diff --git a/cif_ms.dic b/cif_ms.dic index 9a5335c..ce97200 100644 --- a/cif_ms.dic +++ b/cif_ms.dic @@ -402,7 +402,7 @@ save_atom_site_displace_Fourier_param.cos cosine coefficient (Ac) corresponding to the Fourier term defined _atom_site_displace_Fourier.atom_site_label, _atom_site_displace_Fourier.axis and - _atom_site_displace_Fourier.wave_vector.seq_id. Atomic or rigid-group + _atom_site_displace_Fourier.wave_vector_seq_id. Atomic or rigid-group displacements must be expressed as fractions of the unit cell or in angstroms if the modulations are referred to some special axes defined by the items belonging to the ATOM_SITES_AXES @@ -1027,7 +1027,7 @@ save_atom_site_displace_ortho.func_id structural model to describe the displacive modulation of an atom or rigid group. In the case of a rigid group, it applies only to the translational part of the distortion. This code must match - _atom_sites_ortho_func_id. + _atom_sites_ortho.func_id. ; _name.category_id atom_site_displace_ortho _name.object_id func_id @@ -1273,7 +1273,7 @@ save_atom_site_displace_special_func.sawtooth internal space. ux, uy and uz must be expressed in relative units or in angstroms if the modulations are referred to some special axes defined by the items belonging to the ATOM_SITES_AXES - category, through _atom_site_displace_special_funcs.matrix_seq_id. + category, through _atom_site_displace_special_func.matrix_seq_id. The use of this function is restricted to one-dimensional modulated structures. For more details, see @@ -2091,15 +2091,15 @@ save_atom_site_Fourier_wave_vector.q_coeff with integer coefficients of the independent wave vectors given in the _cell_wave_vector. list. Therefore, a generic Fourier wave vector is expressed as k=n(1)q(1)+...+n(p)q(p), where p is given - by _cell_modulation_dimension. In the case of composites + by _cell.modulation_dimension. In the case of composites described in a single data block, these wave vectors are expressed with respect to the three-dimensional reciprocal basis of each subsystem (see _cell_subsystem.matrix_W_*). - _atom_site_Fourier_wave_vector.coeff contains the coefficients that + _atom_site_Fourier_wave_vector.q_coeff contains the coefficients that express a given k as a linear combination of the independent wave vectors - given in _cell_modulation_dimension. The enumeration of the independent + given in _cell.modulation_dimension. The enumeration of the independent wave vectors (1,2, ...) is given by the value of - _atom_site_Fourier_wave_vector_.q_coeff_seq_id matching the + _atom_site_Fourier_wave_vector.q_coeff_seq_id matching the corresponding value of _cell_wave_vector.seq_id ; _name.category_id atom_site_Fourier_wave_vector @@ -2121,7 +2121,7 @@ save_atom_site_Fourier_wave_vector.q_coeff #Not meaningful coefficients are removed here atom_site_Fourier_wave_vector.q_coeff = - temp.q_coeff[0:_cell_modulation_dimension-1] + temp.q_coeff[0:_cell.modulation_dimension-1] ; save_ @@ -2135,7 +2135,7 @@ save_atom_site_Fourier_wave_vector.q_coeff_seq_id The list of codes that identifies each independent wave vector appearing in the linear combination that expresses a generic Fourier wave vector as k=n(1)q(1)+...+n(p)q(p), where p is given - by _cell_modulation_dimension. In the case of composites + by _cell.modulation_dimension. In the case of composites described in a single data block, these wave vectors are expressed with respect to the three-dimensional reciprocal basis of each subsystem (see _cell_subsystem.matrix_W_*). @@ -2161,7 +2161,7 @@ save_atom_site_Fourier_wave_vector.q_coeff_seq_id #Not meaningful identifiers are removed here atom_site_Fourier_wave_vector.q_coeff_seq_id = - temp.q_coeff_seq_id[0:_cell_modulation_dimension-1] + temp.q_coeff_seq_id[0:_cell.modulation_dimension-1] ; save_ @@ -2183,7 +2183,7 @@ save_atom_site_Fourier_wave_vector.x with integer coefficients of the independent wave vectors given in the _cell_wave_vector_ list. Therefore, a generic Fourier wave vector is expressed as k=n(1)q(1)+...