ABINIT Discussion Forums

Hi, everyone. i am a new user of abinit. i had a problem to set up the rprim for AlLa (Cmcm #63 space group). i got the rprim and atomic coordinates from its prototype CrB.(see the nrl.navy website). but when i changed the acell for AlLa calculation, the out file give me another structure (#11space group).


even if i fix
spgaxor 1
spgroup 63
spgorig 1
brvltt -1
angdeg 90 90 90
it reports error during the calculation.
symatm : ERROR -
Largest error (above) is so large that either input atomic coordinates (xred)
are wrong or space group symmetry data is wrong.
Action : correct your input file.
-P-0000
-P-0000 leave_new : decision taken to exit ...

could you please explain to me what happened?
is the atomic coordinates data from nrl.navy website not correct? how you build the crystal structure information normally? materials studio software?

thanks very much

Hi,
Could you provide your input file?


Emmanuel

Hi, Emmanuel,

thanks a lot for the reply,the following is my input file,
# dilatmx 1.1 # Maximum scaling allowed for lattice parameters
# ionmov 2 # Use BFGS algorithm
# ntime 50 # Maximum number of optimization steps
# optcell 0 # Fully optimize unit cell geometry, keeping symmetry
# tolmxf 5.0e-6 # Convergence limit for forces as above

#Starting approximation for the unit cell
acell 9.531 7.734 5.809 angstrom #this is a guess,
rprim 0.5 -0.5 0.0
0.5 0.5 0.0
0.0 0.0 1.0
#Definition of the atom types and atoms
ntypat 2
znucl 57 13
natom 2
typat 1 1 2 2

#Starting approximation for atomic positions in REDUCED coordinates
#based on ideal tetrahedral bond angles
xred -0.14600000 0.14600000 0.25000000
0.14600000 -0.14600000 -0.25000000
-0.44000000 0.44000000 0.25000000
0.44000000 -0.44000000 -0.25000000

#Definition of the plane wave basis set
# ndtset 1
ecut 25.0 # Maximum kinetic energy cutoff (Hartree)
# ecut+ 2
ecutsm 0.5 # Smoothing energy needed for lattice paramete
# optimization. This will be retained for
# consistency throughout.

#Definition of the k-point grid
ngkpt 12 12 12 # 4x4x4 Monkhorst-Pack grid
nshiftk 1 # Use one copy of grid only (default) n=4 for fcc 3 bcc,,,,check
shiftk 0.5 0.5 0.5 # This choice of origin for the k point grid for hexagonal please change for other structure
kptopt 1 # preserves the hexagonal symmetry of the grid,
occopt 7
tsmear 300 K # which would be broken by the default choice.

#Definition of the self-consistency procedure
iscf 7 # Pulay mixing algorithm 14 pour PAW (PSEUDO DE SIMON)
nstep 150 # Maxiumum number of SCF iterations
tolvrs 1.0d-10 # Strict tolerance on (squared) residual of the
ixc 11 # SCF potential needed for accurate forces and
# stresses in the structural optimization, and
# accurate wave functions in the RF calculations

the partial output file is:
DATASET 1 : space group P2_1/m (# 11); Bravais mP (primitive monocl.)
================================================================================
Values of the parameters that define the memory need for DATASET 1.
intxc = 0 ionmov = 0 iscf = 7 xclevel = 2
lmnmax = 3 lnmax = 3 mband = 4 mffmem = 1
P mgfft = 60 mkmem = 54 mpssoang= 4 mpw = 8665
mqgrid = 3001 natom = 2 nfft = 144000 nkpt = 432
nloalg = 4 nspden = 1 nspinor = 1 nsppol = 1
nsym = 4 n1xccc = 2501 ntypat = 2 occopt = 7
================================================================================
P This job should need less than 81.801 Mbytes of memory.
Rough estimation (10% accuracy) of disk space for files :
WF disk file : 228.474 Mbytes ; DEN or POT disk file : 1.101 Mbytes.
================================================================================

arras wrote:Hi,
Could you provide your input file?


