// ## operation writeChemkinSpecies(ReactionModel,SystemSnapshot)
public static String writeChemkinSpecies(
ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) {
// #[ operation writeChemkinSpecies(ReactionModel,SystemSnapshot)
StringBuilder result = new StringBuilder();
result.append("SPECIES\n");
CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
// write inert gas
for (Iterator iter = p_beginStatus.getInertGas(); iter.hasNext(); ) {
String name = (String) iter.next();
result.append('\t' + name + '\n');
}
// write species
for (Iterator iter = cerm.getSpecies(); iter.hasNext(); ) {
Species spe = (Species) iter.next();
result.append('\t' + spe.getChemkinName() + '\n');
}
result.append("END\n");
return result.toString();
// #]
}
public void populate(EvolutionState state, int thread) {
// should we load individuals from a file? -- duplicates are permitted
if (loadInds != null) {
try {
readSubpopulation(state, new LineNumberReader(new FileReader(loadInds)));
} catch (IOException e) {
state.output.fatal(
"An IOException occurred when trying to read from the file "
+ loadInds
+ ". The IOException was: \n"
+ e);
}
} else {
Hashtable h = null;
if (numDuplicateRetries >= 1) h = new Hashtable(individuals.length / 2); // seems reasonable
for (int x = 0; x < individuals.length; x++) {
for (int tries = 0; tries <= /* Yes, I see that*/ numDuplicateRetries; tries++) {
individuals[x] = species.newIndividual(state, thread);
if (numDuplicateRetries >= 1) {
// check for duplicates
Object o = h.get(individuals[x]);
if (o == null) // found nothing, we're safe
// hash it and go
{
h.put(individuals[x], individuals[x]);
break;
}
}
} // oh well, we tried to cut down the duplicates
}
}
}
public void setup(final EvolutionState state, final Parameter base) {
Parameter def = defaultBase();
int size;
// do we load from a file?
loadInds = state.parameters.getFile(base.push(P_FILE), null);
// what species do we use?
species =
(Species)
state.parameters.getInstanceForParameter(
base.push(P_SPECIES), def.push(P_SPECIES), Species.class);
species.setup(state, base.push(P_SPECIES));
// how big should our subpopulation be?
size = state.parameters.getInt(base.push(P_SUBPOPSIZE), def.push(P_SUBPOPSIZE), 1);
if (size <= 0)
state.output.fatal(
"Subpopulation size must be an integer >= 1.\n",
base.push(P_SUBPOPSIZE),
def.push(P_SUBPOPSIZE));
// How often do we retry if we find a duplicate?
numDuplicateRetries = state.parameters.getInt(base.push(P_RETRIES), def.push(P_RETRIES), 0);
if (numDuplicateRetries < 0)
state.output.fatal(
"The number of retries for duplicates must be an integer >= 0.\n",
base.push(P_RETRIES),
def.push(P_RETRIES));
individuals = new Individual[size];
}
// ## operation generateSpeciesStatus(ReactionModel,ArrayList,ArrayList,ArrayList)
private LinkedHashMap generateSpeciesStatus(
ReactionModel p_reactionModel,
ArrayList p_speciesChemkinName,
ArrayList p_speciesConc,
ArrayList p_speciesFlux) {
// #[ operation generateSpeciesStatus(ReactionModel,ArrayList,ArrayList,ArrayList)
int size = p_speciesChemkinName.size();
if (size != p_speciesConc.size() || size != p_speciesFlux.size())
throw new InvalidSpeciesStatusException();
LinkedHashMap speStatus = new LinkedHashMap();
for (int i = 0; i < size; i++) {
String name = (String) p_speciesChemkinName.get(i);
int ID = parseIDFromChemkinName(name);
Species spe = SpeciesDictionary.getInstance().getSpeciesFromID(ID);
double conc = ((Double) p_speciesConc.get(i)).doubleValue();
double flux = ((Double) p_speciesFlux.get(i)).doubleValue();
System.out.println(
String.valueOf(spe.getID())
+ '\t'
+ spe.getName()
+ '\t'
+ String.valueOf(conc)
+ '\t'
+ String.valueOf(flux));
if (conc < 0) {
double aTol = ReactionModelGenerator.getAtol();
// if (Math.abs(conc) < aTol) conc = 0;
// else throw new NegativeConcentrationException("species " + spe.getName() + " has negative
// conc: " + String.valueOf(conc));
if (conc < -100.0 * aTol)
throw new NegativeConcentrationException(
"Species " + spe.getName() + " has negative concentration: " + String.valueOf(conc));
}
SpeciesStatus ss = new SpeciesStatus(spe, 1, conc, flux);
speStatus.put(spe, ss);
}
return speStatus;
// #]
}
/**
* Reads a subpopulation in binary form, from the format generated by writeSubpopulation(...). If
* the number of individuals is not identical, the individuals array will be deleted and replaced
* with a new array, and a warning will be generated as individuals will have to be created using
* newIndividual(...) rather than readIndividual(...)
