2021-01-29 Atsushi Togo * Version 1.16.1 Bug fix of fortran wrapper. 2020-07-30 Atsushi Togo * Version 1.16 Minor update. Symmetry operations in spg_database.c for Hall numbers 212, 213, 214 are re-ordered to start by identity operation. 2020-04-28 Atsushi Togo * Version 1.15.1 Critical bug fix for collinear spin symmetry. * src/spin.c (get_operations): Collinear spin symmetry was wrongly handled. This was fixed at commit bf954039. 2020-04-17 Atsushi Togo * Version 1.15 'crystallographic_orbits' was added to SpglibDataset by Lauri Himanen. Rust interface was implemented by Seaton Ullberg. 2019-07-30 Atsushi Togo * Version 1.14.1 Version number increment just to release pypi package. 2019-07-30 Atsushi Togo * Version 1.14 Improvement against cyclic point change over applying standardizaion repeatedly. More specifically, when we have an input crystal structre, we standardize it by spglib then we may get another structure. We apply the standardization again to this standardized structure and we get another structure. Some people may expect after several iteration, the input and output structures become same. This version provides some improvement on this. But unfortunately it could not be perfect, for example, this can be not working for crystal structures having special metrics given in the table of Euclidean normalizer section of ITA. 2019-07-02 Atsushi Togo * Version 1.13 * src/spacegroup.c (match_hall_symbol_db_ortho, match_hall_symbol_db_monocli): Fix Issue#57 of SeekPath: Standardizations of choices of a,b,c axes for Cmma (67), Ccca(68), Ibca(73), Imma(74) were fixed. For monoclinic systems, lengths of non-unique axes are now checked by a exhaustive way. * src/kpoint.c (check_mesh_symmetry): Issue#79: Treatment of ir-kpoint search for special cases with three fold rotation (e.g., hexagonal or primitive FCC). 2019-02-06 Atsushi Togo * Version 1.12.2 Minor release for memory leak fix (PR#71). 2019-01-30 Atsushi Togo * Version 1.12.1 * src/spglib.h: Bug fix of PR #70. #include is inserted. In principle, this line is necessary to compile. 2019-01-29 Atsushi Togo * Version 1.12.0 After this minor version, addition of new features will be stopped until version 2.0 will be released. * src/sitesym_database.c (ssmdb_get_site_symmetry_symbol): Experimental support of site symmetry symbols. * src/pointgroup.c: Comparisons of basis vector lengths are more carefully done for letting them work for different computer architectures to treat very small numerical different that is close to the machine precision. * src/mathfunc.c (mat_Dmod1): Similarly, MOD-Z operation (bring values x inside the rage of 0<= x < 1) is now done considering the difference of machine precision. * src/kpoint.c (kpt_get_irreducible_reciprocal_mesh): To enable dense k-point mesh sampling, integer types of variables that represent grid point indices were changed from int to size_t. But to support current functions with the same API, adapters were written for these functions (having 'dense' in their function names until v2.0 will be released) and currently they are working in the same way as before. Finally the API change will be realized at the v2.0 2018-12-07 Atsushi Togo * Version 1.11.2 * src/refinement.c (find_similar_bravais_lattice): Bug fix. Again, origin shift was still not correctly computed when the standardized basis vectors are rotated in this method to find most similar choice of basis vectors to the idealized ones. This bug affected to 'origin_shift' and 'std_positions' in spglib dataset and the functions 'spg_standardize_cell', 'spg_find_primitive', and 'spg_refine_cell'. Although there existed this bug, tests unfortunately passed. So a new test to check Wyckoff positions consistency was added to find possible bugs related to origin shift because this bug was found by getting wrong Wyckoff positions reported by a user. 2018-11-12 Atsushi Togo * Version 1.11.1 * src/refinement.c (find_similar_bravais_lattice): Bug fix. Origin shift was not correctly computed when the standardized basis vectors are rotated in this method to find most similar choice of basis vectors to the idealized ones. This bug affected to 'origin_shift' and 'std_positions' in spglib dataset and the functions 'spg_standardize_cell', 'spg_find_primitive', and 'spg_refine_cell'. 2018-11-09 Atsushi Togo * Version 1.11.0 * src/refinement.c (find_similar_bravais_lattice): This looks for a similar choice of starndardized basis vectors to that of idealized starndardized basis vectors among those generated by proper symmetry operations. * src/refinement.c (measure_rigid_rotation): This computes a rigid rotation matrix introduced in the idealization step. The rotation is made to agree a-axes and a-b planes between systems before and after idealization. 2018-08-01 Atsushi Togo * Version 1.10.4 Collection of minor fixes. A text on spglib algorithm is prepared for this version. This text will be available soon at arXiv. To be consistent between text and code, the code refactoring was made. 2018-01-13 Atsushi Togo * Version 1.10.3 * src/overlap.c: New algorithm to search translation part of space group operation is implmented by Michael Lamparski to improving the search speed especially for large unit cell systems. For this, new files 'overlap.*' are added and so the version number is incremented. 2017-12-13 Atsushi Togo * Version 1.10.2 * src/Makefile.am: Automake didn't work due to the lack of determination.{c,h} lines. This was fixed. 