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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <projectDescription> | ||
| <name>QC_JSON_Schema</name> | ||
| <comment></comment> | ||
| <projects> | ||
| </projects> | ||
| <buildSpec> | ||
| </buildSpec> | ||
| <natures> | ||
| </natures> | ||
| </projectDescription> | ||
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| package org.jmol.adapter.readers.quantum; | ||
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Collaborator
There was a problem hiding this comment. Can we simply put this in a |
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| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.Hashtable; | ||
| import java.util.Map; | ||
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| import javajs.util.AU; | ||
| import javajs.util.Lst; | ||
| import javajs.util.SB; | ||
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| import org.jmol.adapter.smarter.Atom; | ||
| import org.jmol.api.JmolAdapter; | ||
| import org.jmol.util.Logger; | ||
| import org.qcschema.QCSchemaUnits; | ||
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| /** | ||
| * A molecular structure and orbital reader for MolDen files. | ||
| * See http://www.cmbi.ru.nl/molden/molden_format.html | ||
| * | ||
| * updated by Bob Hanson <hansonr@stolaf.edu> for Jmol 12.0/12.1 | ||
| * | ||
| * adding [spacegroup] [operators] [cell] [cellaxes] for Jmol 14.3.7 | ||
| * | ||
| * @author Matthew Zwier <mczwier@gmail.com> | ||
| */ | ||
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| public class QCJSONReader extends MoldenReader { | ||
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| private Map<String, Object> job; | ||
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| private int jobCount; | ||
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| private int modelCount; | ||
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| @SuppressWarnings("unchecked") | ||
| @Override | ||
| protected void initializeReader() { | ||
| super.initializeReader(); | ||
| SB sb = new SB(); | ||
| try { | ||
| while (rd() != null) | ||
| sb.append(line); | ||
| Lst<Object> json = vwr.parseJSONArray(sb.toString()); | ||
| // first record is version tag | ||
| Logger.info(json.get(0).toString()); | ||
| // second record is Jmol info; not used here | ||
| jobCount = json.size() - 2; | ||
| for (int i = 0; i < jobCount; i++) | ||
| processJob((Map<String, Object>)json.get(i + 2)); | ||
| } catch (Exception e) { | ||
| e.printStackTrace(); | ||
| } | ||
| continuing = false; | ||
| } | ||
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| /** | ||
| * @param job | ||
| * @throws Exception | ||
| */ | ||
| private void processJob(Map<String, Object> job) throws Exception { | ||
| this.job = job; | ||
| readSteps(); | ||
| /* | ||
| if (loadVibrations) | ||
| readFreqsAndModes(); | ||
| if (loadGeometries) | ||
| readGeometryOptimization(); | ||
| checkSymmetry(); | ||
| if (asc.atomSetCount == 1 && moData != null) | ||
| finalizeMOData(moData); | ||
| */ | ||
| } | ||
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| @Override | ||
| public void finalizeSubclassReader() throws Exception { | ||
| finalizeReaderASCR(); | ||
| } | ||
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| private void readSteps() throws Exception { | ||
| ArrayList<Object> steps = QCSchemaUnits.getList(job, "steps"); | ||
| int nSteps = steps.size(); | ||
| for (int iStep = 0; iStep < nSteps; iStep++) { | ||
| if (!doGetModel(++modelCount, null)) { | ||
| if (!checkLastModel()) | ||
| return; | ||
| continue; | ||
| } | ||
| asc.newAtomSet(); | ||
| @SuppressWarnings("unchecked") | ||
| Map<String, Object> step = (Map<String, Object>) steps.get(iStep); | ||
| Map<String, Object> topology = getMapSafely(step, "topology"); | ||
| Map<String, Object> atoms = getMapSafely(topology, "atoms"); | ||
