part怎么用？Python check_vtens_part使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了check_vtens_part函数的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_gpos_vtens_oopdist_formaldehyde
def test_gpos_vtens_oopdist_formaldehyde():
system = get_system_formaldehyde()
system.pos[0,0] += 0.0*angstrom
part = ForcePartValence(system)
part.add_term(Harmonic(0.0,0.0*angstrom,OopDist(2,3,1,0)))
check_gpos_part(system, part)
check_vtens_part(system, part)示例2: test_bks_vtens_gpos_parts
def test_bks_vtens_gpos_parts():
system = get_system_quartz()
fn_pars = context.get_fn('test/parameters_bks.txt')
ff = ForceField.generate(system, fn_pars, smooth_ei=True, reci_ei='ignore')
for part in ff.parts:
check_vtens_part(system, part, ff.nlist)
check_gpos_part(system, part, ff.nlist)示例3: test_gpos_vtens_quartz
def test_gpos_vtens_quartz():
system = get_system_quartz()
rv_table = {
('Si', 'O'): 3.24970,
('O', 'Si', 'O'): 2.06457,
('Si', 'O', 'Si'): 1.80173,
}
fc_table = {
('Si', 'O'): 0.30978,
('O', 'Si', 'O'): 0.19282,
('Si', 'O', 'Si'): 0.00751,
}
part = ForcePartValence(system)
for i, j in system.bonds:
key = system.get_ffatype(i), system.get_ffatype(j)
part.add_term(Harmonic(fc_table[key], rv_table[key], Bond(i, j)))
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
key = system.get_ffatype(i0), system.get_ffatype(i1), system.get_ffatype(i2)
if i0 > i2:
part.add_term(Harmonic(fc_table[key], rv_table[key], BendAngle(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)示例4: test_gpos_vtens_bond_fues_water32
def test_gpos_vtens_bond_fues_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(Fues(0.3, 1.7, Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)示例5: test_gpos_vtens_dihedral_cos_mil53
def test_gpos_vtens_dihedral_cos_mil53():
system = get_system_mil53()
forbidden_dihedrals = [
["O_HY","AL","O_HY","AL"],
["O_HY","AL","O_HY","H_HY"],
["O_CA","AL","O_CA","C_CA"],
["O_CA","AL","O_HY","H_HY"],
["H_PH","C_PH","C_PC","C_PH"],
["H_PH","C_PH","C_PC","C_CA"],
["C_PH","C_PH","C_PC","C_PH"],
["C_PH","C_PH","C_PC","C_CA"],
["C_PC","C_PH","C_PH","H_PH"],
["C_PC","C_PH","C_PH","C_PC"],
["H_PH","C_PH","C_PH","H_PH"],
["C_PH","C_PC","C_CA","O_CA"],
]
idih = -1
for i1, i2 in system.bonds:
for i0 in system.neighs1[i1]:
if i0==i2: continue
for i3 in system.neighs1[i2]:
if i3==i1: continue
types = [system.get_ffatype(i0), system.get_ffatype(i1), system.get_ffatype(i2), system.get_ffatype(i3)]
if types in forbidden_dihedrals or types[::-1] in forbidden_dihedrals: continue
idih += 1
fc = 2.1 + 0.01*(0.3*i1 + 0.7*i2)
part = ForcePartValence(system)
part.add_term(PolyFour([-2.0*fc,0.0001,0.0,0.0],DihedCos(i0,i1,i2,i3)))
check_gpos_part(system, part)
check_vtens_part(system, part)示例6: test_gpos_vtens_polyfour_water32
def test_gpos_vtens_polyfour_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(PolyFour([-0.5, 0.3, -0.16, 0.09], Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)示例7: test_ewald_vtens_neut_water32
def test_ewald_vtens_neut_water32():
# fake water model, negative oxygens and neutral hydrogens
system = get_system_water32()
system.charges -= 0.1
for alpha in 0.05, 0.1, 0.2:
part_ewald_neut = ForcePartEwaldNeutralizing(system, alpha)
check_vtens_part(system, part_ewald_neut)示例8: test_ewald_gpos_vtens_corr_water32
def test_ewald_gpos_vtens_corr_water32():
system = get_system_water32()
scalings = Scalings(system, 0.0, 0.0, 0.5)
for alpha in 0.05, 0.1, 0.2:
part_ewald_corr = ForcePartEwaldCorrection(system, alpha, scalings, dielectric=0.8)
