Contents of The I.S.A.A.C.S. Project File format

I.S.A.A.C.S. program uses an intuitive format for a project file (see Tab. 2.1) which contains all parameters needed to set up a calculation of structural characteristics of a 3D model. The structure of the file follows the XML coding [2] and allows to store detailed information about the system to be analyzed: chemical composition, chemical and physical properties of each atomic species (e.g. atomic weight and x-ray/neutron scattering amplitudes), size of the model box, atomic coordinates type (e.g. Cartesian or fractional), time series properties, description of the bonding between atoms. The information is provided by the user and may be re-used/modified during I.S.A.A.C.S. execution.

Table 2.1: Example of I.S.A.A.C.S. project file '*.ipf' in XML format for glassy silica.

<?xml version="1.0" encoding="UTF-8"?>
<!-- I.S.A.A.C.S. v1.1 XML file -->
<isaacs-xml>
 <!-- Format and file of the configuration(s) -->
 <data>
  <type>Chem3D file</type>
  <file>/home/leroux/Desktop/sio2.chem3d</file>
 </data>
 <!-- Chemistry information -->
 <chemistry>
  <atoms>3000</atoms>
  <species number="2">
   <label id="0">O </label>
   <label id="1">Si</label>
  </species>
  <element symbol="O ">
   <name>Oxygen         </name>
   <z>8</z>
   <mass>16.000000</mass>
   <rad>0</rad>
   <radius>0.660000</radius>
   <nscatt>5.803000</nscatt>
   <xscatt>8.000000</xscatt>
  </element>
  <element symbol="Si">
   <name>Silicon        </name>
   <z>14</z>
   <mass>28.090000</mass>
   <rad>0</rad>
   <radius>1.110000</radius>
   <nscatt>4.153000</nscatt>
   <xscatt>14.000000</xscatt>
  </element>
 </chemistry>
 <!-- Box information -->
 <box>
  <edges>
   <a>35.662100</a>
   <b>35.662100</b>
   <c>35.662100</c>
  </edges>
  <angles>
   <alpha>90.000000</alpha>
   <beta>90.000000</beta>
   <gamma>90.000000</gamma>
  </angles>
  <vectors>
   <a.x>35.662100</a.x>
   <a.y>0.000000</a.y>
   <a.z>0.000000</a.z>
   <b.x>0.000000</b.x>
   <b.y>35.662100</b.y>
   <b.z>0.000000</b.z>
   <c.x>0.000000</c.x>
   <c.y>0.000000</c.y>
   <c.z>35.662100</c.z>
  </vectors>
 </box>
 <!-- PBC information -->
 <pbc>
  <apply>TRUE</apply>
  <fractional>FALSE</fractional>
  <fractype>0</fractype>
 </pbc>
 <!-- Bonds information -->
 <cutoffs>
  <total>2.184304</total>
  <partials>
   <O-O>2.808390</O-O>
   <O-Si>2.184304</O-Si>
   <Si-O>2.184304</Si-O>
   <Si-Si>3.432477</Si-Si>
  </partials>
 </cutoffs>
 <!-- Time series -->
 <time-series>
   <dt>2.500000</dt>
   <unit>t [fs]</unit>
   <ndt>20</ndt>
 </time-series>
 >!-- Apply project -->
 <project>TRUE</project>
</isaacs-xml>