ABINIT Discussion Forums

Hello, Dear colleagues!
I want to calculate of elastic constants of MgSiO3 with Pbcn space group.
My telast_3.files is:
telast_3.in
telast_3.out
telast_2o_DS3_DDB
dummy_moldyn
dummy_GKK
dummy
dum
.....
However, anaddb writes follow in log file:
...........
-begin at tcpu 0.001 and twall 0.000 sec
inprep8 : open file telast_2o_DS3_DDB
inprep8 : nband(1)= 96
occ 0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
0.20000000000000D+01 0.20000000000000D+01 0.20000000000000D+01
instrng : 11 lines of input have been read
will read the inputs completely
read the inputs completely

================================================================================

-outvars9: echo values of input variables ----------------------

Flags :
elaflag 3
instrflag 1
piezoflag 3
Miscellaneous information :
chneut 1

================================================================================

read the DDB information and perform some checks

-begin at tcpu 0.026 and twall 0.025 sec

Unit cell volume ucvol= 2.9885975E+03 bohr^3
Angles (23,13,12)= 9.00000000E+01 9.00000000E+01 9.00000000E+01 degrees
symatm: atom number 1 is reached starting at atom
1 2 1 2 3 4 3 4
symatm: atom number 2 is reached starting at atom
2 1 2 1 4 3 4 3
symatm: atom number 3 is reached starting at atom
3 4 3 4 1 2 1 2
symatm: atom number 4 is reached starting at atom
4 3 4 3 2 1 2 1
symatm: atom number 5 is reached starting at atom
5 6 5 6 7 8 7 8
symatm: atom number 6 is reached starting at atom
6 5 6 5 8 7 8 7
symatm: atom number 7 is reached starting at atom
7 8 7 8 5 6 5 6
symatm: atom number 8 is reached starting at atom
8 7 8 7 6 5 6 5
symatm: atom number 9 is reached starting at atom
9 10 13 14 11 12 15 16
symatm: atom number 10 is reached starting at atom
10 9 14 13 12 11 16 15
symatm: atom number 11 is reached starting at atom
11 12 15 16 9 10 13 14
symatm: atom number 12 is reached starting at atom
12 11 16 15 10 9 14 13
symatm: atom number 13 is reached starting at atom
13 14 9 10 15 16 11 12
symatm: atom number 14 is reached starting at atom
14 13 10 9 16 15 12 11
symatm: atom number 15 is reached starting at atom
15 16 11 12 13 14 9 10
symatm: atom number 16 is reached starting at atom
16 15 12 11 14 13 10 9
symatm: atom number 17 is reached starting at atom
17 18 21 22 19 20 23 24
symatm: atom number 18 is reached starting at atom
18 17 22 21 20 19 24 23
symatm: atom number 19 is reached starting at atom
19 20 23 24 17 18 21 22
symatm: atom number 20 is reached starting at atom
20 19 24 23 18 17 22 21
symatm: atom number 21 is reached starting at atom
21 22 17 18 23 24 19 20
symatm: atom number 22 is reached starting at atom
22 21 18 17 24 23 20 19
symatm: atom number 23 is reached starting at atom
23 24 19 20 21 22 17 18
symatm: atom number 24 is reached starting at atom
24 23 20 19 22 21 18 17
symatm: atom number 25 is reached starting at atom
25 26 29 30 27 28 31 32
symatm: atom number 26 is reached starting at atom
26 25 30 29 28 27 32 31
symatm: atom number 27 is reached starting at atom
27 28 31 32 25 26 29 30
symatm: atom number 28 is reached starting at atom
28 27 32 31 26 25 30 29
symatm: atom number 29 is reached starting at atom
29 30 25 26 31 32 27 28
symatm: atom number 30 is reached starting at atom
30 29 26 25 32 31 28 27
symatm: atom number 31 is reached starting at atom
31 32 27 28 29 30 25 26
symatm: atom number 32 is reached starting at atom
32 31 28 27 30 29 26 25
symatm: atom number 33 is reached starting at atom
33 34 37 38 35 36 39 40
symatm: atom number 34 is reached starting at atom
34 33 38 37 36 35 40 39
symatm: atom number 35 is reached starting at atom
35 36 39 40 33 34 37 38
symatm: atom number 36 is reached starting at atom
36 35 40 39 34 33 38 37
symatm: atom number 37 is reached starting at atom
37 38 33 34 39 40 35 36
symatm: atom number 38 is reached starting at atom
38 37 34 33 40 39 36 35
symatm: atom number 39 is reached starting at atom
39 40 35 36 37 38 33 34
symatm: atom number 40 is reached starting at atom
40 39 36 35 38 37 34 33