2017-10-27 Atsushi Togo * Version 1.10.1 * src/spglib.c (get_dataset): A large refactoring was made to replace the outer-most iteration loop of symmetry search algorithm to a new file 'determination.c'. * src/spglib.c (spg_get_schoenflies,spg_get_international): These routines had accessed directly to a function close to spacegroup.c. Now these are replaced by passing through 'get_dataset'. 2017-10-22 Atsushi Togo * Version 1.10.0 'mapping_to_primitive' and 'std_mapping_to_primitive' in the spglib dataset are put available on the spglib document. 'spg_get_hall_number_from_symmetry' function ('get_hall_number_from_symmetry' method for python) is also available on the spglib document. 2017-10-02 Atsushi Togo * Version 1.9.10 Many minor fixes and updates after many months from v1.9.9. * src/symmetry.c (search_pure_translations): Pure translation search is made faster using a property of group, which is significantly effective for supercells with large multiplicity. 2016-12-14 Atsushi Togo * Version 1.9.9 * src/kpoint.c: 'get_ir_reciprocal_mesh' was supporsed to work with mesh numbers that are consistent with symmetry. Now this function somehow supports when mesh numbers are symmetrically broken. 2016-12-09 Atsushi Togo * src/symmetry.c: static variable of 'angle_tolerance', 'sym_set_angle_tolerance', 'sym_get_angle_tolerance' were removed toward letting it thread-safe. Now 'angle_tolerance' is passed as an argument to many functions in spglib. 2016-11-02 Atsushi Togo * Version 1.9.8 * src/cell.c (cel_is_overlap_with_same_type): 'cel_is_overlap_with_same_type' is implemented to check overlapping of atoms along with checking atom type agreement. Using this, atoms that have about the same position but with different types can be separately handled. 2016-10-19 Atsushi Togo * Version 1.9.6 Collection of minor fixes. * src/cell.c (cel_set_cell): Reduced atomic positions of the input cell are inisitalized by their moving in the range between -0.5 and 0.5. The cell shape is kept unchanged but this may need to be considered to handle some extreme case in the future. 2016-09-05 Atsushi Togo * Version 1.9.5 * src/spglib.h (SpglibError): 'spg_get_error_code' and 'spg_get_error_message' were made to handle a few types of internal errors. * src/spglib.c, src/cell.c (cel_any_overlap_with_same_type): To check overlap of atoms, 'cel_any_overlap' and 'cel_any_overlap_with_same_type' were implemented. The former doesn't check atomic type but the later does. Currently this check is done before symmetry search and the later is used for it. Therefore overlap of different types of atoms is allowed. 2016-05-06 Atsushi Togo * Version 1.9.4 * src/spglib.h (SpglibDataset): The member of SpglibDataset, 'setting', is renamed to 'choice', and 'pointgroup_number' is removed. * src/cell.c (get_overlap_table): Fix unexpected behavior. This might happen in a rare case with large tolerance. 2016-04-28 Atsushi Togo * src/spglib.c (spg_get_spacegroup_type): Arithmetic crystal class number and symbol are returned. Python interface 'get_spacegroup_type' was created. * src/spglib.c (get_dataset): * src/site_symmetry.c (ssm_get_exact_positions, set_exact_location): Two iterative loops are implemented. The outer one is in get_dataset, and the inner one is in ssm_get_exact_positions. Each site-symmetry is checked in set_exact_location. In the inner loop, symmetry tolerance is controled until all site-symmetries become reasonable. If the inner loop finally fails, the symmetry tolerance in the outer loop is reduced and the symmetry search starts from the begginig. 2016-04-17 Atsushi Togo * Version 1.9.2 * src/symmetry.c (get_lattice_symmetry): The treatment after the conditon, order of point symmetry becomes larger than 48, is found was bad and it induced segfault. It is fixed and a better treatment for angle_tolerance is implemented as an iterative method. * src/spglib.c (spg_delaunay_reduce): spg_delaunay_reduce is made as an interface to the Delaunay reduction. * src/spacegroup.c (search_spacegroup): A check if excess symmetry operations are found for a primitive cell is inserted by watching its point group. This made the algorithm of database matching safer. 2016-04-11 Atsushi Togo * src/delaunay.c: lattice.{c,h} are renamed to delaunay.{c.h}, respectively. Function names in them, *get_smallest_lattice, are changed to *delaunay_reduce. 2016-04-06 Atsushi Togo * Version 1.9.1 This is a minor update. Only a small notable change is in the python wrapper, where for crystal structure, now a tuple format can be sued. 2015-12-20 Atsushi Togo * Version 1.9.0 Pyspglib was considered as a special extention of spglib, but now it starts to be a part of spglib as a usual extention. Therefore the package name is changed to spglib, and this python wrapper will be maintained to work at every update of c-spglib. Scripts for pypi and conda package environments are prepared in python wrapper by a lot of help from Paweł T. Jochym. In previous versions, tests were in the test directory and space group numbers were checked for many POSCARs by using combination of ruby-spglib and shell script. Now a similar test is written in a form of python unit test in the 'python' directory. Previous 'test' directory is renamed to 'ruby' and the POSCARs were moved under the 'python/test' directory. 2015-12-13 Atsushi Togo * Version 1.8.3 * src/version.h: Made functions to return spglib version number, 'spg_get_major_version()', 'spg_get_minor_version()', 'spg_get_micro_version()' in 'spglib.c'. This version number is stored in 'version.h'. 