/* $RCSfile$ * $Author: hansonr $ * $Date: 2006-08-27 21:07:49 -0500 (Sun, 27 Aug 2006) $ * $Revision: 5420 $ * * 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.quantum; import java.util.Hashtable; import java.util.Map; import org.jmol.adapter.smarter.Atom; import org.jmol.quantum.QS; import org.jmol.util.Escape; import org.jmol.util.Logger; import javajs.util.AU; import javajs.util.Lst; import javajs.util.PT; /** * Reads ORCA input and output files * */ public class OrcaReader extends MOReader { private String chargeTag; private int atomCount; private boolean xyzBohr; private int moModelSet; @Override protected void initializeReader() throws Exception { chargeTag = (checkAndRemoveFilterKey("CHARGE=LOW") ? "LOEW" : "MULL"); } @Override protected boolean checkLine() throws Exception { if (line.startsWith("! Bohrs")) { xyzBohr = true; return true; } if (line.startsWith("* xyz") || line.startsWith("*xyz")) { processInputFile(); continuing = false; return false; } if (line.indexOf("CARTESIAN COORDINATES (ANG") >= 0) { processAtoms(); return true; } if (line.indexOf("ATOMIC CHARGES") >= 0 && line.indexOf(chargeTag) >= 0) { processAtomicCharges(); return true; } if (line.startsWith("Total Energy")) { processEnergyLine(); return true; } if (line.indexOf("BASIS SET IN INPUT FORMAT") == 0) { processBasis(); } if (line.trim().equals("MOLECULAR ORBITALS")) { processMolecularOrbitals(); } return true; } // Total Energy : -76.36038546 Eh -2077.87173 eV private void processEnergyLine() { String[] tokens = getTokens(); asc.setAtomSetEnergy(tokens[3], Float.parseFloat(tokens[3])); } // # Simple Calculation // ! B3LYP def2-SVP opt // // * xyz 0 1 // // C -2.48753 2.50320 0.45149 // O -1.37907 2.85206 0.73571 // O -3.59614 2.15450 0.16756 // * private void processInputFile() throws Exception { while (rd() != null) { while (line.trim().length() == 0 || line.startsWith("#")) { rd(); } if (line.indexOf("*") >= 0) break; String[] tokens = getTokens(); Atom a = addAtomXYZSymName(tokens, 1, tokens[0], null); if (xyzBohr) a.scale(ANGSTROMS_PER_BOHR); } } // CARTESIAN COORDINATES (ANGSTROEM) // --------------------------------- // N -1.547600 0.308690 0.000000 // H -0.527600 0.308690 0.000000 // H -1.887600 -0.336090 -0.713490 // H -1.887600 1.248970 -0.201650 void processAtoms() throws Exception { modelNumber++; if (!doGetModel(modelNumber, null)) return; asc.newAtomSet(); baseAtomIndex = asc.ac; rd(); // ------------- while (rd() != null) { String[] tokens = getTokens(); if (tokens.length != 4) break; addAtomXYZSymName(tokens, 1, tokens[0], null); } if (baseAtomIndex == 0) atomCount = asc.ac; } //----------------------- //MULLIKEN ATOMIC CHARGES //----------------------- // 0 N : -0.267065 // 1 H : 0.089379 // 2 H : 0.089033 // 3 H : 0.088654 //Sum of atomic charges: 0.0000000 //LOEWDIN ATOMIC CHARGES //---------------------- // 0 N : -0.159838 // 1 H : 0.053364 // 2 H : 0.053340 // 3 H : 0.053134 void processAtomicCharges() throws Exception { rd(); for (int i = 0; i < atomCount; i++) { rd(); asc.atoms[i + baseAtomIndex].partialCharge = Float.parseFloat(line.substring(line.indexOf(":") + 1)); } } // ------------------------------- // AUXILIARY BASIS SET INFORMATION // ------------------------------- // There are 2 groups of distinct atoms // // Group 1 Type O : 12s5p4d2f1g contracted to 6s4p3d1f1g pattern {711111/2111/211/2/1} // Group 2 Type H : 5s2p1d contracted to 3s1p1d pattern {311/2/1} // // Atom 0O basis set group => 1 // Atom 1H basis set group => 2 // Atom 2H basis set group => 2 // // ----------------------------------- // AUXILIARY BASIS SET IN INPUT FORMAT // ----------------------------------- // // # Auxiliary basis set for element : H // NewAuxGTO H // S 3 // 1 15.6752927000 0.1007184237 // 2 3.6063578000 0.3404257499 // 3 1.2080016000 0.6491996172 // S 1 // 1 0.4726794000 1.0000000000 // S 1 // 1 0.2018100000 1.0000000000 // P 2 // 1 2.0281365000 0.5596620919 // 2 0.5358730000 0.5596620919 // D 1 // 1 2.2165124000 1.0000000000 // end; // private void processBasis() throws Exception { if (shells != null) return; shells = new Lst(); Lst gdata = new Lst(); boolean doSphericalF = true, doSphericalD = true; // ? calculationType = "5D7F"; // ? Map> basisLines = new Hashtable>(); rd(); while (discardLinesUntilContains2("#", "-----").indexOf("#") >= 0) { String element = line.substring(line.indexOf(":") + 1).trim(); Lst lines = new Lst(); basisLines.put(element, lines); rd(); while (rd().indexOf("end;") < 0) { if (line.length() > 10) line = line.substring(4); // skip index on gaussian line lines.addLast(getTokens()); } } // S 3 // 1 15.6752927000 0.1007184237 // 2 3.6063578000 0.3404257499 // 3 1.2080016000 0.6491996172 // S 1 // 1 0.4726794000 1.0000000000 // S 1 // 1 0.2018100000 1.0000000000 // P 2 // 1 2.0281365000 0.5596620919 // 2 0.5358730000 0.5596620919 // D 1 // 1 2.2165124000 1.0000000000 for (int ac = 0; ac < atomCount; ac++) { Lst lines = basisLines.get(asc.atoms[ac].elementSymbol); for (int j = 0; j < lines.size();) { String[] tokens = lines.get(j++); shellCount++; int[] slater = new int[4]; slater[0] = ac + 1; String oType = tokens[0]; if (doSphericalF && oType.indexOf("F") >= 0 || doSphericalD && oType.indexOf("D") >= 0) slater[1] = BasisFunctionReader.getQuantumShellTagIDSpherical(oType); else slater[1] = BasisFunctionReader.getQuantumShellTagID(oType); int nGaussians = parseIntStr(tokens[1]); slater[2] = gaussianCount + 1; // or parseInt(tokens[7]) slater[3] = nGaussians; if (debugging) Logger.debug("Slater " + shells.size() + " " + Escape.eAI(slater)); shells.addLast(slater); gaussianCount += nGaussians; for (int i = 0; i < nGaussians; i++) { tokens = lines.get(j++); if (debugging) Logger .debug("Gaussians " + (i + 1) + " " + Escape.eAS(tokens, true)); gdata.addLast(tokens); } } } gaussians = AU.newFloat2(gaussianCount); for (int i = 0; i < gaussianCount; i++) { String[] tokens = gdata.get(i); gaussians[i] = new float[tokens.length]; for (int j = 0; j < tokens.length; j++) gaussians[i][j] = parseFloatStr(tokens[j]); } Logger.info(shellCount + " slater shells read"); Logger.info(gaussianCount + " gaussian primitives read"); } // ------------------ // MOLECULAR ORBITALS // ------------------ // 0 1 2 3 4 5 // -18.75649 -0.88651 -0.46852 -0.29897 -0.23062 0.03125 // 2.00000 2.00000 2.00000 2.00000 2.00000 0.00000 // -------- -------- -------- -------- -------- -------- // 0O 1s 0.988667 