def debye_waller_factors(self, miller_index=None, miller_indices=None, u_iso=None, b_iso=None, u_cart=None, b_cart=None, u_cif=None, u_star=None, exp_arg_limit=50, truncate_exp_arg=False): assert [miller_index, miller_indices].count(None) == 1 assert [u_iso, b_iso, u_cart, b_cart, u_cif, u_star].count(None) == 5 from cctbx import adptbx h = miller_index if (h is None): h = miller_indices if (u_iso is not None): b_iso = adptbx.u_as_b(u_iso) if (b_iso is not None): return adptbx.debye_waller_factor_b_iso( self.stol_sq(h), b_iso, exp_arg_limit, truncate_exp_arg) if (b_cart is not None): u_cart = adptbx.b_as_u(b_cart) if (u_cart is not None): u_star = adptbx.u_cart_as_u_star(self, u_cart) if (u_cif is not None): u_star = adptbx.u_cif_as_u_star(self, u_cif) assert u_star is not None return adptbx.debye_waller_factor_u_star( h, u_star, exp_arg_limit, truncate_exp_arg)
def exercise_interface(): episq = 8 * (math.pi**2) assert approx_equal(adptbx.u_as_b(2.3), 2.3 * episq) assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(2.3)), 2.3) u = (3, 4, 9, 2, 1, 7) assert approx_equal(adptbx.u_as_b(u), [x * episq for x in u]) assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(u)), u) uc = uctbx.unit_cell((5, 4, 7, 80, 110, 100)) for fw, bw in ((adptbx.u_cif_as_u_star, adptbx.u_star_as_u_cif), (adptbx.u_cart_as_u_star, adptbx.u_star_as_u_cart), (adptbx.u_cart_as_u_cif, adptbx.u_cif_as_u_cart), (adptbx.u_cart_as_beta, adptbx.beta_as_u_cart), (adptbx.u_cif_as_beta, adptbx.beta_as_u_cif)): assert approx_equal(bw(uc, fw(uc, u)), u) assert approx_equal(adptbx.beta_as_u_star(adptbx.u_star_as_beta(u)), u) assert approx_equal(adptbx.u_cart_as_u_iso(adptbx.u_iso_as_u_cart(2.3)), 2.3) for fw, bw in ((adptbx.u_iso_as_u_star, adptbx.u_star_as_u_iso), (adptbx.u_iso_as_u_cif, adptbx.u_cif_as_u_iso), (adptbx.u_iso_as_beta, adptbx.beta_as_u_iso)): assert approx_equal(bw(uc, fw(uc, 2.3)), 2.3) fc = adptbx.factor_u_cart_u_iso(u_cart=u) assert approx_equal(fc.u_iso, adptbx.u_cart_as_u_iso(u)) assert approx_equal(fc.u_cart_minus_u_iso, [uii - fc.u_iso for uii in u[:3]] + list(u[3:])) f = adptbx.factor_u_star_u_iso(unit_cell=uc, u_star=adptbx.u_cart_as_u_star(uc, u)) assert approx_equal(f.u_iso, fc.u_iso) assert approx_equal(f.u_star_minus_u_iso, adptbx.u_cart_as_u_star(uc, fc.u_cart_minus_u_iso)) f = adptbx.factor_u_cif_u_iso(unit_cell=uc, u_cif=adptbx.u_cart_as_u_cif(uc, u)) assert approx_equal(f.u_iso, fc.u_iso) assert approx_equal(f.u_cif_minus_u_iso, adptbx.u_cart_as_u_cif(uc, fc.u_cart_minus_u_iso)) f = adptbx.factor_beta_u_iso(unit_cell=uc, beta=adptbx.u_cart_as_beta(uc, u)) assert approx_equal(f.u_iso, fc.u_iso) assert approx_equal(f.beta_minus_u_iso, adptbx.u_cart_as_beta(uc, fc.u_cart_minus_u_iso)) assert approx_equal(adptbx.debye_waller_factor_b_iso(0.25, 2.3), math.exp(-2.3 * 0.25)) assert approx_equal(adptbx.debye_waller_factor_u_iso(0.25, 2.3), math.exp(-2.3 * episq * 0.25)) assert approx_equal( adptbx.debye_waller_factor_b_iso(uc, (1, 2, 3), 2.3), adptbx.debye_waller_factor_u_iso(uc, (1, 