Adding an nwchem file to be run by Jumbo
jens....@stfc.ac.uk
I'm trying to get jumbo to convert one of the NWChem files from our test set (http://quixote.wikispot.org/Three_Gaussian03_and_NWChem_6.0_single-points).
I'm starting with the file RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out and have copied it into the directory:
jumbo-converters-compchem/src/test/resources/compchem/nwchem/log/in
when I run "mvn clean test", the output file ends up in:
jumbo-converters-compchem/target/test-classes/compchem/nwchem/log/in
but nothing else happens.
What other steps do I need to do to get the file converted to xml?
Thanks,
Jens
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Peter Murray-Rust
Hi Peter,
I'm trying to get jumbo to convert one of the NWChem files from our test set (http://quixote.wikispot.org/Three_Gaussian03_and_NWChem_6.0_single-points).
I'm starting with the file RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out and have copied it into the directory:
I am hacking through the new version of the parser (I have forked the code) and will suggest we move to it next week.
Meanwhile continue with the version you have
jumbo-converters-compchem/src/test/resources/compchem/nwchem/log/in
Correct
when I run "mvn clean test", the output file ends up in:
jumbo-converters-compchem/target/test-classes/compchem/nwchem/log/in
By output you mean RHF_6-31Gdp_sp_HCO-L-Ala-NH2.xml?
This should be output under target/test/compchem/nwchem/log/out/RHF_6-31Gdp_sp_HCO-L-Ala-NH2.xml
copy this to:
jumbo-converters-compchem/src/test/resources/compchem/nwchem/log/ref/
and it will act as a regression test.
but nothing else happens.
What other steps do I need to do to get the file converted to xml?
This needs to be written up...
Thanks,
Jens
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Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
jens....@stfc.ac.uk
> From: peter.mu...@googlemail.com [peter.mu...@googlemail.com] on behalf of Peter Murray-Rust [pm...@cam.ac.uk]
> Sent: 08 March 2011 17:42
> To: quixote-...@googlegroups.com
> Cc: Thomas, Jens (STFC,DL,CSE)
> Subject: Re: [quixote-qcdb-dev] Adding an nwchem file to be run by Jumbo
>
>
>
> On Tue, Mar 8, 2011 at 5:03 PM, <jens....@stfc.ac.uk> wrote:
>
> Hi Peter,
>
> I'm trying to get jumbo to convert one of the NWChem files from our test set (http://quixote.wikispot.org/Three_Gaussian03_and_NWChem_6.0_single-points).
>
> I'm starting with the file RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out and have copied it into the directory:
>
>
> I am hacking through the new version of the parser (I have forked the code) and will suggest we move to it next week.
>
> Meanwhile continue with the version you have
>
>
> jumbo-converters-compchem/src/test/resources/compchem/nwchem/log/in
>
>
> Correct
>
>
> when I run "mvn clean test", the output file ends up in:
>
> jumbo-converters-compchem/target/test-classes/compchem/nwchem/log/in
>
>
> By output you mean RHF_6-31Gdp_sp_HCO-L-Ala-NH2.xml?
No - sorry I wasn't clear. My original file RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out gets copied into:
jumbo-converters-compchem/target/test-classes/compchem/nwchem/log/in
but nothing else happens.
Under target/test/compchem there is only a gaussian directory - nothing else.
Peter Murray-Rust
No - sorry I wasn't clear. My original file RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out gets copied into:
jumbo-converters-compchem/target/test-classes/compchem/nwchem/log/in
That is where it is meant to start..
I don't understand how it gets copied... from where? The tests are looking for files in the ../log/in directory
but nothing else happens.
Under target/test/compchem there is only a gaussian directory - nothing else.
Jens
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jens....@stfc.ac.uk
All I have done is copied the file RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out into the directory:
jumbo-converters-compchem/src/test/resources/compchem/nwchem/log/in
Whilst sat in jumbo-converters-compchem
I run "mvn clean" so there is no target directory.
I run "mvn test".
