From 53aacb27019cdd20942850473aee08b1e3252613 Mon Sep 17 00:00:00 2001 From: vaitkus Date: Fri, 7 Nov 2025 16:27:40 +0200 Subject: [PATCH 1/2] Fix typos in data names appearing in descriptions --- cif_ms.dic | 57 +++++++++++++++++++++++++++--------------------------- 1 file changed, 28 insertions(+), 29 deletions(-) diff --git a/cif_ms.dic b/cif_ms.dic index e3906f8..fce7f1b 100644 --- a/cif_ms.dic +++ b/cif_ms.dic @@ -222,7 +222,7 @@ save_ATOM_SITE_ANHARMONIC_ADP environment variation induced by the modulation, the components of the tensors describing the anharmonicity could become also modulated. In that case, the additional modulation parameters would be - described by items belong to the _ATOM_SITE_ANHARMONIC_ADP_FOURIER + described by items belong to the ATOM_SITE_ANHARMONIC_ADP_FOURIER category. References: Kuznetsov, P.I., Stratonovich, R.L. & Tikhonov, V.I. (1960). @@ -1126,7 +1126,7 @@ save_atom_site_anharmonic_adp_fourier_param.phase _definition.update 2025-10-20 _description.text ; - _The phase [\q(j...)n/2\\p], in cycles, of the complex amplitude + The phase [\q(j...)n/2\\p], in cycles, of the complex amplitude corresponding to the Fourier term defined by _atom_site_anharmonic_ADP_Fourier.atom_site_label, _atom_site_anharmonic_ADP_Fourier.tens_elem and @@ -1179,7 +1179,7 @@ save_atom_site_anharmonic_adp_fourier_param.sin The sine coefficient [T(j...)sn] corresponding to the Fourier term defined by _atom_site_anharmonic_ADP_Fourier.atom_site_label, _atom_site_anharmonic_ADP_Fourier.tens_elem and - _atom_site_anharmonic_AD_Fourier.wave_vector_seq_id. + _atom_site_anharmonic_ADP_Fourier.wave_vector_seq_id. ; _name.category_id atom_site_anharmonic_ADP_Fourier_param _name.object_id sin @@ -1343,7 +1343,7 @@ save_atom_site_anharmonic_adp_legendre.tens_elem A label identifying the anharmonic ADP tensor elements of a given atom whose modulation is being parameterized by Legendre polynomials. This code must match one of the codes listed in - 'atom_site_anharmonic_ADP.tens_elem. + _atom_site_anharmonic_ADP.tens_elem. ; _name.category_id atom_site_anharmonic_ADP_Legendre _name.object_id tens_elem @@ -2280,7 +2280,7 @@ save_atom_site_displace_fourier_param.cos The cosine coefficient (Acn) corresponding to the Fourier term defined by _atom_site_displace_Fourier.atom_site_label, _atom_site_displace_Fourier.axis and - _atom_site_displace_Fourier_wave_vector.seq_id. + _atom_site_displace_Fourier.wave_vector_seq_id. ; _name.category_id atom_site_displace_Fourier_param _name.object_id cos @@ -3057,7 +3057,7 @@ save_atom_site_displace_ortho.func_id ; A code identifying the orthogonalized function used in the structural model to describe the displacive 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_displace_ortho _name.object_id func_id @@ -4092,7 +4092,7 @@ save_ATOM_SITE_FOURIER_WAVE_VECTOR details about the wave vectors of the Fourier terms used in the structural model to describe the atomic modulation functions. They are linear combinations with integer coefficients of the independent - wave vectors given in the _cell_wave_vector. list. Therefore, wave + wave vectors given in the CELL_WAVE_VECTOR list. Therefore, wave vectors are expressed with respect to the three-dimensional reciprocal basis that spans the lattice of main reflections. However, in the case of composites these wave vectors are expressed with respect to @@ -4105,11 +4105,11 @@ save_ATOM_SITE_FOURIER_WAVE_VECTOR or expressed as k=n(1)q(1)+...+n(p)q(p), where p is given by _cell_modulation_dimension (with a maximum value of 8). - In that case, _atom_site_Fourier_wave_vector.coeff contains the + In that case, _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 the CELL_WAVE_VECTOR category. The enumeration of the independent wave vectors (1,2, ...,9) is given by - the value of _atom_site_Fourier_wave_vector_.q_coeff_seq_id matching + the value of _atom_site_Fourier_wave_vector.q_coeff_seq_id matching the corresponding value of _cell_wave_vector.seq_id. ; @@ -4537,7 +4537,7 @@ save_atom_site_fourier_wave_vector.q_coeff of the _cell_modulation_dimension