2015-08-19 Atsushi Togo * Version 1.8.2.2 * src/spglib.c (is_rhombohedral): Regardless of rhombohedral or hexagonal setting, a primitive rhombohedral is found when using finding primitive cell functions. 2015-08-03 Atsushi Togo * Version 1.8.2.1 * src/spacegroup.c (spa_transform_to_primitive): Bug fix of transformation matrix with centering. The side to be multiplied was wrong. * Version 1.8.2 * k-points and tetrahedron method k-point grid definitions are separated to 'kgrid.c'. 'kgrid.{c,h}' and 'tetrahedron_method.{c,h}' are moved to a new git repository of kspclib (https://github.com/atztogo/kspclib). Tetrahedron method related spglib-APIs are removed. * Choice of triclinic basis vector directions is implemented and the definition is written in the document. 2015-07-09 Atsushi Togo * Version 1.8.1 In SpglibDataset, definitions of transformation matrix and origin shift are changed, member names of '*brv_*' are changed to '*std_*', and the members, pointgroup_number and pointgroup_symbol, are added. New function 'spg_standardize_cell' is implemented. This can also give 'standardized primitive cell' with 'to_primitive = 1'. Due to change of internal implementation, the order of symmetry operations obtained can be different from the recently released versions, but the set is the same. 2015-06-25 Atsushi Togo * Version 1.8 Relatively large code refactoring was made. Especially 'primitive.c' was changed a lot. Write license statement (New BSD) in the source codes. * src/spglib.c: A new function 'spg_find_standardized_primitive' is implemented. This function allows to create a primitive cell from the obtained standardized conventional unit cell with transformation using pre-determined choice of centring basis vectors. 2015-06-15 Atsushi Togo * Version 1.7.4 Wyckoff position database for rhombohedral cell was wrong. Probably this bug was hidden by the previous default choice of basis vectors but from version 1.7.3 it became revealed. 2015-06-14 Atsushi Togo * src/sitesym_database.c Bug in database of hP of rhombohedral was fixed. This bug was affected after version 1.7.3. 'make_Wyckoff_db.py' is fixed and then the database in 'sitesym_database.c' is recreated by make_Wyckoff_db.py. 2015-04-06 Atsushi Togo * Version 1.7.3 2015-04-05 Atsushi Togo * src/triplet_kpoint.{c,h}: Code to handle triplets of kpoints was separated from kpoint.c. Detail of functions was revisited and modified, e.g., taking modulo of grid address is now included in get_grid_point_double_mesh in most cases. This is probably safe change, but may induce some tricky bug, which has to be remembered. kpt_get_grid_point should be moved to spglib.c with calling kpt_get_grid_point_double_mesh someday soon. It is noted here for not forgetting that get_third_q_of_triplets_at_q in triplet_kpoint.c might be written better around the point using mat_modulo_i3. In triplet_kpoint.c, mat_modulo_i3 is used only here, so eliminating this can move mat_modulo_i3 to kpoint.c as a local function as before. 2015-04-03 Atsushi Togo * src/spacegroup.c (match_hall_symbol_db_ortho): Change the convention of lengths of basis vector preference to: a < b < c for hall number 290 and a < c < b for 291 or a < b < c for hall number 291 and a < c < b for 290, to preserve a < b convention found in Parthe et al, Journal of Alloys and Compounds, 197 (1993) 291-301. 2015-03-31 Atsushi Togo * src/spacegroup.c (match_hall_symbol_db_ortho): Fix choice of lengths of basis vectors in orthorhombic Pbca. There are two choices for Pbca. The basis vectors can be chosen so as to a < b < c or b < a < c, which correspond to these two choices, respectively. The correspondance can be flipped, i.e., in a case, a < b < c for hall number 290 and b < a < c for 291, but in some other case, a < b < c for hall number 291 and b < a < c for 290. 2015-03-20 Atsushi Togo * src/hall_symbol.c (find_hall_symbol): A critical bug was found in version 1.7.2, where origin shift was given for the primitive cell but not for the Bravais lattice. This was fixed. The version 1.7.2 was removed from the download site and temporary 1.7.3-pre is put on the download site. 2015-03-08 Atsushi Togo * Version 1.7.2 * src/niggli.*: Routine of Niggli cell reduction is imported from https://github.com/atztogo/niggli. 2015-02-24 Atsushi Togo * src/spacegroup.c (get_symmetry_settings): Monoclinic lattice vectors are chosen as |a| < |c| with b as the unique axis. This is achieved by get_Delaunay_reduction_2D. * src/lattice.c (get_Delaunay_reduction_2D): 2D Delaunay reduction is implemented based on that of 3D. * src/lattice.c (lat_smallest_lattice_vector_2D): Create an interface to access 2D Delaunay reduction. 2015-02-11 Atsushi Togo * Version 1.7.1 There are minor changes to make functions robust and code clean. * src/spglib.c spg(at)_get_symmetry_with_collinear_spin is changed to return equivalent atoms. spg_get_international and spg_get_schoenflies call iterative routine to determine space group type. * src/primitive.h: Primitive structure is defined. This is expected to make routines related to primitive cell comprehensive. Memory for a pointer of the Primitive variable may be allocated using prm_alloc_primitive and freed by prm_free_primitive. * src/spacegroup.c: spa_get_spacegroup was replaced by iterative routine and now returns a Primitive structure. 