Hey bob, I am sorry for wasting your time again. can you try the crystal class attached below opening whatever frequency files you like! I tried to extend it to fragment calculations! Jmol comes out with an error like : ERROR: Error reading file at line 4001: FREQ(CM**-1) 25.21 28.35 32.20 41.27 42.40 66.19 -1 java.lang.ArrayIndexOutOfBoundsException: -1
I cannot figure out what is happening! However I will send you on file which contains frequency for a fragment ! The error java.lang.ArrayIndexOutOfBoundsException: -1 sounds really strange ! Thank you ,Piero /* $RCSfile$ * $Author: hansonr $ * * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org * * Contact: jmol-develop...@lists.sf.net * * Copyright (C) 2009 Piero Canepa, University of Kent, UK * * Contact: pc...@kent.ac.uk or pieremanuele.can...@gmail.com * * 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 org.jmol.adapter.smarter.*; import org.jmol.util.Logger; import org.jmol.util.TextFormat; import java.util.Vector; /** * * http://www.crystal.unito.it/ * * @author Pieremanuele Canepa, Room 104, FM Group School of Physical Sciences, * Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United * Kingdom, pc...@kent.ac.uk * * @version 1.3 * * for a specific model in the set, use * * load "xxx.out" n * * as for all readers, where n is an integer > 0 * * for final optimized geometry use * * load "xxx.out" 0 * * (that is, "read the last model") as for all readers * * for conventional unit cell -- input coordinates only, use * * load "xxx.out" filter "conventional" * * to NOT load vibrations, use * * load "xxx.out" FILTER "novibrations" * * TODO: fix frequency reader for fragment case * * */ public class CrystalReader extends AtomSetCollectionReader { private boolean isPrimitive = true; private boolean isPolymer = false; private boolean isSlab = false; private boolean isMolecular = false; private boolean doReadAtoms = false; private boolean haveCharges = false; private boolean addVibrations = false; private int atomCount; protected void initializeReader() throws Exception { isPrimitive = (filter == null || filter.indexOf("conv") < 0); addVibrations = (filter == null || filter.indexOf("novib") < 0); atomSetCollection.setAtomSetCollectionAuxiliaryInfo("unitCellType", (isPrimitive ? "primitive" : "conventional")); setFractionalCoordinates(readHeader()); } protected boolean checkLine() throws Exception { // starting point for any calculation is the definition of the lattice // parameters similar to the "data" statement of a CIF file if (line.startsWith(" LATTICE PARAMETER") && (isPrimitive && (line.contains("- PRIMITIVE") || line.contains("- BOHR")) || !isPrimitive && line.contains("- CONVENTIONAL"))) { if (doneReadingModels()) { continuing = false; return false; } if (!isPrimitive || doGetModel(++modelNumber)) { readCellParams(); doReadAtoms = true; } else { doReadAtoms = false; } return true; } if (!doReadAtoms) return true; if (!isPrimitive) { if (line.startsWith(" INPUT COORDINATES")) { readInputCoords(); continuing = false; // because if we are reading the conventional cell, // there won't be anything else we can do here. } return true; } // from here on -- must be primitive if (line.startsWith(" ATOMS IN THE ASYMMETRIC UNIT")) { readFractionalCoords(); return true; } if (line.startsWith(" TOTAL ENERGY")) { readEnergy(); readLine(); if (line.startsWith(" ********")) discardLinesUntilContains("SYMMETRY ALLOWED"); if (line.startsWith(" TTTTTTTT")) discardLinesUntilContains("PREDICTED ENERGY CHANGE"); return true; } if (line.startsWith(" TYPE OF CALCULATION")) { calculationType = line.substring(line.indexOf(":") + 1).trim(); return true; } if (line.startsWith(" MULLIKEN POPULATION