/* $RCSfile$ * $Author: hansonr $ * $Date: 2006-10-22 14:12:46 -0500 (Sun, 22 Oct 2006) $ * $Revision: 5999 $ * * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org * * Contact: jmol-developers@lists.sf.net * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public * License as published by the Free Software Foundation; either * version 2.1 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this library; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. */ package org.jmol.adapter.readers.xml; import org.jmol.adapter.smarter.Atom; import org.jmol.util.Logger; import javajs.util.PT; import javajs.util.SB; import javajs.util.V3; /** * * Vasp vasprun.xml reader * * @author hansonr * */ public class XmlVaspReader extends XmlReader { private SB data; private String name; private int ac; private int iAtom; private boolean isE_wo_entrp = false; private boolean isE_fr_energy = false; private String enthalpy = null; private String gibbsEnergy = null; // private String[] myAttributes = { "name" }; public XmlVaspReader() { } // @Override // protected String[] getDOMAttributes() { // return myAttributes; // } @Override protected void processXml(XmlReader parent, Object saxReader) throws Exception { parent.doProcessLines = true; processXml2(parent, saxReader); } @Override public void processStartElement(String localName, String nodeName) { if (debugging) Logger.debug("xmlvasp: start " + localName); if (!parent.continuing) return; if ("calculation".equals(localName)) { enthalpy = null; gibbsEnergy = null; return; } if ("i".equals(localName)) { String s = atts.get("name"); if (s.charAt(0) != 'e') return; isE_wo_entrp = s.equals("e_wo_entrp"); isE_fr_energy = s.equals("e_fr_energy"); setKeepChars(isE_wo_entrp || isE_fr_energy); return; } if ("structure".equals(localName)) { if (!parent.doGetModel(++parent.modelNumber, null)) { parent.checkLastModel(); return; } parent.setFractionalCoordinates(true); asc.doFixPeriodic = true; asc.newAtomSet(); if (enthalpy != null) { asc.setCurrentModelInfo("enthalpy", Double.valueOf(enthalpy)); } if (gibbsEnergy != null) { asc.setAtomSetEnergy("" + gibbsEnergy, parseFloatStr(gibbsEnergy)); asc.setCurrentModelInfo("gibbsEnergy", Double.valueOf(gibbsEnergy)); } if (enthalpy != null && gibbsEnergy != null) asc.setAtomSetName("Enthalpy = " + enthalpy + " eV Gibbs Energy = " + gibbsEnergy + " eV"); return; } if (!parent.doProcessLines) return; if ("v".equals(localName)) { setKeepChars(data != null); return; } if ("c".equals(localName)) { setKeepChars(iAtom < ac); return; } if ("varray".equals(localName)) { name = atts.get("name"); if (name != null && PT.isOneOf(name, ";basis;positions;forces;")) data = new SB(); return; } if ("atoms".equals(localName)) { setKeepChars(true); return; } } boolean haveUnitCell = false; String[] atomNames; String[] atomSyms; String atomName; String atomSym; float a; float b; float c; float alpha; float beta; float gamma; @Override void processEndElement(String localName) { if (debugging) Logger.debug("xmlvasp: end " + localName); while (true) { if (!parent.doProcessLines) break; if (isE_wo_entrp) { isE_wo_entrp = false; enthalpy = chars.toString().trim(); break; } if (isE_fr_energy) { isE_fr_energy = false; gibbsEnergy = chars.toString().trim(); break; } if ("v".equals(localName) && data != null) { data.append(chars.toString()); break; } if ("c".equals(localName)) { if (iAtom < ac) { if (atomName == null) { atomName = atomSym = chars.toString().trim(); } else { atomNames[iAtom++] = atomName + chars.toString().trim(); atomName = null; } } break; } if ("atoms".equals(localName)) { ac = parseIntStr(chars.toString()); atomNames = new String[ac]; atomSyms = new String[ac]; iAtom = 0; break; } if ("varray".equals(localName) && data != null) { if (name == null) { } else if ("basis".equals(name) && !haveUnitCell) { haveUnitCell = true; float[] ijk = getTokensFloat(data.toString(), null, 9); V3 va = V3.new3(ijk[0], ijk[1], ijk[2]); V3 vb = V3.new3(ijk[3], ijk[4], ijk[5]); V3 vc = V3.new3(ijk[6], ijk[7], ijk[8]); a = va.length(); b = vb.length(); c = vc.length(); va.normalize(); vb.normalize(); vc.normalize(); alpha = (float) (Math.acos(vb.dot(vc)) * 180 / Math.PI); beta = (float) (Math.acos(va.dot(vc)) * 180 / Math.PI); gamma = (float) (Math.acos(va.dot(vb)) * 180 / Math.PI); } else if ("positions".equals(name)) { parent.setUnitCell(a, b, c, alpha, beta, gamma); float[] fdata = new float[ac * 3]; getTokensFloat(data.toString(), fdata, ac * 3); int fpt = 0; for (int i = 0; i < ac; i++) { Atom atom = asc.addNewAtom(); parent.setAtomCoordXYZ(atom, fdata[fpt++], fdata[fpt++], fdata[fpt++]); atom.elementSymbol = atomSyms[i]; atom.atomName = atomNames[i]; } } else if ("forces".equals(name)) { float[] fdata = new float[ac * 3]; getTokensFloat(data.toString(), fdata, ac * 3); int fpt = 0; int i0 = asc.getLastAtomSetAtomIndex(); //TODO question here as to whether these need transformation for (int i = 0; i < ac; i++) asc.addVibrationVector(i0 + i, fdata[fpt++], fdata[fpt++], fdata[fpt++]); } data = null; break; } if ("structure".equals(localName)) { try { parent.applySymmetryAndSetTrajectory(); } catch (Exception e) { // TODO } break; } return; } setKeepChars(false); } }