Difference between revisions of "Matgen toolkit"
From wiki
(→Find Space Groups) |
(→In-Cell) |
||
| Line 68: | Line 68: | ||
=== In-Cell === | === In-Cell === | ||
==== Description ==== | ==== Description ==== | ||
| + | This program will obtain its in-cell structure based on the space group information of the unit cell. | ||
==== Usage ==== | ==== Usage ==== | ||
<pre> | <pre> | ||
| − | .. | + | usage: ./bin/in_cell --input_path=string --output_path=string [options] ... |
| + | options: | ||
| + | -i, --input_path input MOF cif file (string) | ||
| + | -o, --output_path output file path (string) | ||
| + | -?, --help print this message | ||
</pre> | </pre> | ||
==== Example ==== | ==== Example ==== | ||
<pre> | <pre> | ||
| − | .. | + | $ ./bin/in_cell -i ./examples/cod/WAJZUE.cif -o ./examples/result |
| + | Getting some known resources... | ||
| + | Parsing the cif file - WAJZUE.cif | ||
| + | Exporting in-cell result... | ||
| + | Export file ./examples/result/WAJZUE_in_cell.cif successfully! | ||
</pre> | </pre> | ||
Revision as of 13:22, 14 February 2020
Contents
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
Description
This program will obtain its in-cell structure based on the space group information of the unit cell.
Usage
usage: ./bin/in_cell --input_path=string --output_path=string [options] ... options: -i, --input_path input MOF cif file (string) -o, --output_path output file path (string) -?, --help print this message
Example
$ ./bin/in_cell -i ./examples/cod/WAJZUE.cif -o ./examples/result Getting some known resources... Parsing the cif file - WAJZUE.cif Exporting in-cell result... Export file ./examples/result/WAJZUE_in_cell.cif successfully!
ICSD' Classify And Unique =
Description
Usage
..
Example
..
CSD' Classify
Description
Usage
..
Example
..
Format
Description
Usage
..
Example
..
Splice Molecule
Description
Usage
..
Example
..