ANALYSIS")) { readPartialCharges(); return true; } if (addVibrations && line.contains("FRQFRQFRQFRQFRQFRQFRQFRQ")) { readFrequencies(); return true; } if (line.startsWith(" ATOMIC SPINS SET")) { readSpins(); return true; } if (line.startsWith(" TOTAL ATOMIC SPINS :")) { readMagneticMoments(); return true; } return true; } /* SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS ATOMIC SPINS SET TO (ATOM, AT. N., SPIN) 1 26-1 2 8 0 3 8 0 4 8 0 5 26 1 6 26 1 7 8 0 8 8 0 9 8 0 10 26-1 11 26-1 12 8 0 13 8 0 14 8 0 15 26 1 16 26 1 17 8 0 18 8 0 19 8 0 20 26-1 21 26-1 22 8 0 23 8 0 24 8 0 25 26 1 26 26 1 27 8 0 28 8 0 29 8 0 30 26-1 ALPHA-BETA ELECTRONS LOCKED TO 0 FOR 50 SCF CYCLES */ private void readSpins() throws Exception { String[] spins = new String[atomCount]; String data = ""; while (readLine() != null && line.indexOf("ALPHA") < 0) data += line; data = TextFormat.simpleReplace(data, "-", " -"); String[] tokens = getTokens(data); for (int i = 0, pt = 2; i < atomCount; i++, pt += 3) spins[i] = tokens[pt]; data = TextFormat.join(spins, '\n', 0); atomSetCollection.setAtomSetAuxiliaryProperty("spin", data); } private void readMagneticMoments() throws Exception { String data = ""; while (readLine() != null && line.indexOf("TTTTTT") < 0) data += line; data = TextFormat.join(getTokens(data), '\n', 0); atomSetCollection.setAtomSetAuxiliaryProperty("magneticMoment", data); } protected void finalizeReader() throws Exception { if (energy != null) setEnergy(); super.finalizeReader(); } private boolean readHeader() throws Exception { discardLinesUntilContains("* CRYSTAL"); discardLinesUntilContains("EEEEEEEEEE"); atomSetCollection.setCollectionName(readLine().trim() + (desiredModelNumber == 0 ? " (optimized)" : "")); readLine(); String type = readLine().trim(); /* * This is when the initial geometry is read from an external file GEOMETRY * INPUT FROM EXTERNAL FILE (FORTRAN UNIT 34) */ if (type.indexOf("EXTERNAL FILE") >= 0) { type = readLine().trim(); isPolymer = (type.equals("1D - POLYMER")); isSlab = (type.equals("2D - SLAB")); } else { isPolymer = (type.equals("POLYMER CALCULATION")); isSlab = (type.equals("SLAB CALCULATION")); } atomSetCollection.setAtomSetCollectionAuxiliaryInfo("symmetryType", type); if (type.indexOf("MOLECULAR") >= 0) { isMolecular = doReadAtoms = true; readLine(); atomSetCollection.setAtomSetCollectionAuxiliaryInfo( "molecularCalculationPointGroup", line.substring( line.indexOf(" OR ") + 4).trim()); return false; } if (!isPrimitive) { discardLines(5); setSpaceGroupName(line.substring(line.indexOf(":") + 1).trim()); } return true; } private void readCellParams() throws Exception { newAtomSet(); if (isPolymer && !isPrimitive) { float a = parseFloat(line.substring(line.indexOf("CELL") + 4)); setUnitCell(a, -1, -1, 90, 90, 90); return; } discardLinesUntilContains("GAMMA"); String[] tokens = getTokens(readLine()); if (isSlab) { if (isPrimitive) setUnitCell(parseFloat(tokens[0]), parseFloat(tokens[1]), -1, parseFloat(tokens[3]), parseFloat(tokens[4]), parseFloat(tokens[5])); else setUnitCell(parseFloat(tokens[0]), parseFloat(tokens[1]), -1, 90, 90, parseFloat(tokens[2])); } else if (isPolymer) { setUnitCell(parseFloat(tokens[0]), -1, -1, parseFloat(tokens[3]), parseFloat(tokens[4]), parseFloat(tokens[5])); } else { setUnitCell(parseFloat(tokens[0]), parseFloat(tokens[1]), parseFloat(tokens[2]), parseFloat(tokens[3]), parseFloat(tokens[4]), parseFloat(tokens[5])); } } int atomIndexLast; /* * ATOMS IN THE ASYMMETRIC UNIT 30 - ATOMS IN THE UNIT CELL: 30 ATOM X/A Y/B * Z(ANGSTROM) * ***************************************************************** 1 T 26 FE * 3.332220233571E-01 1.664350001467E-01 5.975038441891E+00 2 T 8 O * -3.289334452690E-01 1.544678332212E-01 5.601153565811E+00 */ private void readFractionalCoords() throws Exception { if (isMolecular) newAtomSet(); readLine(); readLine(); int i = atomIndexLast; atomIndexLast = atomSetCollection.getAtomCount(); boolean doNormalizePrimitive = isPrimitive && !isMolecular && !isPolymer && !isSlab; while (readLine() != null && line.length() > 0) { Atom atom = atomSetCollection.addNewAtom(); String[] tokens = getTokens(); int atomicNumber = getAtomicNumber(tokens[2]); atom.atomName = getAtomName(tokens[3]); float x = parseFloat(tokens[4]); float y = parseFloat(tokens[5]); float z = parseFloat(tokens[6]); if (haveCharges) atom.partialCharge = atomSetCollection.getAtom(i++).partialCharge; // because with these we cannot use the "packed" keyword if (x < 0 && (isPolymer || isSlab || doNormalizePrimitive)) x += 1; if (y < 0 && (isSlab || doNormalizePrimitive)) y += 1; if (z < 0 && doNormalizePrimitive) z += 1; setAtomCoord(atom, x, y, z); atom.elementSymbol = getElementSymbol(atomicNumber); } atomCount = atomSetCollection.getAtomCount() - atomIndexLast; } private String getAtomName(String s) { String atomName = s; if (atomName.length() > 1 && Character.isLetter(atomName.charAt(1))) atomName = atomName.substring(0, 1) + Character.toLowerCase(atomName.charAt(1)) + atomName.substring(2); return atomName; } /* * Crystal adds 100 to the atomic number when the same atom will be described * with different basis sets. It also adds 200 when ECP are used: * * 1 T 282 PB 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2 T 16 * S -5.000000000000E-01 -5.000000000000E-01 -5.000000000000E-01 */ private int getAtomicNumber(String token) { int atomicNumber = parseInt(token); while (atomicNumber >= 100) atomicNumber -= 100; return atomicNumber; } /* * INPUT COORDINATES * * ATOM AT. N. COORDINATES 1 12 0.000000000000E+00 0.000000000000E+00 * 0.000000000000E+00 2 8 5.000000000000E-01 5.000000000000E-01 * 5.000000000000E-01 */ private void readInputCoords() throws Exception { readLine(); readLine(); while (readLine() != null && line.length() > 0) { Atom atom = atomSetCollection.addNewAtom(); String[] tokens = getTokens(); int atomicNumber = getAtomicNumber(tokens[1]); float x = parseFloat(tokens[2]); float y = parseFloat(tokens[3]); float z = parseFloat(tokens[4]); /* * we do not do this, because we have other ways to do it namely, "packed" * or "{555 555 1}" In this way, we can check those input coordinates * exactly * * if (x < 0) x += 1; if (y < 0) y += 1; if (z < 0) z += 1; */ setAtomCoord(atom, x, y, z); atom.elementSymbol = getElementSymbol(atomicNumber); } } private void newAtomSet() throws Exception { if (atomSetCollection.getAtomCount() == 0) return; applySymmetryAndSetTrajectory(); atomSetCollection.newAtomSet(); } private Double energy; private void readEnergy() { line = TextFormat.simpleReplace(line, "( ", "("); String[] tokens = getTokens(); energy = new Double(Double.parseDouble(tokens[2])); setEnergy(); } private void setEnergy() { atomSetCollection.setAtomSetAuxiliaryInfo("Energy", energy); atomSetCollection.setAtomSetCollectionAuxiliaryInfo("Energy", energy); atomSetCollection.setAtomSetName("Energy = " + energy + " Hartree"); } /* * MULLIKEN POPULATION ANALYSIS - NO. OF ELECTRONS 152.000000 * * ATOM Z CHARGE A.O. POPULATION * * 1 FE 26 23.991 2.000 1.920 2.057 2.057 2.057 0.384 0.674 0.674 */ private void readPartialCharges() throws Exception { if (haveCharges) return; haveCharges = true; discardLines(3); Atom[] atoms = atomSetCollection.getAtoms(); int i = atomSetCollection.getLastAtomSetAtomIndex(); while (readLine() != null && line.length() > 3) if (line.charAt(3) != ' ') atoms[i++].partialCharge = parseFloat(line.substring(9, 