package org.jmol.adapter.readers.more; import java.util.Arrays; import java.util.Hashtable; import java.util.Map; import java.util.Map.Entry; import javajs.util.Lst; import javajs.util.PT; import javajs.util.SB; import org.jmol.adapter.readers.xtal.VaspPoscarReader; import javajs.util.BS; import org.jmol.util.Logger; /** * A reader for various AFLOW file types. * * For starters, we have output from the binaries page. * * see http://www.aflowlib.org/binary_alloys.php * * or, in Jmol, from: * * print load("http://aflowlib.mems.duke.edu/php/apool.php?POST?job=awrapper_apool&lattice=all&alloy=AgAu") * * Unit cells are centered. * * Selected compositions can be obtained using the filter "Ca=0.5" for example. * * @author Bob Hanson * * @version 1.0 */ public class AFLOWReader extends VaspPoscarReader { private String aabb; private boolean readPRE; // private boolean readPOST; private float fracB = Float.NaN; private Map compositions; private boolean getComposition; private String listKey, listKeyCase; private int fileModelNumber; private boolean havePRE; private String titleMsg; //Looking for: // //[NbRh] # WEB file for ALL NbRh (Nb_svRh_pv) [calcs=285] [date=2015-05-29] [aflow 31010 (C) 2003-2015 Stefano Curtarolo] //[NbRh] REFERENCE: G. L. W. Hart, S. Curtarolo, T.B. Massalski, and O. Levy, Comprehensive Search for New Phases and Compounds in Binary Alloy Systems Based on Platinum-Group Metals, Using a Computational First-Principles Approach, Phys. Rev. X 3, 041035 (2013). //[NbRh] REFERENCE: S. Curtarolo, W. Setyawan, S. Wang, J. Xue, K. Yang, R. H. Taylor, L. J. Nelson, G. L. W. Hart, S. Sanvito, M. Buongiorno Nardelli, N. Mingo, and O. Levy, AFLOWLIB.ORG: a distributed materials properties repository from high-throughput ab initio calculations, Comp. Mat. Sci. 58, 227-235 (2012). //[NbRh] REFERENCE: S. Curtarolo, W. Setyawan, G. L. W. Hart, M. Jahnatek, R. V. Chepulskii, R. H. Taylor, S. Wang, J. Xue, K. Yang, O. Levy, M. Mehl, H. T. Stokes, D. O. Demchenko, and D. Morgan, AFLOW: an automatic framework for high-throughput materials discovery, Comp. Mat. Sci. 58, 218-226 (2012). //[NbRh] REFERENCE: R. H. Taylor, S. Curtarolo, and G. L. W. Hart, Predictions of the Pt8Ti phase in unexpected systems, J. Am. Chem. Soc. 132, 6851-6854 (2010). //[NbRh] REFERENCE: O. Levy, R. V. Chepulskii, G. L. W. Hart, and S. Curtarolo, The new face of rhodium alloys: revealing ordered structures from first principles, J. Am. Chem. Soc. 132, 833-837 (2010). //[NbRh] REFERENCE: S. Curtarolo, D. Morgan, and G. Ceder, Accuracy of ab-initio methods in predicting the crystal structures of metals: review of 80 binary alloys, Calphad 29, 163-211 (2005). //[NbRh] PROTOTYPES: http://aflowlib.mems.duke.edu/AFLOW/proto.pdf //[NbRh/1] # ************************************************************************************************************** //[NbRh/1] # ----------------------------------------------------------------------- //[NbRh/1] NbRh/1 //[NbRh/1] # ---- Structure PRE ---------------------------------------------------- //[NbRh/1] Nb_svRh_pv/1 - (1) - FCC A1 [B] (1) (htqc library) (swap of 2) //[NbRh/1] -14.173100 //[NbRh/1] 0.50000000000000 0.00000000000000 -0.50000000000000 //[NbRh/1] 0.50000000000000 -0.50000000000000 0.00000000000000 //[NbRh/1] 0.00000000000000 -0.50000000000000 -0.50000000000000 //[NbRh/1] 1 //[NbRh/1] Direct(1) [A1] //[NbRh/1] 0.00000000000000 0.00000000000000 0.00000000000000 Rh_pv //[NbRh/1] # ---- Structure POST --------------------------------------------------- //[NbRh/1] Nb_svRh_pv/1 - (1) - FCC A1 [B] (1) (ht //[NbRh/1] 1.244826 //[NbRh/1] 0.00000000000000 1.54318346068944 1.54318346068944 //[NbRh/1] 1.54318346068944 0.00000000000000 1.54318346068944 //[NbRh/1] 1.54318346068944 1.54318346068944 0.00000000000000 //[NbRh/1] 1 //[NbRh/1] Direct(1) [A1] //[NbRh/1] 0.00000000000000 0.00000000000000 0.00000000000000 //[NbRh/1] # ---- DATA ------------------------------------------------------------- //[NbRh/1] -7.34073000000000 # H [eV] (VASP) //[NbRh/1] -7.34073000000000 # H/at [eV] (VASP) //[NbRh/1] 0.00000000000000 # Hf_atom [eV] (VASP) //[NbRh/1] 0.00000000000000 # Mom/at //[NbRh/1] 14.17780000000000 # Volume/at //[NbRh/1] 0.00000000000000 # Ca //[NbRh/1] 1.00000000000000 # Cb //[NbRh/1] Fm-3m #225 # space group PRE //[NbRh/1] Fm-3m #225 # space group POST //[NbRh/1] # ---- URL -------------------------------------------------------------- //[NbRh/1] http://materials.duke.edu/AFLOWDATA/LIB2_RAW/Nb_svRh_pv/1/index.php //[NbRh/1] # ---- aflowlib.out ----------------------------------------------- //[NbRh/1] aurl=aflowlib.duke.edu:AFLOWDATA/LIB2_RAW/Nb_svRh_pv/1 | auid=aflow:e57e1645ae54fc4b | data_api=aapi1.1 | data_source=aflowlib | loop=lock,thermodynamics | code=vasp.4.6.35 | compound=Rh1 | prototype=1 | nspecies=1 | natoms=1 | composition=1 | density=12.0526 | scintillation_attenuation_length=0.96579 | stoichiometry=1 | species=Rh | species_pp=Rh_pv | dft_type=PAW_PBE | species_pp_version=Rh_pv:PAW_PBE:06Sep2000 | species_pp_ZVAL=15 | valence_cell_iupac=6 | valence_cell_std=9 | volume_cell=14.1778 | volume_atom=14.1778 | pressure=0 | geometry=2.716697,2.716697,2.716697,60,60,60 | energy_cell=-7.34073 | energy_atom=-7.34073 | enthalpy_cell=-7.34073 | enthalpy_atom=-7.34073 | eentropy_cell=9.706e-05 | eentropy_atom=9.706e-05 | enthalpy_formation_cell=-0.000163 | enthalpy_formation_atom=-0.000163 | entropic_temperature=0 | PV_cell=0 | PV_atom=0 | spin_cell=0 | spin_atom=0 | stoich=1.0000 | calculation_time=1879.86 | calculation_memory=636.17 | calculation_cores=8 | nbondxx=1.1225 | sg=Fm-3m #225,Fm-3m #225,Fm-3m #225 | sg2=Fm-3m #225,Fm-3m #225,Fm-3m #225 | spacegroup_orig=225 | spacegroup_relax=225 | forces=0,0,0 | positions_cartesian=0,0,0 | Bravais_lattice_orig=FCC | lattice_variation_orig=FCC | lattice_system_orig=cubic | Pearson_symbol_orig=cF4 | Bravais_lattice_relax=FCC | lattice_variation_relax=FCC | lattice_system_relax=cubic | Pearson_symbol_relax=cF4 | files=CONTCAR.relax,CONTCAR.relax.abinit,CONTCAR.relax.qe,CONTCAR.relax.vasp,CONTCAR.relax1,CONTCAR.relax2,LOCK,POSCAR.orig,POSCAR.relax2,aflow.in,aflow.qmvasp.out,edata.orig.out,edata.relax.out | aflow_version=aflow30069 | aflowlib_version=31007 | aflowlib_date=20150417_04:32:31_GMT-5 //[NbRh/1] # ************************************************************************************************************** //[NbRh/2] # ************************************************************************************************************** //[NbRh/2] # ----------------------------------------------------------------------- //[NbRh/2] NbRh/2 //[NbRh/2] # ---- Structure PRE ---------------------------------------------------- //[NbRh/2] Nb_svRh_pv/2 - (2) - FCC A1 [A] (2) (htqc library) //[NbRh/2] -18.313200 //... //[NbRh] PROTOTYPES: http://aflowlib.mems.duke.edu/awrapper.html //[NbRh] REFERENCE: G. L. W. Hart, S. Curtarolo, T.B. Massalski, and O. Levy, Comprehensive Search for New Phases and Compounds in Binary Alloy Systems Based on Platinum-Group Metals, Using a Computational First-Principles Approach, Phys. Rev. X 3, 041035 (2013). //[NbRh] REFERENCE: S. Curtarolo, W. Setyawan, S. Wang, J. Xue, K. Yang, R. H. Taylor, L. J. Nelson, G. L. W. Hart, S. Sanvito, M. Buongiorno Nardelli, N. Mingo, and O. Levy, AFLOWLIB.ORG: a distributed materials properties repository from high-throughput ab initio calculations, Comp. Mat. Sci. 58, 227-235 (2012). //[NbRh] REFERENCE: S. Curtarolo, W. Setyawan, G. L. W. Hart, M. Jahnatek, R. V. Chepulskii, R. H. Taylor, S. Wang, J. Xue, K. Yang, O. Levy, M. Mehl, H. T. Stokes, D. O. Demchenko, and D. Morgan, AFLOW: an automatic framework for high-throughput materials discovery, Comp. Mat. Sci. 58, 218-226 (2012). //[NbRh] REFERENCE: R. H. Taylor, S. Curtarolo, and G. L. W. Hart, Predictions of the Pt8Ti phase in unexpected systems, J. Am. Chem. Soc. 132, 6851-6854 (2010). //[NbRh] REFERENCE: O. Levy, R. V. Chepulskii, G. L. W. Hart, and S. Curtarolo, The new face of rhodium alloys: revealing ordered structures from first principles, J. Am. Chem. Soc. 132, 833-837 (2010). //[NbRh] REFERENCE: S. Curtarolo, D. Morgan, and G. Ceder, Accuracy of ab-initio methods in predicting the crystal structures of metals: review of 80 binary alloys, Calphad 29, 163-211 (2005). //[NbRh] # WEB file for ALL NbRh (Nb_svRh_pv) [calcs=285] [date=2015-05-29] [aflow 31010 (C) 2003-2015 Stefano Curtarolo] @Override protected void initializeReader() throws Exception { readPRE = checkFilterKey("PRE"); // readPOST = !checkFilterKey("NOPOST"); // forcePacked = !checkFilterKey("NOPACK"); String s; s = getFilter("CA="); if (s != null) fracB = (1 - parseFloatStr(s)); s = getFilter("CB="); if (s != null) fracB = parseFloatStr(s); s = getFilter("LIST="); listKey = (s == null ? "HF" : s); listKeyCase = listKey; getComposition = !Float.isNaN(fracB); discardLinesUntilStartsWith("["); //asc.setAtomSetName(title = line.trim()); aabb = line.substring(1, line.indexOf("]")); int pt = (PT.isUpperCase(aabb.charAt(1)) ? 1 : 2); defaultLabels = new String[] { aabb.substring(0, pt), aabb.substring(pt) }; while (rd().indexOf("] REFERENCE:") >= 0) appendLoadNote(line); compositions = new Hashtable(); quiet = true; asc.bsAtoms = new BS(); addJmolScript("unitcell off;axes off;"); havePRE = (line.indexOf("Structure PRE") >= 0); } @Override protected boolean checkLine() throws Exception { if (!havePRE) discardLinesUntilContains("Structure PRE"); havePRE = false; if (line == null) return false; continuing &= readPrePost(); return continuing; } private boolean readPrePost() throws Exception { fileModelNumber++; titleMsg = "#" + (modelNumber+1) + (getComposition ? "," + fileModelNumber + ", Cb=" + fracB : ""); elementLabel = null; int n0 = asc.bsAtoms.cardinality(); if (readPRE) { readStructure(titleMsg); } else { readElementLabelsOnly(); discardLinesUntilContains("Structure POST"); readStructure(titleMsg); } if (getData()) { applySymmetryAndSetTrajectory(); // XtalSymmetry sym = asc.getXSymmetry(); // T3 offset = sym.getOverallSpan(); // offset.scale(-0.5f); //asc.setModelInfoForSet(JC.INFO_UNIT_CELL_OFFSET, offset, asc.iSet); } else { asc.bsAtoms.clearBits(asc.getLastAtomSetAtomIndex(), asc.ac); doCheckUnitCell = false; } finalizeModel(); if (n0 != asc.bsAtoms.cardinality()) Logger.info("AFLOW: file#, saved#, atoms: " + fileModelNumber + " " + modelNumber + " " + (asc.bsAtoms.cardinality() - n0)); return !haveModel || modelNumber != desiredModelNumber; } private void finalizeModel() throws Exception { asc.removeLastUnselectedAtoms(); } /** * scan the AFLOWReader PRE structure for elements in coord section * @throws Exception */ private void readElementLabelsOnly() throws Exception { readLines(5); rdline(); int n = getTokens().length; elementLabel = new