Discussion:
[Wien] Wien97 struct file execution
Naseem Hassan
2013-12-15 10:47:33 UTC
Permalink
Respected Senior Members,

I am trying to initialize Wien97 struct file generated by XCrySDen
program. I am trying to execute relaxed structures from SIESTA through
wien2k code.

In general what is the proper alteration in Wien97 structure file to
execute it without error ? Also Kindly guide how to avoid the fallowing
warnings ''xnn'' step of the Initialization

pecify nn-bondlength factor: (usually=2) [and optionally dlimit (about
1.d-5)]
DSTMAX: 23.0526088200000
iix,iiy,iiz 3 3 2

ATOM 1 C ATOM 6 C
RMT( 1)=1.28500 AND RMT( 6)=1.28500
SUMS TO 2.57000 LT. NN-DIST= 2.67007

ATOM 2 C ATOM 1 C
RMT( 2)=1.32720 AND RMT( 1)=1.28500
SUMS TO 2.61220 LT. NN-DIST= 2.75434

ATOM 3 C ATOM 4 C
RMT( 3)=1.27920 AND RMT( 4)=1.27920
SUMS TO 2.55840 LT. NN-DIST= 2.65833

ATOM 4 C ATOM 3 C
RMT( 4)=1.27920 AND RMT( 3)=1.27920
SUMS TO 2.55840 LT. NN-DIST= 2.65833

ATOM 5 C ATOM 12 C
RMT( 5)=1.32280 AND RMT( 12)=1.32200
SUMS TO 2.64480 LT. NN-DIST= 2.74554

ATOM 6 C ATOM 1 C
RMT( 6)=1.28500 AND RMT( 1)=1.28500
SUMS TO 2.57000 LT. NN-DIST= 2.67008

ATOM 7 C ATOM 4 C
RMT( 7)=1.28150 AND RMT( 4)=1.27920
SUMS TO 2.56070 LT. NN-DIST= 2.66301

ATOM 8 Si ATOM 7 C
RMT( 8)=1.52980 AND RMT( 7)=1.28150
SUMS TO 2.81130 LT. NN-DIST= 3.15951

ATOM 9 C ATOM 10 C
RMT( 9)=1.27720 AND RMT( 10)=1.27720
SUMS TO 2.55440 LT. NN-DIST= 2.65443

ATOM 10 C ATOM 9 C
RMT( 10)=1.27720 AND RMT( 9)=1.27720
SUMS TO 2.55440 LT. NN-DIST= 2.65443

ATOM 11 C ATOM 12 C
RMT( 11)=1.32200 AND RMT( 12)=1.32200
SUMS TO 2.64400 LT. NN-DIST= 2.74393

ATOM 12 C ATOM 11 C
RMT( 12)=1.32200 AND RMT( 11)=1.32200
SUMS TO 2.64400 LT. NN-DIST= 2.74393
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file

NN created a new 2.struct_nn file
NN created a new CASE.STRUCT_NN FILE
0.0u 0.0s 0:00.03 66.6% 0+0k 0+376io 0pf+0w

Thank You
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20131215/cd64fefc/attachment.htm>
Gavin Abo
2013-12-15 17:48:50 UTC
Permalink
You might need to use the script 100atomfix_lapw
[http://www.wien2k.at/reg_user/faq/99atoms.html].

To remove those "x nn" warnings, you can accept the use of the new
struct file that the initialization suggests
[http://zeus.theochem.tuwien.ac.at/pipermail/wien/2012-January/015966.html],
but it's a good idea to check afterwards that the structure looks
correct in xcrysden.
Post by Naseem Hassan
Respected Senior Members,
I am trying to initialize Wien97 struct file generated by XCrySDen
program. I am trying to execute relaxed structures from SIESTA
through wien2k code.
In general what is the proper alteration in Wien97 structure file to
execute it without error ? Also Kindly guide how to avoid the
fallowing warnings ''xnn'' step of the Initialization
pecify nn-bondlength factor: (usually=2) [and optionally dlimit (about
1.d-5)]
DSTMAX: 23.0526088200000
iix,iiy,iiz 3 3 2
ATOM 1 C ATOM 6 C
RMT( 1)=1.28500 AND RMT( 6)=1.28500
SUMS TO 2.57000 LT. NN-DIST= 2.67007
ATOM 2 C ATOM 1 C
RMT( 2)=1.32720 AND RMT( 1)=1.28500
SUMS TO 2.61220 LT. NN-DIST= 2.75434
ATOM 3 C ATOM 4 C
RMT( 3)=1.27920 AND RMT( 4)=1.27920
SUMS TO 2.55840 LT. NN-DIST= 2.65833
ATOM 4 C ATOM 3 C
RMT( 4)=1.27920 AND RMT( 3)=1.27920
SUMS TO 2.55840 LT. NN-DIST= 2.65833
ATOM 5 C ATOM 12 C
RMT( 5)=1.32280 AND RMT( 12)=1.32200
SUMS TO 2.64480 LT. NN-DIST= 2.74554
ATOM 6 C ATOM 1 C
RMT( 6)=1.28500 AND RMT( 1)=1.28500
SUMS TO 2.57000 LT. NN-DIST= 2.67008
ATOM 7 C ATOM 4 C
RMT( 7)=1.28150 AND RMT( 4)=1.27920
SUMS TO 2.56070 LT. NN-DIST= 2.66301
ATOM 8 Si ATOM 7 C
RMT( 8)=1.52980 AND RMT( 7)=1.28150
SUMS TO 2.81130 LT. NN-DIST= 3.15951
ATOM 9 C ATOM 10 C
RMT( 9)=1.27720 AND RMT( 10)=1.27720
SUMS TO 2.55440 LT. NN-DIST= 2.65443
ATOM 10 C ATOM 9 C
RMT( 10)=1.27720 AND RMT( 9)=1.27720
SUMS TO 2.55440 LT. NN-DIST= 2.65443
ATOM 11 C ATOM 12 C
RMT( 11)=1.32200 AND RMT( 12)=1.32200
SUMS TO 2.64400 LT. NN-DIST= 2.74393
ATOM 12 C ATOM 11 C
RMT( 12)=1.32200 AND RMT( 11)=1.32200
SUMS TO 2.64400 LT. NN-DIST= 2.74393
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
NN created a new 2.struct_nn file
NN created a new CASE.STRUCT_NN FILE
0.0u 0.0s 0:00.03 66.6% 0+0k 0+376io 0pf+0w
Thank You
Naseem Hassan
2013-12-16 10:37:28 UTC
Permalink
Respected Sir Gavin Abo