independent wave vectors given in CELL_WAVE_VECTOR category. The enumeration of the independent wave vectors (1,2, ...,9) is given by thes 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 @@ -5628,7 +5628,7 @@ save_ATOM_SITE_OCC_ORTHO Data items in the ATOM_SITE_OCC_ORTHO category record details about the orthogonalized functions (see - ATOM_SITE_DISPLACE_ORTHO)defined to solve correlation problems + ATOM_SITE_DISPLACE_ORTHO) defined to solve correlation problems during the refinement of the occupational modulation when the atomic domain of a given atom is restricted by a crenel function. The functions are constructed selecting Fourier harmonics until the @@ -5715,7 +5715,7 @@ 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 @@ -7135,7 +7135,7 @@ 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 @@ -7740,7 +7740,7 @@ save_atom_site_rot_zigzag.atom_site_label a zigzag function that describes the rotational part of its displacive modulation is being defined. This code must match the _atom_site.label of the associated coordinate list and conform to the rules described - in_atom_site.label. + in _atom_site.label. ; _name.category_id atom_site_rot_zigzag _name.object_id atom_site_label @@ -9769,7 +9769,7 @@ save_atom_sites_ortho.coeff_cos_list _description.text ; 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 @@ -9791,7 +9791,7 @@ save_atom_sites_ortho.coeff_sin_list _description.text ; 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 @@ -15981,7 +15981,7 @@ save_geom_hbond.angle_dha_av _description.text ; The average value of the angle subtended by the sites identified by - the _geom_hbond key names.The hydrogen at site *_H is at the apex + the GEOM_HBOND key names. The hydrogen at site *_H is at the apex of the angle. ; _name.category_id geom_hbond @@ -16021,7 +16021,7 @@ save_geom_hbond.angle_dha_max _description.text ; The maximum value of the angle subtended by the sites identified by - the _geom_hbond key names.The hydrogen at site *_H is at the apex + the GEOM_HBOND key names. The hydrogen at site *_H is at the apex of the angle. ; _name.category_id geom_hbond @@ -16061,7 +16061,7 @@ save_geom_hbond.angle_dha_min _description.text ; The minimum value of the angle subtended by the sites identified by - the _geom_hbond key names.The hydrogen at site *_H is at the apex + the GEOM_HBOND key names. The hydrogen at site *_H is at the apex of the angle. ; _name.category_id geom_hbond @@ -16101,7 +16101,7 @@ save_geom_hbond.distance_da_av _description.text ; The average distance between the donor and acceptor sites in the - hydrogen bond identified by the _geom_hbond key names. + hydrogen bond identified by the GEOM_HBOND key names. ; _name.category_id geom_hbond _name.object_id distance_DA_av @@ -16140,7 +16140,7 @@ save_geom_hbond.distance_da_max _description.text ; The maximum distance between the donor and acceptor sites in the - hydrogen bond identified by the _geom_hbond key names. + hydrogen bond identified by the GEOM_HBOND key names. ; _name.category_id geom_hbond _name.object_id distance_DA_max @@ -16179,7 +16179,7 @@ save_geom_hbond.distance_da_min _description.text ; The minimum distance between the donor and acceptor sites in the - hydrogen bond identified by the _geom_hbond key names. + hydrogen bond identified by the GEOM_HBOND key names. ; _name.category_id geom_hbond _name.object_id distance_DA_min @@ -16218,7 +16218,7 @@ save_geom_hbond.distance_dh_av _description.text ; The average distance between the donor and hydrogen sites in the - hydrogen bond identified by the _geom_hbond key names. + hydrogen bond identified by the GEOM_HBOND key names. ; _name.category_id geom_hbond _name.object_id distance_DH_av @@ -16239,7 +16239,6 @@ save_geom_hbond.distance_dh_av_su ; Standard uncertainty of the average angle given in _geom_hbond.distance_DH_av. - ; _name.category_id geom_hbond _name.object_id distance_DH_av_su @@ -16258,7 +16257,7 @@ save_geom_hbond.distance_dh_max _description.text ; The maximum distance between the donor and hydrogen sites in the - hydrogen bond identified