String[n]; rdline(); // DIRECT line = ""; String s = null, last = null; for (int i = 0; i < n; i++) { while (s == null || s.equals(last)) { rdline(); String[] tokens = getTokens(); if (tokens.length != 4 || (s = elementLabel[i] = getElement(tokens[3])) == null) { i = n + 1; break; } } last = s; } if (s == null) elementLabel = defaultLabels; } private boolean getData() throws Exception { discardLinesUntilContains("- DATA -"); Map htAFLOW = new Hashtable(); htAFLOW.put("fileModelNumber", Integer.valueOf(fileModelNumber)); htAFLOW.put("modelNumber", Integer.valueOf(modelNumber + 1)); htAFLOW.put("AaBb", aabb); int pt = 0; SB sb = new SB(); float listVal = Float.MAX_VALUE; String strcb = "?"; String listValStr = null; float cb = 0; while (rdline() != null && (pt = line.indexOf(" # ")) >= 0) { String key = line.substring(pt + 3).trim(); String val = line.substring(0, pt).trim(); sb.append(key).append("=").append(val).append(" | "); if (key.toUpperCase().startsWith(listKey)) { listKey = key.toUpperCase(); listKeyCase = key; listValStr = val; listVal = parseFloatStr(val); } if (key.equals("Ca")) { float ca = parseFloatStr(val); if (getComposition && Math.abs((1 - ca) - fracB) > 0.01f) return false; } else if (key.equals("Cb")) { cb = parseFloatStr(strcb = val); if (getComposition && Math.abs(cb - fracB) > 0.01f) return false; } else if (key.equals("Hf_atom [eV] (VASP)")) { float e = parseFloatStr(val); asc.setAtomSetEnergy(val, e); } } asc.setAtomSetName(titleMsg + (getComposition ? "" : " Cb=" + cb) + " " + listKey + "=" + listValStr); float[] count_min = compositions.get(strcb); if (!doGetModel(++modelNumber, null)) return false; if (count_min == null) compositions.put(strcb, count_min = new float[] { 0, Float.MAX_VALUE, 0 }); count_min[0]++; if (listVal < count_min[1]) { count_min[1] = listVal; count_min[2] = fileModelNumber; } while (line.indexOf("- URL -") < 0) rdline(); sb.append("URL=" + rdline() + "|"); while (line.indexOf("aurl=") < 0) rdline(); sb.append(line); String[] pairs = PT.split(sb.toString(), " | "); for (int i = pairs.length; --i >= 0;) { String[] kv = pairs[i].split("="); if (kv.length < 2) continue; float f = parseFloatStr(kv[1]); Object o = Float.isNaN(f) ? kv[1] : Float.valueOf(f); htAFLOW.put(kv[0], o); String kvclean = cleanKey(kv[0]); if (kvclean != kv[0]) htAFLOW.put(kvclean, o); } asc.setCurrentModelInfo("aflowInfo", htAFLOW); return true; } private Map keyMap = new Hashtable(); /** * cleans key to just letters and digits * * @param key * @return cleaned key */ private String cleanKey(String key) { String kclean = keyMap.get(key); if (kclean != null) return kclean; char[] chars = key.toCharArray(); for (int i = chars.length; --i >= 0;) if (!PT.isLetterOrDigit(chars[i])) chars[i] = '_'; keyMap.put(key, kclean = PT.trim(PT.rep(new String(chars), "__", "_"), "_")); return kclean; } @Override protected void finalizeSubclassReader() throws Exception { alignUnitCells(); listCompositions(); finalizeReaderASCR(); } @SuppressWarnings("cast") private void listCompositions() { Lst list = new Lst(); for (Entry e : compositions.entrySet()) { float[] count_min = (float[]) e.getValue(); list.addLast(e.getKey() + "\t" + ((int) count_min[0]) + "\t" + (int) count_min[2] + "\t" + listKeyCase + "\t" + count_min[1]); } String[] a = new String[list.size()]; list.toArray(a); Arrays.sort(a); for (int i = 0, n = a.length; i < n; i++) appendLoadNote(aabb + "\t" + a[i]); } private void alignUnitCells() { // for (int i = asc.atomSetCount; --i >= 0;) { // //// M3 matUnitCellOrientation = (M3) modelAuxiliaryInfo.get("matUnitCellOrientation"); // // // } } }