*/
public void readSubpopulation(final EvolutionState state, final DataInput dataInput)
throws IOException {
int numIndividuals = dataInput.readInt();
if (numIndividuals != individuals.length) {
state.output.warnOnce(
"On reading subpopulation from binary stream, the subpopulation size was incorrect.\n"
+ "Had to resize and use newIndividual() instead of readIndividual().");
individuals = new Individual[numIndividuals];
for (int i = 0; i < individuals.length; i++)
individuals[i] = species.newIndividual(state, dataInput);
} else
for (int i = 0; i < individuals.length; i++) individuals[i].readIndividual(state, dataInput);
}
/**
* Reads a subpopulation from the format generated by printSubpopulation(....). If the number of
* individuals is not identical, the individuals array will be deleted and replaced with a new
* array, and a warning will be generated as individuals will have to be created using
* newIndividual(...) rather than readIndividual(...).
*/
public void readSubpopulation(final EvolutionState state, final LineNumberReader reader)
throws IOException {
// read in number of individuals and check to see if this appears to be a valid subpopulation
int numIndividuals = Code.readIntegerWithPreamble(NUM_INDIVIDUALS_PREAMBLE, state, reader);
// read in individuals
if (numIndividuals != individuals.length) {
state.output.warnOnce(
"On reading subpopulation from text stream, the subpopulation size didn't match.\n"
+ "Had to resize and use newIndividual() instead of readIndividual().");
individuals = new Individual[numIndividuals];
for (int i = 0; i < individuals.length; i++) {
int j = Code.readIntegerWithPreamble(INDIVIDUAL_INDEX_PREAMBLE, state, reader);
// sanity check
if (j != i)
state.output.warnOnce(
"On reading subpopulation from text stream, some individual indexes in the subpopulation did not match.");
individuals[i] = species.newIndividual(state, reader);
}
} else
for (int i = 0; i < individuals.length; i++) {
int j = Code.readIntegerWithPreamble(INDIVIDUAL_INDEX_PREAMBLE, state, reader);
// sanity check
if (j != i)
state.output.warnOnce(
"On reading subpopulation from text stream, some individual indexes in the subpopulation did not match.");
if (individuals[i] != null) individuals[i].readIndividual(state, reader);
else {
state.output.warnOnce(
"On reading subpopulation from text stream, some of the preexisting subpopulation's slots were null.\n"
+ "Had to use newIndividual() instead of readIndividual(). If you're starting an evolutionary run by reading an\n"
+ "existing population from a file, this is expected -- ignore this message.");
individuals[i] = species.newIndividual(state, reader);
}
}
}
// ## operation writeReactorInputFile(ReactionModel,ReactionTime,ReactionTime,SystemSnapshot)
public boolean writeReactorInputFile(
ReactionModel p_reactionModel,
ReactionTime p_beginTime,
ReactionTime p_endTime,
SystemSnapshot p_beginStatus) {
// #[ operation writeReactorInputFile(ReactionModel,ReactionTime,ReactionTime,SystemSnapshot)
// construct "input" string
String input = "<?xml version=\"1.0\" standalone=\"no\"?>" + "\n";
String dir = System.getProperty("RMG.workingDirectory");
if (!dir.endsWith("/")) dir += "/";
String dtd = dir + "software/reactorModel/documentTypeDefinitions/reactorInput.dtd";
input += "<!DOCTYPE reactorinput SYSTEM \"" + dtd + "\">" + "\n";
input += "<reactorinput>" + "\n";
input += "<header>" + "\n";
input += "<title>Reactor Input File</title>" + "\n";
