ABINIT Discussion Forums

Dear abinit users,
I am trying to calculate some properties of Eu2(MoO4)3, but it give me error as following. can you help me for correct input file. My input file is following.
thanks a lot.

ERROR:
chkinp: ERROR -
Atoms number 1 and 5 are located at the same point of the unit cell
(periodic images are taken into account).
Action: change the coordinate of one of these atoms in the input file.

#My input file:
# Eu2(MoO43_Monoclinic (space group:C2/c) : computation of the total energy
# Convergence with respect to the number of k points.

ndtset 25

#Definition of the k-point grids
kptopt 1 # Option for the automatic generation of k points, taking
# into account the symmetry
#nshiftk 4
#shiftk 0.5 0.5 0.5 # These shifts will be the same for all grids
#0.5 0.0 0.0
#0.0 0.5 0.0
#0.0 0.0 0.5

#ngkpt1 2 2 2 # Definition of the different grids
#ngkpt2 4 4 4
#ngkpt3 6 6 6
ngkpt4 8 8 8
ecut: 20 ecut+ 2

getwfk -1 # This is to speed up the calculation, by restarting
# from previous wavefunctions, transferred from the old
# to the new k-points.



#Definition of the unit cell
acell 14.29 21.68 21.575 # This is equivalent to 10.18 10.18 10.18

angdeg 90 109.3093 90
spgroup 15
brvltt -1

#Definition of the atom types
ntypat 3 # There is only one type of atom
znucl 63 42 8 # The keyword "znucl" refers to the atomic number of the
# possible type(s) of atom. The pseudopotential(s)
# mentioned in the "files" file must correspond
# to the type(s) of atom. Here, the only type is Silicon.


#Definition of the atoms
natom 68 # There are two atoms
typat 8*1 12*2 48*3 # They both are of type 1, that is, Silicon
xred # This keyword indicate that the location of the atoms
# will follow, one triplet of number for each atom

0.332560 0.377130 0.408920
0.667440 0.377130 0.091080
0.667440 0.622870 0.591080
0.332560 0.622870 0.908920
0.832560 0.877130 0.408920
0.167440 0.877130 0.091080
0.167440 0.122870 0.591080
0.832560 0.122870 0.908920
0.000000 0.129350 0.250000
0.000000 0.870650 0.750000
0.500000 0.629350 0.250000
0.500000 0.370650 0.750000
0.149180 0.388530 0.059420
0.850820 0.388530 0.440580
0.850820 0.611470 0.940580
0.149180 0.611470 0.559420
0.649180 0.888530 0.059420
0.350820 0.888530 0.440580
0.350820 0.111470 0.940580
0.649180 0.111470 0.559420
0.449300 0.208200 0.064200
0.550700 0.208200 0.435800
0.550700 0.791800 0.935800
0.449300 0.791800 0.564200
0.949300 0.708200 0.064200
0.050700 0.708200 0.435800
0.050700 0.291800 0.935800
0.949300 0.291800 0.564200
0.136300 0.211200 0.387200
0.863700 0.211200 0.112800
0.863700 0.788800 0.612800
0.136300 0.788800 0.887200
0.636300 0.711200 0.387200
0.363700 0.711200 0.112800
0.363700 0.288800 0.612800
0.636300 0.288800 0.887200
0.250300 0.313200 0.198200
0.749700 0.313200 0.301800
0.749700 0.686800 0.801800
0.250300 0.686800 0.698200
0.750300 0.813200 0.198200
0.249700 0.813200 0.301800
0.249700 0.186800 0.801800
0.750300 0.186800 0.698200
0.346300 0.461100 0.039200
0.653700 0.461100 0.460800
0.653700 0.538900 0.960800
0.346300 0.538900 0.539200
0.846300 0.961100 0.039200
0.153700 0.961100 0.460800
0.153700 0.038900 0.960800
0.846300 0.038900 0.539200
0.033300 0.475200 0.394200
0.966700 0.475200 0.105800
0.966700 0.524800 0.605800
0.033300 0.524800 0.894200
0.533300 0.975200 0.394200
0.466700 0.975200 0.105800
0.466700 0.024800 0.605800
0.533300 0.024800 0.894200
0.449300 0.208200 0.064200
0.550700 0.208200 0.435800
0.550700 0.791800 0.935800
0.449300 0.791800 0.564200
0.949300 0.708200 0.064200
0.050700 0.708200 0.435800
0.050700 0.291800 0.935800
0.949300 0.291800 0.564200


#Definition of the planewave basis set
#ecut 8.0 # Maximal kinetic energy cut-off, in Hartree

#Definition of the SCF procedure
nstep 1000 # Maximal number of SCF cycles
toldfe 1.0d-6 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of total energy
# differ by less than toldfe (in Hartree)
#diemac 12.0 # Although this is not mandatory, it is worth to
# precondition the SCF cycle. The model dielectric
# function used as the standard preconditioner
# is described in the "dielng" input variable section.
# Here, we follow the prescription for bulk silicon.