2014-11-19 Atsushi Togo * Version 1.7 Space group operations for non-standard setting can be determined using spg_get_dataset_with_hall_number. To achieve this, many lines are added and changed. Due to the big change of the code, there may be bugs, and maybe it's safer to wait for a while to use this version for mission critical systems. Two important changes are: * src/spglib.c (spg_get_dataset_with_hall_number) In space group type determination, Hall symbol serial number can be specified. * src/spglib.h (SpglibDataset) Crystallographic setting information is stored in 'setting'. Symmetrized and standarized crsytal structure is stored in 'n_brv_atoms', 'brv_lattice', 'brv_types', and 'brv_positions', which are the same information obtained using 'spg_refine_cell', except that non-standard setting can be specified in 'spg_get_dataset_with_hall_number'. 2014-10-16 Atsushi Togo * Version 1.6.4 * src/refinement.c (refine_cell): An iterative approach is implemented for refine_cell. 2014-09-12 Atsushi Togo * Version 1.6.3 * src/primitive.c: Atom type is checked in finding a primitive cell. This enables to handle different types of atoms that locate at the same position. for the case of an automatically generated crystal structure data from a fractional occupancy, etc. * Version 1.6.2 Minor bug fixes. * src/spglib.c (spg_get_symmetry_from_database): An API to access space group operations database is implemented. 2014-08-04 Atsushi Togo * Version 1.6.1: * src/{refinement.*,primitive.*,spglib.c} Fix symmetry finding bug for supercell that has lower point group than the primitive cell. * src/spglib.* New functions of spg_get_spacegroup_type and spg_get_grid_point. The former offers difrect access to space group type database using hall symbol number. The later perfoms converting grid address to grid point index on the reciprocal mesh. * pyspglib update. 2014-02-17 Atsushi Togo * Version 1.6.0: * src/spglib.c (spg_get_spacegroup_type): A function is made for accessing space-group-type database. 2014-01-07 Atsushi Togo * src/tetrahedron_method.*: Tetrahedron method is implemented. Example is found in the example directory. 2013-09-10 Atsushi Togo * Version 1.5.2: * kpoint.c (kpt_relocate_BZ_grid_address): New function kpt_relocate_BZ_grid_address is implemented in kpoint.c. k-points on the mesh of the reciprocal primitive lattice are relocated to fit in the Brillouin zone. To treat translationally equivalent k-points, the memory space of bz_grid_address[prod(mesh + 1)][3] is required. bz_map[prod(mesh * 2 - 1)] is used to map k-points on the expanded k-space where the shape is same as the reciprocal primitive lattice but the size along each lattice vector is multiplied by mesh * 2 - 1. BZ zone is included in this expanded k-space, so the bz_map can hold the location of relocated k-points. Irreducible k-points are stored from 0 to index of prod(mesh) - 1 in bz_grid_address in the same order of grid_address, and the translationally equivalent k-points are stored after that. Fast indexing of the location of relocated k-points can be executed using bz_map with similar way to usual grid_address scheme. * kpoint.c (kpt_get_BZ_triplets_at_q): New function kpt_get_BZ_triplets_at_q is implemented using relocate_BZ_grid_address. This generates a set of triplets that cleanly fit in BZ. 2013-09-10 Atsushi Togo * kpoint.c: Remove get_triplets_reciprocal_mesh and extract_triplets_reciprocal_mesh_at_q. Add get_grid_triplets_at_q. This function treats q-points on boundary correctly. * spglib.c (spg_get_symmetry): Previously symmetry operations were obtained by sym_get_operation. Now it is changed so that they are extracted from spglib_dataset. 2013-04-16 Atsushi Togo * symmetry.c (get_operation): In some case, get_space_group_operation returns more than 48 symmetry operations for a primitive cell. To avoid this, an iterative approach, which is just reducing tolerance gradually to achieve number of symmetry operations <= 48, is implemented. * symmetry.c: In the symmetry operation search, rot[] and trans[] were used. Now they are replaced by Symmetry *symmetry in symmetry.c. 2013-04-14 Atsushi Togo * Fortran interface given by Dimitar Pashov: The new fortran interface is given by Dimitar Pashov, which is much safer than the previous one. The new fortran interface, its example, and makefile are found in the example directory as spglib_f08.f90, example_f08.f90 and Makefile_f08. * spglib.h, spglib.c, kpoint.h, kpoint,c: Symprec parameter was removed from spg_get_stabilized_reciprocal_mesh. 2013-01-28 Atsushi Togo * spglib.c, spglib_f.c: Pointerd out by Michael Rutter that the length of charasters of space-group type symbol (International table) was wrong in spglib_f.c. That of Schoenflies symbol was also found wrong. The former and latter were fixed as from 21 to 11 and from 10 to 7, respectively. 2012-10-10 Atsushi Togo * Version 1.3 Rethink algorithms to search symmetry operations for speed-up and stability. Many small modifications are applied. Some parts of the codes that look unnecessary were removed but this change might make the code unstable. * symmetry.c (get_translation): Improve OpenMP efficiency. Number of atoms to enable OpenMP concurrency is set as 1000 (NUM_ATOMS_CRITERION_FOR_OPENMP). 2012-10-09 Atsushi Togo * symmetry.c (sym_get_pure_translation, get_translation): In 'sym_get_pure_translation', iterative approach to search pure_translation was employed. But 'sym_get_pure_translation' was only used from two functions in primitive.c. In these two functions, tolerance is iteratively reduced when the search fails. Because there is no need to do iteration twice, the iteration part in 'sym_get_pure_translation' was removed. * primitive.