[CPMD-list] monoclinic cell

[Samir H. Mushrif]

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