input +=
"<description>RMG-generated file used to call an external reactor model</description>"
+ "\n";
input += "</header>" + "\n";
input += "<inputvalues>" + "\n";
input += "<integrationparameters>" + "\n";
input += "<reactortype>" + reactorType + "</reactortype>" + "\n";
input +=
"<starttime units=\""
+ p_beginTime.getUnit()
+ "\">"
+ MathTool.formatDouble(p_beginTime.getTime(), 15, 6)
+ "</starttime>"
+ "\n";
input +=
"<endtime units=\""
+ p_endTime.getUnit()
+ "\">"
+ MathTool.formatDouble(p_endTime.getTime(), 15, 6)
+ "</endtime>"
+ "\n";
// input += "<starttime units=\"" + p_beginTime.unit + "\">" +
// MathTool.formatDouble(p_beginTime.time,15,6) + "</starttime>" + "\n";
// input += "<endtime units=\"" + p_endTime.unit + "\">" +
// MathTool.formatDouble(p_endTime.time,15,6) + "</endtime>" + "\n";
input += "<rtol>" + rtol + "</rtol>" + "\n";
input += "<atol>" + atol + "</atol>" + "\n";
input += "</integrationparameters>" + "\n";
input += "<chemistry>" + "\n";
input += "</chemistry>" + "\n";
input += "<systemstate>" + "\n";
input +=
"<temperature units=\"K\">"
+ MathTool.formatDouble(p_beginStatus.getTemperature().getK(), 15, 6)
+ "</temperature>"
+ "\n";
input +=
"<pressure units=\"Pa\">"
+ MathTool.formatDouble(p_beginStatus.getPressure().getPa(), 15, 6)
+ "</pressure>"
+ "\n";
for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) {
SpeciesStatus spcStatus = (SpeciesStatus) iter.next();
Species thisSpecies = spcStatus.getSpecies();
CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
if (cerm.containsAsReactedSpecies(thisSpecies)) {
String spcChemkinName = thisSpecies.getChemkinName();
double concentration = spcStatus.getConcentration();
input +=
"<amount units=\"molPerCm3\" speciesid=\""
+ spcChemkinName
+ "\">"
+ concentration
+ "</amount>"
+ "\n";
}
}
for (Iterator iter = p_beginStatus.getInertGas(); iter.hasNext(); ) {
String name = (String) iter.next();
double conc = p_beginStatus.getInertGas(name);
if (conc != 0.0)
input +=
"<amount units=\"molPerCm3\" speciesid=\"" + name + "\">" + conc + "</amount>" + "\n";
}
input += "</systemstate>" + "\n";
input += "</inputvalues>" + "\n";
input += "</reactorinput>" + "\n";
// write "input" string to file
try {
String file = "chemkin/reactorInput.xml";
FileWriter fw = new FileWriter(file);
fw.write(input);
fw.close();
return true;
} catch (Exception e) {
System.out.println("Error in writing reactorInput.xml!");
System.out.println(e.getMessage());
return false;
}
// #]
}
// ## operation writeChemkinThermo(ReactionModel)
public static String writeChemkinThermo(ReactionModel p_reactionModel) {
// #[ operation writeChemkinThermo(ReactionModel)
/*
String thermoHeader = "! neon added by pey (20/6/04) - used thermo for Ar\n";
thermoHeader += "Ne 120186Ne 1 G 0300.00 5000.00 1000.00 1\n";
thermoHeader += " 0.02500000E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2\n";
thermoHeader += "-0.07453750E+04 0.04366001E+02 0.02500000E+02 0.00000000E+00 0.00000000E+00 3\n";
thermoHeader += " 0.00000000E+00 0.00000000E+00-0.07453750E+04 0.04366001E+02 4\n";
thermoHeader += "N2 121286N 2 G 0300.00 5000.00 1000.00 1\n";
thermoHeader += " 0.02926640e+02 0.01487977e-01-0.05684761e-05 0.01009704e-08-0.06753351e-13 2\n";
thermoHeader += "-0.09227977e+04 0.05980528e+02 0.03298677e+02 0.01408240e-01-0.03963222e-04 3\n";
thermoHeader += " 0.05641515e-07-0.02444855e-10-0.01020900e+05 0.03950372e+02 4\n";