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| // one or the other of these is required: | ||
| String[] symbols = QCSchemaUnits.getStringArray(atoms, "symbol"); | ||
| int[] atomNumbers = QCSchemaUnits.getIntArray(atoms, "atom_number"); | ||
| String[] atom_names = QCSchemaUnits.getStringArray(atoms, "atom_names"); | ||
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| double[] coords = QCSchemaUnits.getDoubleArray(atoms, "coords"); | ||
| modelAtomCount = coords.length / 3; | ||
| double f = QCSchemaUnits.getConversionFactor(atoms, "coords", QCSchemaUnits.UNITS_ANGSTROMS); | ||
| boolean isFractional = (f == 0); | ||
| setFractionalCoordinates(isFractional); | ||
| if (isFractional) { | ||
| f = QCSchemaUnits.getConversionFactor(atoms, "unit_cell", QCSchemaUnits.UNITS_ANGSTROMS); | ||
| double[] cell = QCSchemaUnits.getDoubleArray(atoms, "unit_cell"); | ||
| // a b c alpha beta gamma | ||
| // m.m00, m.m10, m.m20, // Va | ||
| // m.m01, m.m11, m.m21, // Vb | ||
| // m.m02, m.m12, m.m22, // Vc | ||
| // dimension, (float) volume, | ||
| if (cell == null) { | ||
| Logger.error("topology.unit_cell is missing even though atoms are listed as fractional"); | ||
| } else { | ||
| for (int i = 0; i < 6; i++) { | ||
| switch (i) { | ||
| case 3: | ||
| f = 1; | ||
| //$FALL-THROUGH$ | ||
| default: | ||
| setUnitCellItem(i, (float)(cell[i] * f)); | ||
| break; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| for (int i = 0, pt = 0; i < modelAtomCount; i++) { | ||
| Atom atom = asc.addNewAtom(); | ||
| setAtomCoordXYZ(atom, (float)(coords[pt++] * f), (float)(coords[pt++] * f), (float) (coords[pt++] | ||
| * f)); | ||
| String sym = (symbols == null ? JmolAdapter | ||
| .getElementSymbol(atomNumbers[i]) : symbols[i]); | ||
| atom.atomName = (atom_names == null ? sym : atom_names[i]); | ||
| atom.elementNumber = (short) (atomNumbers == null ? JmolAdapter | ||
| .getElementNumber(sym) : atomNumbers[i]); | ||
| } | ||
| if (doReadMolecularOrbitals) { | ||
| readMolecularOrbitals(getMapSafely(step, "molecular_orbitals")); | ||
| clearOrbitals(); | ||
| } | ||
| applySymmetryAndSetTrajectory(); | ||
| if (loadVibrations) { | ||
| readFreqsAndModes(QCSchemaUnits.getList(step, "vibrations")); | ||
| } | ||
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| } | ||
| } | ||
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| private boolean readFreqsAndModes(ArrayList<Object> vibrations) throws Exception { | ||
| // "frequency":{"value":-0.00,"units":["cm^-1","?"]}, | ||
| // "ir_intensity":{"value":0.000005,"units":["au",1]}, | ||
| // "vectors":[ | ||
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| if (vibrations != null) { | ||
| int n = vibrations.size(); | ||
| for (int i = 0; i < n; i++) { | ||
| @SuppressWarnings("unchecked") | ||
| Map<String, Object> vib = (Map<String, Object>) vibrations.get(i); | ||
| double freq = QCSchemaUnits.getDouble(vib, "frequency", QCSchemaUnits.UNITS_CM_1); | ||
| double[] vectors = QCSchemaUnits.getDoubleArray(vib, "vectors"); | ||
| if (i > 0) | ||
| asc.cloneLastAtomSet(); | ||
| asc.setAtomSetFrequency(null, null, "" + freq, QCSchemaUnits.UNITS_CM_1); | ||
| int i0 = asc.getLastAtomSetAtomIndex(); | ||
| for (int j = 0, pt = 0; j < modelAtomCount; j++) { | ||
| asc.addVibrationVector(j + i0, (float) (vectors[pt++] * ANGSTROMS_PER_BOHR), | ||
| (float) (vectors[pt++] * ANGSTROMS_PER_BOHR), (float) (vectors[pt++] | ||
| * ANGSTROMS_PER_BOHR)); | ||
| } | ||
| } | ||
| } | ||
| return true; | ||
| } | ||
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| private boolean haveEnergy = true; | ||
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| /** | ||
| * Read basis and orbital information. | ||
| * | ||
| * @param molecular_orbitals | ||
|
Collaborator
There was a problem hiding this comment. Can we provide much more information of what the |
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| * @return true if successful | ||
| * | ||
| * @throws Exception | ||
