diff --git a/README.md b/README.md new file mode 100644 index 0000000..9049055 --- /dev/null +++ b/README.md @@ -0,0 +1,12 @@ +# The Modulated Structures dictionary + +A repository for developing CIF definitions for describing modulated and composite structures. Do +not rely on the contents of this repository for authoritative information about data names. You +may rely on released versions, or versions found on +[the IUCr website](https://www.iucr.org/resources/cif/dictionaries/cif_ms) for this purpose. + +## Contributing + +Please feel free to raise issues, including asking questions about dictionary usage +and suggestions of new data names, using the usual Github mechanisms. Participation +in ongoing discussions of issues and PRs is also welcome. diff --git a/cif_ms.dic b/cif_ms.dic index 251292f..be5f7f8 100644 --- a/cif_ms.dic +++ b/cif_ms.dic @@ -1,5 +1,5 @@ #\#CIF_2.0 -############################################################################### +################################################################################ # # # CIF Dictionary for Modulated Structures # # --------------------------------------- # @@ -49,7 +49,7 @@ save_MS_GROUP ; _name.category_id CIF_MS _name.object_id MS_GROUP - _import.get [{"file":"cif_core.dic" "save":"CIF_CORE" "mode":"Full"}] + _import.get [{"file":"cif_core.dic" "save":"CIF_CORE" "mode":"Full" "dupl":"Ignore"}] save_ @@ -399,8 +399,8 @@ 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 displacements must be expressed as fractions of the unit + _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 category, through _atom_site_displace_Fourier.matrix_seq_id. @@ -479,8 +479,8 @@ save_atom_site_displace_Fourier_param.modulus 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. Atomic or rigid- - group displacements must be expressed as fractions of the unit + _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 category, through _atom_site_displace_Fourier.matrix_seq_id. @@ -579,8 +579,8 @@ save_atom_site_displace_Fourier_param.sin sine coefficient (As) 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 displacements must be expressed as fractions of the unit + _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 @@ -647,7 +647,6 @@ save_ATOM_SITE_DISPLACE_LEGENDRE ATOM_SITE_ROT_LEGENDRE category. The coefficients of each Legendre function belong to the category ATOM_SITE_DISPLACE_LEGENDRE_PARAM and are listed separately. -. References: Petricek, V., Van Der Lee & Evain, M. (1995). Acta Cryst. A51, 529-535. DOI 10.1107/S0108767395000365 @@ -741,7 +740,7 @@ save_atom_site_displace_Legendre.coeff _atom_site_displace_Legendre.axis and _atom_site_displace_Legendre.order. 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 defined by the items belonging to the + special axes defined by the items belonging to the ATOM_SITES_AXES category, through _atom_site_rot_Legendre.matrix_seq_id. ; _name.category_id atom_site_displace_Legendre @@ -855,7 +854,7 @@ save_atom_site_displace_Legendre_param.coeff _atom_site_displace_Legendre.axis and _atom_site_displace_Legendre.order. 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 defined by the items belonging to the + special axes defined by the items belonging to the ATOM_SITES_AXES category, through _atom_site_rot_Legendre.matrix_seq_id. ; _name.category_id atom_site_displace_Legendre_param @@ -1001,7 +1000,7 @@ save_atom_site_displace_ortho.coeff _atom_site_displace_ortho.axis and _atom_site_displace_ortho.func_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 defined by the items belonging to the + special axes defined by the items belonging to the ATOM_SITES_AXES category, through _atom_site_rot_ortho.matrix_seq_id. ; _name.category_id atom_site_displace_ortho @@ -1029,7 +1028,7 @@ save_atom_site_displace_ortho.func_id ; _name.category_id atom_site_displace_ortho _name.object_id func_id - _name.linked_item_id '_atom_sites_ortho.func_id ' + _name.linked_item_id '_atom_sites_ortho.func_id' _type.purpose Link _type.source Related _type.container Single @@ -1117,7 +1116,7 @@ save_atom_site_displace_ortho_param.coeff _atom_site_displace_ortho.axis and _atom_site_displace_ortho.func_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 defined by the items belonging to the + special axes defined by the items belonging to the ATOM_SITES_AXES category, through _atom_site_rot_ortho.matrix_seq_id. ; _name.category_id atom_site_displace_ortho_param @@ -1859,7 +1858,7 @@ save_atom_site_displace_xharm.coeff _atom_site_displace_xharm.axis and _atom_site_displace_xharm.order. 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 defined by the items belonging to the + special axes defined by the items belonging to the ATOM_SITES_AXES category, through _atom_site_rot_xharm.matrix_seq_id. ; _name.category_id atom_site_displace_xharm @@ -1970,7 +1969,7 @@ save_atom_site_displace_xharm_param.coeff _atom_site_displace_xharm.axis and _atom_site_displace_xharm.order. 