{c,h}: 'get_primitive_with_pure_translation' was replaced by 'get_primitive_and_pure_translation'. The former was only used from 'get_operation' in symmetry.c and the interative approach was implemented in 'get_operation'. The iterative part was moved into 'get_primitive_and_pure_translation'. The Primitive structure was defined in primitive.h. This just packs Cell * primitive_cell and VecDBL * pure_trans. The Primitive structure is only used in 'get_operation' in symmetry.c and '(prm_)get_primitive_and_pure_translation' in primitive.c. 2012-10-08 Atsushi Togo * spacegroup.c (get_hall_number_local_iteration): REDUCE_RATE to reduce number of symmetry operations is changed from 0.2 to 0.95. Symmetry operations depend on tolerance delicately. * Remove many lines of debug_print: Now to follow the flow is more important than to see the detailed behavior of implementation. 2012-10-03 Atsushi Togo * Version 1.2.5 * primitive.c: Separate out get_primitive_with_mapping_table from prm_get_primitive_with_mapping_table. Rename prm_get_primitive_with_all to get_primitive_with_pure_translation. In get_primitive_with_pure_translation, it was if (pure_trans->size > 0) but not it was fixed to if (pure_trans->size > 1) not to search primitive cell when pure_trans->size == 1. 2012-10-01 Atsushi Togo * Version 1.2.4 * kpoint.c (get_ir_reciprocal_mesh): In spglib, k-point grid is indexed as, for example, 0 1 2 3 4 5 6 -5 -4 -3 -2 -1 for 12 points mesh. Now the different index style such as 0 1 2 3 4 5 -6 -5 -4 -3 -2 -1 is activated by CFLAGS='-DGRID_BOUNDARY_AS_NEGATIVE' before running configure script at the compilation time. * symmetry.c (get_operation): In the iterative reduction of tolerance of primitive cell search, pure_trans was searched by a fixed tolerance rather than the reduced one. This is fixed to use the reduced tolerance at each iteration. 2012-08-13 Atsushi Togo * Version 1.2.3 * symmetry.c (is_identity_metric): To check identity of metric tensors, too small angle induces numerical size error, so if the dtheta is calculated smaller than 1e-6, automatically set the angles be identical. * spacegroup.c (get_hall_number_local_iteration): Implementation of iterative reduction of symmetry tolerance to search symmetry operation to get Hall symbol is separated as the function get_hall_number_local_iteration and the tolerance reduction rate of REDUCE_RATE is changed from 0.2 from 0.95. 2012-07-17 Atsushi Togo * Version 1.2.2 * lattice.c (get_centering): Tranformation A-centring monoclinic lattice to C-centring monoclinic lattice preserving b-axis is not well handled and now the matrix 'monocli_a2c' is used for it. 2012-07-14 Atsushi Togo * Version 1.2.1 * pointgroup.c (laue_one_axis): Transformation matrix is expected to be always positive, but it was not correctly implemented. 2012-05-28 Atsushi Togo * refinement.c (reduce_symmetry_in_frame): Fix memory leak by freeing lattice_trans. 2012-04-26 Atsushi Togo The numbering of the hall symbol is included in the 'struct SpglibDataset'. This starts from 1 to 530. 2012-04-25 Atsushi Togo * spglib.c, spglib.h: To find symmetry with angle tolerance, for spg_* functions, respective spgat_* functions are prepared. In the spgat_* functions, the last variable is the angle tolerance (in degrees). * symmetry.c: The way to find lattice symmetry is changed. Now a new static variable, 'angle_tolerance', can be used for the tolerance of angle. Therefore the non-diagonal elements of metric tensor are directry compared with this angle. 'angle_tolerance' can be accessed via 'sym_set_angle_tolerance' inside spglib. However the default behavior does not use the angle tolerance. In the default behavior, averaged_lattice_vector_length * sin(delta_theta) is compared with usual 'symprec'. The default behavior is invoked when 'angle_tolerance' has negative value. These are implemented in 'is_identity_metric' in symmetry.c. 2012-04-12 Atsushi Togo * lattice.c (get_centering): Correction matrix for I-centring monoclinic was implemented. 2012-03-03 Atsushi Togo * primitive.c: The functions of 'prm_get_current_tolerance', 'set_current_tolerance' and the value of static double current_tolerance were introduced in 'primitive.c'. These are used to return reduced tolerance value that is iteratively determined in 'prm_get_primitive_with_mapping_table'. The interative technique is used in several parts to obtain possible primitive cell parameters by reducing symmetry tolerance. Only in 'get_overlap_table' in 'primitive.c', the interative techinique is used with reducing and increasing the tolerance, i.e., in the other parts, only reducing. 2012-03-02 Atsushi Togo * Version 1.1.2 * refinement.c, primitive.c, symmetry.c: Modifications at many small parts of the code for improve robustness with large symmetry tolerance values. 2012-02-28 Atsushi Togo * primitive.c (get_overlap_table): Simplify the algorithm for search overlapping table. The new algorithm is as follows: Symmetry tolerance monotonically decreases by REDUCE_RATE = 0.95 when the search is failed. When number of overlapping atoms is found smaller than the ratio of number of atoms between original and primitive cells, the symmetry tolerance is doubled. For this algorithm, 'check_overlap_table' function was implemented. 2012-02-09 Atsushi Togo * spin.{c,h}: 'spin.