segmentation fault while reading nwchem output

From NWChem

Viewed 3010 times, With a total of 5 Posts
Jump to: navigation, search

Clicked A Few Times
Threads 4
Posts 5
Dear Ecce developers and users,
while attempting to read a specific nwchem output,
eviewer aborts with segmentation fault.
You can find the output here:
http://puccini.chimica.uniba.it/sample_code/h2o_ecce.out
Edited On 10:26:43 AM PDT - Fri, Apr 12th 2013 by Edoapra

Gets Around
Threads 16
Posts 115
I'm not a developer, but from running your input file it seems to be a combination of zcoord and your use of 'Oxygen' instead of 'O' in the geometry section e.g.

Your input was:
start
memory 300 mb
scratch_dir /scratch
ecce_print h2o_ecce.out
echo

geometry
Oxygen  0  0  0
H  0.7  0  0.3 
H -0.7  0  0.3 
  zcoord
    angle 2 1 3 120.0 constant
  end 
end

basis
  h  library  pc-1
  o  library  pc-1
end

scf
thresh 1.0e-6
end

dft
  xc b3lyp
end

driver
  xyz 
end

task dft optimize

which leads to an ecce.out that causes segfaults, whereas
start
memory 300 mb
scratch_dir /scratch
ecce_print h2o_ecce.out
echo

geometry
O  0  0  0
H  0.7  0  0.3 
H -0.7  0  0.3 
  zcoord
    angle 2 1 3 120.0 constant
  end 
end

basis
  h  library  pc-1
  o  library  pc-1
end

scf
thresh 1.0e-6
end

dft
  xc b3lyp
end

driver
  xyz 
end

task dft optimize

works fine. Either the zcoord section or 'Oxygen' on their own are fine, but the combination isn't.
Edited On 12:13:52 AM PDT - Mon, Apr 15th 2013 by Ohlincha

Gets Around
Threads 2
Posts 82
I'm not sure why this is, but I don't have time to investigate it and the workaround looks reasonable to me. This would be one of many potential issues ECCE has with importing existing calculation output so hacking the output file a bit before doing an import isn't unusual. I do know that ECCE doesn't support Z matrix coordinates so that could be related. I'm guessing it just ignores that zcoord block, although not sure why the full element name would cause it to fail completely in combination with zcoord.

Gary

Just Got Here
Threads 1
Posts 3
How to link Molden or ECCE with NWchem ? I have tried many ways but, I cannot view my work.

Just Got Here
Threads 1
Posts 3
visualization
How can I view output file of NWchem with Molden or Gabedit? I have tried many, but I can't view anything. Thank you.

Gets Around
Threads 16
Posts 115
Auwalu,
You should make a separate post if you have a question.

To view output from nwchem in ECCE you need to use the ecce_print directive in your nwchem input: [1]. Even better, set up and launch the job via ecce. There are a lot of resources online that you can use to help you set up ECCE properly.

It's off-topic, but to view your output in GabEdit simply pipe the output to a file and open it. See e.g. [2]. Do make sure to patch nwchem if you want to do that though.
Edited On 3:57:20 AM PDT - Fri, May 17th 2013 by Ohlincha


Forum >> ECCE: Extensible Computational Chemistry Environment >> General ECCE Topics



Who's here now Members 0 Guests 1 Bots/Crawler 0


AWC's: 2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC