[CPMD-list] monoclinic cell
Juerg Hutter
hutter at pci.uzh.ch
Tue Jul 10 08:57:35 CEST 2007
Hi
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.
regards
Juerg Hutter
----------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Physical Chemistry Institute FAX : ++41 44 635 6838
University of Zurich E-mail: hutter at pci.uzh.ch
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
----------------------------------------------------------
On Mon, 9 Jul 2007, Samir H. Mushrif wrote:
> Hello CPMD Users,
> First of all I would like to thank Axel for replying
> to my previous mails. Continuing my work on the same topic, I am having
> difficulties getting the correct crystal information of the molecule in
> CPMD. I want to simulate Palladium (II) acetylacetonate [Pd(C5O2H7)2]
> which has following lattice structure:
>
> Monoclinic symmetry
> a=9.9119 A, b=5.2232 A, c=10.3877 A, and beta = 95.807 degrees
> P 21/n space group
> Z=2
>
> Relevant sections of the input file are as follows:
>
> &CPMD
> OPTIMIZE WAVEFUNCTION
> PCG MINIMIZE
> TIMESTEP
> 20
> CONVERGENCE ORBITALS
> 1.0d-6 CENTER MOLECULE OFF
> LSD
> MAXSTEP
> 1 &END
> .
> .
> .
>
> &SYSTEM
> ANGSTROM
> SYMMETRY
> 12 ***(Monoclinic cell)
> SCALE
> POINT GROUP MOLECULE
> CNH 2 *** (Corresponding Schoenflies notation for the Herman Maguin
> symbol P21/n, as per CPMD manual's instructions)
> CELL
> 9.9119 0.527 1.048 -0.10118 0.0 0.0 ***(Instead of giving
> angles as 0.0 -0.10118 0.0, they are given as -0.10118 0.0 0.0,
> based upon the CPMD mailing list discussions on monoclinic cell)
> .
> .
> &END
>
> &ATOMS
> *Pd-q18
> LMAX=D
> 2
> 0.0000 0.0000 0.0000
> 0.5000 0.5000 0.5000
>
> *C-q4
> LMAX=P
> 20
> -0.0069 0.3901 0.195
> 0.1949 0.3966 0.0698
> .
> .
>
> *O-q6
> LMAX=P
> 8
> 0.1691 0.2016 -0.0024
> -0.068 0.194 0.1444
> .
> .
>
> *H-q1
> LMAX=S
> 28
> 0.1505 0.6343 0.2119
> -0.1572 0.422 0.3156
> .
> .
> &END
>
> All the fractional coordinates are obtained from the Cambridge
> Structural Database information file, using MERCURY software. As per
> the suggestions from CPMD mailing list, two molecules are taken without
> splitting them, even though they are outside the unit cell. I have also
> tried splitting the molecules from surrounding unit cells and taking
> atoms that are inside the unit cell but the results are the same.
>
> Relevant section of the output file is as follows:
>
> LOCAL SPIN DENSITY APPROXIMATION
> PATH TO THE RESTART FILES: /home/grad/samir/lat_wav3/
> GRAM-SCHMIDT ORTHOGONALIZATION
> MAXIMUM NUMBER OF STEPS: 1 STEPS
> PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
> STORE INTERMEDIATE RESULTS EVERY 10001 STEPS
> NUMBER OF DISTINCT RESTART FILES: 1
> TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR FICTITIOUS
> ELECTRON MASS: 400.0000
> TIME STEP FOR ELECTRONS: 20.0000
> TIME STEP FOR IONS: 20.0000
> CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-06
> WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED CG
> THRESHOLD FOR THE HESSIAN IS 0.5000
> PERFORM QUADRATIC LINE SEARCH
> FULL ELECTRONIC GRADIENT IS USED SPLINE INTERPOLATION IN G-SPACE FOR
> PSEUDOPOTENTIAL FUNCTIONS
> NUMBER OF SPLINE POINTS: 5000
>
> EXCHANGE CORRELATION FUNCTIONALS LDA EXCHANGE:
> NONE
> LDA XC THROUGH PADE APPROXIMATION
> S.GOEDECKER, J.HUTTER, M.TETER PRB 54 1703 (1996)
>
> ***(I did not understand the following section)
>
> *** DETSP| SIZE OF THE PROGRAM IS 2128/ 72744 kBYTES ***
> !!! 2 OPERATION NOT CORRECT!!!
> !!! 3 OPERATION NOT CORRECT!!!
> !!! 4 OPERATION NOT CORRECT!!!
>
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !! CHKSYM| NUMBER OF SYMMETRY OPERATIONS HAS BEEN CHANGED !!
> !! FROM 4 TO 1 !!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>
> MOLECULAR SYSTEM WITH 1 OPERATIONS
>
> SYMMETRY UNIQUE (INEQUIVALENT) ATOMS: 58
> REQUIRED PRECISION FOR SYMMETRY: 1.00E-06
>
> NUMBER OF IRREDUCIBLE REPRESENTATIONS: 1
> DIMENSION OF IR: 1
> .
> .
> .
> ************************** SUPERCELL ***************************
> SYMMETRY: MONOCLINIC
> MOLECULAR POINT GROUP : CNH 2
> POINT GROUP : SUBGROUP OF CNH GROUP ORDER= 1
> 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
> REAL SPACE MESH: 150 80 160
> WAVEFUNCTION CUTOFF(RYDBERG): 150.00000
> DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 600.00000
> NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 56021
> NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 448063
> ****************************************************************
> I do not understand if the CPMD recognizes the group information given
> by me or it changes something that I am not understanding. I also tried
> using POINT GROUP AUTO option (with "splitted" molecules and
> "unsplitted" molecules) but it gives me 1 (c1) as the symmetry group
> which I don't think is correct.
>
> Can someone please help me in this aspect?
>
> Thanks a lot for your help and time.
>
> Best Regards
> Samir
> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
>
> Samir H. Mushrif
> Department of Chemical Engineering
> Mcgill University
> 3610 University Street
> Montreal, Quebec H3A2B2
> Canada
> Ph: (Lab)514-398-5170
> (Off)514-398-4169
>
>
>
>
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