I need to model in LAMMPS a small molecular crystal described in CIF format. The structure is triclinic. I need to model it as 3D periodic. I see from manula creating a 3D periodic triclinix box is a bit complex. Can anybody show me some tutorial/sample data how to solve such problem ?
You can convert a cif file to lammps data file using this utility
There are other tools listed in the pre/post processing section of the manual though
HTH
I was going throug all this utilites and it looks to me none work correctly with triclinic systems nor correctly supports space group informations from CIF. What will help me is an acces to a functional tested lammps input + cif from witch it was genarated. I had found only some trivial cubic alloys examples, but never some triclinic or monoclinic sample of pure organic molecular crystal … If I will see a functional input/output I can write the data transformation code myself … Does anybody have such example ?
I was trying to make cif2cell-lammps working for 3 hours. It depends on another code PyCifRW. The actual 3.12 python does not work with the old PyCifRW 3.3 code from cif2-cell. I was able to install actual version of PyCifRW (4.4.6), but it does not work with cif2cell-lammps … Is there anybody who had successfully made this working ?
I don’t know about PyCifRW or cif2cell-lammps. But the best place to ask for help for the tool is to the developer of the said tool. That said, I highly doubt that ALL tools dedicated to reading/converting CIF files do not “correctly support space group information from CIF”. OVITO or VESTA can generally reproduce quite complex structure well from CIF and write lammps data or XYZ files that can be read from LAMMPS.
Note that I don’t think cif file contain any bond or angle information so those should be added as a post process on your own.
The topic is a bit complex to understand - some of the mentioned tools works but:
- they generetate molecule in vacuum
- they generate a simulation cluster
I need something generatin periodic box corresponding to crystallographic unit cell. And woking correctly for non rectangular cells = monoclinic and triclinic.
If anybody hava a tested functiona workflow for such proces, it will be helpful.
I took the following file randomly from the COD, here:
#------------------------------------------------------------------------------
#$Date: 2019-10-10 12:58:52 +0300 (Thu, 10 Oct 2019) $
#$Revision: 219250 $
#$URL: file:///home/coder/svn-repositories/cod/cif/2/00/00/2000097.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/
#
# All data on this site have been placed in the public domain by the
# contributors.
#
data_2000097
loop_
_publ_author_name
'Gimbert, Yves'
'Robert, Fr\'ed\'eric'
'Durif, Andr\'e'
'Averbuch, Marie-Th\'er\`ese'
'Kann, Nina'
'Greene, Andrew E.'
_publ_section_title
;
Synthesis and Characterization of New Binuclear Co(0) Complexes with
Diphosphinoamine Ligands. A Potential Approach for Asymmetric
Pauson-Khand Reactions
;
_journal_coden_ASTM JOCEAH
_journal_issue 10
_journal_name_full 'The Journal of Organic Chemistry'
_journal_page_first 3492
_journal_page_last 3497
_journal_paper_doi 10.1021/jo982245o
_journal_volume 64
_journal_year 1999
_chemical_formula_sum 'C25 H13 Co2 F24 N O8 P2'
_space_group_IT_number 2
_symmetry_cell_setting triclinic
_symmetry_Int_Tables_number 2
_symmetry_space_group_name_Hall '-P 1'
_symmetry_space_group_name_H-M 'P -1'
_cell_angle_alpha 111.07(4)
_cell_angle_beta 98.14(2)
_cell_angle_gamma 76.85(3)
_cell_formula_units_Z 2
_cell_length_a 10.611(2)
_cell_length_b 12.401(6)
_cell_length_c 15.960(4)
_cell_volume 1904.192
_diffrn_ambient_temperature ?
_exptl_crystal_colour 'dark red'
_exptl_crystal_density_diffrn 1.9
_refine_ls_R_factor_gt 0.039
_refine_ls_wR_factor_gt 0.039
_cod_depositor_comments
;
Updated bibliographic information.