check_gpos_part(system, part_ewald_corr)
check_vtens_part(system, part_ewald_corr)示例9: test_ewald_gpos_vtens_corr_quartz
def test_ewald_gpos_vtens_corr_quartz():
system = get_system_quartz().supercell(2, 2, 2)
scalings = Scalings(system, np.random.uniform(0.1, 0.9), np.random.uniform(0.1, 0.9), np.random.uniform(0.1, 0.9))
for alpha in 0.1, 0.2, 0.5:
part_ewald_corr = ForcePartEwaldCorrection(system, alpha, scalings)
check_gpos_part(system, part_ewald_corr)
check_vtens_part(system, part_ewald_corr)示例10: test_gpos_vtens_morse_water32
def test_gpos_vtens_morse_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(Morse(0.3, 1.7, 2.0, Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)示例11: test_ewald_gpos_vtens_reci_water32
def test_ewald_gpos_vtens_reci_water32():
system = get_system_water32()
dielectric = 1.4
for alpha in 0.05, 0.1, 0.2:
part_ewald_reci = ForcePartEwaldReciprocal(system, alpha, gcut=alpha / 0.75, dielectric=dielectric)
check_gpos_part(system, part_ewald_reci)
check_vtens_part(system, part_ewald_reci)示例12: test_gpos_vtens_mm3quartic_water32
def test_gpos_vtens_mm3quartic_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(MM3Quartic(1.5, 2.0+0.01*i, Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)示例13: test_gpos_vtens_2T
def test_gpos_vtens_2T():
system = get_system_2T()
rv_table = {
('H', 'Si', 'H'): 1.80861,
('Si', 'O'): 3.24970,
('H', 'O'): 1.96022,
('O', 'Si', 'O'): 2.06457,
('O', 'Si'): 3.24970,
('O', 'Si', 'H'): 1.85401,
('Si', 'O', 'Si'): 1.80173,
('Si', 'O', 'H'): 1.55702,
('H', 'O', 'Si'): 1.55702,
('Si', 'H'): 2.87853,
('H', 'Si'): 2.87853,
('H', 'Si', 'O'): 1.85401,
('O', 'H'): 1.96022,
}
fc_table = {
('H', 'Si', 'H'): 0.09376,
('Si', 'O'): 0.30978,
('H', 'O'): 0.60322,
('O', 'Si', 'O'): 0.19282,
('O', 'Si'): 0.30978,
('O', 'Si', 'H'): 0.11852,
('Si', 'O', 'Si'): 0.00751,
('Si', 'O', 'H'): 0.04271,
('H', 'O', 'Si'): 0.04271,
('Si', 'H'): 0.18044,
('H', 'Si'): 0.18044,
('H', 'Si', 'O'): 0.11852,
('O', 'H'): 0.60322,
}
part = ForcePartValence(system)
for i, j in system.bonds:
key = system.get_ffatype(i), system.get_ffatype(j)
part.add_term(Harmonic(fc_table[key], rv_table[key], Bond(i, j)))
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
key = system.get_ffatype(i0), system.get_ffatype(i1), system.get_ffatype(i2)
if i0 > i2:
part.add_term(Harmonic(fc_table[key], rv_table[key], BendAngle(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)
# same test but with Fues bonds instead of Harmonic bonds
part = ForcePartValence(system)
for i, j in system.bonds:
key = system.get_ffatype(i), system.get_ffatype(j)
part.add_term(Fues(fc_table[key], rv_table[key], Bond(i, j)))
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
key = system.get_ffatype(i0), system.get_ffatype(i1), system.get_ffatype(i2)
if i0 > i2:
part.add_term(Harmonic(fc_table[key], rv_table[key], BendAngle(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)示例14: test_gpos_vtens_bend_cos_water32
def test_gpos_vtens_bend_cos_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
part.add_term(Harmonic(1.1+0.01*i0, -0.2, BendCos(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)示例15: test_gpos_vtens_ub_water
def test_gpos_vtens_ub_water():
system = get_system_water32()
part = ForcePartValence(system)
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
part.add_term(Harmonic(2.1,2.0*angstrom,UreyBradley(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)