Matgen toolkit

Descriptions

Remove Solvents

Description

The program is a tool to remove solvents from MOF.

Usagen

usage: ./bin/rm_mof_solvents --cif_in=string [options] ...
options:
  -i, --cif_in         input MOF cif file (string)
  -o, --output_path    output filepath (string [=])
  -f, --force          remove solvent molecules anyway
  -?, --help           print this message

Example

$ ./bin/rm_mof_solvents -i ./examples/cod/ABAGAO.MOF_subset.cif -o ./examples/result
Parsing the cif file - ABAGAO.MOF_subset.cif
Getting some known resources...
Building base cell...
The number of bonded atom pairs is 80
Looking for solvent in ABAGAO.MOF_subset.cif
The calculated solvent molecule to be screened is [ H2O<known>  ]
The MOF framework is  [ C14CuH13N3O4  ]
Exporting result...
Export file ./example/result/ABAGAO_clean.cif successfully!

Find Space Groups

Description

The program is used to obtain the space group information in the cif file.(base on spglib)

Usage

usage: ./bin/find_space_groups --input=string [options] ...
options:
  -i, --input         input cif file name (string)
  -v, --version       return the version of spglib
  -w, --why           this method is used to see roughly why  spglib failed
  -s, --spacegroup    internatioanl space group short symbol and number are obtained as a string
  -m, --symmetry      symmetry operations are obtained as a dictionary
  -r, --refine        standardized crystal structure is obtained as a tuple of lattice (a 3x3 numpy array), atomic scaled positions (a numpy array of [number_of_atoms,3]), and atomic numbers (a 1D numpy array) that are symmetrized following space group type.
  -p, --primitive     is found, lattice parameters (a 3x3 numpy array), scaled positions (a numpy array of [number_of_atoms,3]), and atomic numbers (a 1D numpy array) is returned.
  -d, --dataset       dataset,cell and symprec;angle_tolerance;hall_number;number;choice;transformation_matrix;origin shift;wyckoffs;site_symmetry_symbols;equivalent_atoms;mapping_to_primitive;rotations and translations;pointgroup;std_lattice;std_positions;std_types;std_rotation_matrix;std_mapping_to_primitive
  -c, --symmfdset     A set of crystallographic symmetry operations corresponding to hall_number is returned by a dictionary where rotation parts and translation parts are accessed by the keys rotations and translations, respectively.
  -f, --spgfdset      This function allows to directly access to the space-group-type database in spglib (spg_database.c). A dictionary is returned. To specify the space group type with a specific choice, hall_number is used.
  -n, --niggli        Niggli reduction is achieved using this method.
  -l, --delaunay      Delaunay reduction is achieved using this method.
  -k, --irrkpoints    Irreducible k-points are obtained from a sampling mesh of k-points
  -?, --help          print this message

Example

$ ./bin/find_space_groups -i ./examples/cod/WAJZUE.cif -s
Parsing the cif file - ABETIN_clean.cif
Getting some known resources...
The space group is: I4_1/acd 142

Problem && Solution

error while loading shared libraries: libsymspg.so.1: cannot open shared object file: No such file or directory because the program will default to /lib64/libsymspg.so not in /lib64/. Therefore, the following commands need to be added to allow the program to find the library in the directory of the instruction.

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:./include/spglib/_build

spglib path please change according to the actual

In-Cell

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ICSD' Classify And Unique =

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CSD' Classify

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Format

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Splice Molecule

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