lensfield2, testing

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Pablo Echenique

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Jun 1, 2011, 1:38:30 PM6/1/11
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Hi,
I am running lensfield2 in a folder with a lot of subfolders, and in each subfolder 144 gaussian logfiles called, say N.log, where N=1,...,144.
I am using the following lf file and it seems it works perfectly!

---------

; Build file taking all files **/*.log, and transforming all to **/*.cml


(source
    logfiles    **/*.log)  
;    cmlraw    **/*.raw.cml)

(build
    cmlraw      org.xmlcml.cml.converters.compchem.gaussian.log.GaussianLog2XMLConverter/convert
; turns raw into XML
    :input      logfiles
    :output     **/*.raw.cml
    :depends    cml:jumbo-converters-compchem-gaussian:0.3-SNAPSHOT)

(build
    cmlfull      org.xmlcml.cml.converters.compchem.gaussian.log.GaussianLogXML2CompchemConverter/convert
    ; truns XML into compchem CML
    :input      cmlraw
    :output     **/*.cml
    :depends    cml:jumbo-converters-compchem-gaussian:0.3-SNAPSHOT)

-------

It creates the N.raw.cml files and the N.cml ones, each one with the appropriate names and in the approrpiate folders, and seemingly with the appropriate contents.
But, for each file, it gives the following error:

-------

[DEBUG] (cmlraw) writing heterolevel/MP2_3-21G_MP2_6-311ppG2df2pd/f-165_p-15.raw.cml
[DEBUG] (cmlraw) reading heterolevel/MP2_3-21G_MP2_6-311ppG2df2pd/f-165_p-165.log
PREVIOUS...1
[org.xmlcml.cml.element.CMLList: list]
ERROR org.xmlcml.cml.converters.text.Template - Null line (1)
java.lang.RuntimeException: java.lang.RuntimeException: addArrays (3)out of sync with atoms: 14 != 15
at org.xmlcml.cml.converters.text.TransformElement.createMolecule(TransformElement.java:1011)
at org.xmlcml.cml.converters.text.TransformElement.applyMarkup(TransformElement.java:394)
at org.xmlcml.cml.converters.text.TransformElement.applyMarkup(TransformElement.java:354)
at org.xmlcml.cml.converters.text.Template.applyMarkup(Template.java:361)
at org.xmlcml.cml.converters.text.TemplateListElement.applyMarkup(TemplateListElement.java:60)
at org.xmlcml.cml.converters.text.Template.applyMarkup(Template.java:361)
at org.xmlcml.cml.converters.text.TemplateProcessor.applyMarkup(TemplateProcessor.java:37)
at org.xmlcml.cml.converters.text.Text2XMLTemplateConverter.convertToXML(Text2XMLTemplateConverter.java:65)
at org.xmlcml.cml.converters.AbstractConverter.convert(AbstractConverter.java:374)
at sun.reflect.GeneratedMethodAccessor11.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.lensfield.process.ProcessRunner.runArgsTask(ProcessRunner.java:294)
at org.lensfield.process.ProcessRunner.runProcess(ProcessRunner.java:166)
at org.lensfield.Lensfield.run(Lensfield.java:655)
at org.lensfield.Lensfield.runKtoLStep(Lensfield.java:459)
at org.lensfield.Lensfield.processBuildStep(Lensfield.java:419)
at org.lensfield.Lensfield.build(Lensfield.java:357)
at org.lensfield.Lensfield.processBuildSteps(Lensfield.java:712)
at org.lensfield.Lensfield.build(Lensfield.java:128)
at org.lensfield.cli.LensfieldCli.run(LensfieldCli.java:87)
at org.lensfield.cli.LensfieldCli.main(LensfieldCli.java:69)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.lensfield.launcher.load.Loader.run(Loader.java:65)
at org.lensfield.launcher.load.Loader.main(Loader.java:94)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.lensfield.launcher.boot.Bootstrap.main(Bootstrap.java:52)
Caused by: java.lang.RuntimeException: addArrays (3)out of sync with atoms: 14 != 15
at org.xmlcml.cml.converters.text.TransformElement.addArrays(TransformElement.java:1896)
at org.xmlcml.cml.converters.text.TransformElement.createMolecule(TransformElement.java:1009)
... 32 more
ERROR org.xmlcml.cml.converters.text.TransformElement - Cannot parse/set date/duration: 0 days  0 hours  0 minutes 23.3 seconds. (format='DHMS'); java.lang.ClassCastException: org.joda.time.Duration cannot be cast to org.joda.time.DateTime
**/*.raw.cml <0>/<1>.raw.cml {*=f-165_p-165, **=heterolevel/MP2_3-21G_MP2_6-311ppG2df2pd/}
[DEBUG] (cmlraw) writing heterolevel/MP2_3-21G_MP2_6-311ppG2df2pd/f-165_p-165.raw.cml
[DEBUG] (cmlraw) reading heterolevel/MP2_3-21G_MP2_6-311ppG2df2pd/f-165_p-45.log
PREVIOUS...1

--------

Any idea?
Best,
  Pablo.

Peter Murray-Rust

unread,
Jun 1, 2011, 2:01:28 PM6/1/11
to quixot...@googlegroups.com, Sam Adams
On Wed, Jun 1, 2011 at 6:38 PM, Pablo Echenique <echen...@gmail.com> wrote:
Hi,
I am running lensfield2 in a folder with a lot of subfolders, and in each subfolder 144 gaussian logfiles called, say N.log, where N=1,...,144.
I am using the following lf file and it seems it works perfectly!

Good

---------

; Build file taking all files **/*.log, and transforming all to **/*.cml


(source
    logfiles    **/*.log)  
;    cmlraw    **/*.raw.cml)

(build
    cmlraw      org.xmlcml.cml.converters.compchem.gaussian.log.GaussianLog2XMLConverter/convert
; turns raw into XML
    :input      logfiles
    :output     **/*.raw.cml
    :depends    cml:jumbo-converters-compchem-gaussian:0.3-SNAPSHOT)

(build
    cmlfull      org.xmlcml.cml.converters.compchem.gaussian.log.GaussianLogXML2CompchemConverter/convert
    ; truns XML into compchem CML
    :input      cmlraw
    :output     **/*.cml
    :depends    cml:jumbo-converters-compchem-gaussian:0.3-SNAPSHOT)

Looks good. (You might use *.compchem.cml as you cannot easily separate *.cml from *.raw.cml

This is a misparse and I will get it to add a line into the output rather than throwing an error
Best,
  Pablo.




--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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