Warning: a number of old tutorials which have not been checked recently but which may contain important information can be found at old - Tutorials and problems.
First of all
You will need to have the following components installed to use the Quixote infrastructure:
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![[WWW]](http://wikispot.org/wiki/eggheadbeta/img/sycamore-www.png)
Java JDK You can check if you have the jdk installed by running the following command at the command-line: javac -version
If that gives a command not found type error, you need to install the Java Development Kit.
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Maven for resolving Java dependencies. Check Maven for a basic tutorial and known problems.
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Mercurial for interacting with software repositories. Check Mercurial for a basic tutorial and known problems.
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Avogadro for visualizing the parsed output. Check Avogadro for instructions about how to install it.
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A source code editor (
jEdit, Emacs, etc.) or IDE (such as Eclipse).
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A command-line window where to enter commands (Windows, Mac and Linux, all have it). The commands may, alternatively, be run from the IDE.
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Some tricks of the trade
Conventions:
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The root folder for the cloned project code will be identified by <project-root>.
Useful commands:
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Use a name of your choice for the folder that will contain the cloned project code:
hg clone https://bitbucket.org/petermr/jumbo-converters myFolder
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Obtain source code changes from the original cloned repository; then compile, test and install everything again. Run from <project-root>:
hg pull hg update mvn clean install
At the moment, the developing environment is a bit unstable, so, if you happen to have some problems with the tutorials here, it is sometimes a good idea to "restart" your environment before trying anything out. Some possible "restarting steps" are:
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Delete your jumbo-converters folder and clone again:
hg clone https://bitbucket.org/petermr/jumbo-converters
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Issue. If running the examples seems to be using an old version of the project software, try the following (from <project-root>):
mvn clean install
and Delete the .m2 hidden folder in your home.
JUMBO-Converters basic compiling and setup
Clone the JUMBO-converters repository with the command (be patient; it may take several minutes):
hg clone https://bitbucket.org/petermr/jumbo-converters
A jumbo-converters directory (this will be the <project-root>) will be created in the directory where you issued the command to clone the repository. Enter into this directory with:
cd jumbo-converters
Run the command:
mvn clean install
This will download the java jar files required by the converters into your local maven repository (~/.m2/repository on unix), compile, test and install the code into your local maven repository. Everything will then be ready for using the JUMBO-Converters software.
Running JUMBO-Converters for NWChem and Gaussian
Gaussian
To use the Gaussian parser, cd into the <project-root>/jumbo-converters-compchem/jumbo-converters-compchem-gaussian directory.
cd jumbo-converters-compchem/jumbo-converters-compchem-gaussian
and run the converter. With the command:
mvn -e exec:java -Dexec.mainClass="org.xmlcml.cml.converters.compchem.gaussian.log.GaussianLog2CompchemConverter" -Dexec.args="logfile.out"
where logfile.out is the path to a gaussian logfile you wish to convert. This will then create a cml file named logfile.cml in the directory that the command was executed.
mvn exec:java takes care of setting up the Java environment (the classpath) so as to locate all compiled files needed for the execution. For this to happen, the previous command must be executed at the jumbo-converters-compchem-gaussian folder.
The argument -Dexec.mainClass states the Java class to execute (in this case, the Gaussian converter), and the -Dexec.args argument passes the space-separated strings in the argument as arguments to the main class.
NWChem
To use the NWChem converter, go into the jumbo-converters-compchem-nwchem folder:
cd jumbo-converters-compchem-nwchem
and run the converter (it will use a test file, and it will create as output the file ch3f_rot.xml:
mvn -e exec:java -Dexec.mainClass=org.xmlcml.cml.converters.compchem.nwchem.log.NWChemLogCompchemConverter
This will take one of the nwchem output files in jumbo-converters-compchem-nwchem/src/test/resources/compchem/nwchem/log/in/ and create cml file in the directory jumbo-converters-compchem-nwchem/test folder (for details of what happens, see the file src/main/java/org/xmlcml/cml/converters/compchem/nwchem/log/NWChemLog2CompchemConverter.java.
Status
Use this section to indicate if the tutorial works for you, if it doesn't, if you needed to do something differently, etc.:
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Pablo Echenique, success! MacOSX 10.6, 2011-03-22.
