NMR NICS

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Hello NWCHEM-users,

I want to calculate the chemical shift on benzene [color=black]inside the ring,[/color,] not for special Atoms like, Carbon or Hydrogen!
Is this possible and how can I do that ?

thank you in advance

greetings
Alfred

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Something like the input deck below would do it. This is a QA test case in our development branch.

Bert




echo

start benzene_nics2

title "benzene nics2"

symmetry c1
C 0.98348719 0.98348719 0.00000000
C -1.34346849 0.35998130 0.00000000
C 0.35998130 -1.34346849 0.00000000
C -0.98348719 -0.98348719 0.00000000
C 1.34346849 -0.35998130 0.00000000
C -0.35998130 1.34346849 0.00000000
H 1.74853940 1.74853940 0.00000000
H -2.38854924 0.64000984 0.00000000
H 0.64000984 -2.38854924 0.00000000
H -1.74853940 -1.74853940 0.00000000
H 2.38854924 -0.64000984 0.00000000
H -0.64000984 2.38854924 0.00000000
bqH 0.00000000 0.0000000 0.00000000
end

basis "ao basis" spherical
c library 6-31g*
h library 6-31g*
bqH library H 6-31g*
end

dft
xc b3lyp
end

property
shielding 1 13
end

task dft property


Quote:Clusterix Sep 27th 10:53 am
Hello NWCHEM-users,

I want to calculate the chemical shift on benzene [color=black]inside the ring,[/color,] not for special Atoms like, Carbon or Hydrogen!
Is this possible and how can I do that ?

thank you in advance

greetings
Alfred
Edited On 12:30:06 PM PDT - Fri, Sep 28th 2012 by Bert

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NICS revised
Hello Bert,

thank you for your reply and your input-example! I had the idea, that is has something to do with Bq, but the meaning of Bq is not still clear to me! I Ususally I use X, as a ghost atom for generating z-matrices, but what is the difference between Bq and X ?
Does your input also works for other symmetries than C1 or should it always be C1 !?


greetings

and kindly regards

Alfred

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NICS again
Hello Bert,

Sorry to ask you again, but I have tried as you suggested me, however the program runs to a certain point and then it fails--> attached files
Moreover what I noticed, was when I used
mpirun -np 2 ./nwchem file.nw > file.nwo & it runs and crashes later
but with
mpirun -np 1 ./nwchem file.nw > file.nwo & it crashes immediately

Compiling nwchem-6.1.1 with openmpi-1.6.1 and with the newest blas library intel-mkl runs fine.
It seems there is a problem with bq; without bq, the program finished correctly!
I'm not sure what goes wrong!

Greetings
Alfred

P.S.: input & output


.......................... input
echo

start benzene_nics2

title "benzene nics2"

geometry
symmetry C1
 C   0.99   0.98  0.0 
........
bqH   0.0    0.0   0.0
end
basis "ao basis" spherical
c library 6-31g*
h library 6-31g*
bqH library H 6-31g*
end

dft
xc b3lyp
end
property
shielding 1  13
end
task dft property




............ output


         Chemical Shielding Tensors (GIAO, in ppm)
-----------------------------------------

                               NWChem CPHF Module
------------------


 scftype          =     RHF 
nclosed = 21
nopen = 0
variables = 1617
# of vectors = 3
tolerance = 0.10D-03
level shift = 0.00D+00
max iterations = 50
max subspace = 30


Integral file          = ./benzene_nics2.aoints.0
Record size in doubles = 65536 No. of integs per rec = 43688
Max. records in memory = 185 Max. records in file = 18347
No. of bits per label = 8 No. of bits per value = 64


#quartets = 7.491D+05 #integrals = 6.061D+06 #direct =  0.0% #cached =100.0%


File balance: exchanges= 1 moved= 4 time= 0.0

SCF residual:   7.90565231570597703E-005


Iterative solution of linear equations
 No. of variables     1617
No. of equations 3
Maximum subspace 30
Iterations 50
Convergence 1.0D-04
Start time 120.4


  iter   nsub   residual    time
---- ------ -------- ---------
1 3 5.56D-01 135.7
2 6 9.42D-03 150.5
3 9 8.53D-04 165.7
4 12 2.99D-05 181.9