| */ | ||
| private boolean readMolecularOrbitals(Map<String, Object> molecular_orbitals) throws Exception { | ||
| if (molecular_orbitals == null) | ||
| return false; | ||
| String moBasisID = molecular_orbitals.get("basis_id").toString();//:"MOBASIS_1" | ||
| if (!readBasis(moBasisID)) | ||
| return false; | ||
| Boolean isNormalized = (Boolean) molecular_orbitals.get("__jmol_normalized"); | ||
| if (isNormalized != null && isNormalized.booleanValue()) | ||
| moData.put("isNormalized", isNormalized); | ||
| calculationType = (String) molecular_orbitals.get("__jmol_calculation_type"); | ||
| if (calculationType == null) | ||
| calculationType = "?"; | ||
| moData.put("calculationType", calculationType); | ||
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| ArrayList<Object> mos = QCSchemaUnits.getList(molecular_orbitals, "orbitals"); | ||
| int n = mos.size(); | ||
| for (int i = 0; i < n; i++) { | ||
| @SuppressWarnings("unchecked") | ||
| Map<String, Object> thisMO = (Map<String, Object>) mos.get(i); | ||
| double energy = QCSchemaUnits.getDouble(thisMO, "energy", "ev"); | ||
| double occupancy = QCSchemaUnits.getDouble(thisMO, "occupancy", null); | ||
| String symmetry = (String) thisMO.get("symmetry"); | ||
| String spin = (String) thisMO.get("type"); | ||
| if (spin != null) { | ||
| if (spin.indexOf("beta") >= 0) | ||
| alphaBeta = "beta"; | ||
| else if (spin.indexOf("alpha") >= 0) | ||
| alphaBeta = "alpha"; | ||
| } | ||
| float[] coefs = toFloatArray(QCSchemaUnits.getDoubleArray(thisMO, "coefficients")); | ||
| line = "" + symmetry; | ||
| if (filterMO()) { | ||
| Map<String, Object> mo = new Hashtable<String, Object>(); | ||
| mo.put("coefficients", coefs); | ||
| if (Double.isNaN(energy)) { | ||
| haveEnergy = false; | ||
| } else { | ||
| mo.put("energy", Float.valueOf((float) energy)); | ||
| } | ||
| if (!Double.isNaN(occupancy)) | ||
| mo.put("occupancy", Float.valueOf((float) occupancy)); | ||
| if (symmetry != null) | ||
| mo.put("symmetry", symmetry); | ||
| if (alphaBeta.length() > 0) | ||
| mo.put("type", alphaBeta); | ||
| setMO(mo); | ||
| if (debugging) { | ||
| Logger.debug(coefs.length + " coefficients in MO " + orbitals.size()); | ||
| } | ||
| } | ||
| } | ||
| if (debugging) | ||
| Logger.debug("read " + orbitals.size() + " MOs"); | ||
| ArrayList<Object> units = QCSchemaUnits.getList(molecular_orbitals, "orbitals_energy_units"); | ||
| String sunits = (units == null ? null : units.get(0).toString()); | ||
| setMOs(sunits == null || sunits.equals("?") ? "?" : sunits); | ||
| if (haveEnergy && doSort) | ||
| sortMOs(); | ||
| return false; | ||
| } | ||
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| private float[] toFloatArray(double[] da) { | ||
| float[] fa = new float[da.length]; | ||
| for (int j = da.length; --j >= 0;) | ||
| fa[j] = (float) da[j]; | ||
| return fa; | ||
| } | ||
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| String lastBasisID = null; | ||
| private boolean readBasis(String moBasisID) throws Exception { | ||
| Map<String, Object> moBasisData = getMapSafely(job, "mo_bases"); | ||
| Map<String, Object> moBasis = getMapSafely(moBasisData, moBasisID); | ||
| if (moBasis == null) { | ||
| Logger.error("No job.mo_bases entry for " + moBasisID); | ||
| return false; | ||
| } | ||
| if (moBasisID == lastBasisID) | ||
| return true; | ||
| lastBasisID = moBasisID; | ||
| ArrayList<Object> listG = QCSchemaUnits.getList(moBasis, "gaussians"); | ||
| ArrayList<Object> listS = QCSchemaUnits.getList(moBasis, "shells"); | ||
| if (listG == null && listS == null) { | ||
| listG = listS = QCSchemaUnits.getList(moBasis, "slaters"); | ||
| } | ||
| if ((listG == null) != (listS == null)) { | ||
| Logger.error("gaussians/shells or slaters missing"); | ||
| return false; | ||
| } | ||
| if (listG == listS) { | ||
| readSlaterBasis(listS); | ||
| } else { | ||
| readGaussianBasis(listG, listS); | ||
| } | ||