I selected new generated structure file suggested by you and Wien2k.

I face the new error in initializing step as fallow,

Commandline: *x symmetry *
Program input is: *""*

alpha(3) .lt. 89.8; reset to 90.1
ERROR: negative position in rstruc. Please report
0.000u 0.000s 0:00.04 0.0% 0+0k 1952+16io 6pf+0w

Kindly suggest remedy

Thank You
You might need to use the script 100atomfix_lapw [
http://www.wien2k.at/reg_user/faq/99atoms.html].
To remove those "x nn" warnings, you can accept the use of the new struct
file that the initialization suggests [http://zeus.theochem.tuwien.
ac.at/pipermail/wien/2012-January/015966.html], but it's a good idea to
check afterwards that the structure looks correct in xcrysden.
Post by Naseem Hassan
Respected Senior Members,
I am trying to initialize Wien97 struct file generated by XCrySDen
program. I am trying to execute relaxed structures from SIESTA through
wien2k code.
In general what is the proper alteration in Wien97 structure file to
execute it without error ? Also Kindly guide how to avoid the fallowing
warnings ''xnn'' step of the Initialization
pecify nn-bondlength factor: (usually=2) [and optionally dlimit (about
1.d-5)]
DSTMAX: 23.0526088200000
iix,iiy,iiz 3 3 2
ATOM 1 C ATOM 6 C
RMT( 1)=1.28500 AND RMT( 6)=1.28500
SUMS TO 2.57000 LT. NN-DIST= 2.67007
ATOM 2 C ATOM 1 C
RMT( 2)=1.32720 AND RMT( 1)=1.28500
SUMS TO 2.61220 LT. NN-DIST= 2.75434
ATOM 3 C ATOM 4 C
RMT( 3)=1.27920 AND RMT( 4)=1.27920
SUMS TO 2.55840 LT. NN-DIST= 2.65833
ATOM 4 C ATOM 3 C
RMT( 4)=1.27920 AND RMT( 3)=1.27920
SUMS TO 2.55840 LT. NN-DIST= 2.65833
ATOM 5 C ATOM 12 C
RMT( 5)=1.32280 AND RMT( 12)=1.32200
SUMS TO 2.64480 LT. NN-DIST= 2.74554
ATOM 6 C ATOM 1 C
RMT( 6)=1.28500 AND RMT( 1)=1.28500
SUMS TO 2.57000 LT. NN-DIST= 2.67008
ATOM 7 C ATOM 4 C
RMT( 7)=1.28150 AND RMT( 4)=1.27920
SUMS TO 2.56070 LT. NN-DIST= 2.66301
ATOM 8 Si ATOM 7 C
RMT( 8)=1.52980 AND RMT( 7)=1.28150
SUMS TO 2.81130 LT. NN-DIST= 3.15951
ATOM 9 C ATOM 10 C
RMT( 9)=1.27720 AND RMT( 10)=1.27720
SUMS TO 2.55440 LT. NN-DIST= 2.65443
ATOM 10 C ATOM 9 C
RMT( 10)=1.27720 AND RMT( 9)=1.27720
SUMS TO 2.55440 LT. NN-DIST= 2.65443
ATOM 11 C ATOM 12 C
RMT( 11)=1.32200 AND RMT( 12)=1.32200
SUMS TO 2.64400 LT. NN-DIST= 2.74393
ATOM 12 C ATOM 11 C
RMT( 12)=1.32200 AND RMT( 11)=1.32200
SUMS TO 2.64400 LT. NN-DIST= 2.74393
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
NN created a new 2.struct_nn file
NN created a new CASE.STRUCT_NN FILE
0.0u 0.0s 0:00.03 66.6% 0+0k 0+376io 0pf+0w
Thank You
_______________________________________________
Wien mailing list
Wien at zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at: http://www.mail-archive.com/
wien at zeus.theochem.tuwien.ac.at/index.html
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20131216/032363b4/attachment.htm>
Gavin Abo
2013-12-16 16:54:19 UTC
Permalink
You can try "x patchsymm"
[https://www.mail-archive.com/wien at zeus.theochem.tuwien.ac.at/msg07063.html].

However, if it doesn't fix the problem, then it probably means that your
software conversion of the structure from SIESTA to Wien2k failed. You
would then likely need to look at your struct file, identity what is
wrong with it, and fix it in StructGen by hand.
Post by Naseem Hassan
Respected Sir Gavin Abo
I selected new generated structure file suggested by you and Wien2k.
I face the new error in initializing step as fallow,
Commandline: *x symmetry *
Program input is: *""*
alpha(3) .lt. 89.8; reset to 90.1
ERROR: negative position in rstruc. Please report
0.000u 0.000s 0:00.04 0.0% 0+0k 1952+16io 6pf+0w
Kindly suggest remedy
Thank You
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20131216/cd99902f/attachment.htm>
Loading...