Emmanuel

Hi,

here is another input file, which i am trying to use spgroup,
# dilatmx 1.1 # Maximum scaling allowed for lattice parameters
# ionmov 2 # Use BFGS algorithm
# ntime 50 # Maximum number of optimization steps
# optcell 0 # Fully optimize unit cell geometry, keeping symmetry
# tolmxf 5.0e-6 # Convergence limit for forces as above

#Starting approximation for the unit cell
acell 9.531 7.734 5.809 angstrom #this is a guess, with the c/a
spgaxor 1
spgroup 63
spgorig 1
brvltt -1
angdeg 90 90 90
# chkprim 0
#Definition of the atom types and atoms
ntypat 2
znucl 57 13
natom 2
natrd 2
typat 1 2

#Starting approximation for atomic positions in REDUCED coordinates
#based on ideal tetrahedral bond angles
xred -0.14600000 0.14600000 0.25000000
0.14600000 -0.14600000 -0.25000000
-0.44000000 0.44000000 0.25000000
0.44000000 -0.44000000 -0.25000000

#Definition of the plane wave basis set
ndtset 1
ecut: 15.0 # Maximum kinetic energy cutoff (Hartree)
ecut+ 2
ecutsm 0.5 # Smoothing energy needed for lattice paramete
# optimization. This will be retained for
# consistency throughout.

#Definition of the k-point grid
ngkpt 12 12 12 # 4x4x4 Monkhorst-Pack grid
nshiftk 1 # Use one copy of grid only (default) n=4 for fcc 3 bcc,,,,check
shiftk 0.5 0.5 0.5 # This choice of origin for the k point grid for hexagonal please change for other structure
kptopt 1 # preserves the hexagonal symmetry of the grid,
occopt 7
tsmear 300 K # which would be broken by the default choice.

#Definition of the self-consistency procedure
iscf 7 # Pulay mixing algorithm 14 pour PAW (PSEUDO DE SIMON)
nstep 150 # Maxiumum number of SCF iterations
tolvrs 1.0d-10 # Strict tolerance on (squared) residual of the
ixc 11 # SCF potential needed for accurate forces and
# stresses in the structural optimization, and
# accurate wave functions in the RF calculations

the log file tell me the error,

symatm : ERROR -
Largest error (above) is so large that either input atomic coordinates (xred)
are wrong or space group symmetry data is wrong.
Action : correct your input file.-P-0000
-P-0000 leave_new : decision taken to exit ...

thank you very much

jin

Hi, Emmanuel,

the LaAl lattice parameter: a=9.531 b=7.734 c= 5.809, space group: Cmcm (63) , prototype:CrB, Pearson Symbol: oC8.

i also have a question, the space group is given based on the conventional cell, right?
if so,the crystal structure of the primitive cell could change, and also the space group of the primitive cell might change, too. it is right?
if this is the case, how you can verify that you have the right input file?

sorry if i asked the dummy question!

arras wrote:Hi,
Could you provide your input file?


Emmanuel

Hi Jin,

There are 3 problems, one of which is not your fault.
First, there seem to be a problem on the nrl.navy website. Indeed, reduced coordinates should not bee :
-0.146 0.146 0.25
0.146 -0.146 -0.25
-0.440 0.440 0.25
0.440 -0.440 -0.25
but should be
0.146 0.146 0.25
-0.146 -0.146 -0.25
0.440 0.440 0.25
-0.440 -0.440 -0.25

Second, your unit cell is ill defined. Neither:

acell 9.531 7.734 5.809 angstrom #this is a guess,
rprim 0.5 -0.5 0.0
0.5 0.5 0.0
0.0 0.0 1.0

Nor

acell 9.531 7.734 5.809 angstrom #this is a guess, with the c/a
spgaxor 1
spgroup 63
spgorig 1
brvltt -1
angdeg 90 90 90

are good. You should use either:

acell 2*9.531 5.809 bohr
angdeg 90 90 41.4

wich is the simplest, Or

acell 3*10 angstrom
rprim
0.12725884 0.33681374 0.00000000
-0.12725884 0.33681374 0.00000000
0.00000000 0.00000000 0.34106412

which is taken directly from the nrl.navy website (thus it is the CrB lattice).

And third, you have natom 2 whereas it should be 4.

the first point is the case of the problem:

symatm : ERROR -
Largest error (above) is so large that either input atomic coordinates (xred)
are wrong or space group symmetry data is wrong.
Action : correct your input file.-P-0000
-P-0000 leave_new : decision taken to exit ...