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This tutorial has been checked on 2011-05-10 (Linux, Java 1.6, JUMBO-Converters changeset 332:1db5c3ee0b74).
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Bert, mostly success! Windows7, 2011-05-11. When building the Quantum Expresso build fails.
How to run tutorial 1
"Tutorial 1" (which can be found at your local cloned <project-root>/jumbo-converters-core/tutorial/tutorial1.html), needs the following setup:
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Go to the jumbo-converters-core folder:
cd jumbo-converters-core
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Create an examples folder:
mkdir examples
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Copy the tutorial files there:
cp tutorial/amber.inp examples/ cp tutorial/amber.template.xml examples/ cp tutorial/amber.ref.xml examples/
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Run the tutorial program:
mvn -e exec:java -Dexec.mainClass=org.xmlcml.cml.converters.text.Examples
The result of the execution will be found at examples/amber.out.xml.
When modifying the template used, or when using a different input file, you should run the tutorial program with 3 arguments (in -Dexec.args) as follows:
mvn -e exec:java -Dexec.mainClass=org.xmlcml.cml.converters.text.Examples -Dexec.args="examples/amber.template.xml examples/amber.inp examples/amber.out.xml"
First argument is the name of the template file, second one is the name of the input file, and the third and last one is the name of the output file.
Writing a small parser
At present, the JUMBO-Converters for compchem work in a declarative manner, i.e., you don't need to know Java to write a parser; you just need to know the output of your favourite compchem code, a bit of regular expressions and some very basic XPath (both of which you could even infer from already made examples). Then you edit some XML files that tell the JUMBO-Converters what they have to do and you are done.
Here, I will describe a small bit of Gaussian parsing and how to develop it. For more details, check JUMBO-Converters and the rest of tutorials in this page.
Also, see Declarative parsing syntax for a complete list of the rules followed by the parsers and their relations to the template XML files.
The first thing to know is that Gaussian runs are separated into links, which seem to be some kind of internal modules, each of which is in charge of a more or less conceptually bounded task. The important issue for us is that, if the calculation has been run with the #P level of verbosity, as in
%Mem=900MB #P RHF/6-31G(d,p) 5D 7F SCF=(Conver=10) TrackIO GFInput MaxDisk=16GB HCO-L-Ala-NH2 RHF/6-31(d,p) single point calculation close to the polyproline II minimum 0 1 H1 C2 1 rC2H1 N3 2 rN3C2 1 aN3C2H1 O4 2 rO4C2 3 aO4C2N3 1 pO4C2N3H1 C5 3 rC5N3 2 aC5N3C2 1 dC5N3C2H1 ...
then the points at which Gaussian enters or exits a link are clearly printed into the logfile; which is a very helpful feature for parsing.
For example, at the middle of the logfile that we will use in this tutorial,
jumbo-converters/jumbo-converters-compchem/src/test/resources/echeniquep/inputQC/g03_threeSPs/RHF_6-31Gdp_sp_HCO-L-Ala-NH2_hashP.log
you can read:
(Enter /apps/apps64/g03/l302.exe)
NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1
NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0.
One-electron integrals computed using PRISM.
NBasis= 152 RedAO= T NBF= 152
NBsUse= 152 1.00D-06 NBFU= 152
Leave Link 302 at Thu Feb 17 17:30:34 2011, MaxMem= 117964800 cpu: 0.2
However, we will not try to parse now this obscure information about the 1-electron integrals. Instead, we will go for the molecular formula, which can be found in link 202, in the middle of it, in a line which begins by a space (as all lines in the logfile do) and the word Stoichiometry:
(Enter /apps/apps64/g03/l202.exe)
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 1 0 0.000000 0.000000 0.000000
...
16 1 0 -0.696737 1.335650 3.331321
---------------------------------------------------------------------
Distance matrix (angstroms):
1 2 3 4 5
1 H 0.000000
2 C 1.088294 0.000000
...
16 H 0.000000
Stoichiometry C4H8N2O2
Framework group C1[X(C4H8N2O2)]
Deg. of freedom 42
Full point group C1
Largest Abelian subgroup C1 NOp 1
Largest concise Abelian subgroup C1 NOp 1
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 1 0 2.673167 -0.694356 1.176039
...
