[CPMD-list] monoclinic cell

[Axel Kohlmeyer]

On Mon, 9 Jul 2007, Samir H. Mushrif wrote:


SM> Hello CPMD Users,

hi samir,

SM>                   First of all I would like to thank Axel for replying 
SM> to my previous mails. Continuing my work on the same topic, I am having 

you're welcome. i'd appreciate it a lot, if you (and others) would 
drop me a line about whether my suggestions are actually helpful 
and particularly where not. this would help to give better advice
the next time.

[...]


SM> ***(I did not understand the following section)
SM> 
SM> ***     DETSP| SIZE OF THE PROGRAM IS    2128/  72744 kBYTES ***
SM> !!!  2 OPERATION NOT CORRECT!!!
SM> !!!  3 OPERATION NOT CORRECT!!!
SM> !!!  4 OPERATION NOT CORRECT!!!
SM> 
SM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
SM> !! CHKSYM| NUMBER OF SYMMETRY OPERATIONS HAS BEEN CHANGED     !!
SM> !!         FROM  4 TO  1                                      !!
SM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
SM> 
SM> MOLECULAR SYSTEM  WITH  1 OPERATIONS
SM>
SM>
SM> SYMMETRY UNIQUE (INEQUIVALENT) ATOMS:                         58
SM> REQUIRED PRECISION FOR SYMMETRY:                        1.00E-06

ok, so the way you entered the coordinates, did not
match with the point group symmetry. 

your coordinates input is not overly precise, perhaps
you need to relax the tolerance for symmetry detection
a little and then ask CPMD to symmetrize the coordinates,
or enter them with more significant digits. 
your symmetry tolerance is at 0.000001!

did you check if you have to rotate the coordinates 
along with the swapping of the cell parameters?

generally, enforcing point group symmetry is rarely
needed (see other posts on that subject in the mailing list),
and particularly meant for isolated molecules (which have
to be oriented correctly) when looking at vibrational modes
and geometry optimization.

if you want to use it to check your input, here is 
an alternative:

turn off symmetry, set MAXSTEP to 1 and add RHOOUT.
this should give you the coordinates and the density
of the initial guess in a DENSITY file which you can
convert into a cube file with cpmd2cube.x 

if you load this cube file into a visualization program
which supports periodicity (xcrysden, VMD), you can
look at the structure with multiple copies of the principle
cell and compare to your reference and see whether
CPMD 'got it'.

SM> 
SM> NUMBER OF IRREDUCIBLE REPRESENTATIONS:                         1
SM> DIMENSION OF IR:                                               1

[...]

SM> I do not understand if the CPMD recognizes the group information given 
SM> by me or it changes something that I am not understanding. I also tried 
SM> using POINT GROUP AUTO option (with "splitted" molecules and 
SM> "unsplitted" molecules) but it gives me 1 (c1) as the symmetry group 
SM> which I don't think is correct.

[...]

SM> Can someone please help me in this aspect?

one question remains: do you really 
want to enforce that symmetry?

most calculations will run fine without.

cheers,
   axel.

SM> 
SM> Thanks a lot for your help and time.
SM> 
SM> Best Regards
SM> Samir
SM> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
SM> 
SM> Samir H. Mushrif
SM> Department of Chemical Engineering
SM> Mcgill University
SM> 3610 University Street
SM> Montreal, Quebec H3A2B2
SM> Canada
SM> Ph: (Lab)514-398-5170
SM>     (Off)514-398-4169
SM> 
SM> 
SM> 
SM> 
SM> _______________________________________________
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SM> CPMD-list at cpmd.org
SM> http://cpmd.org/mailman/listinfo/cpmd-list
SM> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.