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:
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[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.