2, 3), 2.3 / episq)) u_star = adptbx.u_cart_as_u_star(uc, u) dw = adptbx.debye_waller_factor_u_star((1, 2, 3), u_star) assert approx_equal( dw, adptbx.debye_waller_factor_beta((1, 2, 3), adptbx.u_star_as_beta(u_star))) assert approx_equal( dw, adptbx.debye_waller_factor_u_cif(uc, (1, 2, 3), adptbx.u_star_as_u_cif(uc, u_star))) assert approx_equal( dw, adptbx.debye_waller_factor_u_cart(uc, (1, 2, 3), adptbx.u_star_as_u_cart(uc, u_star))) for e in adptbx.eigenvalues(u): check_eigenvalue(u, e) assert not adptbx.is_positive_definite(adptbx.eigenvalues(u)) assert not adptbx.is_positive_definite(adptbx.eigenvalues(u), 0) assert adptbx.is_positive_definite(adptbx.eigenvalues(u), 1.22) assert not adptbx.is_positive_definite(u) assert not adptbx.is_positive_definite(u, 0) assert adptbx.is_positive_definite(u, 1.22) up = (0.534, 0.812, 0.613, 0.0166, 0.134, -0.0124) s = adptbx.eigensystem(up) assert approx_equal(s.values(), (0.813132, 0.713201, 0.432668)) for i in xrange(3): check_eigenvector(up, s.values()[i], s.vectors(i)) c = (1, 2, 3, 3, -4, 5, 4, 5, 6) v = (198, 18, 1020, 116, 447, 269) assert approx_equal(adptbx.c_u_c_transpose(c, u), v) assert approx_equal( adptbx.eigensystem(u).values(), (14.279201519086316, 2.9369143826320214, -1.2161159017183376)) s = adptbx.eigensystem(up) try: s.vectors(4) except RuntimeError, e: assert str(e).endswith("Index out of range.")
def exercise_interface(): episq = 8*(math.pi**2) assert approx_equal(adptbx.u_as_b(2.3), 2.3*episq) assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(2.3)), 2.3) u = (3,4,9, 2,1,7) assert approx_equal(adptbx.u_as_b(u), [x*episq for x in u]) assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(u)), u) uc = uctbx.unit_cell((5,4,7,80,110,100)) for fw,bw in ((adptbx.u_cif_as_u_star, adptbx.u_star_as_u_cif), (adptbx.u_cart_as_u_star, adptbx.u_star_as_u_cart), (adptbx.u_cart_as_u_cif, adptbx.u_cif_as_u_cart), (adptbx.u_cart_as_beta, adptbx.beta_as_u_cart), (adptbx.u_cif_as_beta, adptbx.beta_as_u_cif)): assert approx_equal(bw(uc, fw(uc, u)), u) assert approx_equal(adptbx.beta_as_u_star(adptbx.u_star_as_beta(u)), u) assert approx_equal(adptbx.u_cart_as_u_iso(adptbx.u_iso_as_u_cart(2.3)), 2.3) for fw,bw in ((adptbx.u_iso_as_u_star, adptbx.u_star_as_u_iso), (adptbx.u_iso_as_u_cif, adptbx.u_cif_as_u_iso), (adptbx.u_iso_as_beta, adptbx.beta_as_u_iso)): assert approx_equal(bw(uc, fw(uc, 2.3)), 2.3) fc = adptbx.factor_u_cart_u_iso(u_cart=u) assert approx_equal(fc.u_iso, adptbx.u_cart_as_u_iso(u)) assert approx_equal( fc.u_cart_minus_u_iso, [uii-fc.u_iso for uii in u[:3]]+list(u[3:])) f = adptbx.factor_u_star_u_iso( unit_cell=uc, u_star=adptbx.u_cart_as_u_star(uc, u)) assert approx_equal(f.u_iso, fc.u_iso) assert approx_equal( f.u_star_minus_u_iso, adptbx.u_cart_as_u_star(uc, fc.u_cart_minus_u_iso)) f = adptbx.factor_u_cif_u_iso( unit_cell=uc, u_cif=adptbx.u_cart_as_u_cif(uc, u)) assert approx_equal(f.u_iso, fc.u_iso) assert approx_equal( f.u_cif_minus_u_iso, adptbx.u_cart_as_u_cif(uc, fc.u_cart_minus_u_iso)) f = adptbx.factor_beta_u_iso( unit_cell=uc, beta=adptbx.u_cart_as_beta(uc, u)) assert approx_equal(f.u_iso, fc.u_iso) assert approx_equal( f.beta_minus_u_iso, adptbx.u_cart_as_beta(uc, fc.u_cart_minus_u_iso)) assert approx_equal(adptbx.debye_waller_factor_b_iso(0.25,2.3), math.exp(-2.3*0.25)) assert approx_equal(adptbx.debye_waller_factor_u_iso(0.25,2.3), math.exp(-2.3*episq*0.25)) assert approx_equal(adptbx.debye_waller_factor_b_iso(uc, (1,2,3), 2.3), adptbx.debye_waller_factor_u_iso(uc, (1,2,3), 2.3/episq)) u_star = adptbx.u_cart_as_u_star(uc, u) dw = adptbx.debye_waller_factor_u_star((1,2,3), u_star) assert approx_equal(dw, adptbx.debye_waller_factor_beta((1,2,3), adptbx.u_star_as_beta(u_star))) assert approx_equal(dw, adptbx.debye_waller_factor_u_cif(uc, (1,2,3), adptbx.u_star_as_u_cif(uc, u_star))) assert approx_equal(dw, adptbx.debye_waller_factor_u_cart(uc, (1,2,3), adptbx.u_star_as_u_cart(uc, u_star))) for e in adptbx.eigenvalues(u): check_eigenvalue(u, e) assert not adptbx.is_positive_definite(adptbx.eigenvalues(u)) assert not adptbx.is_positive_definite(adptbx.eigenvalues(u), 0) assert adptbx.is_positive_definite(adptbx.eigenvalues(u), 1.22) assert not adptbx.is_positive_definite(u) assert not adptbx.is_positive_definite(u, 0) assert adptbx.is_positive_definite(u, 1.22) up = (0.534, 0.812, 0.613, 0.0166, 0.134, -0.0124) s = adptbx.eigensystem(up) assert approx_equal(s.values(), (0.813132, 0.713201, 0.432668)) for i in xrange(3): check_eigenvector(up, s.values()[i], s.vectors(i)) c = (1,2,3, 3,-4,5, 4,5,6) v = (198,18,1020,116,447,269) assert approx_equal(adptbx.c_u_c_transpose(c, u), v) assert approx_equal(adptbx.eigensystem(u).values(), (14.279201519086316, 2.9369143826320214, -1.2161159017183376)) s = adptbx.eigensystem(up) try: s.vectors(4) except RuntimeError, e: assert str(e).endswith("Index out of range.") else: raise Exception_expected uf = adptbx.eigenvalue_filtering(u_cart=u, u_min=0) assert approx_equal(uf, (3.0810418, 4.7950710, 9.3400030, 1.7461615, 1.1659954, 6.4800706)) uf = adptbx.eigenvalue_filtering(u_cart=u, u_min=0, u_max=3) assert approx_equal(uf, (2.7430890, 1.0378360, 2.1559895, 0.6193215, -0.3921632, 1.2846854)) uf = adptbx.eigenvalue_filtering(u_cart=u, u_min=0, u_max=3) assert approx_equal(scitbx.linalg.eigensystem.real_symmetric(u).values(), (14.2792015, 2.9369144, -1.2161159)) assert approx_equal(scitbx.linalg.eigensystem.real_symmetric(uf).values(), (3, 2.9369144, 0)) uf = adptbx.eigenvalue_filtering(up) assert approx_equal(uf, up)
def exercise_interface(): episq = 8 * (math.pi ** 2) assert approx_equal(adptbx.u_as_b(2.3), 2.3 * episq) assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(2.3)), 2.3) u = (3, 4, 9, 2, 1, 7) assert approx_equal(adptbx.u_as_b(u), [x * episq for x in u]) assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(u)), u) uc = uctbx.unit_cell((5, 4, 7, 80, 110, 100)) for fw, bw in ( (adptbx.u_cif_as_u_star, adptbx.u_star_as_u_cif), (adptbx.u_cart_as_u_star, adptbx.u_star_as_u_cart), (adptbx.u_cart_as_u_cif, adptbx.u_cif_as_u_cart), (adptbx.u_cart_as_beta, adptbx.beta_as_u_cart), (adptbx.u_cif_as_beta, adptbx.beta_as_u_cif), ): assert