0.276495 -0.000052 -0.109450 -0.000142 0.112677 // 0O 2s -0.040154 0.551582 -0.000072 -0.215647 -0.000273 0.208186 // 0O 3s 0.014488 0.264791 -0.000120 -0.355545 -0.000390 0.910843 // 0O 1pz -0.001944 0.081875 -0.234942 0.364091 0.373345 0.172906 // 0O 1px -0.001697 0.071503 0.410331 0.317584 0.000634 0.149709 // 0O 1py -0.001408 0.059231 -0.170031 0.264432 -0.514361 0.125934 // 0O 2pz 0.000045 0.004964 -0.090187 0.236855 0.289093 0.211428 // 0O 2px 0.000038 0.004074 0.158193 0.208582 0.000093 0.181044 // 0O 2py 0.000033 0.003627 -0.065232 0.172655 -0.399112 0.152738 // 0O 1dz2 0.000165 -0.000331 -0.011144 0.002751 0.012835 0.001386 // 0O 1dxz 0.000580 -0.000950 0.005623 0.012048 0.006499 0.005722 // 0O 1dyz -0.000943 0.005511 -0.009325 0.010295 -0.004904 0.004642 // 0O 1dx2y2 -0.000904 0.004175 0.013190 0.001900 0.007385 0.000600 // 0O 1dxy 0.000420 -0.000714 0.004074 0.008787 -0.008972 0.004113 // 1H 1s 0.002519 0.201346 0.333263 0.188938 0.000585 -0.152228 // 1H 2s -0.002454 0.014310 0.100167 0.067086 -0.000213 -0.784160 // 1H 1pz -0.000026 0.006148 -0.009444 0.021537 0.018322 0.004870 // 1H 1px -0.003374 -0.032789 -0.025691 -0.007750 -0.000079 -0.013472 // 1H 1py -0.000019 0.004435 -0.006851 0.015565 -0.025143 0.003594 // 2H 1s 0.002518 0.201043 -0.333152 0.190099 0.000600 -0.152926 private void processMolecularOrbitals() throws Exception { if (shells == null) return; Map[] mos = AU.createArrayOfHashtable(6); Lst[] data = AU.createArrayOfArrayList(6); int nThisLine = 0; rd(); Lst labels = new Lst(); while (rd() != null && line.indexOf("----") < 0) { if (line.length() == 0) continue; String[] tokens; if (line.startsWith(" ")) { addMODataOR(nThisLine, labels, data, mos); labels.clear(); rd(); // energy line tokens = getTokens(); nThisLine = tokens.length; for (int i = 0; i < nThisLine; i++) { mos[i] = new Hashtable(); data[i] = new Lst(); mos[i].put("energy", Float.valueOf(tokens[i])); } rd(); // occupancy line tokens = getTokens(); for (int i = 0; i < nThisLine; i++) { mos[i].put("occupancy", Float.valueOf(tokens[i])); } rd(); // ---- continue; } try { tokens = getTokens(); String type = tokens[tokens.length - nThisLine - 1].substring(1).toUpperCase(); labels.addLast(type); if (PT.isDigit(type.charAt(0))) type = type.substring(1); // "1S" if (!QS.isQuantumBasisSupported(type.charAt(0)) && "XYZ".indexOf(type.charAt(0)) >= 0) type = (type.length() == 2 ? "D" : "F") + type; if (!QS.isQuantumBasisSupported(type.charAt(0))) continue; tokens = getStrings(line.substring(line.length() - 10 * nThisLine), nThisLine, 10); for (int i = 0; i < nThisLine; i++) data[i].addLast(tokens[i]); } catch (Exception e) { Logger.error("Error reading Gaussian file Molecular Orbitals at line: " + line); break; } } addMODataOR(nThisLine, labels, data, mos); setMOData(moModelSet != asc.atomSetCount); moModelSet = asc.atomSetCount; } private void addMODataOR(int nThisLine, Lst labels, Lst[] data, Map[] mos) { if (labels.size() == 0) return; for (int i = 0; i < labels.size(); i++) { if (labels.get(i).equals("PZ")) { // Switch PX and PZ for (int j = 0; j < nThisLine; j++) { Lst d = data[j]; String s = d.removeItemAt(i); d.add(i+2, s); } // } } addMOData(nThisLine, data, mos); } }