NMR NICS

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3:53:18 AM PDT - Thu, Sep 27th 2012
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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12:29:14 PM PDT - Fri, Sep 28th 2012
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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Threads 4
Posts 9
1:40:34 AM PDT - Sat, Sep 29th 2012
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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Posts 9
3:42:09 AM PDT - Sun, Sep 30th 2012
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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1:38:00 PM PDT - Mon, Oct 1st 2012
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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