package org.jmol.adapter.readers.xtal; /** * Piero Canepa * * Dmol3 http://people.web.psi.ch/delley/dmol3.html * * @author Pieremanuele Canepa, Room 104, FM Group School of Physical Sciences, * Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United * Kingdom, pc229@kent.ac.uk * * @version 1.0 */ import javajs.util.DF; import javajs.util.PT; import org.jmol.adapter.smarter.AtomSetCollectionReader; import org.jmol.adapter.smarter.Atom; import org.jmol.util.Logger; public class DmolReader extends AtomSetCollectionReader { private float[] unitCellData; private Double totE; private boolean geomOpt; @Override protected boolean checkLine() throws Exception { //discardLinesUntilContains("INCOOR, atomic coordinates"); if (line.contains("** GEOMETRY OPTIMIZATION IN DELOCALIZED COORDINATES **")) { geomOpt = true; } else if (line.contains("INCOOR, atomic coordinates")) { geomOpt = false; } else if (!geomOpt ? line.contains("$cell vectors") : line .contains("Lattice:")) { readCellParam(); } else if (!geomOpt ? line.contains("$coordinates") : line .contains("Input Coordinates")) { readCoord(); } else if (line.contains(" Total Energy")) { readEnergy(); } else if (line.contains("Frequencies (cm-1)")) { readFreq(); } return true; } /* This is the intial cell in Bohr $cell vectors 29.35935199573791 0.00000000000000 0.00000000000000 0.00000000000000 25.95066401147447 0.00000000000000 1.69922562728373 0.00000000000000 17.54793198563486 */ private void readCellParam() throws Exception { unitCellData = new float[9]; for (int n = 0, i = 0; n < 3; n++) { String[] tokens = PT.getTokens(rd()); unitCellData[i++] = parseFloatStr(!geomOpt ? tokens[0] : tokens[4]) * ANGSTROMS_PER_BOHR; unitCellData[i++] = parseFloatStr(!geomOpt ? tokens[1] : tokens[5]) * ANGSTROMS_PER_BOHR; unitCellData[i++] = parseFloatStr(!geomOpt ? tokens[2] : tokens[6]) * ANGSTROMS_PER_BOHR; } } private void newAtomSet() throws Exception { applySymmetryAndSetTrajectory(); asc.newAtomSet(); if (totE != null) setEnergy(); doApplySymmetry = true; if (unitCellData != null) { addExplicitLatticeVector(0, unitCellData, 0); addExplicitLatticeVector(1, unitCellData, 3); addExplicitLatticeVector(2, unitCellData, 6); setSpaceGroupName("P1"); } setFractionalCoordinates(false); } /* * This are the initial coordinates in Bohr $coordinates Cl 9.46746707483118 -14.23892561172251 16.08667007245203 N 14.21326641906855 -5.69691653093388 24.31834296217202 C 13.13775850152313 -6.97234560502355 18.68982922572976 C 14.29353578655659 -4.55611608133144 19.67134825073612 C 13.37907463795869 -3.79263006614721 22.32571709227506 H 14.26305374826999 -2.21782944550038 22.73141162261102 C 14.74314585128389 -4.50474463251394 26.82192772160853 ....................... O 21.48475665233617 -3.60840142211203 27.57186515636701 H 20.70238433631352 -2.51542956278797 26.79973685669534 H 21.31202510204545 -4.76514473514059 26.64610779191174 $end */ private void readCoord() throws Exception { newAtomSet(); if (geomOpt) readLines(2); while (rd() != null && !geomOpt ? !line.contains("$end") : !line .contains("-----")) { String[] tokens = getTokens(); Atom atom = asc.addNewAtom(); atom.atomName = !geomOpt ? tokens[0] : tokens[1]; float factor = (float) (!geomOpt ? ANGSTROMS_PER_BOHR : 1.00); float x = parseFloatStr(!geomOpt ? tokens[1] : tokens[2]) * factor; float y = parseFloatStr(!geomOpt ? tokens[2] : tokens[3]) * factor; float z = parseFloatStr(!geomOpt ? tokens[3] : tokens[4]) * factor; atom.set(x, y, z); setAtomCoord(atom); } } private void readEnergy() throws Exception { rd(); if (line.contains("Ef")) totE = Double.valueOf(Double.parseDouble(PT.getTokens(line.substring(line.indexOf("Ef") +1 , line.indexOf("Ha") ))[1])); } private void setEnergy() { asc.setAtomSetEnergy("" + totE, totE.floatValue()); asc.setInfo("Energy", totE); asc.setAtomSetName("E = " + totE + " Hartree"); } /* Frequencies (cm-1) and normal modes 1: -16.6 2: -0.5 3: 0.2 4: 0.5 5: 10.0 6: 21.4 7: 22.1 8: 24.2 9: 31.1 Cl x -0.0864 -0.1628 -0.0005 0.0046 -0.0891 0.1852 -0.0800 0.0329 0.1295 y -0.2307 -0.0001 -0.1628 0.0000 0.0146 0.1332 -0.0101 0.0200 0.1026 z 0.0153 -0.0045 0.0008 -0.1628 0.1962 -0.0105 0.2003 -0.1943 -0.0911 N x -0.0093 -0.1023 -0.0002 0.0028 -0.0387 0.0737 -0.0256 -0.0017 0.0623 y -0.0556 0.0000 -0.1024 0.0000 -0.0197 -0.0288 -0.0228 0.0123 -0.0237 z -0.0199 -0.0029 0.0001 -0.1023 0.0245 0.0262 0.0117 -0.0891 0.0026 C x -0.0136 -0.0947 -0.0002 0.0026 -0.0490 0.0799 -0.0309 -0.0026 0.0752 y -0.1142 0.0000 -0.0947 0.0000 0.0277 0.0368 0.0096 0.0001 0.0191 z -0.0166 -0.0026 0.0004 -0.0947 0.1016 0.0271 0.1004 -0.0962 -0.0305 C x -0.0130 */ private void readFreq() throws Exception { int lastAtomCount = 0; int ac = asc.getLastAtomSetAtomCount(); while (rd() != null && line.charAt(1) == ' ') { String[] tokens = getTokens(); int frequencyCount = tokens.length / 2; float[] frequencies = new float[frequencyCount]; for (int i = 1, n = 0; i < tokens.length; i += 2, n++) { frequencies[n] = parseFloatStr(tokens[i]); if (debugging) Logger.debug((vibrationNumber + n) + " frequency=" + frequencies[n]); } boolean[] ignore = new boolean[frequencyCount]; int iAtom0 = 0; for (int i = 0; i < frequencyCount; i++) { ignore[i] = (!doGetVibration(++vibrationNumber)); if (ignore[i]) continue; applySymmetryAndSetTrajectory(); lastAtomCount = cloneLastAtomSet(ac, null); if (i == 0) iAtom0 = asc.getLastAtomSetAtomIndex(); asc.setAtomSetFrequency(vibrationNumber, null, null, String.valueOf(frequencies[i]), null); asc.setAtomSetName(DF.formatDecimal( frequencies[i], 2) + " cm-1"); } rd(); fillFrequencyData(iAtom0, ac, lastAtomCount, ignore, false, 5, 13, null, 0, null); readLines(2); } } }