{c,h}' are added. Colliear spins on atoms are employed as additional constraints to search symmetry. The API is 'spg_get_symmetry_with_collinear_spin'. (reduce_symmetry_in_frame): Bug fix to get refined symmetry operations. When the original cell is not primitive and the lattice symmetry is lower than that primitive lattice, the symmetry of primitive has to be reduced to those belongs to the lower symmetry. But this was not correctly done. 2011-10-05 Atsushi Togo * spglib.c (spg_get_pointgroup): 'spg_get_pointgroup' is implemented. This is used to obtain point group symbols. 2011-09-30 Atsushi Togo * site_symmetry.c (get_Wyckoff_notation): Bug fix of assignment of Wyckoff letters 'sitesym_database.c' is compressed. Now only the first element of 'coordinates' is used to aasign a Wyckoff letter. 2011-08-09 Atsushi Togo * symmetry.c (sym_get_pure_translation): Iterative reduction of symmetry tolerance to find pure translations is implemented as well as different parts. 2011-07-29 Atsushi Togo * kpoint.c, kpoint.h: symmetry_kpoint.c and symmetry_kpoint.h are renamed as kpoint.c and kpoint.h, respectively. 2011-07-06 Atsushi Togo * site_symmetry.c: A set of equivalent atoms is returned. It is accessible through spg_get_dataset. (spglib-1.0.7) 2011-07-05 Atsushi Togo * site_symmetry.c, sitesym_database.c, spglib-1.0.6: Newly added two source files (and also *.h). The part related to site symmetry in refinement.c is moved to site_symmetry.c. Wyckoff position determination is implemented in site_symmetry.c and the database is in sitesym_database.c. The pointers in the structure SpglibDataset are made free by calling spg_free_dataset. It was difficult to implement Wyckoff position determination without Yusuke Seko's formated crystallographic database. I appreciate his kind offer. (spglib-1.0.6) * primitive.c (prm_get_primitive): The function is modified to return mapping table from input cell to primitive cell as the first argument. 2011-06-18 Atsushi Togo * symmetry.c: OpenMP is included to search translations with each rotation. Compilation with gcc is achived by '-lgomp' and '-fopenmp'. * refinement.c: Performance tuning was made for 'get_refined_symmetry_operations'. 2011-06-18 Atsushi Togo * refinement.c: In 'ref_get_refined_symmetry_operations', it was forgotten to consider origin shift to obtain symmetry operations from database. This is fixed by modifying translations in 'set_translation_with_origin_shift'. 2011-06-15 Atsushi Togo * spglib-1.0.4: The new version of spglib is released. To the next version, implementation of Wyckoff positions is planed. 2011-06-15 Atsushi Togo * pyspglib: pyspglib didn't work correctly. It was fixed. 2011-06-15 Atsushi Togo * spglib.c: A new function 'spg_get_dataset is implmented. This returns a 'SpglibDataset' type structure that is defined in 'spglib.h'. This includes refined informations of crystal symmetry. For example, the symmetry operations are derived based on the operations in database and so they are different from those obtained from 'spg_get_symmetry'. Wyckoff positions are to be impmemented. 2011-06-13 Atsushi Togo * spg_database.c: A static array of 'symmetry_operations' is compressed because it was very large. It contains symmetry operations of 530 hall symbols. Each space group operation requires a rotation 3x3 matrix and a translation vector, therefore 12 elements were implemented for that. Now it is compressed using ternary numerical system for rotation and duodecimal system for translation. This is achieved because each element of rotation matrix can have only one of {-1,0,1}, and the translation can have one of {0,2,3,4,6,8,9,10} divided by 12. Therefore 3^9 * 12^3 = 34012224 different values can map space group operations. In principle, octal numerical system can be used for translation, but duodecimal system is used for the convenient. The fact that determinant of rotation matrix is -1 or 1 could be used as a constraint to reduce the number of mapping space. These may be implemented if more compression is required. 2011-06-10 Atsushi Togo * spglib.c: spg_show_symmetry was removed. 2011-05-17 Atsushi Togo * primitive.c, etc A tolerance to find primitive lattice vectors sometimes fails because found pure translations do not give possible lattice vectors in which the volume ratio of the input cell and primitive cell does not match to the number of pure translations. So iterative tolerance reduction is implemented. The reduced tolerance should be used to find spacegroup and refined cell because to hold consistency with symmetry operations to be found for primitive cell. The reduced tolerance is not used inside symmetry opration search. The tolerance used to find primitive cell is stored in a static variable 'tolerance' in primitive.c and this can be accessed via prm_get_tolerance(). Old 'prm_get_primitive' was removed and new one is that of 'prm_get_primitive_with_pure_trans' renamed. So now pure translations are always required to call to obtain primitive cell. When calling 'prm_get_primitive' and if the input cell is already primitive, primitive->size=0 was returned in the previous implementation, but in the new implementation, primitive cell that has smallest lattice vectors is returned. 2011-04-21 Atsushi Togo * refinement.c (refine_cell): When an input structure is a primitive cell but the lattice is not smallest, 'refine_cell' didn't work correctly. This is fixed by using new function of 'prm_get_cell_with_smallest_lattice' in primitive.c. This function was originally in spacegroup.c as 'get_cell_with_smallest_lattice'. Following this, spacegroup.c, primitive.c, and primitive.h were modified. 