/* $RCSfile$ * $Author: hansonr $ * $Date: 2006-09-30 10:16:53 -0500 (Sat, 30 Sep 2006) $ * $Revision: 5778 $ * * 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.xtal; import javajs.util.PT; import org.jmol.adapter.smarter.AtomSetCollectionReader; import org.jmol.adapter.smarter.Atom; /** * A reader for Wein2k DFT files. * * http://www.wien2k.at/reg_user/textbooks/usersguide.pdf * * Bob Hanson hansonr@stolaf.edu 5/14/2009 * */ public class Wien2kReader extends AtomSetCollectionReader { private boolean isrhombohedral; private char latticeCode = '\0'; private boolean doSymmetry = true; @Override public void initializeReader() throws Exception { doSymmetry = !sgName.equals("none"); setFractionalCoordinates(true); asc.setCollectionName(rd()); readUnitCell(); readAtoms(); readSymmetry(); readEmbeddedScript(); continuing = false; } /* from HallInfo: * final static String[] latticeTranslationData = { "\0", "unknown", "" ,"P", "primitive", "" ,"I", "body-centered", " 1n" ,"R", "rhombohedral", " 1r 1r" ,"F", "face-centered", " 1ab 1bc 1ac" ,"A", "A-centered", " 1bc" ,"B", "B-centered", " 1ac" ,"C", "C-centered", " 1ab" ,"S", "rhombohedral(S)", " 1s 1s" ,"T", "rhombohedral(T)", " 1t 1t" }; from Wien2k user manual: P all primitive lattices except hexagonal (trigonal lattice is also supported) [a sin(gamma), a cos(gamma), 0], [0, b, 0], [0, 0, c] F face-centered [a/2, b/2, 0], [a/2, 0, c/2], [0, b/2, c/2] B body-centered [a/2, -b/2, c/2],[a/2, b/2, -c/2], [-a/2, b/2, c/2] CXY C-base-centered (orthorhombic only) [a/2, -b/2, 0], [a/2, b/2, 0], [0, 0, c] CYZ A-base-centered (orthorhombic only) [a, 0, 0], [0, -b/2, c/2], [0, b/2, c/2] CXZ B-base-centered (orthorh. and monoclinic symmetry) [a sin(gamma)/2, a cos(gamma)/2, -c/2], [0, b, 0], [a sin(gamma)/2, a cos(gamma)/2, c/2] R rhombohedral [a/sqrt(3)/2, -a/2, c/3],[a/sqrt(3)/2, a/2, c/3],[-a/sqrt(3), 0, c/3] H hexagonal [sqrt(3)a/2, -a/2, 0],[0, a, 0],[0, 0, c] * */ private void readUnitCell() throws Exception { rd(); isrhombohedral = ((latticeCode = line.charAt(0)) == 'R'); //CXY --> "C" SHELX // x+1/2, y+1/2, z if (line.startsWith("CYZ")) latticeCode = 'A'; // x,y+1/2,z+1/2 else if (line.startsWith("CXZ")) latticeCode = 'B'; // provided gamma is 90 -- x+1/2,y,z+1/2 else if (line.startsWith("B")) latticeCode = 'I'; // x+1/2,y+1/2,z+1/2 if (latticeCode != 'R' && latticeCode != 'H') asc.getXSymmetry().setLatticeParameter(latticeCode); if (line.length() > 32) { String name = line.substring(32).trim(); if (name.indexOf(" ") >= 0) name = name.substring(name.indexOf(" ") + 1); if (name.indexOf("_") >= 0) name = name.substring(name.indexOf("_") + 1); setSpaceGroupName(name); } float factor = (rd().toLowerCase().indexOf("ang") >= 0 ? 1f : ANGSTROMS_PER_BOHR); rd(); float a = parseFloatRange(line, 0,10) * factor; float b = parseFloatRange(line, 10,20) * factor; float c = parseFloatRange(line, 20,30) * factor; int l = line.length(); float alpha = (l >= 40 ? parseFloatRange(line, 30,40) : 0); float beta = (l >= 50 ? parseFloatRange(line, 40,50) : 0); float gamma = (l >= 60 ? parseFloatRange(line, 50,60) : 0); if (isrhombohedral) { float ar = (float) Math.sqrt(a * a /3 + c * c / 9) ; alpha = beta = gamma = (float) (Math.acos( (2*c * c - 3 * a * a) / (2 * c * c + 6 * a * a)) * 180 / Math.PI); a = b = c = ar; } if (Float.isNaN(alpha) || alpha == 0) alpha = 90; if (Float.isNaN(beta) || beta == 0) beta = 90; if (Float.isNaN(gamma) || gamma == 0) gamma = 90; setUnitCell(a, b, c, alpha, beta, gamma); } private void readAtoms() throws Exception { // format (4X,I4,4X,F10.8,3X,F10.8,3X,F10.8) rd(); while (line != null && (line.indexOf("ATOM") == 0 || !doSymmetry && line.indexOf(":") == 8)) { int thisAtom = asc.ac; addAtom(); if (rd().indexOf("MULT=") == 10) for (int i = parseIntRange(line, 15,18); --i >= 0; ) { rd(); if (!doSymmetry) addAtom(); } // format (A10,5X,I5,5X,F10.8,5X,F10.5,5X,F5.2) String atomName = line.substring(0, 10); String sym = atomName.substring(0,2).trim(); if (sym.length() == 2 && PT.isDigit(sym.charAt(1))) sym = sym.substring(0, 1); atomName = PT.rep(atomName, " ", ""); int n = 0; for (int i = asc.ac; --i >= thisAtom; ) { Atom atom = asc.atoms[i]; atom.elementSymbol = sym; atom.atomName = atomName + "_" + (n++); } while (rd() != null && line.indexOf("ATOM") < 0 && line.indexOf("SYMMETRY") < 0) { } } // return with "SYMMETRY" line in buffer } private void addAtom() { float a = parseFloatRange(line, 12,22); float b = parseFloatRange(line, 25,35); float c = parseFloatRange(line, 38,48); /* if (false && isrhombohedral) { float ar = a; float br = b; float cr = c; a = ar * 2 / 3 - br * 1 / 3 - cr * 1 / 3; b = ar * 1 / 3 + br * 1 / 3 - cr * 2 / 3; c = ar * 1 / 3 + br * 1 / 3 + cr * 1 / 3; } */ Atom atom = asc.addNewAtom(); setAtomCoordXYZ(atom, a, b, c); } private void readSymmetry() throws Exception { if (line.indexOf("SYMMETRY") < 0) return; int n = parseIntRange(line, 0, 4); for (int i = n; --i >= 0;) { String xyz = getJones() + "," + getJones() + "," + getJones(); if (doSymmetry) setSymmetryOperator(xyz); rd(); } } private final String cxyz = " x y z"; private String getJones() throws Exception { rd(); String xyz = ""; // 1 0 0 0.0000000 float trans = parseFloatStr(line.substring(6)); for (int i = 0; i < 6; i++) { if (line.charAt(i) == '-') xyz += "-"; if (line.charAt(++i) == '1') { xyz += cxyz.charAt(i); if (trans > 0) xyz += "+"; if (trans != 0) xyz += trans; } } return xyz; } private void readEmbeddedScript() throws Exception { while (line != null) { checkCurrentLineForScript(); rd(); } } }