rdddb9 : read 1 blocks from the input DDB
symq3 : found symmetry 1 preserves q
symq3 : found symmetry 1 + TimeReversal preserves q
symq3 : found symmetry 2 preserves q
symq3 : found symmetry 2 + TimeReversal preserves q
symq3 : found symmetry 3 preserves q
symq3 : found symmetry 3 + TimeReversal preserves q
symq3 : found symmetry 4 preserves q
symq3 : found symmetry 4 + TimeReversal preserves q
symq3 : found symmetry 5 preserves q
symq3 : found symmetry 5 + TimeReversal preserves q
symq3 : found symmetry 6 preserves q
symq3 : found symmetry 6 + TimeReversal preserves q
symq3 : found symmetry 7 preserves q
symq3 : found symmetry 7 + TimeReversal preserves q
symq3 : found symmetry 8 preserves q
symq3 : found symmetry 8 + TimeReversal preserves q
symq3 : able to use time-reversal symmetry.
(except for gamma, not yet able to use time-reversal symmetry)
Now the whole DDB is in central memory
gtblk9 : enter gtblk9
gtblk9 : found blok number 1 agree with specifications
gtblk9 : enter gtblk9
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 1 42 1 4217098
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 2 42 2 4217237
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 3 42 3 4217376
gtblk9 :
Unable to find block corresponding to the following specifications :
Type (rfmeth) = 1
ider qphon(3) qphnrm rfphon rfelfd rfstrs
1 0.00 0.00 0.00 0.00 1 2 0
2 0.00 0.00 0.00 0.00 1 2 0

================================================================================

Calculation of the internal-strain tensor

-begin at tcpu 0.067 and twall 0.066sec
anaddb : instrflag=1, so extract the internal strain constant from the 2DTE
gtblk9 : enter gtblk9
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 1 43 1 4417929
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 1 43 2 4418067
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 1 43 3 4418205
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 2 43 1 4417930
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 2 43 2 4418068
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 2 43 3 4418206
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 3 43 1 4417931
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 3 43 2 4418069
gtblk9 : COMMENT -
The blok 1 does not match the requirement
because it lacks the element with
idir1,ipert1,idir2,ipert2,index= 3 43 3 4418207
gtblk9 :
Unable to find block corresponding to the following specifications :
Type (rfmeth) = 1
ider qphon(3) qphnrm rfphon rfelfd rfstrs
1 0.00 0.00 0.00 0.00 0 0 3
2 0.00 0.00 0.00 0.00 0 0 3
forrtl: severe (174): SIGSEGV, segmentation fault occurred

Where is the mistake here?
--
Best regards,
Andrey Chibisov.
Numerical method of mathematical physics Laboratory
Computing Center of Far Eastern Branch of Russian Academy of Sciences.

2 possible problems:

1)
Unable to find block corresponding to the following specifications :
Type (rfmeth) = 1
ider qphon(3) qphnrm rfphon rfelfd rfstrs
1 0.00 0.00 0.00 0.00 0 0 3
2 0.00 0.00 0.00 0.00 0 0 3

indicates that you are missing strain perturbations.

2) the segfault is strange. Run anaddb using gdb or valgrind to see where the error appears.

3) you may just be missing a ddb in the mrgddb run. Check the DDB files you have produced (before merge) for the corresponding perturbations: see http://www.abinit.org/documentation/hel ... tml#rfstrs


matthieu

dear Dr Mathieu,
i have the same problem but with LiBH4 (pnma) and i don't know if the problem of Andrey Chibisov is solved. also I don't know exactly what you mean with "you are missing strain perturbations" ?
here you can found my input and output files.

i forget to say THANK YOU

hi,
my problem is solved. in fact, I just put rfstr3 = 3 (in the libh4.in)
thanks

hello,
i'm new user of abinit i'm traying to have propreties of BaSnO3, how to find varition of parameter mail versus cohesive energy??i have excuted t43.in file but the out file is not comleted, pleas ho can help me??
best re gards.

bouhadda wrote:hi,
my problem is solved. in fact, I just put rfstr3 = 3 (in the libh4.in)
thanks

correct! Same goes for Andrey Chibisov - you need the full set of elastic dfpt calculations to combine with phonons and ddk in anaddb.

Cheers

Matthieu