[CPMD-list] Problems optimizing monoclinic unit cell
Dr. Balasubramanian Sundaram
bala at jncasr.ac.in
Fri Sep 10 10:16:26 CEST 2004
Dear Ewald,
> Perhaps one further question on this matter is why to put the 'cos
> beta' value first (i.e. on position d)? Is there a specific reason for
> this choice?
I wouldn't know, as I am only an user of the code like you. My guess
would
be that it may be to remove redundant reading of data. If something is
not
necessary, why should it be read from the input? (in this instance, the
cosine of those cell angles that are 90 degrees).
Cheers,
Bala
> Thanks,
> Ewald.
>
> Dr. Balasubramanian Sundaram wrote:
>
> > Dear Ewald,
> > We have been doing geometry optimization (ion coordinates) in
> > a monoclinic cell, without problems. Our CPMD version 3.9.1.
> > I feel that the following lines in your input file may not be
> > correct.
> >
> >
> >
> >> CELL
> >> 5.0872 2.314338 1.073321 0.0 -0.374493314 0.0
> >>
> >>
> > In the new version (v. 3.9.1), in file "sysin.F", there are a few
> > lines
> > that
> > say:
> > ELSE IF (IBRAV.EQ.12) THEN
> > IF ((ABS(CELLDM(5)).GT.BOXEPS)
> > $ .OR.(ABS(CELLDM(6)).GT.BOXEPS)) THEN
> > WRITE(0,*) 'SUPERCELL IS NOT MONOCLINIC'
> > WRITE(0,'(A,A)') 'EXPECTED FORM:',
> > $ ' a b c d 0.0 0.0'
> > CELLOK=.FALSE.
> > ENDIF
> >
> > It appears that the correct way to put the cell info for you would
> > be:
> >
> >
> >
> >> CELL
> >> 5.0872 2.314338 1.073321 -0.374493314 0.0 0.0
> >>
> >>
> > The previous version (v. 3.7.2) did not have this check and error
> > msg.
> > This is probably a reason why the molecular conformation got messy.
> >
> > Best Wishes,
> > Bala
> >
> >
> >
> > Ewald Pauwels wrote:
> >
> >
> >> Dear all,
> >>
> >> Does anybody have any experience with applying CPMD on monoclinic
> >> crystals?
> >> The system I am studying contains four (organic) molecules in the
> >> unit
> >> cell. When I optimize these molecules (only the atomic coordinates
> >> - not
> >> the cell constants), I find that the unit cell no longer satisfies
> >> the
> >> original symmetry. I.e. all four molecules have a substantially
> >> different conformation!
> >>
> >> I suspect that I must be doing something wrong here. Below is my
> >> inputfile.
> >>
> >> Thanks in advance,
> >> Ewald.
> >>
> >> -------------------------------------------------------
> >> inputfile
> >> -------------------------------------------------------
> >> &CPMD
> >> RESTART LATEST GEOFILE WAVEFUNCTION
> >> OPTIMIZE GEOMETRY
> >> LSD
> >> ODIIS NO_RESET=50
> >> 10
> >> TIMESTEP
> >> 20
> >> PRINT
> >> 10
> >> STRUCTURE BONDS ANGLES
> >> &END
> >>
> >> &SYSTEM
> >> ANGSTROM
> >> SYMMETRY
> >> 12
> >> CELL
> >> 5.0872 2.314338 1.073321 0.0 -0.374493314 0.0
> >> CUTOFF
> >> 25.
> >> MULTIPLICITY
> >> 1
> >> &END
> >>
> >> &ATOMS
> >> *C_VDB_U BINARY NEWF
> >> LMAX=P
> >> 8
> >> 0.218182218417937 1.473520453 0.333090471110274
> >> 0.732546560623109 1.717103823 -1.08374897292691
> >> 1.30308357695184 7.360020453 2.1982999039374
> >> 0.788719234746671 7.603603823 3.61513934797459
> >> -0.218182218417937 -1.473520453 -0.333090471110274
> >> -0.732546560623109 -1.717103823 1.08374897292691
> >> 1.73944801378772 4.412979547 2.86448084615795
> >> 2.25381235599289 4.169396177 1.44764140212077
> >> *N_VDB_U BINARY NEWF
> >> LMAX=P
> >> 4
> >> 2.03113800324446 1.040509513 -1.31410549705625
> >> -0.509872207874679 6.927009513 3.84549587210393
> >> -2.03113800324446 -1.040509513 1.31410549705625
> >> 3.55240379861424 4.845990487 1.21728487799143
> >> *O_VDB_U BINARY NEWF
> >> LMAX=P
> >> 8
> >> 1.05333382374583 1.104201443 1.19695275049904
> >> -1.00750738194352 1.676251513 0.53944941448416
> >> 0.467931971623952 6.990701443 1.33443762454863
> >> 2.5287731773133 7.562751513 1.99194096056352
> >> -1.05333382374583 -1.104201443 -1.19695275049904
> >> 1.00750738194352 -1.676251513 -0.53944941448416
> >> 2.57459961911561 4.782298557 3.72834312554672
> >> 0.513758413426261 4.210248487 3.07083978953184
> >> *H_VDB_U BINARY NEWF
> >> LMAX=S
> >> 20
> >> 2.33817143317496 1.18130282 -2.29299415508719
> >> 2.75812420631155 1.37791192 -0.67745575495101
> >> 1.93653355901116 0.03473035 -1.14763114043162
> >> 0.875530385150063 2.77889892 -1.22357285168305
> >> 0.0131007466085907 1.35318862 -1.81758891709173
> >> -0.816905637805185 7.06780282 4.82438453013487
> >> -1.23685841094177 7.26441192 3.20884612999869
> >> -0.415267763641377 5.92123035 3.67902151547929
> >> 0.645735410219716 8.66539892 3.75496322673072
> >> 1.50816504876119 7.23968862 4.34897929213941
> >> -2.33817143317496 -1.18130282 2.29299415508719
> >> -2.75812420631155 -1.37791192 0.67745575495101
> >> -1.93653355901116 -0.03473035 1.14763114043162
> >> -0.875530385150063 -2.77889892 1.22357285168305
> >> -0.0131007466085907 -1.35318862 1.81758891709173
> >> 3.85943722854474 4.70519718 0.23839621996049
> >> 4.27939000168133 4.50858808 1.85393462009667
> >> 3.45779935438094 5.85176965 1.38375923461606
> >> 2.39679618051984 3.10760108 1.30781752336463
> >> 1.53436654197837 4.53331138 0.713801457955944
> >> &END
> >>
> >> &DFT
> >> LDA CORRELATION PZ
> >> FUNCTIONAL BP
> >> GC-CUTOFF
> >> 5.D-5
> >> &END
> >> ------------------------------------------------------------------
> >>
> >> --
> >> Ewald Pauwels
> >> Centre for Molecular Modelling
> >> Laboratory of Theoretical Physics
> >> Ghent University
> >> Proeftuinstraat 86
> >> B-9000 Gent
> >> Belgium
> >> ewald.pauwels at UGent.be
> >> +32 9 264 65 76
> >>
> >> _______________________________________________
> >> CPMD-list mailing list
> >> CPMD-list at cpmd.org
> >> http://cpmd.org/mailman/listinfo/cpmd-list
> >>
> >>
>
> --
> Ewald Pauwels
> Centre for Molecular Modelling
> Laboratory of Theoretical Physics
> Ghent University
> Proeftuinstraat 86
> B-9000 Gent
> Belgium
> ewald.pauwels at UGent.be
> +32 9 264 65 76
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