MolStart

This is a specific MolStart interface developed for communicating with other programs. The functions are implemented and included in the current version. The interface GUI is designed dynamically based on the information provided by the XML data. The first window of the interface contains Tabs to take users to different programming interfaces,

The tabs are defined by the xml file named program.xml. The contents of the XML looks like,

<xml version="1.0" encoding="utf-8">
<programs>
<program>
    <title>Gaussian</title>
    <name>gaussian.xml</name>
    <value>URLString|NameSpace</value>
</program>
<program>
    <title>Gamess/Newton</title>
    <name>gamess.xml</name>
    <value>URLString|NameSpace</value>
</program>
<program>
    <title>NWChem/Bartman<title>
    <name>nwchem.xml</name>
    <value>URLString|NameSpace</value>
</program>
<program>
    <title>Dmol/Newton</title>
    <name>dmol.xml</name>
    <value>URLString|NameSpace</value>
</program>
</programs>

This XML file, program.xml, provides the names of the applications we can interface with and also the xml file needed to construct the contents of the interface. The Url and NameSpace in the value tag are used to define the web service location where the job will be sent. Please contact your web administrator to install the web services in the computer where Gaussian and other chemistry applications located. There are Gaussian, Gamess, NWChem and Dmol programs defined in this XML data and they are shown in the four different tabs. The names, Newton and Bartman, are names of the computers in NCSC. The XML to construct the contents of the Gaussian interface, gaussian.xml, is shown below,

<gaussian>
    <title>Job Script, Number of Processor,Basis set</title>
    <name>textfield, textfield,combobox</name>
    <value>nqe_script.xml, gncpu.xml,gbasis.xml</value>
</gaussian>

<gaussian>
   < title>Charge/Multiplicity,SCF method,Calculation</title>
   <name>textfield2, combobox,radiobutton</name>
   <value>gcharge.xml, gscf_type.xml,gcal_type.xml</value>
</gaussian>

It is easy to understand from the XML data: there are two groups of GUIs to be displayed in the interface. First group contains only textfields and the second group contains textfields, comboboxes, and radiobuttons.

For example, the first group with textfields is defined with nqe_script.xml. This nqe_script.xml is a simple example for the NQE queuing system,

<xml version="1.0" encoding="utf-8">
<scripts>
  <jobscript>
   <title>Shell</title>
   <name>#SUB -csh</name>
   <value>/bin/csh</value>
</jobscript>
   <jobscript>
   <title>Memory</title>
   <name>#SUB -M</name>
   <value>40MG</value>
</jobscript>
   <jobscript>
   <title>CPU Time</title>
   <name>#SUB -t</name>
   <value>4000</value>
</jobscript>
   <jobscript>
   <title>Processor #</title>
   <name>#SUB -np</name>
   <value>4</value>
   </jobscript>
</scripts>

You should be able to match the XML data with the graphics shown in the upper part of the page, or the picture shown below,

Edit and Launch Job

The "Edit" button is used to bring up an editing panel containing the job script that will be submitted to the web services. The user can edit the contents of the script before submitting the job. MolStart will contact the web services for the job submission when users click on the "Launch" button. A warning dialog will popup if the web services is not available.

Edit input panel

Input & Output Files

Click on the "Output" button to view the input and output files that are located on the computer where the web service is implemented. A message, "No job found", is shown in the Status area, if there is no job submitted to the web service.

Input and output file list

Double click on an item in the file list to obtain the contents of the file from the web service,

File contents from Web Services

Please note that in this MolStart release the submitted job information is stored in the memory of the "Compute" window, so the information will be lost if the user closes the "Compute" window.

The release version is configured to submit GAMESS to the Web Services located at the NEWTON.NCSC.ORG computer. This setting is only for test purpose, so we might terminate your job at any time.

Gamess input panel

The xml files for the Dmol interface are,

dmol.xml
Calculation Type
Functionals
Contents of the DMol interface