30 atoms in the cell ... down below are the cartesian (!) coordinates:

Eu 0.970612033 4.326812490 4.407173767
Eu -2.858723927 4.326812490 0.981623268
Eu -4.746835820 7.146187510 6.370420302
Eu -0.917499861 7.146187510 9.795970801
Mo -0.944055947 1.484032550 2.694398517
Mo -2.832167841 9.988967450 8.083195551
Mo 0.903701025 4.457604690 0.640404640
Mo -2.791812918 4.457604690 4.748392395
Mo -4.679924812 7.015395310 10.137189429
Mo -0.984410869 7.015395310 6.029201674
O -0.625821897 8.125178600 0.691921539
O -1.262289997 8.125178600 4.696875495
O -3.150401890 3.347821400 10.085672529
O -2.513933791 3.347821400 6.080718573
O -0.431466881 2.423097600 4.173084423
O -1.456645013 2.423097600 1.215712611
O -3.344756907 9.049902400 6.604509645
O -2.319578774 9.049902400 9.561881458
O 1.144296015 3.593343600 2.136119144
O -3.032407909 3.593343600 3.252677890
O -4.920519803 7.879656400 8.641474924
O -0.743815878 7.879656400 7.524916179
O 2.470657998 5.290200300 0.422481687
O -4.358769891 5.290200300 4.966315347
O -6.246881785 6.182799700 10.355112381
O 0.582546104 6.182799700 5.811278722
O -1.236776147 5.451969600 4.248527582
O -0.651335747 5.451969600 1.140269452
O -2.539447640 6.021030400 6.529066487
O -3.124888041 6.021030400 9.637324616

Kind regards,

Alain

Dear Alian,

First of all, thank you for your reply.

My srtucture has C2/c (No:15) space group and Z=4.

in unit cell of Eu2(MoO4)3, There are 2 Eu atoms, 3 Mo atoms and 12 O atoms. namely Eu2Mo3O12.
in this instance, When is Z=4, Should not Eu2(MoO4)3 has 68 atoms in unit cell.

I apologize for you. But I could not understand, How did you find 30 atoms in unit cell of Eu2(MoO4)3.

Can you explain how you find 30 atoms.

Dear Sevket,

If you look at the abinit output, you'll see error messages saying that you list in the xred section atomic positions that are in fact the same i.e. several coordinates are redundant (not because of symmetry). I removed the duplicates, reduced to a primitive cell and gave you those 30 unique positions. That's plain application of crystallography properties with zero understanding of chemistry. Now you can say that stoichiometry is wrong and atoms are missing but, if any, it's because they are absent from your list.

A way to check if the structure I provided is the one you expect is to run the following abinit input Display the resulting cif file with jmol or Avogadro, fill the unit cell and superpose with your own structure. Anything missing?

Kind regards,

Alain

Honorary member of Space Cadet Academy ... and polyoxometalates vet

Hi, I used the following procedure (I'm currently writing a tutorial for abinit for how to do this in general):

I installed two python packages on my machine, PyCifRW and cif2cell. Get them both from sourceforge. Then I downloaded a cif file for Eu2Mo3O12 (I'm a subscriber). I used cif2cell to generate abinit input from the cif file, and here's what I get. Notice that natom = 34; indeed with Z = 4, there are 68 atoms in the CONVENTIONAL unit cell, but in the PRIMITIVE unit cell, in this case, there are half as many (2 formula units instead of 4). There are always an integer multiple of the formula unit. The clue that this unit cell will have a smaller primitive cell than conventional cell is that the name begins with a letter other than P (P stands for primitive). C cells are body centered and have primitive cells half as big as the conventional cells.

#*************************************************************************************
#* Generated by cif2cell 1.0.8 2013-04-22 20:20 *
#* Data obtained from ICSD. Reference number : 153371 *
#* Eu2 (Mo3 O12) (Dieuropium trimolybdate(VI)) *
#* Boulahya, K. et al., European Journal of Inorganic Chemistry 2005, 967-970 (2005) *
#*************************************************************************************
# Structural parameters
acell 3*14.2887859599

rprim 0.500000000000000 -0.758368270006480 0.000000000000000
0.500000000000000 0.758368270006480 0.000000000000000
-0.503146153538979 0.000000000000000 1.436036710951808

natom 34
ntypat 3
typat 1 1 1 1 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
znucl 63 42 8
xred 0.955400000000000 0.709600000000000 0.408900000000000
0.290400000000000 0.044600000000000 0.091100000000000
0.044600000000000 0.290400000000000 0.591100000000000
0.709600000000000 0.955400000000000 0.908900000000000
0.870700000000000 0.129300000000000 0.250000000000000
0.129300000000000 0.870700000000000 0.750000000000000
0.760600000000000 0.537600000000000 0.059400000000000
0.462400000000000 0.239400000000000 0.440600000000000
0.239400000000000 0.462400000000000 0.940600000000000
0.537600000000000 0.760600000000000 0.559400000000000
0.127000000000000 0.219000000000000 0.214000000000000
0.781000000000000 0.873000000000000 0.286000000000000
0.873000000000000 0.781000000000000 0.786000000000000
0.219000000000000 0.127000000000000 0.714000000000000
0.925000000000000 0.347000000000000 0.387000000000000
0.653000000000000 0.075000000000000 0.113000000000000
0.075000000000000 0.653000000000000 0.613000000000000
0.347000000000000 0.925000000000000 0.887000000000000
0.937000000000000 0.563000000000000 0.198000000000000
0.437000000000000 0.063000000000000 0.302000000000000
0.063000000000000 0.437000000000000 0.802000000000000
0.563000000000000 0.937000000000000 0.698000000000000
0.885000000000000 0.807000000000000 0.039000000000000
0.193000000000000 0.115000000000000 0.461000000000000
0.115000000000000 0.193000000000000 0.961000000000000
0.807000000000000 0.885000000000000 0.539000000000000
0.558000000000000 0.508000000000000 0.394000000000000
0.492000000000000 0.442000000000000 0.106000000000000
0.442000000000000 0.492000000000000 0.606000000000000
0.508000000000000 0.558000000000000 0.894000000000000
0.241000000000000 0.657000000000000 0.064000000000000
0.343000000000000 0.759000000000000 0.436000000000000
0.759000000000000 0.343000000000000 0.936000000000000
0.657000000000000 0.241000000000000 0.564000000000000