+n(p)q(p), where p is given - by _cell_modulation_dimension. In the case of composites + by _cell.modulation_dimension. In the case of composites described in a single data block, these wave vectors are expressed with respect to the three-dimensional reciprocal basis of each subsystem (see _cell_subsystem.matrix_W_*). @@ -2222,7 +2222,7 @@ save_atom_site_Fourier_wave_vector.xyz with integer coefficients of the independent wave vectors given in the _cell_wave_vector. list. Therefore, a generic Fourier wave vector is expressed as k=n(1)q(1)+...+n(p)q(p), where p is given - by _cell_modulation_dimension. In the case of composites + by _cell.modulation_dimension. In the case of composites described in a single data block, these wave vectors are expressed with respect to the three-dimensional reciprocal basis of each subsystem (see _cell_subsystem.matrix_W_*). @@ -2286,7 +2286,7 @@ save_atom_site_Fourier_wave_vector.y with integer coefficients of the independent wave vectors given in the _cell_wave_vector_ list. Therefore, a generic Fourier wave vector is expressed as k=n(1)q(1)+...+n(p)q(p), where p is given - by _cell_modulation_dimension. In the case of composites + by _cell.modulation_dimension. In the case of composites described in a single data block, these wave vectors are expressed with respect to the three-dimensional reciprocal basis of each subsystem (see _cell_subsystem.matrix_W_*). @@ -2329,7 +2329,7 @@ save_atom_site_Fourier_wave_vector.z with integer coefficients of the independent wave vectors given in the _cell_wave_vector_ list. Therefore, a generic Fourier wave vector is expressed as k=n(1)q(1)+...+n(p)q(p), where p is given - by _cell_modulation_dimension. In the case of composites + by _cell.modulation_dimension. In the case of composites described in a single data block, these wave vectors are expressed with respect to the three-dimensional reciprocal basis of each subsystem (see _cell_subsystem.matrix_W_*). @@ -2369,7 +2369,7 @@ save_atom_site_Fourier_wave_vector.q1_coeff with integer coefficients of the independent wave vectors given in the _cell_wave_vector. list. Therefore, a generic Fourier wave vector is expressed as k=n(1)q(1)+...+n(p)q(p), where p is given - by _cell_modulation_dimension. In the case of composites + by _cell.modulation_dimension. In the case of composites described in a single data block, these wave vectors are expressed with respect to the three-dimensional reciprocal basis of each subsystem (see _cell_subsystem.matrix_W_*). @@ -2377,7 +2377,7 @@ save_atom_site_Fourier_wave_vector.q1_coeff of the contribution of the first independent wave vector to the above linear combination. The enumeration of the involved independent wave vectors (1,2, ...) is given by the value of - _atom_site_Fourier_wave_vecto_.q1_coeff_seq_id matching the + _atom_site_Fourier_wave_vector.q1_coeff_seq_id matching the corresponding value of _cell_wave_vector.seq_id. ; _name.category_id atom_site_Fourier_wave_vector @@ -2408,7 +2408,7 @@ save_atom_site_Fourier_wave_vector.q1_coeff_seq_id A code identifying the first independent wave vector, q(1), in the linear combination that expresses a generic Fourier wave vector as k=n(1)q(1)+...+n(p)q(p), where p is given by - _cell_modulation_dimension. It must match a code given in + _cell.modulation_dimension. It must match a code given in _cell_wave_vector.seq_id. ; _name.category_id atom_site_Fourier_wave_vector @@ -3044,7 +3044,7 @@ save_atom_site_occ_Fourier_param.modulus and the modulus-argument form, |P| cos(\2\p k r+\\d), where k is the wave vector of the term and r is the atomic - average position. _atom_site_occ_Fourier.param_modulus is the + average position. _atom_site_occ_Fourier_param.modulus is the modulus (|P|) of the complex amplitude corresponding to the Fourier term defined by _atom_site_occ_Fourier.atom_site_label and _atom_site_occ_Fourier.wave_vector_seq_id. @@ -3417,7 +3417,7 @@ save_atom_site_occ_ortho.func_id A code identifying the orthogonalized function used in the structural model to describe the occupational modulation of an atom - or rigid group. This code must match _atom_sites_ortho_func_id. + or rigid group. This code must match _atom_sites_ortho.func_id. ; _name.category_id atom_site_occ_ortho _name.object_id func_id @@ -4194,7 +4194,7 @@ save_atom_site_rot_Fourier_param.cos and the modulus-argument form, |R| cos(2\\p k