/* $RCSfile: ADFReader.java,v $ * $Author: egonw $ * $Date: 2004/02/23 08:52:55 $ * $Revision: 1.3.2.4 $ * * Copyright (C) 2002-2004 The Jmol Development Team * * 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., 59 Temple Place, Suite 330, Boston, MA * 02111-1307 USA. */ package org.jmol.adapter.readers.quantum; import org.jmol.adapter.smarter.Atom; import org.jmol.quantum.SlaterData; import org.jmol.util.Logger; import javajs.util.PT; import javajs.util.SB; import java.util.Hashtable; import java.util.Map; /** * A reader for Dgrid BASISFILE data. http://www.scm.com/News/DGrid.html * http://www.scm.com/Doc/Doc2009.01/ADF/ADFUsersGuide/page430.html * * */ public class DgridReader extends SlaterReader { private String title; @Override protected boolean checkLine() throws Exception { if (line.indexOf(":title") == 0) { title = rd().substring(2); return true; } if (line.indexOf("basis: CARTESIAN STO") >= 0) { readSlaterBasis(); // Cartesians return true; } if (line.indexOf(":atom") == 0) { readCoordinates(); return true; } if (line.indexOf(" MO DATA ") >= 0) { if (doReadMolecularOrbitals) readMolecularOrbitals(); return true; } return true; } /** * Reads a set of coordinates * * @exception Exception if an I/O error occurs */ private void readCoordinates() throws Exception { /* * :atom No. x y z charge :--------------------------------------------------------- N 1: 0.0000 0.0000 4.8054 5.00 O 2: 0.0000 0.0000 7.0933 6.00 C 3: 0.0000 0.0000 -0.0761 4.00 C 4: 0.0000 0.0000 2.6002 4.00 C 5: 2.3400 0.0000 -1.3762 4.00 * */ asc.newAtomSet(); asc.setAtomSetName(title); discardLinesUntilContains("----"); while (rd() != null && !line.startsWith(":-----")) { String[] tokens = getTokens(); if (tokens.length < 5) break; setAtomCoordScaled(null, tokens, 2, ANGSTROMS_PER_BOHR).elementSymbol = tokens[0]; } } Map htExponents = new Hashtable(); private void readSlaterBasis() throws Exception { /* : +--------------------------+ : basis: CARTESIAN STO : : +--------------------------+ : atom No. type exponents and coefficients :----------------------------------------------------------------------------------- N 1 1s exp: 6.38000000e+00 N 1 2s exp: 1.50000000e+00 N 1 2s exp: 2.50000000e+00 N 1 2s exp: 5.15000000e+00 N 1 2p exp: 1.00000000e+00 N 1 2p exp: 1.88000000e+00 */ discardLinesUntilContains(":-"); char ch = 'a'; while (rd() != null && line.indexOf(":-") < 0) { String atomSymbol = line.substring(3,6).trim(); String xyz = line.substring(19, 21); String code = atomSymbol + xyz; if (htExponents.get(code) == null) { ch = 'a'; } else { code += "_" + ch++; } String exp = line.substring(34); htExponents.put(code, Float.valueOf(parseFloatStr(exp))); } } private Map htFuncMap; private void readMolecularOrbitals() throws Exception { /* sym: A1 1 1s 2 1s 3 1s 4 1s 5 1s 9 1s 6 1s 8 1s 7 1s 10 1s 11 1s 1 2s 1 2s_a 1 2s_b 1 2pz 1 2pz_a 1 2pz_b 1 3dz2 1 3dx2 1 3dy2 */ htFuncMap = new Hashtable(); readLines(3); getSlaters(); while (line != null && line.indexOf(":") != 0) { discardLinesUntilContains("sym: "); String symmetry = line.substring(4, 10).trim(); if (symmetry.indexOf("_FC") >= 0) break; SB data = new SB(); data.append(line.substring(15)); while (rd() != null && line.length() >= 15) data.append(line); String[] tokens = PT.getTokens(data.toString()); int nFuncs = tokens.length / 2; int[] ptSlater = new int[nFuncs]; Atom[] atoms = asc.atoms; for (int i = 0, pt = 0; i < tokens.length;) { int iAtom = parseIntStr(tokens[i++]) - 1; String code = tokens[i++]; String key = iAtom + "_" + code; if (htFuncMap.containsKey(key)) { ptSlater[pt++] = htFuncMap.get(key).intValue(); } else { int n = slaters.size(); ptSlater[pt++] = n; htFuncMap.put(key, Integer.valueOf(n)); //System.out.println(code + " " + key); addSlater(createSlaterData(iAtom + 1, atoms[iAtom].elementSymbol, code), n); } } discardLinesUntilContains(":-"); rd(); while (line != null && line.length() >= 20) { int iOrb = parseIntRange(line, 0, 10); float energy = parseFloatRange(line, 10, 20); SB cData = new SB(); cData.append(line.substring(20)); while (rd() != null && line.length() >= 10) { if (line.charAt(3) != ' ') break; cData.append(line); } float[] list = new float[slaters.size()]; tokens = PT.getTokens(cData.toString()); if (tokens.length != nFuncs) Logger .error("DgridReader: number of coefficients (" + tokens.length + ") does not equal number of functions (" + nFuncs + ")"); for (int i = 0; i < tokens.length; i++) { int pt = ptSlater[i]; list[pt] = parseFloatStr(tokens[i]); } Map mo = new Hashtable(); mo.put("energy", Float.valueOf(energy)); mo.put("coefficients", list); mo.put("symmetry", symmetry + "_" + iOrb); setMO(mo); //System.out.println(orbitals.size() + " " + symmetry + "_" + iOrb); } } /* : +------------+ | OCCUPATION | : +------------+ :------------------------------------------------------------ : # symmetry orb ALPHA BETA :------------------------------------------------------------ 1 A1 1 1.00000000000 1.00000000000 2 A1 2 1.00000000000 1.00000000000 3 A1 3 1.00000000000 1.00000000000 */ discardLinesUntilContains(": # symmetry"); rd(); for (int i = 0; i < orbitals.size(); i++) { rd(); float occupancy = parseFloatRange(line, 31, 45) + parseFloatRange(line, 47, 61); orbitals.get(i).put("occupancy", Float.valueOf(occupancy)); } sortOrbitals(); //System.out.println(Escape.escape(list, false)); setSlaters(true); setMOs("eV"); } private SlaterData createSlaterData(int iAtom, String atomSymbol, String xyz) { char ch; char abc = ' '; char type = ' '; int exp = 1; int el = 0; int x = 0; int y = 0; int z = 0; for (int i = xyz.length(); --i >= 0;) { switch (ch = xyz.charAt(i)) { case '_': type = abc; break; case '1': case '2': case '3': case '4': exp = ch - '0'; break; case 'x': x = exp; el += exp; exp = 1; break; case 'y': y = exp; el += exp; exp = 1; break; case 'z': z = exp; el += exp; exp = 1; break; case 's': case 'p': case 'd': case 'f': default: abc = ch; } } int r = (exp - el - 1); String code = atomSymbol + xyz.substring(0, 2); if (type != ' ') code += "_" + type; Float f = htExponents.get(code); float zeta = 0; if (f == null) Logger.error("Exponent for " + code + " not found"); else zeta = f.floatValue(); //System.out.println("DgridReader [" + iAtom + " " //+ x + " " + y + " " + z + " " + r + "]" + " " + alpha); return new SlaterData(iAtom, x, y, z, r, zeta, 1); } }