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 defined by the items belonging to the + special axes defined by the items belonging to the ATOM_SITES_AXES category, through _atom_site_rot_xharm.matrix_seq_id. ; _name.category_id atom_site_displace_xharm_param @@ -3419,7 +3418,7 @@ save_atom_site_occ_ortho.func_id ; _name.category_id atom_site_occ_ortho _name.object_id func_id - _name.linked_item_id '_atom_sites_ortho.func_id ' + _name.linked_item_id '_atom_sites_ortho.func_id' _type.purpose Link _type.source Related _type.container Single @@ -4159,7 +4158,7 @@ save_ATOM_SITE_ROT_FOURIER_PARAM a given rigid group. The translational part would appear in a separate list of items belonging to the ATOM_SITE_DISPLACE_FOURIER_PARAM category. The Fourier components - are defined in the parent category ATOM_SITE_ROT_FOURIER Notice + are defined in the parent category ATOM_SITE_ROT_FOURIER. Notice that items in this category may be listed together with those of the ATOM_SITE_DISPLACE_FOURIER category. ; @@ -4656,7 +4655,7 @@ save_ATOM_SITE_ROT_ORTHO Data items in the ATOM_SITE_ROT_ORTHO category record details about the orthogonalized functions defined to solve correlation problems during the refinement of displacive - modulations when the the atomic domain of a given atom is + modulations when the atomic domain of a given atom is restricted by a crenel function. The functions are constructed selecting Fourier harmonics until the desired degree of orthogonality and completeness is reached (see @@ -4758,7 +4757,7 @@ save_atom_site_rot_ortho.func_id ; _name.category_id atom_site_rot_ortho _name.object_id func_id - _name.linked_item_id '_atom_sites_ortho.func_id ' + _name.linked_item_id '_atom_sites_ortho.func_id' _type.purpose Link _type.source Related _type.container Single @@ -6395,7 +6394,7 @@ save_atom_site_U_ortho.func_id ; _name.category_id atom_site_U_ortho _name.object_id func_id - _name.linked_item_id '_atom_sites_ortho.func_id ' + _name.linked_item_id '_atom_sites_ortho.func_id' _type.purpose Link _type.source Related _type.container Single @@ -6740,7 +6739,7 @@ save_ATOM_SITES_AXES _name.category_id MS_GROUP _name.object_id ATOM_SITES_AXES loop_ - _category_key.name '_atom_site_sites_axes.matrix_seq_id' + _category_key.name '_atom_sites_axes.matrix_seq_id' save_ save_atom_sites_axes.matrix @@ -7175,9 +7174,9 @@ save_atom_sites_modulation.global_phase_list & Garcia Arribas, A. (1987). Acta Cryst. A43, 216-226. On the structure and symmetry of incommensurate phases. A practical formulation - Smaalen, S. van(1995). Crystallogr. Rev. 4, 79-202. + Smaalen, S. van (1995). Crystallogr. Rev. 4, 79-202. Incommensurate crystal structures - Smaalen, S. van(2012). + Smaalen, S. van (2012). Incommensurate Crystallography. Oxford University Press. ; _name.category_id atom_sites_modulation @@ -7512,7 +7511,7 @@ save_atom_sites_ortho.coeff_sin_list vector list given by _atom_sites_ortho.wave_vector_seq_id_list ; _name.category_id atom_sites_ortho - _name.object_id coeff_sin + _name.object_id coeff_sin_list _type.purpose Number _type.source Assigned _type.container List @@ -7524,7 +7523,7 @@ save_ save_atom_sites_ortho.func_id - _definition.id '_atom_sites_ortho.func_id ' + _definition.id '_atom_sites_ortho.func_id' _definition.update 2017-03-11 _description.text ; @@ -7892,7 +7891,7 @@ save_cell_subsystem.matrix_W Smaalen, S. van (1995). Crystallogr. Rev. 4, 79-202. Incommensurate crystal structures - Smaalen, S. van(2012). + Smaalen, S. van (2012). Incommensurate Crystallography. Oxford University Press. ; @@ -9301,7 +9300,7 @@ save_cell_wave_vectors.meas_details _name.category_id cell_wave_vectors _name.object_id meas_details _type.purpose Describe - _type.source Asd + _type.source Assigned _type.container Single _type.contents Text @@ -10353,7 +10352,7 @@ save_exptl_crystal_face.index_m_list _name.object_id index_m_list _type.purpose Number _type.source Assigned - _type.container Single + _type.container List _type.contents Integer _type.dimension '[8]' loop_ @@ -10609,7 +10608,7 @@ save_function.Sawtooth 2* a * ((x4-c)/w) for x4 belonging to the interval [c-(w/2), c+(w/2)], where a is the array - containing the the amplitudes (maximum displacements) along each + containing the amplitudes (maximum displacements) along each crystallographic axis, w is the width of the sawtooth, x4 is a particular value of the internal coordinate and c is the centre of the function in internal space. The use of this function is restricted to one-dimensional @@ -10690,7 +10689,7 @@ save_function.Zigzag for x4 in the interval [c+1/2-(w/2), c+1/2+(w/2)] - where a is the array containing the the amplitudes (maximum displacements) + where a is the array containing the amplitudes (maximum displacements) along each crystallographic axis, w is the width of the zigzag, x4 is a particular value of the internal coordinate and c is the centre of the function in internal space. The use of this function is restricted to one-dimensional @@ -10863,7 +10862,7 @@ _units.code degrees save_ -save_save_geom_angle.site_ssg_symmetry_1 +save_geom_angle.site_ssg_symmetry_1 _definition.id '_geom_angle.site_ssg_symmetry_1' _definition.update 2014-06-27 @@ -10899,9 +10898,9 @@ save_save_geom_angle.site_ssg_symmetry_1 loop_ _description_example.case _description_example.detail - "." 'no symmetry or translation to site' - "4" '4th symmetry operation applied' - "7_645" '7th symmetry position; +a on x, -b on y' + . 'no symmetry or translation to site' + 4 '4th symmetry operation applied' + 7_645 '7th symmetry position; +a on x, -b on y' save_