Problem linking NBO6 with G09.D01

Problem linking NBO6 with G09.D01

Postby giberger » Thu Jun 25, 2015 10:25 pm

Dear Eric,

I have a problem very similar to the one described by gost with G09W.
I use rev D of g09 (x64) and modified gaunbo accordingly (set INT = i8 and set BINDIR = /opt/nbo6/bin).
Here is the output:
***
Running external command "gaunbo6 R"
input file "/work/giberger/Gau-20505.EIn"
output file "/work/giberger/Gau-20505.EOu"
message file "/work/giberger/Gau-20505.EMs"
fchk file "/work/giberger/Gau-20505.EFC"
mat. el file "/work/giberger/Gau-20505.EUF"

Writing Wrt12E file "/work/giberger/Gau-20505.EUF"
Gaussian matrix elements Version 1 NLab= 7 Len12L=8 Len4L=8
Write GAUSSIAN SCALARS from file 501 offset 0 to matrix element file.
Write OVERLAP from file 514 offset 0 to matrix element file.
Write CORE HAMILTONIAN ALPHA from file 515 offset 0 to matrix element file.
Write CORE HAMILTONIAN BETA from file 515 offset 67161 to matrix element file.
Write KINETIC ENERGY from file 516 offset 0 to matrix element file.
Write ORTHOGONAL BASIS from file 685 offset 0 to matrix element file.
Write DIPOLE INTEGRALS from file 518 offset 0 to matrix element file.
Array DIP VEL INTEGRALS on file 572 does not exist.
Array R X DEL INTEGRALS on file 572 does not exist.
Write ALPHA ORBITAL ENERGIES from file 0 offset 0 to matrix element file.
Write ALPHA MO COEFFICIENTS from file 10524 offset 0 to matrix element file.
Write ALPHA DENSITY MATRIX from file 0 offset 0 to matrix element file.
Write ALPHA SCF DENSITY MATRIX from file 10528 offset 0 to matrix element file.
Write ALPHA FOCK MATRIX from file 10536 offset 0 to matrix element file.
No 2e integrals to process.
Read Unf file /work/giberger/Gau-20505.EUF:
Label Gaussian matrix elements IVers= 1 NLab= 7 Version=AM64L-G09RevD.01
Title Title Card Required
NAtoms= 39 NBasis= 366 NBsUse= 366 ICharg= 0 Multip= 1 NE= 142 Len12L=8 Len4L=8
Label GAUSSIAN SCALARS NI= 1 NR= 1 NTot= 7 LenBuf= 2000 N= 1000 1 1 1 1
Label OVERLAP NI= 0 NR= 1 NTot= 67161 LenBuf= 4000 N= -366 366 0 0 0
Label CORE HAMILTONIAN ALPHA NI= 0 NR= 1 NTot= 67161 LenBuf= 4000 N= -366 366 0 0 0
Label CORE HAMILTONIAN BETA NI= 0 NR= 1 NTot= 67161 LenBuf= 4000 N= -366 366 0 0 0
Label KINETIC ENERGY NI= 0 NR= 1 NTot= 67161 LenBuf= 4000 N= -366 366 0 0 0
Label ORTHOGONAL BASIS NI= 0 NR= 1 NTot= 133956 LenBuf= 4000 N= 366 366 0 0 0
Label DIPOLE INTEGRALS NI= 0 NR= 1 NTot= 201483 LenBuf= 4000 N= -366 366 3 0 0
Label ALPHA ORBITAL ENERGIES NI= 0 NR= 1 NTot= 366 LenBuf= 4000 N= 366 0 0 0 0
Label ALPHA MO COEFFICIENTS NI= 0 NR= 1 NTot= 133956 LenBuf= 4000 N= 366 366 0 0 0
Store file 524 Len= 133956.
Label ALPHA DENSITY MATRIX NI= 0 NR= 1 NTot= 67161 LenBuf= 4000 N= -366 366 0 0 0
Store file 528 Len= 67161.
Label ALPHA SCF DENSITY MATRIX NI= 0 NR= 1 NTot= 67161 LenBuf= 4000 N= -366 366 0 0 0
Label ALPHA FOCK MATRIX NI= 0 NR= 1 NTot= 67161 LenBuf= 4000 N= -366 366 0 0 0
Store file 536 Len= 67161.
External program failed.
Error termination via Lnk1e
***

