ABINIT Discussion Forums

Hi
I want to relax 2 of 98 atoms, so I should fix 96 atoms.
I have tested every way but It didn't work :
iatfix 96*1
or
iatfix 1 2 3 4 5 6 7 ......
now I'm confused and was wondering if someone can tell me
how I can fix 96 atom?!

best regards
fariba

Hello,

I guess you set natfix 96 ?
Then you have to specify which atoms you want to fix. If you want to fix all the atoms except the two last ones for example, you have to put
iatfix 1 2 3 4 5 6 7 ......... 93 94 95 96
Of course, you have to type the indices of all the atoms you want to fix !

David

Hi
thanks a lot for your sincerely attention!
yes,I let the two last atoms to fix but in this way:

iatfix 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
19 20 21 22 23 24 25 26 27 28 29 30 31 32 33
34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
49 50 51 52 53 54 55 56 57 58 59 60 61 62 63
64 65 66 67 68 69 70 71 72 73 74 75 76 77 78
79 80 81 82 83 84 85 86 87 88 89 90 91 92 93
94 95 96

is it true? or I should go at the end of the line?

best regards
fariba

Hello,

If you could post the error that you get in the log file (part of it, usually the end of the log file is enough), it would be easier to tell you what's wrong there.
Did you specify the natfix variable explicitely ? (indicates how many atoms are fixed, otherwise abinit considers natfix as 0 !)

David

Hello
I specified natfix as well, (natfix=96) and I got these :

WARNING - These should obey zval-nelect_occ=charge to better than 0.10E-10
Action : check input file for occ,wtk, and charge.
Note that wtk is NOT automatically normalized when occopt=2,
but IS automatically normalized otherwise.


memana : ERROR -
Test failed to allocate 839745.910 Mbytes
It is not worth to continue
Action : modify input variable to fit the available memory.
or increase limit on available memory.
leave_new : decision taken to exit ...symbrav : COMMENT -
The Bravais lattice determined from modified primitive
vectors, bravais(1)= 3, has a lower symmetry than before,
but is still more symmetric than the real one, iholohedry= 1
obtained by taking into account the atomic positions.



symbrav : COMMENT -
The Bravais lattice determined from modified primitive
vectors, bravais(1)= 3, has a lower symmetry than before,
but is still more symmetric than the real one, iholohedry= 1
obtained by taking into account the atomic positions.

I think it can't understand the fixed atoms and It is going to relax all the atoms !!!
I don't know, I did my best but nothing worked!!

Here is my input file:

acell 17.21657000 17.21657000 10.00000000 angstrom
angdeg 90 90 120
nsym 1
kptopt 1
wtk 1
ngkpt 15 24 9
nshiftk 1
shiftk 0.0 0.0 0.5
nband 394
occopt 1
getwfk -1
enunit 2
natom 98
ntypat 1
typat 98*1
znucl 6.0
xred
0.047619 0.095238 0.500000
........
........
0.047619 0.238095 0.500000 (I wrote hear the all xreds)
nstep 20
tolmxf 1.85d-7
tolwfr 1.0d-13
ionmov 2
ntime 10
natfix 96
iatfix 1 2 3 4 5 6........ 92 93 94 95 96
ecutsm 0.5 ev
dilatmx 1.05
intxc 0
ixc 11
iscf 3
iprcel 45
ecut 2.0d01

really sorry....
best regards

fariba

Hello,

It seems that your system is way too big. You are using a LOT of k-points, with a very big unit cell. You will definitely not be able to do your simulations with these parameters. Abinit tells you that you need 800 GB of memory for the wavefunction and does not go beyond (because it tried to allocate this amount of memory and could not do it). You should try to reduce the number of k points or the size of your supercell (maybe a lesser number of atoms if possible ?).

David

Dear David
thanks a lot.It is working now!!!!! I just corrected the ngkpt! that you said !!
thank you!! I didn't pay attention to it.
I never forget you.I wish the bests for you!! Thank you......

best regards
fariba