ABINIT Discussion Forums

Dear all,
There is a problem confused me recently. That is definition of unit cell. Sometimes, we will build a crystal by other software. Then we will write the atomic position, from the former one, in input file to define a crystal for abinit calculation conveniently. For example, GaPO4, abinit cannot read the atomic position from paper in which authors often give us 4 fractional coordinates, so I obtain the 18 atomic position from Material Studio. But the new problem appears. That is the input files
#Structural optimisation
chksymbreak 0
chkprim 0
acell 4.9080000000 4.9080000000 11.0500000000 Angstroms
angdeg 90 90 120
natom 18
znucl 8 15 31
ntypat 3
typat 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 3 3 3
xred 0.434000 0.316000 0.398000
0.409000 0.263000 0.882000
-0.316000 0.118000 0.731333
-0.263000 0.146000 1.215333
-0.118000 -0.434000 1.064667
-0.146000 -0.409000 1.548667
0.316000 0.434000 -0.398000
0.263000 0.409000 -0.882000
……（18 atomic position in total）
#Definition of the scf procedure
#******************************
iscf 7
nstep 300
ixc 1
#Definition of the plane wave basis
#************************************
ecut 100.0
ecutsm 14.0
dilatmx 1.05
ngkpt 4 4 2
nshiftk 1
shiftk 0.0 0.0 0.5

And the warning in out file is
The space group number is 5, C2，……

Then if I add some other variables as following，
Spgroup 152
brvltt -1
……
The warning in log file is
Symatm.F90:163:WARNING
Trouble finding symmetrically equivalent atoms
Applying inv of symm number 2 to atom number 1 of typat 1
gives tratom =-3.1600E-01 1.1800E-01 7.3133E-01
this is further away from every atom in crystal than the allowed tolerance.
The inverse symmetry matrix is 0 1 0
-1 -1 0
0 0 1
And the nonsymmorphic transl. tnons =0.0000000 0.0000000 -0.3333333
The nearest caardinate differs by 0.000E+00 -2.776E-17 3.333E-07
for indsym(nearest atom )= 3

sometimes， I write a primitive cell in input file，when the code run I get P1 structure. Why ?
I really need your help. Hope for your reply, thanks!

Best wishes!

nannan

The symmetry finder in abinit is extremely good. If it says your input is spacegroup 5, then it almost certainly is, and changing the spacegroup is 154 in the input won't change the fact that the atoms are located in spacegroup 5. The place to look for errors or inconsistencies in the input itself. You might install the python package cif2cell and use it to interpret .cif files into abinit format. For example, here's the output I get for Ga(PO)4:

#*******************************************************************************************
#* Generated by cif2cell 1.0.10 2013-05-04 13:37 *
#* Data obtained from ICSD. Reference number : 30881 *
#* Ga (P O4) (Gallium phosphate(V)) *
#* Baumgartner, O. et al., Zeitschrift fuer Kristallographie (149,1979-) 168, 83-91 (1984) *
#*******************************************************************************************
# Structural parameters
acell 3*9.2615476161

rprim 0.866025403784439 -0.500000000000000 0.000000000000000
0.000000000000000 1.000000000000000 0.000000000000000
0.000000000000000 0.000000000000000 2.254233829830647

natom 18
ntypat 3
typat 1 1 1 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3
znucl 31 15 8
xred 0.456400000000000 0.000000000000000 0.333333333333333
0.543600000000000 0.543600000000000 0.000000000000000
0.000000000000000 0.456400000000000 0.666666666666667
0.456400000000000 0.000000000000000 0.833333333333333
0.543600000000000 0.543600000000000 0.500000000000000
0.000000000000000 0.456400000000000 0.166666666666667
0.409000000000000 0.317400000000000 0.392700000000000
0.591000000000000 0.908400000000000 0.940633333333333
0.682600000000000 0.091600000000000 0.726033333333333
0.908400000000000 0.591000000000000 0.059366666666667
0.317400000000000 0.409000000000000 0.607300000000000
0.091600000000000 0.682600000000000 0.273966666666667
0.409600000000000 0.273000000000000 0.872600000000000
0.590400000000000 0.863400000000000 0.460733333333333
0.727000000000000 0.136600000000000 0.205933333333333
0.863400000000000 0.590400000000000 0.539266666666667
0.273000000000000 0.409600000000000 0.127400000000000
0.136600000000000 0.727000000000000 0.794066666666667