Thanks for your help!
Gilles
giberger
 
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Re: Problem linking NBO6 with G09.D01

Postby ericg » Mon Jun 29, 2015 9:39 am

Gilles,

It appears to me that gaunbo6.bat doesn't ever get the NBO executables started. Is BINDIR set to /opt/nbo6/bin, or /opt/nbo6w/bin? If you have the Windows distribution of NBO6 (NBO6W) I suspect that you'll want the latter.

Eric
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Re: Problem linking NBO6 with G09.D01

Postby giberger » Fri Jul 03, 2015 1:36 am

Hi Eric,

I use the linux version of G09 and NBO6. BINDIR seems correctly set to point my nbo directory on the HPC cluster...

Best,
Gilles
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Re: Problem linking NBO6 with G09.D01

Postby ericg » Sun Jul 05, 2015 4:41 pm

Gilles,

Try changing the first line of gaunbo6 to

#!/bin/csh -fx

The "x" flag forces gaunbo6 to echo its commands immediately before they are executed.

Does this produce any extra output, just after the "No 2e integrals to process." line in the G09 output? If not, then G09 can't find gaunbo6 (its directory probably isn't in your path).

Eric
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Re: Problem linking NBO6 with G09.D01

Postby giberger » Thu Jul 30, 2015 6:35 am

Dear Eric,

Sorry for the very late answer, I just moved from Belgium for a postdoc position at MIT in Boston.
Moreover, they are upgrading the computing cluster and I was not able to access my account.

Here is the ouptut obtained after adding the x flag in gaunbo6:

Running external command "gaunbo6 R"
input file "/work/giberger/Gau-25693.EIn"
output file "/work/giberger/Gau-25693.EOu"
message file "/work/giberger/Gau-25693.EMs"
fchk file "/work/giberger/Gau-25693.EFC"
mat. el file "/work/giberger/Gau-25693.EUF"