r+\\y), where k is the wave vector of the term and r is the atomic - average position. _atom_site_rot_Fourier_param_cos is the cosine + average position. _atom_site_rot_Fourier_param.cos is the cosine coefficient (Rc) in degrees corresponding to the Fourier term defined by _atom_site_rot_Fourier.atom_site_label, @@ -4756,7 +4756,7 @@ save_atom_site_rot_ortho.func_id structural model to describe the displacive modulation of an atom or rigid group. In the case of a rigid group, it applies only to the rotational part of the distortion. This code must match - _atom_sites_ortho_func_id. + _atom_sites_ortho.func_id. ; _name.category_id atom_site_rot_ortho _name.object_id func_id @@ -7418,7 +7418,7 @@ save_ATOM_SITES_ORTHO by a Crenel function (see Petricek et al., 2016). The functions are constructed selecting Fourier harmonics until a desired degree of orthogonality and completeness is - reached (see_atom_site_occ_special_func.crenel_ortho_eps). + reached (see _atom_site_occ_special_func.crenel_ortho_eps). References: Petricek, V., Van Der Lee & Evain, M. (1995). Acta Cryst. A51, 529-535. DOI 10.1107/S0108767395000365 @@ -7446,7 +7446,7 @@ save_atom_sites_ortho.coeff_cos The cosine component of each of the harmonics chosen for the definition an orthogonalized function labeled by - atom_site_ortho.func_id corresponding to the wave + _atom_sites_ortho.func_id corresponding to the wave vector given by _atom_sites_ortho.wave_vector_seq_id ; _name.category_id atom_sites_ortho @@ -7466,7 +7466,7 @@ save_atom_sites_ortho.coeff_cos_list ; The list of cosine components of an orthogonalized function - labeled by atom_sites_ortho.func_id corresponding to the wave + labeled by _atom_sites_ortho.func_id corresponding to the wave vector list given by _atom_sites_ortho.wave_vector_seq_id_list ; _name.category_id atom_sites_ortho @@ -7489,7 +7489,7 @@ save_atom_sites_ortho.coeff_sin The sine component of each of the harmonics chosen for the definition an orthogonalized function labeled by - atom_sites_ortho.func_id corresponding to the wave + _atom_sites_ortho.func_id corresponding to the wave vector given by _atom_sites_ortho.wave_vector_seq_id ; _name.category_id atom_sites_ortho @@ -7510,7 +7510,7 @@ save_atom_sites_ortho.coeff_sin_list ; The list of sine components of an orthogonalized function - labeled by atom_sites_ortho.func_id corresponding to the wave + labeled by _atom_sites_ortho.func_id corresponding to the wave vector list given by _atom_sites_ortho.wave_vector_seq_id_list ; _name.category_id atom_sites_ortho @@ -7826,7 +7826,7 @@ save_cell_subsystem.matrix_W defined in van Smaalen (1991); [see also van Smaalen (1995) or van Smaalen (2012)]. Its dimension must match - (_cell_modulation_dimension+3)*(_cell_modulation_dimension+3). + (_cell.modulation_dimension+3)*(_cell.modulation_dimension+3). Intergrowth compounds are composed of several periodic substructures in which the reciprocal lattices of two different @@ -7875,7 +7875,7 @@ save_cell_subsystem.matrix_W *_subsystem_code pointers, the cell parameters, the superspace group and the measured modulation wave vectors (see CELL_WAVE_VECTOR below) correspond to the reciprocal basis - described in _cell_reciprocal_basis_description and coincide + described in _cell.reciprocal_basis_description and coincide with the reciprocal basis of the specific subsystem (if any) whose W matrix is the unit matrix. The cell parameters and the symmetry of the remaining subsystems can be derived using the @@ -9287,7 +9287,7 @@ save_cell_wave_vector.xyz the case of composites, the modulation wave vectors of each subsystem are expressed in terms of the reciprocal basis of its corresponding reference structure. Their number must match - _cell_modulation_dimension. In the case of composites described + _cell.modulation_dimension. In the case of composites described in a single data block, the wave vectors are expressed in the three-dimensional basis chosen as reference in _cell.reciprocal_basis_description, which would @@ -9599,7 +9599,7 @@ save_diffrn_refln.index_m_list Additional Miller indices needed to write the reciprocal vector of a certain reflection in the basis described in - _cell_reciprocal_basis_description. Following the usual + _cell.reciprocal_basis_description. Following the usual convention, such a vector would be expressed as H=h*a*+k*b*+l*c*+m1*q(1)+...