Antanas Vaitkus,
2019-10-10
;
_cod_original_formula_sum 'C25 H13 Co2 F24 N1 O8 P2'
_cod_database_code 2000097
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 -x,-y,-z
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Co1 Co 0.76581(4) 0.91080(3) 0.82927(2)
Co2 Co 0.75520(4) 0.95255(3) 0.68975(2)
P1 P 0.84007(6) 0.72676(6) 0.77427(4)
P2 P 0.86540(7) 0.78247(6) 0.61952(4)
F1 F 0.8708(2) 0.4382(2) 0.7882(2)
F2 F 0.6917(3) 0.4057(2) 0.7210(2)
F3 F 0.7194(3) 0.4374(2) 0.8605(2)
F4 F 0.4989(2) 0.5943(3) 0.7325(2)
F5 F 0.5185(2) 0.7501(2) 0.8369(2)
F6 F 0.5050(2) 0.5984(2) 0.8652(2)
F7 F 0.9182(2) 0.6866(2) 0.9993(1)
F8 F 1.1122(2) 0.7066(2) 1.0421(1)
F9 F 1.0708(2) 0.5467(2) 0.9435(1)
F10 F 1.2267(2) 0.5878(2) 0.8393(2)
F11 F 1.1578(2) 0.7384(3) 0.8017(2)
F12 F 1.2423(2) 0.7577(3) 0.9324(2)
F13 F 0.6381(2) 0.6106(2) 0.5692(1)
F14 F 0.6917(3) 0.5099(2) 0.4357(2)
F15 F 0.5060(2) 0.6215(2) 0.4585(2)
F16 F 0.7632(2) 0.6329(2) 0.3403(1)
F17 F 0.7157(2) 0.8190(2) 0.3976(1)
F18 F 0.5648(2) 0.7201(2) 0.3512(1)
F19 F 1.1372(3) 0.8721(2) 0.4523(2)
F20 F 1.1861(3) 0.6994(3) 0.4589(2)
F21 F 0.9973(3) 0.7669(3) 0.4214(2)
F22 F 1.1419(2) 0.9192(2) 0.7197(2)
F23 F 1.2704(2) 0.7851(3) 0.6319(2)
F24 F 1.2248(2) 0.9546(3) 0.6209(2)
O1 O 0.7460(2) 0.6308(2) 0.7504(1)
O2 O 0.9560(2) 0.6571(1) 0.8260(1)
O3 O 0.8141(2) 0.7038(2) 0.5192(1)
O4 O 1.0140(2) 0.7611(2) 0.5919(1)
O5 O 0.9813(3) 1.0314(2) 0.9133(2)
O6 O 0.6482(3) 0.9507(3) 0.9946(2)
O7 O 0.9105(3) 1.1375(2) 0.7525(2)
O8 O 0.6078(2) 1.0491(2) 0.5563(2)
N1 N 0.8942(2) 0.6844(2) 0.6725(1)
C1 C 0.9607(3) 0.5611(2) 0.6286(2)
C2 C 0.7007(3) 0.5997(2) 0.8149(2)
C3 C 0.7462(4) 0.4682(3) 0.7952(3)
C4 C 0.5536(3) 0.6352(3) 0.8117(3)
C5 C 1.0351(3) 0.7137(2) 0.8990(2)
C6 C 1.0351(3) 0.6625(3) 0.9720(2)
C7 C 1.1685(3) 0.6974(3) 0.8674(3)
C8 C 0.6840(3) 0.7141(3) 0.4851(2)
C9 C 0.6298(4) 0.6117(3) 0.4865(3)
C10 C 0.6825(4) 0.7206(3) 0.3918(2)
C11 C 1.0616(3) 0.8445(2) 0.5716(2)
C12 C 1.0948(4) 0.7948(4) 0.4746(3)
C13 C 1.1781(4) 0.8746(4) 0.6360(3)
C14 C 0.6279(3) 0.8954(2) 0.7324(2)
C15 C 0.6240(3) 1.0082(2) 0.7790(2)
C16 C 0.5311(3) 1.1172(2) 0.8184(2)
C17 C 0.4023(3) 1.1129(3) 0.8117(3)
C18 C 0.3129(4) 1.2150(5) 0.8488(3)
C19 C 0.3522(4) 1.3182(4) 0.8918(3)
C20 C 0.4783(5) 1.3234(3) 0.8981(3)
C21 C 0.5686(3) 1.2223(3) 0.8618(3)
C22 C 0.8966(3) 0.9854(2) 0.8813(2)
C23 C 0.6927(3) 0.9331(3) 0.9299(2)
C24 C 0.8543(3) 1.0637(2) 0.7276(2)
C25 C 0.6646(3) 1.0072(2) 0.6060(2)
H1 H 0.96370 0.51940 0.66390
H2 H 0.91630 0.52650 0.57920
H3 H 1.02810 0.56170 0.60490
H4 H 0.72910 0.64640 0.88180
H5 H 0.99910 0.80060 0.92400
H6 H 0.62770 0.78830 0.51980
H7 H 0.99160 0.92260 0.57970
H8 H 0.58010 0.82870 0.70270
H9 H 0.37700 1.02460 0.79050
H10 H 0.22430 1.20220 0.83570
H11 H 0.27270 1.38450 0.91320
H12 H 0.50670 1.40480 0.92160
H13 H 0.65770 1.23050 0.85930
loop_
_atom_type_symbol
_atom_type_radius_bond
C 0.68
H 0.23
Co 1.33
F 0.64
N 0.68
O 0.68
P 1.05
This file is correctly opened by Ovito which apparently provides “periodic box corresponding to crystallographic unit cell. […] working correctly for non rectangular cells”. I could successfully export the file as a LAMMPS data file, read it and replicate the box 3 times in each direction keeping the shape triclinic with correct angles and dimensions.
So without more information on the file and software you are trying to use, there is little more we can do than make wild guesses about what could have gone wrong in the format of your file, your workflow or your reading of the software output.