| return true; | ||
| } | ||
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| boolean readSlaterBasis(ArrayList<Object> listS) throws Exception { | ||
| /* | ||
| 1 0 0 0 1 1.5521451600 0.9776767193 | ||
| 1 1 0 0 0 1.5521451600 1.6933857512 | ||
| 1 0 1 0 0 1.5521451600 1.6933857512 | ||
| 1 0 0 1 0 1.5521451600 1.6933857512 | ||
| 2 0 0 0 0 1.4738648100 1.0095121222 | ||
| 3 0 0 0 0 1.4738648100 1.0095121222 | ||
| */ | ||
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| nCoef = listS.size(); | ||
| for (int i = 0; i < nCoef; i++) { | ||
| double[] a = QCSchemaUnits.getDoubleArray(listS.get(i), null); | ||
| addSlater((int) a[0], (int) a[1], (int) a[2], (int) a[3], (int) a[4], (float) a[5], (float) a[6]); | ||
| } | ||
| setSlaters(false, false); | ||
| return true; | ||
| } | ||
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| private boolean readGaussianBasis(ArrayList<Object> listG, ArrayList<Object> listS) throws Exception { | ||
| shells = new Lst<int[]>(); | ||
| for (int i = 0; i < listS.size(); i++) | ||
| shells.addLast(QCSchemaUnits.getIntArray(listS.get(i), null)); | ||
| int gaussianPtr = listG.size(); | ||
| float[][] garray = AU.newFloat2(gaussianPtr); | ||
| // [[exp, coef], [exp, coef],...] with sp [exp, coef1, coef2] | ||
| for (int i = 0; i < gaussianPtr; i++) | ||
| garray[i] = toFloatArray(QCSchemaUnits.getDoubleArray(listG.get(i), null)); | ||
| moData.put("shells", shells); | ||
| moData.put("gaussians", garray); | ||
| Logger.info(shells.size() + " slater shells read"); | ||
| Logger.info(garray.length + " gaussian primitives read"); | ||
| //Logger.info(nCoef + " MO coefficients expected for orbital type " + orbitalType); | ||
| asc.setCurrentModelInfo("moData", moData); | ||
| return false; | ||
| } | ||
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| @SuppressWarnings("unchecked") | ||
| private void sortMOs() { | ||
| Object[] list = orbitals.toArray(new Object[orbitals.size()]); | ||
| Arrays.sort(list, new MOEnergySorter()); | ||
| orbitals.clear(); | ||
| for (int i = 0; i < list.length; i++) | ||
| orbitals.addLast((Map<String, Object>)list[i]); | ||
| } | ||
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| /** | ||
| * Safely get a Map from a Map using a key. | ||
| * @param map | ||
| * @param key | ||
| * @return the Map or null | ||
| */ | ||
| @SuppressWarnings("unchecked") | ||
| private static Map<String, Object> getMapSafely(Map<String, Object> map, String key) { | ||
| return (map == null ? null : (Map<String, Object>) map.get(key)); | ||
| } | ||
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| /////////////////// from Molden reader -- TODO ///////////////// | ||
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| // private boolean checkSymmetry() throws Exception { | ||
| // // extension for symmetry | ||
| // if (line.startsWith("[SPACEGROUP]")) { | ||
| // setSpaceGroupName(rd()); | ||
| // rd(); | ||
| // return true; | ||
| // } | ||
| // if (line.startsWith("[OPERATORS]")) { | ||
| // while (rd() != null && line.indexOf("[") < 0) | ||
| // if (line.length() > 0) { | ||
| // Logger.info("adding operator " + line); | ||
| // setSymmetryOperator(line); | ||
| // } | ||
| // return true; | ||
| // } | ||
| // if (line.startsWith("[CELL]")) { | ||
| // rd(); | ||
| // Logger.info("setting cell dimensions " + line); | ||
| // // ANGS assumed here | ||
| // next[0] = 0; | ||
| // for (int i = 0; i < 6; i++) | ||
| // setUnitCellItem(i, parseFloat()); | ||
| // rd(); | ||
| // return true; | ||
| // } | ||
| // if (line.startsWith("[CELLAXES]")) { | ||
| // float[] f = new float[9]; | ||
| // fillFloatArray(null, 0, f); | ||
| // addExplicitLatticeVector(0, f, 0); | ||
| // addExplicitLatticeVector(1, f, 3); | ||
| // addExplicitLatticeVector(2, f, 6); | ||
| // return true; | ||
| // } | ||
| // return false; | ||
| // } | ||
| // | ||
| } | ||
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