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Fix indentation in QMLibraryEditor.java
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The mixture of spaces and tabs was driving git crazy.
In anticipation of ReactionMechanismGenerator#278 (comment)
I have opted for soft tabs (4 spaces).
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@rwest
rwest committed Nov 26, 2012
1 parent 0861bc7 commit a3a88bc
Showing 1 changed file with 122 additions and 122 deletions.
244 changes: 122 additions & 122 deletions source/RMG/jing/chem/QMLibraryEditor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -48,191 +48,191 @@
*/

public class QMLibraryEditor {
//data fields

//data fields
/** The object representing the dictionary. */
private static BufferedWriter dictionaryFile = null;

/** The object representing the library */
private static BufferedWriter libraryFile = null;
/** The newline character to use. */
private static String newLine = System.getProperty("line.separator");
/** Number of species added to Library used for naming */
//may have to get rid of this if I find naming is important
private static int counter = 0;

//Constructor
//methods
/** Initializes the two files Dictionary.txt and Library.txt */
public static void initialize() {
try {

/** The newline character to use. */
private static String newLine = System.getProperty("line.separator");

/** Number of species added to Library used for naming */
//may have to get rid of this if I find naming is important
private static int counter = 0;

//Constructor

//methods
/** Initializes the two files Dictionary.txt and Library.txt */
public static void initialize() {
try {
// Open the log file (throws IOException if unsuccessful)
dictionaryFile = new BufferedWriter(new FileWriter("QMThermoLibrary/Dictionary.txt", true));
Logger.info("Creating Dictionary for QM Thermo Library");
}
catch (IOException e) {
// This is pretty essential to new QMTP regime. Stop if it fails
Logger.critical("Could not create QM Thermo Dictionary");
Logger.critical("Could not create QM Thermo Dictionary");
System.exit(0);
}
try {

try {
// Open the log file (throws IOException if unsuccessful)
// Boolean Argument in FileWriter means that it will append to existing files.
// Boolean Argument in FileWriter means that it will append to existing files.
libraryFile = new BufferedWriter(new FileWriter("QMThermoLibrary/Library.txt", true));
Logger.info("Creating Library for QM Thermo Library");
}
catch (IOException e) {
// This is pretty essential to new QMTP regime. Stop if it fails
Logger.critical("Could not create QM Thermo Library");
// This is pretty essential to new QMTP regime. Stop if it fails
Logger.critical("Could not create QM Thermo Library");
System.exit(0);
}
}

}

/**
* Close the Dictionary and Library when finished.
*/
public static void finish() {
try {
// Close the log file (throws IOException if unsuccessful)
if (dictionaryFile != null) dictionaryFile.close();
if (dictionaryFile != null) dictionaryFile.close();
if (libraryFile != null) libraryFile.close();
}
catch (IOException e) {
throw new RuntimeException(e);
throw new RuntimeException(e);
}
}

/**
* Adds species to Dictionary.txt and Library.txt
*/
//Will probably require p_graph also
//Using InChI as name as per suggestion by gmagoon
public static void addQMTPThermo(ChemGraph p_graph, String inChI, ThermoData qmResult, String qmMethod, String qmProgram){
//Count the number of species added for naming
counter ++;
//Create comment for logger. I need to double check if naming convention will interfere with model
String comment = "Adding " + inChI + " to the QMTP thermo Library";
// String name = "SQM(";
// name.concat(Integer.toString(counter));
// name.concat(")");

Logger.info(comment);
//finish implementation of this method
addLibraryEntry(inChI, qmResult, qmMethod, qmProgram);
//finish implementation of this method
addDictionaryEntry(inChI, p_graph);
//Count the number of species added for naming
counter ++;
//Create comment for logger. I need to double check if naming convention will interfere with model
String comment = "Adding " + inChI + " to the QMTP thermo Library";
// String name = "SQM(";
// name.concat(Integer.toString(counter));
// name.concat(")");

Logger.info(comment);
//finish implementation of this method
addLibraryEntry(inChI, qmResult, qmMethod, qmProgram);
//finish implementation of this method
addDictionaryEntry(inChI, p_graph);
}
/**
* Adds an entry to the Library of the QMTP thermo library using
* the ThermData calculated from mm4 or pm3.
*/
public static void addLibraryEntry(String inChI, ThermoData qmResult, String qmMethod, String qmProgram) {
//Assumes name in thermo library doesn't have to match the name in RMG
//Not sure how true this is..figures crossed
//line will be the entry to add to Library.txt using the format used in RMG thermo librarys
String line = new String(inChI + " ");
line = (line +Double.toString(qmResult.getH298()) + " ");
line = (line +Double.toString(qmResult.getS298())+ " ");
line = (line +Double.toString(qmResult.getCp300())+ " ");
line = (line +Double.toString(qmResult.getCp400())+ " ");
line = (line +Double.toString(qmResult.getCp500())+ " ");
line = (line +Double.toString(qmResult.getCp600())+ " ");
line = (line +Double.toString(qmResult.getCp800())+ " ");
line = (line +Double.toString(qmResult.getCp1000())+ " ");
line = (line +Double.toString(qmResult.getCp1500())+ " ");
line = (line +Double.toString(qmResult.getDH())+ " ");
line = (line +Double.toString(qmResult.getDS())+ " ");
line = (line +Double.toString(qmResult.getDCp())+ " ");
//include the source of the calculation
line = (line + qmProgram + " " + qmMethod + " Calculation");
//write to Library.txt
//Assumes name in thermo library doesn't have to match the name in RMG
//Not sure how true this is..figures crossed
//line will be the entry to add to Library.txt using the format used in RMG thermo librarys
String line = new String(inChI + " ");
line = (line +Double.toString(qmResult.getH298()) + " ");
line = (line +Double.toString(qmResult.getS298())+ " ");
line = (line +Double.toString(qmResult.getCp300())+ " ");
line = (line +Double.toString(qmResult.getCp400())+ " ");
line = (line +Double.toString(qmResult.getCp500())+ " ");
line = (line +Double.toString(qmResult.getCp600())+ " ");
line = (line +Double.toString(qmResult.getCp800())+ " ");
line = (line +Double.toString(qmResult.getCp1000())+ " ");
line = (line +Double.toString(qmResult.getCp1500())+ " ");
line = (line +Double.toString(qmResult.getDH())+ " ");
line = (line +Double.toString(qmResult.getDS())+ " ");
line = (line +Double.toString(qmResult.getDCp())+ " ");