approx_equal(bw(uc, fw(uc, u)), u) assert approx_equal(adptbx.beta_as_u_star(adptbx.u_star_as_beta(u)), u) assert approx_equal(adptbx.u_cart_as_u_iso(adptbx.u_iso_as_u_cart(2.3)), 2.3) for fw, bw in ( (adptbx.u_iso_as_u_star, adptbx.u_star_as_u_iso), (adptbx.u_iso_as_u_cif, adptbx.u_cif_as_u_iso), (adptbx.u_iso_as_beta, adptbx.beta_as_u_iso), ): assert approx_equal(bw(uc, fw(uc, 2.3)), 2.3) fc = adptbx.factor_u_cart_u_iso(u_cart=u) assert approx_equal(fc.u_iso, adptbx.u_cart_as_u_iso(u)) assert approx_equal(fc.u_cart_minus_u_iso, [uii - fc.u_iso for uii in u[:3]] + list(u[3:])) f = adptbx.factor_u_star_u_iso(unit_cell=uc, u_star=adptbx.u_cart_as_u_star(uc, u)) assert approx_equal(f.u_iso, fc.u_iso) assert approx_equal(f.u_star_minus_u_iso, adptbx.u_cart_as_u_star(uc, fc.u_cart_minus_u_iso)) f = adptbx.factor_u_cif_u_iso(unit_cell=uc, u_cif=adptbx.u_cart_as_u_cif(uc, u)) assert approx_equal(f.u_iso, fc.u_iso) assert approx_equal(f.u_cif_minus_u_iso, adptbx.u_cart_as_u_cif(uc, fc.u_cart_minus_u_iso)) f = adptbx.factor_beta_u_iso(unit_cell=uc, beta=adptbx.u_cart_as_beta(uc, u)) assert approx_equal(f.u_iso, fc.u_iso) assert approx_equal(f.beta_minus_u_iso, adptbx.u_cart_as_beta(uc, fc.u_cart_minus_u_iso)) assert approx_equal(adptbx.debye_waller_factor_b_iso(0.25, 2.3), math.exp(-2.3 * 0.25)) assert approx_equal(adptbx.debye_waller_factor_u_iso(0.25, 2.3), math.exp(-2.3 * episq * 0.25)) assert approx_equal( adptbx.debye_waller_factor_b_iso(uc, (1, 2, 3), 2.3), adptbx.debye_waller_factor_u_iso(uc, (1, 2, 3), 2.3 / episq), ) u_star = adptbx.u_cart_as_u_star(uc, u) dw = adptbx.debye_waller_factor_u_star((1, 2, 3), u_star) assert approx_equal(dw, adptbx.debye_waller_factor_beta((1, 2, 3), adptbx.u_star_as_beta(u_star))) assert approx_equal(dw, adptbx.debye_waller_factor_u_cif(uc, (1, 2, 3), adptbx.u_star_as_u_cif(uc, u_star))) assert approx_equal(dw, adptbx.debye_waller_factor_u_cart(uc, (1, 2, 3), adptbx.u_star_as_u_cart(uc, u_star))) for e in adptbx.eigenvalues(u): check_eigenvalue(u, e) assert not adptbx.is_positive_definite(adptbx.eigenvalues(u)) assert not adptbx.is_positive_definite(adptbx.eigenvalues(u), 0) assert adptbx.is_positive_definite(adptbx.eigenvalues(u), 1.22) assert not adptbx.is_positive_definite(u) assert not adptbx.is_positive_definite(u, 0) assert adptbx.is_positive_definite(u, 1.22) up = (0.534, 0.812, 0.613, 0.0166, 0.134, -0.0124) s = adptbx.eigensystem(up) assert approx_equal(s.values(), (0.813132, 0.713201, 0.432668)) for i in xrange(3): check_eigenvector(up, s.values()[i], s.vectors(i)) c = (1, 2, 3, 3, -4, 5, 4, 5, 6) v = (198, 18, 1020, 116, 447, 269) assert approx_equal(adptbx.c_u_c_transpose(c, u), v) assert approx_equal(adptbx.eigensystem(u).values(), (14.279201519086316, 2.9369143826320214, -1.2161159017183376)) s = adptbx.eigensystem(up) try: s.vectors(4) except RuntimeError, e: assert str(e).endswith("Index out of range.")