2011-03-18 Atsushi Togo * spglib-1.0.3.1: A critical bug in the structure refinment in refinement.c was removed. A tolerance parameter in hall_symbol.c came back to is_hall_symbol. 2011-03-15 Atsushi Togo * spglib-1.0.3: Crystal structure refinement by spg_refine_cell is implemented. Code around tolerance is tunded up, hopefully becoming more robust with large tolerance. * refinement.c: bravais.{c,h} are renamed to refinement.{c,h}. 2011-03-14 Atsushi Togo * debug.h (SPGWARNING): Debug option of SPGWARNING has been defined. This may be used for beta-tests. * bravais.c, spacegrouop.c, hall_symbol.c, lattice.c, primitive.c: Tolerance parameter has been reconsidered to make finding spacegroup robust with a loose tolerance value. Tolerance is used for Cartesian distance, norm squared, or volume. It wold be avoided for ratio, reduced position or distance. * bravais.c: Exact locations of atoms are obtained by get_exact_location in bravais.c. * sapcegroup.c: Iterative search for hall symbol is implemented in get_hall_number. The tolerance is sequentially reduced until finding a hall symbol. With the reduced tolerance, symmetry operations are researched by sym_reduce_operation. The cost of the reduction of symmetry operations is expeted much smaller than that of the increase of symmetry operations with increasing tolerance. * hall_symbol.c: All tolerance parameters were kicked out. * lattice.c: get_base_center is modified to remove the tolerance paremeter. The centring check is now based on integers. lat_smallest_lattice_vector returns 1 or 0 to show if the lattice has non-zero volume or not. * primitive.c: Primitive lattice is made of pure translations. Previously the primitive lattice vectors are constructed from pure translations. Currently, it is set such that the primitive lattice parameters multiplied with 'intergers' become the original latttice parameters. * mathfunc.c (mat_is_int_matrix): A macro of INT_PREC (currently set 0.1 ) is used for checking a value is integer or not in mat_is_int_matrix. 2011-02-18 Atsushi Togo * spglib-1.0.2: Bug fix in finding lattice point symmetry (symmetry.c). spg_get_bravais is added and spg_get_international_with_bravais was removed. 2010-12-26 Atsushi Togo * spglib-1.0.1: By the help of Pawel T. Jochym, the setup.py in the ASE-interface, pysgpblib, has been updated for matching the latest spglib. 2010-11-08 Atsushi Togo * spglib-1.0.0: A lot of source code was re-written for this one month. This release contains the algorithms of symmetry opertation finding and space-group type determination which are different from the versions before spglib 0.7.4. 2010-11-08 Atsushi Togo Algorithm to search basis vectors is changed to that of [Grosse-Kunstleve, Acta Cryst. A55, 383-395 (1999)], which is implemented in lattice.c. bravais.{c,h}, bravais_virtual.{c,h} are removed. spacegroup_type.{c,h} are moved to spacegroup.{c,h}. 2010-11-05 Atsushi Togo * lattice.c: lattice.c and lattice.h are added. Delaunay reduction is moved there from bravais.c. 2010-11-02 Atsushi Togo * spglib 1.0-beta: New release under the modified BSD license. * pointgroup.c: Sometimes symmetry operations that don't match point-group type can be found. In the current implementation, some of non-necessary operations are abandoned. For this, get_cast_symmetry, check_pointgroup_condition, ptg_get_symmetry_pointgroup are added. However still this implementation is not perfect. Maybe another strategy is required. 2010-10-27 Atsushi Togo * primitive.c: trim_cell is divided into trim_cell, set_primitive_positions, get_positions_primitive, get_overlap_table. is_overlap is modified to check Cartesian distance, and moved to cel_is_overlap in cell.c. * symmetry.c (get_translation): Atomic position overlap check part is modified to use cel_is_overlap. * cell.c: cel_frac_to_cart and cel_cart_to_frac are removed. 2010-10-25 Atsushi Togo * bravais_arc.* is renamed to bravais_virtual.* The function is_holohedry is removed. * bravais.c: brv_set_relative_lattice is added. brv_get_brv_lattice_in_loop is modified for handling RHOMB case flexibly. get_metric was removed and moved to mathfunc.c as mat_get_metric. * pointgroup.c: The first argument of ptg_get_holohedry is removed, which was used just for debugging. * symmetry.c: get_space_group_operation is separated from get_operation. sym_get_operation_direct, set_axes and get_lattice_symmetry are newly added. sym_get_operation_direct is the function for finding symmetry operations without relying on Bravais lattice. The lattice symmetry is exhaustively searched through the matrices whose elements are -1, 0, or 1. * mathfunc.c: mat_get_metric and mat_check_identity_matrix_d3 are added. 2010-10-22 Atsushi Togo * bravais.c: The names of local functions starting with brv_... is changed to get_brv_.... Add functions get_brv_cubic_primitive, get_brv_tetra_primitive, get_brv_ortho_primitive to find more variety of lattice transformation matrices. 2010-10-22 Atsushi Togo The space group type finder is replaced completely. spacegroup.*, spacegroup_data.*, spacegroup_database.* are removed. spacegroup_type.*, spg_database.*, and hall_symbol.* are added. The helper tools to create hall symbol related database are in database directories. 