The second one is at the root of your spacegroup problem. I find:

Symmetries : space group Cm c m (# 63); Bravais oC (1-face-center ortho.)

The third one didn't bother you yet.


Also, if you do not have enough precision on you digits (which should not be the case here...) you can also use the variable tolsym
http://www.abinit.org/documentation/hel ... tml#tolsym

Hope that helps.

Emmanuel

Hi, Emmanuel

thanks a lot for your detailed reply, i really appreciate it. i will try these methods immediately.

i always have problems seting rprim or angdeg.
you suggested either using

acell 2*9.531 5.809 bohr
angdeg 90 90 41.4

i would like to know how you set up angdeg, if possible. how you get "41.4"?

another solution you suggested is

acell 3*10 angstrom
rprim
0.12725884 0.33681374 0.00000000
-0.12725884 0.33681374 0.00000000
0.00000000 0.00000000 0.34106412

which is from nrl.navy website.

could you please tell me where you got the rprim from that website?
when i checked the website of CrB crystal strucutre,
it gives me the following information

Primitive vectors
a(1) = 1.48450000 -3.92900000 0.00000000
a(2) = 1.48450000 3.92900000 0.00000000
a(3) = 0.00000000 0.00000000 2.93200000


Volume = 34.20236933


Reciprocal vectors
b(1) = 0.33681374 -0.12725884 0.00000000
b(2) = 0.33681374 0.12725884 0.00000000
b(3) = 0.00000000 0.00000000 0.34106412


Basis Vectors:
Atom Lattice Coordinates Cartesian Coordinates

Cr -0.14600000 0.14600000 0.25000000 0.00000000 1.14726800 0.73300000
Cr 0.14600000 -0.14600000 -0.25000000 0.00000000 -1.14726800 -0.73300000
B -0.44000000 0.44000000 0.25000000 0.00000000 3.45752000 0.73300000
B 0.44000000 -0.44000000 -0.25000000 0.00000000 -3.45752000 -0.73300000

from
download the coordinates of the atoms in these pictures in XYZ format in http://cst-www.nrl.navy.mil/lattice/struk/b33.html.

so my question is how i got the rprim or angdeg information from that website from general point of view.

thanks very much, Emmanuel

jin

HI, Emmanuel

thank you very much, it solves my problem.but i have another two questions.from these two results, i can see that the Xred is always the same no matter what is the rprim. it is supposed to be the same? secondly, how i can calculate the lattice parameter from the results then?

i had the calculation results from two different sets you suggested (i corrected the natom and Xred).
first result,

acell 9.531 9.531 5.809 angstrom #this is a guess, with the c/a
angdeg 90 90 41.4

then the partial output is

DATASET 1 : space group Cm c m (# 63); Bravais oC (1-face-center ortho.)
================================================================================
Values of the parameters that define the memory need for DATASET 1.
intxc = 0 ionmov = 0 iscf = 7 xclevel = 2
lmnmax = 3 lnmax = 3 mband = 8 mffmem = 1
P mgfft = 64 mkmem = 32 mpssoang= 4 mpw = 6563
mqgrid = 3001 natom = 4 nfft = 163840 nkpt = 252
nloalg = 4 nspden = 1 nspinor = 1 nsppol = 1
nsym = 8 n1xccc = 2501 ntypat = 2 occopt = 7
================================================================================
P This job should need less than 82.302 Mbytes of memory.
Rough estimation (10% accuracy) of disk space for files :
WF disk file : 201.891 Mbytes ; DEN or POT disk file : 1.252 Mbytes.
================================================================================
-outvars: echo values of variables after computation --------
acell 1.8010979773E+01 1.8010979773E+01 1.0977419106E+01 Bohr
amu 1.38905500E+02 2.69815390E+01
ecut 1.50000000E+01 Hartree
ecutsm 5.00000000E-01 Hartree
etotal1 -8.5585569523E+00
fcart1 -5.7822746168E-03 -2.1849395041E-03 4.0461683971E-19
5.7822746168E-03 2.1849395041E-03 -4.0461683971E-19
4.5258103752E-03 1.7101612311E-03 -3.1669528213E-19
-4.5258103752E-03 -1.7101612311E-03 3.1669528213E-19
ixc 11
jdtset 1
…
occopt 7
rprim 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00
7.5011106963E-01 6.6131186532E-01 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 1.0000000000E+00
shiftk 5.00000000E-01 5.00000000E-01 5.00000000E-01
spgroup 63