+m8*q(8), @@ -9804,7 +9804,7 @@ save_diffrn_reflns.limit_index_m_max_list appearing in _diffrn_refln.index_m_list. The number of ranges must match _cell.modulation_dimension. The order of the additional indices must be consistent with the codes given in - _cell.wave_vector_seq_id. + _cell_wave_vector.seq_id. ; _name.category_id diffrn_reflns _name.object_id limit_index_m_max_list @@ -9998,7 +9998,7 @@ save_diffrn_reflns.limit_index_m_min_list appearing in _diffrn_refln.index_m_list. The number of ranges must match _cell.modulation_dimension. The order of the additional indices must be consistent with the codes given in - _cell.wave_vector_seq_id. + _cell_wave_vector.seq_id. ; _name.category_id diffrn_reflns _name.object_id limit_index_m_min_list @@ -10466,7 +10466,7 @@ save_exptl_crystal_face.index_m_list ; Additional Miller indices of the crystal face associated with the - value _exptl_crystal_face_perp_dist when the face is indexed + value _exptl_crystal_face.perp_dist when the face is indexed using a multidimensional scheme. The total number of indices must match (_cell.modulation_dimension + 3). The order of the indices must be consistent with the codes given in @@ -11002,13 +11002,13 @@ save_geom_angle.site_ssg_symmetry_1 n_m1...mp. The character string n_m1...mp is composed as follows: 'n' refers to the symmetry operation that is applied to the superspace coordinates. It must match a number given in - _space_group_symop_ssg_id. 'm1...mp' refer to the translations + _space_group_symop.ssg_id. 'm1...mp' refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the angle. These translations (t1,...tp) are related to (m1...mp) by the relations m1=5+t1, ..., mp=5+tp. By adding 5 to the translations, the use of negative numbers is avoided. The number 'p' must agree - with (_cell_modulation_dimension + 3). If there are no cell + with (_cell.modulation_dimension + 3). If there are no cell translations, the translation number may be omitted. If no symmetry operations or translations are applicable, then a single full stop '.' is used. @@ -11184,13 +11184,13 @@ save_geom_bond.site_ssg_symmetry_1 n_m1...mp. The character string n_m1...mp is composed as follows: 'n' refers to the symmetry operation that is applied to the superspace coordinates. It must match a number given in - _space_group_symop_ssg_id. 'm1...mp' refer to the translations + _space_group_symop.ssg_id. 'm1...mp' refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the bond. These translations (t1,...tp) are related to (m1...mp) by the relations m1=5+t1, ..., mp=5+tp. By adding 5 to the translations, the use of negative numbers is avoided. The number 'p' must agree - with (_cell_modulation_dimension + 3). If there are no cell + with (_cell.modulation_dimension + 3). If there are no cell translations, the translation number may be omitted. If no symmetry operations or translations are applicable then a single full stop '.' is used. @@ -11338,13 +11338,13 @@ save_geom_contact.site_ssg_symmetry_1 n_m1...mp. The character string n_m1...mp is composed as follows: 'n' refers to the symmetry operation that is applied to the superspace coordinates. It must match a number given in - _space_group_symop_ssg_id. 'm1...mp' refer to the translations + _space_group_symop.ssg_id. 'm1...mp' refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the contact. These translations (t1,...tp) are related to (m1...mp) by the relations m1=5+t1, ..., mp=5+tp. By adding 5 to the translations, the use of negative numbers is avoided. The number 'p' must agree - with (_cell_modulation_dimension + 3). If there are no cell + with (_cell.modulation_dimension + 3). If there are no cell translations, the translation number may be omitted. If no symmetry operations or translations are applicable, then a single full stop '.' is used. @@ -11502,13 +11502,13 @@ save_geom_torsion.site_ssg_symmetry_1 n_m1...mp. The character string n_m1...mp is composed as follows: 'n' refers to the symmetry operation that is applied to the superspace coordinates. It must match a number given in - _space_group_symop_ssg_id. 