2010-10-09 Atsushi Togo spglib-0.7.4 is released. cel_new_cell is renamed to cel_alloc_cell, and cel_alloc_cell returns a poiter of the Cell structure. cel_delete_cell is renamed to cel_free_cell. sym_new_symmetry is renamed to sym_alloc_symmetry, and sym_alloc_symmetry returns a poiter of the Symmetry structure. sym_delete_symmetry is renamed to sym_free_symmetry. The other functions returns Cell and Symmetry structures are modified to return those pointers. 2010-10-05 Atsushi Togo * symmetry.c (get_index_with_least_atoms): To search translation, it is efficient if an atom in least atoms with an atomic type is used for the search origine. This function looks for it. This is expected to accelerate especially when the cell is huge and the lattice has high symmetry, but the number of atoms of some atomic type is few. 2010-10-04 Atsushi Togo * primitive.c (prm_get_primitive_with_pure_trans): Create new function 'prm_get_primitive_with_pure_trans' to avoid searching same pure translations many times, which leads some speed up. 2010-09-26 Atsushi Togo 'const' of multidimensional arrays are removed. Just to notify it should be 'const', 'SPGCONST' replaces those 'const', however it is defined as nothing in mathfunc.h. This is done because of avoiding lots of waring in C-compiler of 'gcc: incompatible pointer type'. * spglib_f.c: spglib_f.c is updated and some examples are found in example.f90. 2010-04-12 Atsushi Togo * symmetry.c, mathfunc.c: To make the translations clean, sym_get_fractional_translation in symmetry.c and mat_Dmod1 in mathfunc.c are added. sym_get_fractional_translation is supposed to look for the translation that is most closest to one of 0, 1/6, 1/4, 1/3, 1/2, 2/3, 3/4, and 5/6. The first implementation contained a bug and Jorg Meyer solved this. 2010-03-25 Atsushi Togo * bravais_art.c: Space group of the virtual structures in the test directory failed. Fixed points are as follows: P-Cubic, P-Tetra, P-Ortho to Base center monoclinic, which was collect in the old code, and I-Cubic to F-Orthorhombic. Cubic to Rhombohedral. To obtain correct principal axes, 'is_rhombo' was implemented. 2010-03-22 Atsushi Togo * spglib.h, spglib.c: spg_get_bravais_lattice is removed. spg_get_conventional_symmetry is implemented. This is used to get symmetry operations for the conventional unit cell. The conventional unit cell is searched from the primitive cell found from the input cell, i.e., even if the input cell is not primitive, the primitive cell is automatically searched and the conventional cell is determined. The Bravais lattice of the conventinal cell is returned as bravais_lattice. This bravais_lattice is found including the internal atomic positions. Therefore artificial cell is expected to be handled correctly. 2010-02-11 Atsushi Togo * primitive.c: There was a problem that primitive cell is not well found in naive cases (inconsistency between tolerances in finding pure translations and in finding overlapping atoms). David Lonie implemented an iterative way to adjust symmetry finder tolerance on the fly. 2009-07-15 Atsushi Togo * bravais.c: Bug to find bravais lattice in FCC and rhombohedral, when the cell is a supercell. This is probably ad-hoc fix. 2009-05-19 Atsushi Togo * symmetry_kpoint.c: Time reversal symmetry is included. * bravais.c (brv_smallest_lattice_vector): Delaunay reduction is implemented instead of ABINIT implementation. 2009-03-09 Atsushi Togo * symmetry.c: Critical bug for finding symmetry for primitive cell which is reduced from convensional cell. 2009-03-05 Atsushi Togo * symmetry_kpoint.c: Functions to look for the irreducible points in reciprocal space are implemented. 2009-02-25 Atsushi Togo * bravais_art.c: Hexagonal to Orthorhombic symmetry lowering case is implemented. * python module: Python module is implemented. To use them, numpy is required. Interface for ASE is implemented. 2008-08-22 Atsushi Togo * bravais_art.c: This file is used for the cases that the lattice has higher symmetry than the symmetry given by atomic positions. This does not affect to the symmetry operations that is firstly obtained by assuming the bravais lattice having high symmetry. Thus this file works only for changing its bravais lattice. The information about bravais lattice is used for only determing space group. Even if the code in this file fails, or let's say, space group determination fails), we can not say the symmetry operations are wrong. 2008-07-11 Atsushi Togo * Most of the code The procedure for searching a Bravais lattice from a primitive cell is rewritten. The algorithm is also totally changed. * test directory For the test of space group search, 'test' directory is created. Many POSCAR's are prepared in this directory. For running tests, a small ruby code is written and put into this directory. 2008-05-28 Atsushi Togo * spacegroup_data.c (get_spacegroup_data_special_case): Bug fix for space group determinations for special cases (Pcc2, Pbam, Pccn). 2008-05-25 Atsushi Togo * *.c, *.h : Many codes are re-built. Many functions are changed to "static". The first three characters of public functions are re-named using those file names. * bravais.c : Monoclinic is possibly improved. Monoclinic is difficult. It may contain further bugs... 2008-05-01 Atsushi Togo * spacegroup.c (get_proper_rotation_class_6axis): exit(1) is inserted. * bravais.c/h: "lattice_symmetry" is removed from the "Bravais" structure. * spglib.h: Misspelled function prototypes of spg_get_symmetry and spg_check_symmetry are corrected. 2008-04-23 Atsushi Togo * Many patches by Xavier Andrade For fixing many warning in many codes and gcc-4.3 related problem in bravais.c.