Writing Wrt12E file "/work/giberger/Gau-25693.EUF"
Gaussian matrix elements Version 1 NLab= 7 Len12L=8 Len4L=8
Write GAUSSIAN SCALARS from file 501 offset 0 to matrix element file.
Write OVERLAP from file 514 offset 0 to matrix element file.
Write CORE HAMILTONIAN ALPHA from file 515 offset 0 to matrix element file.
Write CORE HAMILTONIAN BETA from file 515 offset 209628 to matrix element file.
Write KINETIC ENERGY from file 516 offset 0 to matrix element file.
Write ORTHOGONAL BASIS from file 685 offset 0 to matrix element file.
Write DIPOLE INTEGRALS from file 518 offset 0 to matrix element file.
Array DIP VEL INTEGRALS on file 572 does not exist.
Array R X DEL INTEGRALS on file 572 does not exist.
Write ALPHA ORBITAL ENERGIES from file 0 offset 0 to matrix element file.
Write ALPHA MO COEFFICIENTS from file 10524 offset 0 to matrix element file.
Write ALPHA DENSITY MATRIX from file 0 offset 0 to matrix element file.
Write ALPHA SCF DENSITY MATRIX from file 10528 offset 0 to matrix element file.
Write ALPHA FOCK MATRIX from file 10536 offset 0 to matrix element file.
No 2e integrals to process.
Read Unf file /work/giberger/Gau-25693.EUF:
Label Gaussian matrix elements IVers= 1 NLab= 7 Version=AM64L-G09RevD.01
Title Title Card Required
NAtoms= 37 NBasis= 647 NBsUse= 647 ICharg= 0 Multip= 1 NE= 130 Len12L=8 Len4L=8
Label GAUSSIAN SCALARS NI= 1 NR= 1 NTot= 7 LenBuf= 2000 N= 1000 1 1 1 1
Label OVERLAP NI= 0 NR= 1 NTot= 209628 LenBuf= 4000 N= -647 647 0 0 0
Label CORE HAMILTONIAN ALPHA NI= 0 NR= 1 NTot= 209628 LenBuf= 4000 N= -647 647 0 0 0
Label CORE HAMILTONIAN BETA NI= 0 NR= 1 NTot= 209628 LenBuf= 4000 N= -647 647 0 0 0
Label KINETIC ENERGY NI= 0 NR= 1 NTot= 209628 LenBuf= 4000 N= -647 647 0 0 0
Label ORTHOGONAL BASIS NI= 0 NR= 1 NTot= 418609 LenBuf= 4000 N= 647 647 0 0 0
Label DIPOLE INTEGRALS NI= 0 NR= 1 NTot= 628884 LenBuf= 4000 N= -647 647 3 0 0
Label ALPHA ORBITAL ENERGIES NI= 0 NR= 1 NTot= 647 LenBuf= 4000 N= 647 0 0 0 0
Label ALPHA MO COEFFICIENTS NI= 0 NR= 1 NTot= 418609 LenBuf= 4000 N= 647 647 0 0 0
Store file 524 Len= 418609.
Label ALPHA DENSITY MATRIX NI= 0 NR= 1 NTot= 209628 LenBuf= 4000 N= -647 647 0 0 0
Store file 528 Len= 209628.
Label ALPHA SCF DENSITY MATRIX NI= 0 NR= 1 NTot= 209628 LenBuf= 4000 N= -647 647 0 0 0
Label ALPHA FOCK MATRIX NI= 0 NR= 1 NTot= 209628 LenBuf= 4000 N= -647 647 0 0 0
Store file 536 Len= 209628.
External program failed.
Error termination via Lnk1e in /apps/brussel/magnycours/software/Gaussian/G09.D01/g09/l612.exe

Thanks
Gilles
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Re: Problem linking NBO6 with G09.D01

Postby ericg » Fri Jul 31, 2015 3:59 pm

Gilles,

gaunbo6 is apparently not in your path when you run G09 calculations. Otherwise you would see "Perform NBO analysis..." immediately after "No 2e integrals to process." in the output file.

Eric
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Re: Problem linking NBO6 with G09.D01

Postby giberger » Sun Aug 02, 2015 7:29 am

Dear Eric,

Bindir is set to my home directory where NBO6 is, so in gaunbo6: "set BINDIR=~/nbo6/bin"

Is something wrong there?

Thanks
Gilles
giberger
 
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Re: Problem linking NBO6 with G09.D01

Postby ericg » Sun Aug 02, 2015 10:47 am

I suspect that nbo6/bin isn't in your path so that G09 can't find the gaunbo6 script in the first place. Try adding:

set path = (~/nbo6/bin $path)

to the script that you use to execute G09 calculations.

Eric
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Re: Problem linking NBO6 with G09.D01

Postby Ubeiden » Thu Jun 09, 2016 11:37 am

Dear Eric,

I have the same problem of Giberger, so when you say "I suspect that nbo6/bin isn't in your path so that G09 can't find the gaunbo6 script in the first place. Try adding:

set path = (~/nbo6/bin $path)"

Where I have to put that path? In my .bashrc or where?

For example the paht of gaussian09 in linux is:

#GAUSSIAN09

export g09root=/home/gaussian
export GAUSS_SCRDIR=/home/scratch
. $g09root/g09/bsd/g09.profile

The path of nb06 is:

/home/nb06/bin

Note: I use the linux version of G09 and NBO6

Thank you,

Ubeiden
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Re: Problem linking NBO6 with G09.D01

Postby ericg » Fri Jun 10, 2016 4:22 am

Try modifying the PATH in your .bashrc (or in the bash script used to execute Gaussian calculations) as follows:

export PATH=/home/nbo6/bin:$PATH

Eric
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