…
xred 1.4600000000E-01 1.4600000000E-01 2.5000000000E-01
-1.4600000000E-01 -1.4600000000E-01 -2.5000000000E-01
4.4000000000E-01 4.4000000000E-01 2.5000000000E-01
-4.4000000000E-01 -4.4000000000E-01 -2.5000000000E-01

second result using: (CrB lattice parameter)

acell 3*10 angstrom
rprim 0.12725884 0.33681374 0.00000000
-0.12725884 0.33681374 0.00000000
0.00000000 0.00000000 0.34106412

output:

DATASET 1 : space group Cm c m (# 63); Bravais oC (1-face-center ortho.)
================================================================================
Values of the parameters that define the memory need for DATASET 1.
intxc = 0 ionmov = 0 iscf = 7 xclevel = 2
lmnmax = 3 lnmax = 3 mband = 8 mffmem = 1
P mgfft = 32 mkmem = 32 mpssoang= 4 mpw = 1198
mqgrid = 3001 natom = 4 nfft = 30720 nkpt = 252
nloalg = 4 nspden = 1 nspinor = 1 nsppol = 1
nsym = 8 n1xccc = 2501 ntypat = 2 occopt = 7
================================================================================
P This job should need less than 16.663 Mbytes of memory.
Rough estimation (10% accuracy) of disk space for files :
WF disk file : 36.855 Mbytes ; DEN or POT disk file : 0.236 Mbytes.
…

-outvars: echo values of variables after computation --------
acell 1.8897261329E+01 1.8897261329E+01 1.8897261329E+01 Bohr
amu 1.38905500E+02 2.69815390E+01
ecut 2.50000000E+01 Hartree
ecutsm 5.00000000E-01 Hartree
etotal1 -6.5897568743E+00
fcart1 0.0000000000E+00 1.8853945389E-01 0.0000000000E+00
0.0000000000E+00 -1.8853945389E-01 0.0000000000E+00
0.0000000000E+00 -1.5836746979E-01 0.0000000000E+00
0.0000000000E+00 1.5836746979E-01 0.0000000000E+00
ixc 11
…
occopt 7
rprim 1.2725884000E-01 3.3681374000E-01 0.0000000000E+00
-1.2725884000E-01 3.3681374000E-01 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 3.4106412000E-01
shiftk 5.00000000E-01 5.00000000E-01 5.00000000E-01
spgroup 63
…
xred 1.4600000000E-01 1.4600000000E-01 2.5000000000E-01
-1.4600000000E-01 -1.4600000000E-01 -2.5000000000E-01
4.4000000000E-01 4.4000000000E-01 2.5000000000E-01
-4.4000000000E-01 -4.4000000000E-01 -2.5000000000E-01

sorry, i am totally a newbie of abinit. would you please explain to me the two questions above, if possible?
i will appreciate it very very very much...

thank you,

jin

Hi,
Actually, it looks like I was too fast, and I took the reciprocal vectors instead of the Primitive vectors... My mistake.

Anyway, by looking at it correctly, there is a one to one correspondance between:
- Primitive vectors -> rprim.
- Lattice Coordinates -> xred
- Cartesian Coordinates -> xcart

So, for CrB, that gives :

rprim
1.48450000 -3.92900000 0.00000000
1.48450000 3.92900000 0.00000000
0.00000000 0.00000000 2.93200000

xred
-0.146 0.146 0.25
0.146 -0.146 -0.25
-0.440 0.440 0.25
0.440 -0.440 -0.25

And I withdraw my remark about the nrl.navy website...

The angdeg notation is extracted from the Primitive vectors. The variable description is pretty self explainatory: http://www.abinit.org/documentation/hel ... tml#angdeg

As for your question about results from abinit... I don't really get it... If you want to find the equilibrium lattice parameters, you can use the optcell variable, with a value of 2 (See : http://www.abinit.org/documentation/hel ... ml#optcell). But before you do anything, I strongly suggest you make a few tutorials:
http://www.abinit.org/documentation/hel ... 7/tutorial
It is time-consuming, but that really is the best way to learn...

