package org.jmol.adapter.readers.xtal; /** * Piero Canepa * * Quantum Espresso * http://www.quantum-espresso.org and http://qe-forge.org/frs/?group_id=10 * @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.PT; import org.jmol.adapter.smarter.AtomSetCollectionReader; import org.jmol.adapter.smarter.Atom; public class EspressoReader extends AtomSetCollectionReader { private float[] cellParams; private Double totEnergy; private boolean endFlag; @Override protected void initializeReader() { setSpaceGroupName("P1"); doApplySymmetry = true; // inputOnly = checkFilter("INPUT"); } @Override protected boolean checkLine() throws Exception { if (line.contains("lattice parameter (a_0)") || line.contains("lattice parameter (alat)")) { readAparam(); } else if (line.contains("crystal axes:")) { readCellParam(false); } else if (line.contains("CELL_PARAMETERS (")) { readCellParam(true); } else if (line.contains("Cartesian axes")) { discardLinesUntilContains("positions ("); if (doGetModel(++modelNumber, null)) readAtoms(); } else if (line.contains("POSITIONS (")) { if (doGetModel(++modelNumber, null)) readAtoms(); } else if (line.contains("! total energy")) { readEnergy(); } else if (line.contains("A final scf")) { endFlag = true; } return true; } private float aPar; private void readAparam() throws Exception { // lattice parameter (alat) = 5.3033 a.u. aPar = parseFloatStr(getTokens()[4]) * ANGSTROMS_PER_BOHR; } /* crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( -0.500000 0.866025 0.000000 ) a(3) = ( 0.000000 0.000000 0.744955 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.000000 0.577350 0.000000 ) b(2) = ( 0.000000 1.154701 0.000000 ) b(3) = ( 0.000000 0.000000 1.342362 ) */ /* CELL_PARAMETERS (alat= 17.62853047) 1.019135101 0.000000000 0.000000000 -0.509567550 0.882596887 0.000000000 0.000000000 0.000000000 0.737221415 */ private void readCellParam(boolean andAPar) throws Exception { int i0 = (andAPar ? 0 : 3); /* in the old version of Espresso optimized cell parameters are expressed in Bohr unit CELL_PARAMETERS (bohr) -4.979256769 4.979256769 9.998215946 4.979256769 -4.979256769 9.998215946 4.979256769 4.979256769 -9.998215946 */ if (line.contains("bohr")) aPar = ANGSTROMS_PER_BOHR; /* in the old version of Espresso optimized cell parameters are expressed in function of the original aPar stored at the beginning CELL_PARAMETERS (alat) 1.001108280 0.000000000 0.000000000 0.000000000 1.001108280 0.000000000 0.000000000 0.000000000 1.301023011 So we also check for = in the line * */ if (andAPar && line.contains("=")) aPar = parseFloatStr(line.substring(line.indexOf("=") + 1)) * ANGSTROMS_PER_BOHR; //Can you look at the example HAP_fullopt_40_r1.fullopt from the 2nd model on the representation is correct //The 1st is wrong. // BH: It's just a bad starting geometry, but the program // very nicely cleans it up in just one step. //PC this is not true as it happens for every 0single jobs and even for single SCF calculations cellParams = new float[9]; for (int n = 0, i = 0; n < 3; n++) { String[] tokens = PT.getTokens(rd()); cellParams[i++] = parseFloatStr(tokens[i0]) * aPar; cellParams[i++] = parseFloatStr(tokens[i0 + 1]) * aPar; cellParams[i++] = parseFloatStr(tokens[i0 + 2]) * aPar; } } private void newAtomSet() throws Exception { asc.newAtomSet(); if (totEnergy != null) setEnergy(); } private void setCellParams() throws Exception { if (cellParams != null) { addExplicitLatticeVector(0, cellParams, 0); addExplicitLatticeVector(1, cellParams, 3); addExplicitLatticeVector(2, cellParams, 6); setSpaceGroupName("P1"); } } /* some have just atoms... site n. atom positions (a_0 units) 1 Ca tau( 1) = ( 0.5000000 -0.2886751 -0.0018296 ) 2 Ca tau( 2) = ( -0.5000000 0.2886751 0.3706481 ) ...some have masses... site n. atom mass positions (a_0 units) 1 Si 28.0800 tau( 1) = ( 0.00000 0.00000 0.00000 ) 2 Si 28.0800 tau( 2) = ( 0.25000 0.25000 0.25000 ) ...some just end with a blank line; others end with a short phrase... O -0.088707198 -0.347657305 0.434774168 O -0.258950107 0.088707198 0.434774168 O 0.000000000 0.000000000 -0.214003341 O 0.000000000 0.000000000 0.286225136 H 0.000000000 0.000000000 -0.071496337 H 0.000000000 0.000000000 0.428733409 End final coordinates */ private void readAtoms() throws Exception { // all atom block types are read here -- BH newAtomSet(); boolean isAlat = (line.contains("alat") || line.contains("a_0")); // This is when coordinates are like //F 3.456262920 8.764752820 1.733918940 0 0 0 boolean firstStr = (line.contains("site n.")); boolean isFractional = line.contains("crystal"); boolean isBohr = line.contains("bohr"); boolean isAngstrom = line.contains("angstrom"); if (isAlat || isFractional || isAngstrom) setCellParams(); setFractionalCoordinates(isFractional); while (rd() != null && line.length() > 45) { String[] tokens = getTokens(); Atom atom = asc.addNewAtom(); atom.atomName = tokens[(isBohr || tokens.length == 4 || !firstStr ? 0 : 1)]; int i1 = (isBohr || tokens.length == 4 || !firstStr ? 1 : tokens.length - 4); float x = parseFloatStr(tokens[i1++]); float y = parseFloatStr(tokens[i1++]); float z = parseFloatStr(tokens[i1++]); atom.set(x, y, z); if (isBohr) { atom.scale(ANGSTROMS_PER_BOHR); } else if (isAlat) { atom.scale(aPar); } setAtomCoord(atom); } applySymmetryAndSetTrajectory(); //This to avoid error when the class reads the FinalRun task /* A final scf calculation at the relaxed structure. The G-vectors are recalculated for the final unit cell Results may differ from those at the preceding step*/ if (endFlag) discardLinesUntilContains("Harris-Foulkes estimate"); } //! total energy = -1668.20791579 Ry private void readEnergy() throws Exception { totEnergy = Double.valueOf(Double.parseDouble(PT.getTokens(line.substring(line .indexOf("=") + 1))[0])); } private void setEnergy() { asc.setAtomSetEnergy("" + totEnergy, totEnergy.floatValue()); asc.setInfo("Energy", totEnergy); asc.setAtomSetName("E = " + totEnergy + " Ry"); } }