16 1 0 0.631638 1.777215 -0.581971
---------------------------------------------------------------------
Rotational constants (GHZ): 2.9412883 1.7541705 1.2354314
Leave Link 202 at Thu Feb 17 17:30:29 2011, MaxMem= 117964800 cpu: 0.1
The minimal set of declarative XML files needed to parse this is as follows:
First you need a file called topTemplate.xml and located at
jumbo-converters/jumbo-converters-compchem/src/main/resources/org/xmlcml/cml/converters/compchem/gaussian/log
It contains the following code:
<?xml version="1.0" encoding="UTF-8"?>
<template id='gaussian.log' output="VERBOSE">
<templateList id='main' xmlns:xi="http://www.w3.org/2001/XInclude">
<xi:include href="l202.temp.xml"/>
</templateList>
</template>
I.e., it includes a list of subtemplates which, in this example, contains only one item, l202.temp.xml, whose task is to capture and parse link 202, which is located at
jumbo-converters/jumbo-converters-compchem/src/main/resources/org/xmlcml/cml/converters/compchem/gaussian/log/templates
and whose contents are:
<template id="l202" repeatCount="*" pattern=".*Enter.*l202[^\d].*"
endPattern=".*Leave Link +202[^\d].*">
<comment>
...
</comment>
<templateList id='l202_list' xmlns:xi="http://www.w3.org/2001/XInclude">
<xi:include href="l202.molformula.temp.xml"/>
</templateList>
</template>
The first two lines tell the JUMBO-Converters, through regular expressions, where link 202 begins and ends, respectively, and everything between those two matches is available for parsing in this file. Then, we see another templateList containing, again, only one item for this example, the file l202.molformula.temp.xml, which is located in the same folder as l202.temp.xml and contains:
<template id="t_molformula" pattern="\sStoichiometry.*"
endPattern="\sFramework.*">
<record id="r_stoichiometry">\sStoichiometry\s+{A,gaussian:molformula}.*</record>
</template>
In this case, we have no further lists of subtemplates and we just take the molecular formula. We detect the piece of text where it lies using pattern and endPattern as before, and this leaves the lines between the two matches available for parsing. The record tag parses the first line using another regular expression, and stores the formula string in a variable identified by gaussian:molformula.
If you now run the maven command in the previous tutorial:
mvn -e exec:java -Dexec.mainClass=org.xmlcml.cml.converters.compchem.gaussian.log.GaussianLog2XMLConverter -Dexec.args="./src/test/resources/echeniquep/inputQC/g03_threeSPs/RHF_6-31Gdp_sp_HCO-L-Ala-NH2_hashP.log ./src/test/resources/echeniquep/outputXML/g03_three_SPs/RHF_6-31Gdp_sp_HCO-L-Ala-NH2_hashP.log.xml"
from
jumbo-converters/jumbo-converters-compchem
this produces the file
jumbo-converters/jumbo-converters-compchem/src/test/resources/echeniquep/outputXML/g03_threeSPs/RHF_6-31Gdp_sp_HCO-L-Ala-NH2_hashP.log.xml
which now contains the expected XML tagging:
<module lineCount="91" templateRef="l202">
(Enter /apps/apps64/g03/l202.exe)
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 1 0 0.000000 0.000000 0.000000
...
16 1 0 -0.696737 1.335650 3.331321
---------------------------------------------------------------------
Distance matrix (angstroms):
1 2 3 4 5
1 H 0.000000
2 C 1.088294 0.000000
...
16 H 0.000000
<module lineCount="1" templateRef="t_molformula">
<list templateRef="r_stoichiometry">
<scalar dataType="xsd:string" dictRef="g:molformula">C4H8N2O2</scalar>
</list>
</module>
Framework group C1[X(C4H8N2O2)]
Deg. of freedom 42
Full point group C1
Largest Abelian subgroup C1 NOp 1
Largest concise Abelian subgroup C1 NOp 1
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 1 0 2.673167 -0.694356 1.176039
...
