[CPMD-list] monoclinic cell
Samir H. Mushrif
samir.mushrif at mail.mcgill.ca
Tue Jul 10 22:58:07 CEST 2007
Hello Axel,
Thanks for your reply. I also got a reply from Juerg Hutter
which states that
**************************
please note that
POINT GROUP MOLECULE
only works for single (isolated) molecules and needs
a special standard orientation of the molecule.
It should not be used for molecular crystals.
**************************
Following your suggestions and Juerg's advice: 1. Relaxing the symmetry
tolerence to 0.0001 (also I tried 0.001)
2. Not using POINT GROUP MOLECULE. Instead I used
POINT GROUP DELTA=0.0001 5
Now the output that I got got this time was something like this:
.
.
.
*** DETSP| SIZE OF THE PROGRAM IS 2076/ 72740 kBYTES ***
!!! 2 OPERATION NOT CORRECT!!!
!!! 3 OPERATION NOT CORRECT!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! CHKSYM| NUMBER OF SYMMETRY OPERATIONS HAS BEEN CHANGED !!
!! FROM 4 TO 2 !!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
THE CRYSTAL SYSTEM IS MONOCLINIC WITH 2 OPERATIONS
THE SPACE GROUP OF THE CRYSTAL IS SYMMORPHIC
NUMBER OF PRIMITIVE CELL: 1
THE POINT GROUP OF THE CRYSTAL CONTAINS THE INVERSION
SYMMETRY UNIQUE (INEQUIVALENT) ATOMS: 30
INDEXES: 1 2 3 4 5 9 10 11 15 16
19 20 23 24 27 28 31 32 33 34 35
36 37 45 46 47 48 49 50 51 REQUIRED PRECISION
FOR SYMMETRY: 1.00E-04
NUMBER OF IRREDUCIBLE REPRESENTATIONS: 2
DIMENSION OF IR: 1 1
.
.
.
SYMMETRY: MONOCLINIC
POINT GROUP : SUBGROUP OF 2/m(c2h) GROUP ORDER= 2
LATTICE CONSTANT(a.u.): 18.73078
CELL DIMENSION: 18.7308 0.5270 1.0480 -0.1012 0.0000 0.0000
VOLUME(OMEGA IN BOHR^3): 3610.81021
LATTICE VECTOR A1(BOHR): 18.7308 0.0000 0.0000
LATTICE VECTOR A2(BOHR): -0.9988 9.8205 0.0000
LATTICE VECTOR A3(BOHR): 0.0000 0.0000 19.6299
RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0534 0.0054 0.0000
RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.1018 0.0000
RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0509
Though I did not get the point group symmetry, the next part of the
output shows POINT GROUP as 2/m(c2h) and that is what we are aiming to
get. I am not clear exactly what is happening here though.
Your other suggestion was:
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. do you really
want to enforce that symmetry? most calculations will run fine without.
Following your suggestion, I did the calculations by turning off the
symmetry and then looked at the structure with multiple cells, using
VMD. What I observed was that the molecules looked same in both the
cases and there was no difference in the arrangement of atoms (and
molecules) in both the cases due to POINT GROUP SYMMETRY.
My aim here is to do geometry and cell optimization (using TSDC option
so as to keep the same shape). I would like to know if having a POINT
GROUP SYMMETRY will have some difference in the results. The geometry
of the molecule that I have put in the cell is already optimized as a
single isolated molecule and I am expecting small change in the
geometry after putting it in the cell with periodic boundary
conditions. With this in mind I don't know if the inclusion of POINT
GROUP SYMMETRY should cause any difference in my final results. May I
know your opinion on this?
Thanks a ton!
Best Regards
Samir
Quoting Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>:
>
> 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> _______________________________________________
> SM> CPMD-list mailing list
> 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.
>
>
>
>
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