'm1...mp' refer to the translations + _space_group_symop.ssg_id. 'm1...mp' refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the angle. These translations (t1,...tp) are related to (m1...mp) by the relations m1=5+t1, ..., mp=5+tp. By adding 5 to the translations, the use of negative numbers is avoided. The number - 'p' must agree with (_cell_modulation_dimension + 3). If there + 'p' must agree with (_cell.modulation_dimension + 3). If there are no cell translations, the translation number may be omitted. If no symmetry operations or translations are applicable, then a single full stop '.' is used. @@ -11762,7 +11762,7 @@ save_refln.index_m_list ; Additional Miller indices of a particular reflection in the basis - described in _cell_reciprocal_basis_description. The total number + described in _cell.reciprocal_basis_description. The total number of indices must match (_cell.modulation_dimension + 3). The order of the additional indices must be consistent with the codes given in _cell_wave_vector.seq_id. @@ -11977,9 +11977,9 @@ save_reflns.limit_index_m_max_list Maximum of the additional Miller indices appearing in _refln.index_m_*. The number of ranges must match - _cell_modulation_dimension. The order of the additional indices + _cell.modulation_dimension. The order of the additional indices must be consistent with the codes given in - _cell.wave_vector_seq_id. These need not be the same as + _cell_wave_vector.seq_id. These need not be the same as the _reflns.limit_index_m_*. ; _name.category_id reflns @@ -12020,9 +12020,9 @@ save_reflns.limit_index_m_min_list Minimum values of the additional Miller indices appearing in _refln.index_m_*. The number of ranges must match - _cell_modulation_dimension. The order of the additional indices + _cell.modulation_dimension. The order of the additional indices must be consistent with the codes given in - _cell.wave_vector_seq_id. These need not be the same as + _cell_wave_vector.seq_id. These need not be the same as the _reflns.limit_index_m_*. ; _name.category_id reflns @@ -12399,8 +12399,8 @@ save_space_group.ssg_name ; Superspace-group symbol conforming to an alternative definition - from that given in _space_group_ssg_name_IT and - _space_group_ssg_name_WJJ for one-dimensional modulated + from that given in _space_group.ssg_name_IT and + _space_group.ssg_name_WJJ for one-dimensional modulated structures or to the superspace-group name for higher dimensions. When necessary, indicate the origin and the setting. Use a colon ':' as a separator between the different parts of the @@ -12408,7 +12408,7 @@ save_space_group.ssg_name between each component. Rules for the notation for Hermann-Mauguin and Hall symbols (if present) are given in the symmetry CIF dictionary (cif_sym.dic) and, partially, in - _space_group_ssg_name_IT and _space_group_ssg_name_WJJ. + _space_group.ssg_name_IT and _space_group.ssg_name_WJJ. For composites described in a single data block, the superspace group describes the symmetry of the whole structure. The symmetry of each subsystem can be derived using the @@ -12576,7 +12576,7 @@ save_space_group_symop.ssg_id ; A numeric code identifying each entry in the - _space_group_symop_ssg_operation_algebraic list. + _space_group_symop.ssg_operation_algebraic list. ; _name.category_id space_group_symop _name.object_id ssg_id @@ -12601,14 +12601,14 @@ save_space_group_symop.ssg_operation_algebraic A parsable string giving one of the symmetry operations of the superspace group in algebraic form. These data will generally be repeated in a loop. Use symbols as necessary according to - _cell_modulation_dimension. + _cell.modulation_dimension. All symmetry operations should be entered, including the identity operation, those for lattice centring and that for a centre of symmetry, if present. The symbolic notation for coordinates is such that the identity operation is expressed as x1,x2,x3,...,xn. - _space_group_symop_ssg_operation_algebraic must always be present + _space_group_symop.ssg_operation_algebraic must always be present in a CIF corresponding to a modulated structure. ; _name.category_id space_group_symop