11)) - parseFloat(line.substring(12, 18)); } private float[] frequencies; private String[] data; private void readFrequencies() throws Exception { discardLines(3); readLine(); /* * FREQUENCIES COMPUTED ON A FRAGMENT OF 36 ATOMS * 2 ( 8 O ) 3 ( 8 O ) 4 ( 8 O ) 85 ( 8 O ) 86 ( 8 O ) * 87( 8 O ) 89( 6 C ) 90( 8 O ) 91( 8 O ) 92( 1 H ) * 93( 1 H ) 94( 6 C ) 95( 1 H ) 96( 8 O ) 97( 1 H ) * 98( 8 O ) 99( 6 C ) 100( 8 O ) 101( 8 O ) 102( 1 H ) * 103( 1 H ) 104( 6 C ) 105( 1 H ) 106( 8 O ) 107( 8 O ) * 108( 1 H ) 109( 6 C ) 110( 1 H ) 111( 8 O ) 112( 8 O ) * 113( 1 H ) 114( 6 C ) 115( 1 H ) 116( 8 O ) 117( 8 O ) * 118( 1 H ) *INFORMATION **** INPFREQ **** ANALYSIS OF THE VIBRATIONAL MODES * */ int numAtomsFrag = 0; boolean fragment = false; if (line.contains("FRAGMENT")) { fragment = true; numAtomsFrag = parseInt(line.substring(39, 44)); int[] atomFrag = new int[numAtomsFrag]; String Sfrag = ""; while (readLine() != null && line.indexOf("INFORMATION **** INPFREQ") < 0) Sfrag += line; Sfrag = TextFormat.simpleReplace(Sfrag, "(", " ("); String[] tokens = getTokens(Sfrag); for (int i = 0, pos = 0; i < numAtomsFrag; i++, pos += 5) atomFrag[i] = parseInt(tokens[pos]); } discardLinesUntilContains("MODES EIGV"); readLine(); Vector vData = new Vector(); int freqAtomCount = atomCount; if(fragment == true) freqAtomCount = numAtomsFrag; while (readLine() != null && line.length() > 0) { int i0 = parseInt(line.substring(1, 5)); int i1 = parseInt(line.substring(6, 10)); String irrep = line.substring(49, 52).trim(); String intens = line.substring(59, 69).replace(')', ' ').trim(); // not all crystal calculations include intensities values // this feature is activated when the keyword INTENS is on the input if (intens == null) intens = "not available"; String irActivity = line.substring(55, 58).trim(); String ramanActivity = line.substring(71, 73).trim(); String[] data = new String[] { irrep, intens, irActivity, ramanActivity }; for (int i = i0; i <= i1; i++) vData.add(data); } discardLinesUntilContains("NORMAL MODES NORMALIZED TO CLASSICAL AMPLITUDES"); readLine(); int lastAtomCount = -1; while (readLine() != null && line.startsWith(" FREQ(CM**-1)")) { int frequencyCount = 0; String[] tokens = getTokens(line.substring(15)); frequencies = new float[tokens.length]; for (int i = 0; i < tokens.length; i++) { float frequency = parseFloat(tokens[i]); frequencies[frequencyCount] = frequency; frequencyCount++; if (Logger.debugging) { Logger.debug((vibrationNumber + 1) + " frequency=" + frequency); } } boolean[] ignore = new boolean[frequencyCount]; int iAtom0 = 0; for (int i = 0; i < frequencyCount; i++) { data = (String[]) vData.get(vibrationNumber); ignore[i] = (!doGetVibration(++vibrationNumber) || data == null); if (ignore[i]) continue; lastAtomCount = cloneLastAtomSet(atomCount); if (i == 0) iAtom0 = atomSetCollection.getLastAtomSetAtomIndex(); setFreqValue(i); } readLine(); fillFrequencyData(iAtom0, freqAtomCount, lastAtomCount, ignore, false, 14, 10); readLine(); } } private void setFreqValue(int i) { String activity = ", IR: " + data[2] + ", Ram. " + data[3]; atomSetCollection.setAtomSetName(data[0] + " " + TextFormat.formatDecimal(frequencies[i], 2) + " cm-1 (" + TextFormat.formatDecimal(Float.parseFloat(data[1]), 0) + " km/Mole)" + activity); atomSetCollection.setAtomSetProperty("Frequency", frequencies[i] + " cm-1"); atomSetCollection.setAtomSetProperty("IR Intensity", data[1] + " km/Mole"); atomSetCollection.setAtomSetProperty("vibrationalSymmetry", data[0]); atomSetCollection.setAtomSetProperty("IR activity ", data[2]); atomSetCollection.setAtomSetProperty("Raman activity ", data[3]); } } -- Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