by the _geom_hbond key names. + hydrogen bond identified by the GEOM_HBOND key names. ; _name.category_id geom_hbond _name.object_id distance_DH_max @@ -16297,7 +16296,7 @@ save_geom_hbond.distance_dh_min _description.text ; The minimum distance between the donor and hydrogen sites in the - hydrogen bond identified by the _geom_hbond key names. + hydrogen bond identified by the GEOM_HBOND key names. ; _name.category_id geom_hbond _name.object_id distance_DH_min @@ -16336,7 +16335,7 @@ save_geom_hbond.distance_ha_av _description.text ; The average distance between the hydrogen and acceptor sites in the - hydrogen bond identified by the _geom_hbond key names. + hydrogen bond identified by the GEOM_HBOND key names. ; _name.category_id geom_hbond _name.object_id distance_HA_av @@ -16375,7 +16374,7 @@ save_geom_hbond.distance_ha_max _description.text ; The maximum distance between the hydrogen and acceptor sites in the - hydrogen bond identified by the _geom_hbond key names. + hydrogen bond identified by the GEOM_HBOND key names. ; _name.category_id geom_hbond _name.object_id distance_HA_max @@ -16414,7 +16413,7 @@ save_geom_hbond.distance_ha_min _description.text ; The minimum distance between the hydrogen and acceptor sites in the - hydrogen bond identified by the _geom_hbond key names. + hydrogen bond identified by the GEOM_HBOND key names. ; _name.category_id geom_hbond _name.object_id distance_HA_min From a25805ea932284c6a9fd53f4cb919a520f5d4382 Mon Sep 17 00:00:00 2001 From: vaitkus Date: Fri, 7 Nov 2025 16:31:42 +0200 Subject: [PATCH 2/2] Replace aliases with canonical data names in descriptions --- cif_ms.dic | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/cif_ms.dic b/cif_ms.dic index fce7f1b..6d40c80 100644 --- a/cif_ms.dic +++ b/cif_ms.dic @@ -4103,7 +4103,7 @@ save_ATOM_SITE_FOURIER_WAVE_VECTOR components (see item _atom_site_Fourier_wave_vector.x, _atom_site_Fourier_wave_vector.y and _atom_site_Fourier_wave_vector.z) or expressed as k=n(1)q(1)+...+n(p)q(p), where p is given by - _cell_modulation_dimension (with a maximum value of 8). + _cell.modulation_dimension (with a maximum value of 8). In that case, _atom_site_Fourier_wave_vector.q_coeff contains the coefficients that express a given k as a linear combination of the @@ -4534,7 +4534,7 @@ save_atom_site_fourier_wave_vector.q_coeff _description.text ; The list of coefficients that express a given k as a linear combination - of the _cell_modulation_dimension independent wave vectors given in + of the _cell.modulation_dimension independent wave vectors given in CELL_WAVE_VECTOR category. The enumeration of the independent wave vectors (1,2, ...,9) is given by thes value of _atom_site_Fourier_wave_vector.q_coeff_seq_id matching the @@ -4586,7 +4586,7 @@ save_atom_site_fourier_wave_vector.q_coeff_seq_id The list of numeric 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 these wave + by _cell.modulation_dimension. In the case of composites these wave vectors are expressed with respect to the three-dimensional reciprocal basis of each subsystem (see _cell_subsystem.matrix_W_).The codes must match those given in _cell_wave_vector.seq_id. @@ -10420,7 +10420,7 @@ 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 @@ -10469,7 +10469,7 @@ 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 @@ -13561,7 +13561,7 @@ 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 @@ -14123,7 +14123,7 @@ 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)+...+m9*q(9), @@ -15198,7 +15198,7 @@ save_exptl_crystal_face.index_m_list _description.text ; 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 @@ -17175,7 +17175,7 @@ save_refln.index_m_list _description.text ; 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. @@ -17621,7 +17621,7 @@ 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 the _diffrn_reflns.limit_index_m_max_list. @@ -17670,7 +17670,7 @@ 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 the _diffrn_reflns.limit_index_m_min_list. @@ -17980,7 +17980,7 @@ save_superspace_group_symop.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