Parallel integral file used     140 records with       0 large values

hnd_giaox: geom_tag_to_element failed        0
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
0:
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error related to the specified geometry
------------------------------------------------------------------------
For more information see the NWChem manual at http://www.nwchem-sw.org/index.php/NWChem_Documentation


For further details see manual section:                                                                                                                                                                                                                                                                
1:1:hnd_giaox: geom_tag_to_element failed:: 0
(rank:1 hostname:nidorix pid:6965):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/armci.c:ARMCI_Error():208 cond:0
hnd_giaox: geom_tag_to_element failed        0
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
36: task dft property
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error related to the specified geometry

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Hi Alfred,

This is a few feature/capability that was implemented in our current development version, and is not working for 6.1.1. You can get the August version of the NWChem development version on our web site.

Bert


Quote:Clusterix Sep 30th 10:42 am
Hello Bert,

Sorry to ask you again, but I have tried as you suggested me, however the program runs to a certain point and then it fails--> attached files
Moreover what I noticed, was when I used
mpirun -np 2 ./nwchem file.nw > file.nwo & it runs and crashes later
but with
mpirun -np 1 ./nwchem file.nw > file.nwo & it crashes immediately

Compiling nwchem-6.1.1 with openmpi-1.6.1 and with the newest blas library intel-mkl runs fine.
It seems there is a problem with bq; without bq, the program finished correctly!
I'm not sure what goes wrong!

Greetings
Alfred

P.S.: input & output


.......................... input
echo

start benzene_nics2

title "benzene nics2"

geometry
symmetry C1
 C   0.99   0.98  0.0 
........
bqH   0.0    0.0   0.0
end
basis "ao basis" spherical
c library 6-31g*
h library 6-31g*
bqH library H 6-31g*
end

dft
xc b3lyp
end
property
shielding 1  13
end
task dft property




............ output


         Chemical Shielding Tensors (GIAO, in ppm)
-----------------------------------------

                               NWChem CPHF Module
------------------


 scftype          =     RHF 
nclosed = 21
nopen = 0
variables = 1617
# of vectors = 3
tolerance = 0.10D-03
level shift = 0.00D+00
max iterations = 50
max subspace = 30


Integral file          = ./benzene_nics2.aoints.0
Record size in doubles = 65536 No. of integs per rec = 43688
Max. records in memory = 185 Max. records in file = 18347
No. of bits per label = 8 No. of bits per value = 64


#quartets = 7.491D+05 #integrals = 6.061D+06 #direct =  0.0% #cached =100.0%


File balance: exchanges= 1 moved= 4 time= 0.0

SCF residual:   7.90565231570597703E-005


Iterative solution of linear equations
 No. of variables     1617
No. of equations 3
Maximum subspace 30
Iterations 50
Convergence 1.0D-04
Start time 120.4


  iter   nsub   residual    time
---- ------ -------- ---------
1 3 5.56D-01 135.7
2 6 9.42D-03 150.5
3 9 8.53D-04 165.7
4 12 2.99D-05 181.9

Parallel integral file used     140 records with       0 large values

hnd_giaox: geom_tag_to_element failed        0
------------------------------------------------------------------------
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
0:
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error related to the specified geometry
------------------------------------------------------------------------
For more information see the NWChem manual at http://www.nwchem-sw.org/index.php/NWChem_Documentation


For further details see manual section:                                                                                                                                                                                                                                                                
1:1:hnd_giaox: geom_tag_to_element failed:: 0
(rank:1 hostname:nidorix pid:6965):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/armci.c:ARMCI_Error():208 cond:0
hnd_giaox: geom_tag_to_element failed        0
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
36: task dft property
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error related to the specified geometry[/quote]


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