Crystal Toolkit -- New structures


#1

I understand that the Crystal Toolkit allows for reporting/calculating new structures that could show on the MP website. I am wondering how the new structure will be linked to the MP user that originally proposed it. Thanks.


#2

Each material detail page has information at the bottom about who submitted the structure. For structures submitted through the Crystal Toolkit, the email address of the user submitting the structure is shown (just like a contact author for a publication), and it is noted next to that, as a remark, that this structure was a “MP user submission”. This information is also stored in the database document as retrieved by API users, in the snl_final.about.authors array. “SNL” stands for structure notation language, and if you report structures via our API (example process here), there is considerable flexibility for associating metadata with your structure such as co-authors, literature references, listing projects / funding sources, and arbitrary short remarks. Such flexibility is not yet available through the web interface, but this is planned.


#3

I am trying to submit a structure from the following cif file to the crystal toolkit but I notice that once uploaded the parameters are not the the same as the ones I created in the .cif file.

#======================================================================

CRYSTAL DATA

#----------------------------------------------------------------------

data_VESTA_phase_1

_chemical_name_common ‘’
_cell_length_a 6.32738
_cell_length_b 6.32738
_cell_length_c 17.07174
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 120
_space_group_name_H-M_alt ‘P 1’
_space_group_IT_number 1

loop_
_space_group_symop_operation_xyz
’x, y, z’

loop_
_atom_site_label
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_adp_type
_atom_site_B_iso_or_equiv
_atom_site_type_symbol
Zn1 1.0 0.000000 0.000000 0.296117 Biso 1.000000 Zn
Zn2 1.0 0.000000 0.000000 0.796117 Biso 1.000000 Zn
Zn3 1.0 0.666667 0.333333 0.629457 Biso 1.000000 Zn
Zn4 1.0 0.666667 0.333333 0.129453 Biso 1.000000 Zn
Zn5 1.0 0.333333 0.666667 0.962788 Biso 1.000000 Zn
Zn6 1.0 0.333333 0.666667 0.462781 Biso 1.000000 Zn
Sn1 1.0 0.000000 0.000000 0.004619 Biso 1.000000 Sn
Sn2 1.0 0.000000 0.000000 0.504603 Biso 1.000000 Sn
Sn3 1.0 0.666667 0.333333 0.337922 Biso 1.000000 Sn
Sn4 1.0 0.666667 0.333333 0.837946 Biso 1.000000 Sn
Sn5 1.0 0.333333 0.666667 0.671273 Biso 1.000000 Sn
Sn6 1.0 0.333333 0.666667 0.171271 Biso 1.000000 Sn
S1 1.0 0.025423 0.374447 0.064152 Biso 1.000000 S
S2 1.0 0.625553 0.650976 0.064152 Biso 1.000000 S
S3 1.0 0.349024 0.974577 0.064152 Biso 1.000000 S
S4 1.0 0.625543 0.974581 0.564156 Biso 1.000000 S
S5 1.0 0.349037 0.374457 0.564156 Biso 1.000000 S
S6 1.0 0.025419 0.650963 0.564156 Biso 1.000000 S
S7 1.0 0.692093 0.707805 0.397497 Biso 1.000000 S
S8 1.0 0.292195 0.984288 0.397497 Biso 1.000000 S
S9 1.0 0.015712 0.307907 0.397497 Biso 1.000000 S
S10 1.0 0.292214 0.307913 0.897486 Biso 1.000000 S
S11 1.0 0.015699 0.707786 0.897486 Biso 1.000000 S
S12 1.0 0.692087 0.984301 0.897486 Biso 1.000000 S
S13 1.0 0.358754 0.041120 0.730823 Biso 1.000000 S
S14 1.0 0.958880 0.317634 0.730823 Biso 1.000000 S
S15 1.0 0.682366 0.641246 0.730823 Biso 1.000000 S
S16 1.0 0.958863 0.641240 0.230828 Biso 1.000000 S
S17 1.0 0.682377 0.041137 0.230828 Biso 1.000000 S
S18 1.0 0.358760 0.317623 0.230828 Biso 1.000000 S


#4

Hi Stephen,

Sorry for the delayed reply. I’ve looked over the code for the crystal toolkit and it appears that your structure is reformatted into the Niggli setting of the primitive cell, primarily because this setting is the most convenient for the transformations which the crystal toolkit allows. You can replicate this transformation in pymatgen using the following code:

from pymatgen import Structure
structure = Structure.from_file("YOUR_FILENAME.cif")
reduced_struct = structure.get_primitive_structure().get_reduced_structure()

One of the reasons this is done automatically is because the symmetry reduction will occur automatically to reduce the computational time of the simulation we would run on your submitted structure, so what you’ll see in the crystal toolkit is what we would likely use for the POSCAR, for example.