Regards

Emmanuel

Hi, Emmanuel

thanks a lot for your patient help. i got the angdeg, and rprim.
put it clear, actually i have the problem with crystal structure. the calculations for CrB and LaAl with the same structure, we can use the same rprim, and same Xred. then how to set up acell? i tested that different acell give totally different space group,
CrB has lattice parameters a=2.96 A, b=7.85 A, C= 2.932 A.
while LaAl has lattice parameters a=9.531A, b=7.734, C= 5.809A

actually, i tried the calculation for CrB with
acell 2 2 1 Angstrom
rprim
1.48450000 -3.92900000 0.00000000
1.48450000 3.92900000 0.00000000
0.00000000 0.00000000 2.9320000
the calculation is right (output file gives me space group Cmcm). but when i tried to change acell into 6 2 2 for LaAl(keep the same rprim and Xred), the results gave me different space group. this bothers me a lot.
by the way, you suggested (for LaAl)

acell 2*9.531 5.809 Angstrom
angdeg 90 90 41.4

why set up acell like that? LaAl has lattice parameters a=9.531A, b=7.734, C= 5.809A,
why not acell 2*7.734 5.809 or acell 9.531 7.734 5.809? i know acell is NOT the length of the conventional orthogonal basis vectors, but the scaling factors of the primitive vectors.normally, i believe we try to set up the initial lattice parameters close to the experimental one to start the optcell optimization.

my impression is if we set up rprim differently, i guess the Xred for the atomic positions should be different. is it right?

all in all, thank you very much, and i have a lot homework to do to learn abinit.

regards,
jin

arras wrote:Hi,
Actually, it looks like I was too fast, and I took the reciprocal vectors instead of the Primitive vectors... My mistake.

Anyway, by looking at it correctly, there is a one to one correspondance between:
- Primitive vectors -> rprim.
- Lattice Coordinates -> xred
- Cartesian Coordinates -> xcart

So, for CrB, that gives :

rprim
1.48450000 -3.92900000 0.00000000
1.48450000 3.92900000 0.00000000
0.00000000 0.00000000 2.93200000

xred
-0.146 0.146 0.25
0.146 -0.146 -0.25
-0.440 0.440 0.25
0.440 -0.440 -0.25

And I withdraw my remark about the nrl.navy website...

The angdeg notation is extracted from the Primitive vectors. The variable description is pretty self explainatory: http://www.abinit.org/documentation/hel ... tml#angdeg

As for your question about results from abinit... I don't really get it... If you want to find the equilibrium lattice parameters, you can use the optcell variable, with a value of 2 (See : http://www.abinit.org/documentation/hel ... ml#optcell). But before you do anything, I strongly suggest you make a few tutorials:
http://www.abinit.org/documentation/hel ... 7/tutorial
It is time-consuming, but that really is the best way to learn...

Regards

Emmanuel

I think you don't undestand the shape of the unit cell.
The base of the cell is a rhombus, thus a=b. That is why I use the line:

acell 2*9.531 5.809 Angstrom

which is equivalent to

acell 9.531 9.531 5.809 Angstrom

You must have a=b in your input file, like

acell 2 2 1 Angstrom

Because when you use

acell 6 2 2 Angstrom

you break the symetry !

Moreover, I don't know where you take your data from (for CrB and LaAl), but they seem really odd.

Hi,

thanks for the reply.

i took the crystal structure from pauling file database for CrB and LaAl, according to the database, both of them are orthorhombic, not rhombohedral.
that is the root of my calculation problem.

Best regards,
jin

arras wrote:I think you don't undestand the shape of the unit cell.
The base of the cell is a rhombus, thus a=b. That is why I use the line:

acell 2*9.531 5.809 Angstrom

which is equivalent to

acell 9.531 9.531 5.809 Angstrom

You must have a=b in your input file, like

acell 2 2 1 Angstrom

Because when you use

acell 6 2 2 Angstrom

you break the symetry !

Moreover, I don't know where you take your data from (for CrB and LaAl), but they seem really odd.

Hi, i m new user of ABINIT How to start optimisation of a b c of ortho structure (SG62)

Dear dal,

You can do that easily. Just read the posts above yours and you will find a few different methods to optimize your cell.

Best regards,

Igor