Not triclinic! [was: Re: [Wien] Problem creating struct files from
VASP contcar files]
Gus Hart
gus.hart at NAU.EDU
Mon Jan 12 22:56:12 CET 2004
Doug du Boulay and Peter Blaha have been thinking in WIEN2K mode to long...
It is NOT TRUE that alpha, beta, gamma all not equal to 90 implies
triclinic. In fact the *primitive cell* for virtually all base-centered
monoclinic cells have this feature. In fact the primitive cell for fcc,
bcc, and others also have all angles not 90.
Flourent correctly points out that a transformation to a NON-PRIMITIVE cell
can be done in which two of the angles are now 90.
The point of Patrick's question is what to do when one DOES NOT KNOW the
transformation. Is the StructGen program incapable of dealing with
primitive cells of arbitrary symmetry? (Pat's experience seems to imply that.)
If one has a primitive cell (say from VASP), how do you convert it to a
struct file? Many cases I have done for base-centered monoclinic are very
difficult. One took me several days before I finally found the *magical*
transformation...
At 09:14 AM 1/7/2004 +0100, you wrote:
>Dear Patrick,
>your cell effectively corresponds to a monoclinic lattice but not a
>primituve one.
Yes it is primitive. That's precisely the problem--WIEN2K doesn't want it
in primitive form. I thought StructGen could generate a struct file from
this. Apparently not.
>I was able to find the monoclinic C centered unit cell doing this
>transformation:
>a' = - c
>b' = 2a + c
>c' = -b
>
>Then I got the following C centered lattice :
>a' = 5.1782
>b' = 8.8046
>c' = 5.1857
>beta = 112.81
>
>In VASP you enter the primitive triclinic unit cell and the program is
>able to find the higher symmetry. Wien works in a different way : you
>enter the non primitive unit cell and it does the job for you to reduce
>the number of k point and find the corresponding primitive cell.
>
>However, for non primitive monoclinic unit cell, WIEN works only with CXZ
>lattice (b-base centered, monoclinic gamma). So you have to use the
>following transformation according to your primitive cell :
>a' = - c
>b' = -b
>c' = -2a - c
>I got :
>Crystal system monoclinic
>Space group B 1 1 2/m (no. 12)
>Unit cell dimensions
>a = 5.1782 Å
>b = 5.1857 Å
>c = 8.8046 Å
>gamma = 112.81 °
>
>I put in attachement a cif file.
>Regards
>Florent
>
>pjr8 a écrit :
>
>>Hello,
>>
>>I'm new to using wien 2k, so I hope I'm not missing a simple solution to
>>this.
>>I'm trying to convert VASP contcar files for low symmetry structures,
>>like monoclinic, into struct files. A sample contcar file is pasted below.
>>
>>GSS check structure #: 81
>> 4.100000000000000
>> 1.0062816128952770 0.5260273706595530 0.5121801204340521
>> -0.4948479628567789 1.0535466565671180 0.4948479628567789
>> -0.4941014924612246 -1.0520547413191060 0.4941014924612247
>> 6 3
>>Direct
>> 0.3333333333333428 0.7607588622281583 0.8969830898152509
>> 0.6694622253955771 0.7390086361365178 0.5980793830199076
>> 0.9972044412710943 0.7390086361365178 0.2619504909576591
>> 0.6694622253955771 0.2609913638634822 0.0713828423756695
>> 0.9972044412710943 0.2609913638634822 0.7352539503134352
>> 0.3333333333333428 0.2392411377718417 0.4363502435180777
>> 0.3333333333333428 0.0000000000000000 0.6666666666666572
>> 0.6680618367231830 0.5000000000000000 0.8340309183616057
>> 0.9986048299434884 0.5000000000000000 0.4993024149717371
>>
>>The first line (after the title) is the scale factor, the next three
>>lines define the basis vectors, and the nine atom positions are listed in
>>direct coordinates. Using StructGen, I entered a=5.105, b=5.187, c=5.178
>>and alpha=112.8, beta=120.5, gamma=78.6. The atom positions were entered
>>in direct coords as above.
>>
>>When I run init_lapw it keeps identifying it as a triclinic structure. I
>>have also tried placing a single atom at 0,0,0 to see if it would show up
>>as monoclinic, but it doesn't.
>>
>>Any help is appreciated.
>>
>>Thanks,
>>
>>Patrick Robbins
>>
>>_______________________________________________
>>Wien mailing list
>>Wien at zeus.theochem.tuwien.ac.at
>>http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>
>>
>
>
>--
>--------------------------------------------------------------------------
>| Florent BOUCHER | |
>| Institut des Matériaux Jean Rouxel | Mailto:Florent.Boucher at cnrs-imn.fr |
>| 2, rue de la Houssinière | Phone: (33) 2 40 37 39 24 |
>| BP 32229 | Fax: (33) 2 40 37 39 95 |
>| 44322 NANTES CEDEX 3 (FRANCE) | http://www.cnrs-imn.fr |
>--------------------------------------------------------------------------
>
>
>data_12_4
>_audit_creation_method 'Created with Diamond v2.0'
>_audit_creation_date 04-01-07
>_audit_update_record 04-01-07
>_chemical_formula_sum 'S12 Ti6'
>_chemical_formula_weight 672.072
>_cell_length_a 5.1782
>_cell_length_b 5.1857
>_cell_length_c 8.8046
>_cell_angle_alpha 90.000
>_cell_angle_beta 90.000
>_cell_angle_gamma 112.810
>_cell_volume 217.9
>_symmetry_int_tables_number 12
>_symmetry_space_group_name_H-M 'B 1 1 2/m'
>_symmetry_space_group_name_Hall '-B_2'
>
>loop_
>_atom_type_symbol
>_atom_type_oxidation_number
>_atom_type_radius_bond
>S ? 1.200
>Ti ? 1.200
>
>
>loop_
>_atom_site_label
>_atom_site_type_symbol
>_atom_site_fract_x
>_atom_site_fract_y
>_atom_site_fract_z
>_atom_site_occupancy
>_atom_site_symmetry_multiplicity
>_atom_site_Wyckoff_symbol
>_atom_site_attached_hydrogens
>_atom_site_calc_flag
>_atom_site_thermal_displace_type
>_atom_site_u_iso_or_equiv
>S1 S 0.2303 0.7608 0.0000 1.000 4 i ? d Uiso 0.50000
>S1 S 0.2367 0.2610 0.8319 1.000 8 j ? d ? ?
>Ti1 Ti 0.0000 0.0000 0.0000 1.000 2 a ? d Uiso 0.25000
>Ti1 Ti 0.0000 0.5000 0.1674 1.000 4 h ? d Uiso 0.50000
++++++++++++++++++++++++++++
Gus Hart (Rm. 312)
Department of Physics and Astronomy
PO Box 6010
Flagstaff AZ 86011-6010
tel. (928)523-0426
fax (928)523-1371
gus.hart at nau.edu
http://www.physics.nau.edu/~hart
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