thermoHeader += "Ar 120186Ar 1 G 0300.00 5000.00 1000.00 1\n";
thermoHeader += " 0.02500000e+02 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 2\n";
thermoHeader += "-0.07453750e+04 0.04366001e+02 0.02500000e+02 0.00000000e+00 0.00000000e+00 3\n";
thermoHeader += " 0.00000000e+00 0.00000000e+00-0.07453750e+04 0.04366001e+02 4\n";
*/
// #]
String thermoHeader =
"! The first four sets of polynomial coefficients (Ar, N2, Ne, He) are from \n";
thermoHeader +=
"! THIRD MILLENIUM IDEAL GAS AND CONDENSED PHASE THERMOCHEMICAL DATABASE FOR \n";
thermoHeader +=
"! COMBUSTION WITH UPDATES FROM ACTIVE THERMOCHENICAL TABLES \n";
thermoHeader +=
"! Authors: Alexander Burcat and Branko Ruscic \n";
thermoHeader +=
"! \n";
thermoHeader +=
"! The rest of the species are estimated by RMG (http://rmg.mit.edu/) \n";
// thermoHeader += "! Ar HF298=0. REF=C.E. Moore 'Atomic Energy Levels' NSRDS-NBS 35 (1971)
// p.211 \n";
// thermoHeader += "! NASA Glen (former Lewis) Research Center (1988)
// \n";
thermoHeader +=
"Ar L 6/88Ar 1 G 200.000 6000.000 1000. 1\n";
thermoHeader +=
" 0.25000000E+01 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2\n";
thermoHeader +=
"-0.74537500E+03 0.43796749E+01 0.25000000E+01 0.00000000E+00 0.00000000E+00 3\n";
thermoHeader +=
" 0.00000000E+00 0.00000000E+00-0.74537500E+03 0.43796749E+01 4\n";
// thermoHeader += "! N2 HF298= 0.0 KJ REF=TSIV Max Lst Sq Error Cp @ 6000 K 0.29%
// \n";
thermoHeader +=
"N2 G 8/02N 2 G 200.000 6000.000 1000. 1\n";
thermoHeader +=
" 2.95257637E+00 1.39690040E-03-4.92631603E-07 7.86010195E-11-4.60755204E-15 2\n";
thermoHeader +=
"-9.23948688E+02 5.87188762E+00 3.53100528E+00-1.23660988E-04-5.02999433E-07 3\n";
thermoHeader +=
" 2.43530612E-09-1.40881235E-12-1.04697628E+03 2.96747038E+00 4\n";
// thermoHeader += "!Ne HF298= 0.0 KJ REF=McBride, Heimel, Ehlers & Gordon
// \n";
// thermoHeader += "! 'Thermodynamic Properties to 6000 K...' NASA SP-3001
// (1963) \n";
thermoHeader +=
"Ne L10/90Ne 1 G 200.0 6000.00 1000.0 1\n";
thermoHeader +=
" 0.25000000E 01 0.00000000E 00 0.00000000E 00 0.00000000E 00 0.00000000E 00 2\n";
thermoHeader +=
"-0.74537500E 03 0.33553227E 01 0.25000000E 01 0.00000000E 00 0.00000000E 00 3\n";
thermoHeader +=
" 0.00000000E 00 0.00000000E 00-0.74537498E 03 0.33553227E 01 4\n";
// thermoHeader += "7440-59-7
// \n";
// thermoHeader += "He HF298=0.0 KJ REF=McBride, Heimel, Ehlers & Gordon "Thermodynamic
// Properties\n";
// thermoHeader += "to 6000K ..." NASA SP-3001 1963.
// \n";
thermoHeader +=
"He REF ELEMENT L10/90HE 1. 0. 0. 0.G 200.000 6000.000 B 4.00260 1\n";
thermoHeader +=
" 2.50000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2\n";
thermoHeader +=
"-7.45375000E+02 9.28723974E-01 2.50000000E+00 0.00000000E+00 0.00000000E+00 3\n";
thermoHeader +=
" 0.00000000E+00 0.00000000E+00-7.45375000E+02 9.28723974E-01 0.00000000E+00 4\n\n";
StringBuilder result = new StringBuilder();
result.append("THERMO ALL\n");
result.append(" 300.000 1000.000 5000.000\n");
result.append(thermoHeader);
CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
for (Iterator iter = cerm.getSpecies(); iter.hasNext(); ) {
Species spe = (Species) iter.next();
if (spe.getNasaThermoSource() != null) {
result.append("!" + spe.getNasaThermoSource() + "\n");
}
result.append(spe.getNasaThermoData() + "\n");
}
result.append("END\n");
// Added by Amrit for Richard's liquid phase chemkin code 05/21/2009
result.append("\n");
return result.toString();
// #]
}