Afterwards there is an additional RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out file in:
jumbo-converters-compchem/target/test-classes/compchem/nwchem/log/in/
but no other file named RHF_6-31Gdp_sp_HCO-L-Ala-NH2 with any extension:
jmht@csevst1:/c/ccg/share/software/quixote/jumbo-converters/jumbo-converters-compchem> find . -name "RHF_6-31Gdp_sp_HCO-L-Ala-NH2*"
./src/test/resources/compchem/nwchem/log/in/RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out
./target/test-classes/compchem/nwchem/log/in/RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out
Jens
________________________________
From: peter.mu...@googlemail.com [peter.mu...@googlemail.com] on behalf of Peter Murray-Rust [pm...@cam.ac.uk]
Sent: 08 March 2011 18:00
To: quixote-...@googlegroups.com
Cc: Thomas, Jens (STFC,DL,CSE)
Subject: Re: [quixote-qcdb-dev] Adding an nwchem file to be run by Jumbo
jumbo-converters-compchem/target/test-classes/compchem/nwchem/log/in
but nothing else happens.
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Peter Murray-Rust
Hi Peter,
All I have done is copied the file RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out into the directory:
Whilst sat in jumbo-converters-compchem
jumbo-converters-compchem/src/test/resources/compchem/nwchem/log/in
I run "mvn clean" so there is no target directory.
I run "mvn test".
Afterwards there is an additional RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out file in:
Do you have someting like:
@Test
public void nwchem2XML() {
RegressionSuite.run("compchem/nwchem/log", "log", "out", converter);
}
if so it should be:
@Test
public void nwchem2XML() {
RegressionSuite.run("compchem/nwchem/log", "log", "xml", converter);
}
[It doesn't HAVE to be , but it avoids confusion]. If this isn't the case we need to skype
jens....@stfc.ac.uk
I've not touched the java code at all so I'm running off what was in the repository as of a couple of hours ago.
The file:
src/test/java/org/xmlcml/cml/converters/compchem/nwchem/log/ConverterTest.java
has:
@Test
public void nwchemOut2XML() {
RegressionSuite.run("compchem/nwchem/log", "out", "xml",
new NWChemLog2XMLConverter());
}
and the file:
src/test/java/org/xmlcml/cml/converters/compchem/nwchem/RegressionTest.java
has:
@Test
@Ignore
public void nwchemOut2XML() {
RegressionSuite.run("compchem/nwchem/log", "out", "xml",
new NWChemLog2XMLConverter());
}
Unfortunately I can't skype now as I don't have my laptop, but I'll bring it in tomorrow.
Best wishes,
Jens
________________________________
From: quixote-...@googlegroups.com [quixote-...@googlegroups.com] on behalf of Peter Murray-Rust [pm...@cam.ac.uk]
Sent: 08 March 2011 18:19
To: quixote-...@googlegroups.com
Cc: Thomas, Jens (STFC,DL,CSE)
Subject: Re: [quixote-qcdb-dev] Adding an nwchem file to be run by Jumbo
On Tue, Mar 8, 2011 at 6:12 PM, <jens....@stfc.ac.uk<mailto:jens....@stfc.ac.uk>> wrote:
Hi Peter,
All I have done is copied the file RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out into the directory:
jumbo-converters-compchem/src/test/resources/compchem/nwchem/log/in
Whilst sat in jumbo-converters-compchem
I run "mvn clean" so there is no target directory.
I run "mvn test".
Afterwards there is an additional RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out file in:
My guess is that this is your XML file and it should have been called *.xml.
Do you have someting like:
@Test
public void nwchem2XML() {
RegressionSuite.run("compchem/nwchem/log", "log", "out", converter);
}
if so it should be:
@Test
public void nwchem2XML() {
RegressionSuite.run("compchem/nwchem/log", "log", "xml", converter);
}
[It doesn't HAVE to be , but it avoids confusion]. If this isn't the case we need to skype
jumbo-converters-compchem/target/test-classes/compchem/nwchem/log/in/
but no other file named RHF_6-31Gdp_sp_HCO-L-Ala-NH2 with any extension:
jmht@csevst1:/c/ccg/share/software/quixote/jumbo-converters/jumbo-converters-compchem> find . -name "RHF_6-31Gdp_sp_HCO-L-Ala-NH2*"
./src/test/resources/compchem/nwchem/log/in/RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out
./target/test-classes/compchem/nwchem/log/in/RHF_6-31Gdp_sp_HCO-L-Ala-NH2.out
Jens
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