16 1 0 0.631638 1.777215 -0.581971
---------------------------------------------------------------------
Rotational constants (GHZ): 2.9412883 1.7541705 1.2354314
</module>
Leave Link 202 at Thu Feb 17 17:30:29 2011, MaxMem= 117964800 cpu: 0.1
Machine-specific known problems
MacOS
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Pablo Echenique: I installed Maven and Mercurial from
MacPorts
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Pablo Echenique: You may have to include this line in your .bashrc, or issue it in command line:
export JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Home
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Pablo Echenique:
It seems that MacOS is stupid enough as not to use UTF-8 as default encoding, which may cause problems. Therefore, you might want to add these lines to your pom.xml file at the top of your maven repository folder:
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
<project.reporting.outputEncoding>
UTF-8
</project.reporting.outputEncoding>
</properties>
25/08/2011 meeting usecase
Machine
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Desktop iMac
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Running Mac OS X 10.7.1 "Lion"
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Processor: 2.66 GHz Intel Core 2 Duo
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Memory: 4 GB 1067 MHz DDR3
Preliminaries
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I installed Maven, Mercurial and dos2unix from
MacPorts.
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I included this line in my .bashrc to inform the compiling system where the proper path to Java is:
export JAVA_HOME=$(/usr/libexec/java_home)
Installing jumbo-converters-compchem
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I moved to a folder of my choice (/Users/pablo/Quixote/ in my case, but this is not relevant) and cloned from the
wwmm BitBucket repository:
hg clone https://bitbucket.org/wwmm/jumbo-converters
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I removed all project artifacts that had been installed into my local maven repository (just in case):
rm -fr ~/.m2
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I moved into the compchem part of jumbo-converters and issued the command for a clean installation:
cd jumbo-converters/jumbo-converters-compchem mvn clean install
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This produces a lot of output, a final report with SUCCESS in all components
[INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] jumbo-converters-compchem-common .................. SUCCESS [1:31.458s] [INFO] jumbo-converters-compchem-testutils ............... SUCCESS [0.853s] [INFO] jumbo-converters-compchem-amber ................... SUCCESS [1.184s] [INFO] jumbo-converters-compchem-cml ..................... SUCCESS [0.951s] [INFO] jumbo-converters-compchem-dalton .................. SUCCESS [0.829s] [INFO] jumbo-converters-compchem-gamessuk ................ SUCCESS [0.826s] [INFO] jumbo-converters-compchem-gamessus ................ SUCCESS [1.251s] [INFO] jumbo-converters-compchem-gaussian ................ SUCCESS [19.494s] [INFO] jumbo-converters-compchem-jaguar .................. SUCCESS [1.138s] [INFO] jumbo-converters-compchem-molcas .................. SUCCESS [1.057s] [INFO] jumbo-converters-compchem-mopac ................... SUCCESS [0.976s] [INFO] jumbo-converters-compchem-nwchem .................. SUCCESS [19.956s] [INFO] jumbo-converters-compchem-qespresso ............... SUCCESS [1.155s] [INFO] jumbo-converters-compchem-turbomole ............... SUCCESS [0.795s] [INFO] jumbo-converters-compchem-all ..................... SUCCESS [0.026s] [INFO] jumbo-converters-compchem-misc .................... SUCCESS [12.102s] [INFO] jumbo-converters-compchem ......................... SUCCESS [0.012s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 2:35.630s [INFO] Finished at: Tue Aug 23 12:58:45 CEST 2011 [INFO] Final Memory: 17M/81M [INFO] ------------------------------------------------------------------------
and it ends the installation of jumbo-converters-compchem in my machine.
Installing lensfield
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I moved to /Users/pablo/Quixote/ and cloned from the
petermr BitBucket repository:
hg clone http://bitbucket.org/petermr/lensfieldjumbo
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I got into the newly created folder, unpacked lensfield and fixed linebreaks and permissions of the main lf script:
cd lensfieldjumbo/ unzip lensfield-0.1.1.zip dos2unix lensfield2-0.1.1/bin/lf chmod u+x lensfield2-0.1.1/bin/lf
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I placed a link to the lf exectutable in my path:
ln -s /Users/pablo/now/Quixote/lensfieldjumbo/lensfield2-0.1.1/bin/lf /Users/pablo/bin/lf
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I updated lensfield, finishing its instalation:
lf --update