//include the source of the calculation
line = (line + qmProgram + " " + qmMethod + " Calculation");

//write to Library.txt
try {
libraryFile.write(line + newLine);
libraryFile.flush();
libraryFile.write(line + newLine);
libraryFile.flush();
}
catch (IOException e) {
// What should we do here?
throw new RuntimeException(e);
throw new RuntimeException(e);
}

}
/**
* Adds an entry to the Dictionary.txt of the QMTP thermo library using
*/
public static void addDictionaryEntry(String inChI, ChemGraph p_graph) {
//Assumes name in thermo library doesn't have to match the name in RMG
//Not sure how true this is..figures crossed
//definition is a string of the name and adjacency list to be added to Dictionary.txt
int i = 1;
String definition = new String(inChI + newLine);
//toString(i) is used as opposed to toString because that seems to give the adjacency list
//without prefacing it with the chemical formula
definition= (definition + p_graph.toString(i) + newLine + newLine);
//write to Dictionary.txt
//Assumes name in thermo library doesn't have to match the name in RMG
//Not sure how true this is..figures crossed
//definition is a string of the name and adjacency list to be added to Dictionary.txt
int i = 1;
String definition = new String(inChI + newLine);
//toString(i) is used as opposed to toString because that seems to give the adjacency list
//without prefacing it with the chemical formula
definition= (definition + p_graph.toString(i) + newLine + newLine);

//write to Dictionary.txt
try {
dictionaryFile.write(definition);
dictionaryFile.flush();
dictionaryFile.write(definition);
dictionaryFile.flush();
}
catch (IOException e) {
// What should we do here?
throw new RuntimeException(e);
throw new RuntimeException(e);
}
}

/**
* Adds an entry to the Dictionary.txt of the QMTP thermo library using
* @throws IOException
*/
public static HashMap readLibrary(String p_qmThermoFileName) throws IOException {
try {
FileReader in = new FileReader(p_qmThermoFileName);
BufferedReader data = new BufferedReader(in);
String line = ChemParser.readMeaningfulLine(data, true);
HashMap <String, ThermoData> library = new HashMap<String, ThermoData>();
while (line!=null){
String [] result = line.split("\\s");
// Construct information to create instance of ThermData
String inChI = result[0];
String thermo = result[1];
for(int i=2; i<13; i++){
thermo = thermo + " " + result[i];
}
int listLength = result.length;
String comments = result[13];
//check this upper bound might need to be listLength + 1 -nyee
for(int i=14; i < listLength; i++){
comments = comments + " " + result[i];
}
//Parse out thermoData, and include name and comments
ThermoData thermoData = ChemParser.parseThermoFromLibrary(thermo);
ThermoData newThermoData = new ThermoData(inChI, thermoData, comments);
library.put(inChI, newThermoData);
line = ChemParser.readMeaningfulLine(data, true);
}
in.close();
return library;
}
catch(IOException e) {
Logger.logStackTrace(e);
throw new IOException("Can't read thermo in primary thermo library!");
}
try {
FileReader in = new FileReader(p_qmThermoFileName);
BufferedReader data = new BufferedReader(in);
String line = ChemParser.readMeaningfulLine(data, true);
HashMap <String, ThermoData> library = new HashMap<String, ThermoData>();
while (line!=null){
String [] result = line.split("\\s");

// Construct information to create instance of ThermData
String inChI = result[0];
String thermo = result[1];

for(int i=2; i<13; i++){
thermo = thermo + " " + result[i];
}

int listLength = result.length;
String comments = result[13];
//check this upper bound might need to be listLength + 1 -nyee
for(int i=14; i < listLength; i++){
comments = comments + " " + result[i];
}

//Parse out thermoData, and include name and comments
ThermoData thermoData = ChemParser.parseThermoFromLibrary(thermo);
ThermoData newThermoData = new ThermoData(inChI, thermoData, comments);

library.put(inChI, newThermoData);
line = ChemParser.readMeaningfulLine(data, true);
}

in.close();
return library;

}

catch(IOException e) {
Logger.logStackTrace(e);
throw new IOException("Can't read thermo in primary thermo library!");
}

}
}

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