public void Initialize(SOCJT nSocjt, FileInfo input, List<ModeInfo> Modes, string[] inputFile, bool isQuad, Eigenvalue[] fitFile)
{
nSoc = nSocjt;
nInput = input;
nModes = Modes;
nInputFile = inputFile;
nIsQuad = isQuad;
nFitFile = fitFile;
}
public List<string> fit(List<ModeInfo> Modes, bool isQuad, string[] inputFile, FileInfo input, String filepath)
{
//string to return
List<string> output = new List<string>();
//reads and parses fit file
string[] fitF = {};
try
{
fitF = FileInfo.FileRead(filepath);
}
catch(FileNotFoundException)
{
throw new FileNotFoundException("The fit file does not exist.");
}
//assign number of eigenvalues to be fit from fitFile
int nToFit = Convert.ToInt16(fitF[0]);
//create new Eigenvalue array to store the values from the fit file for each value being fit
Eigenvalue[] userInput = new Eigenvalue[nToFit];
//initialize the Eigenvalue array for the fit values from the fit file
for (int i = 0; i < nToFit; i++)
{
if (input.useSeed)
{
userInput[i] = new Eigenvalue(Convert.ToDecimal(fitF[i * 5 + 2]), Convert.ToInt16(fitF[i * 5 + 3]), Convert.ToDecimal(fitF[i * 5 + 4]), Convert.ToDouble(fitF[i * 5 + 1]), FileInfo.TorF(fitF[i * 5 + 5]));
}
else // if the seed switch is off, all Lanczos eigenvalues will be labelled as not A1, so we will label all fit file values as not A1
{
userInput[i] = new Eigenvalue(Convert.ToDecimal(fitF[i * 5 + 2]), Convert.ToInt16(fitF[i * 5 + 3]), Convert.ToDecimal(fitF[i * 5 + 4]), Convert.ToDouble(fitF[i * 5 + 1]), false);
}
}
//initializes the X vector, boundary conditions and variable scales
//xList will contain each parameter being fit
List<double> xList = new List<double>();
//the lower bounds for each variable being fit, these are hardcoded
List<double> bndL = new List<double>();
//the upper bounds for each variable being fit, these are hardcoded
List<double> bndU = new List<double>();
//the scaling values for each variable being fit, these are hardcoded
List<double> lScale = new List<double>();
//here I initialize the xList, upper and lower boundaries, and scales for each parameter being fit.
//for Azeta
if (input.FitAzeta == true)
{
xList.Add(input.Azeta);
bndL.Add(double.NegativeInfinity);
bndU.Add(double.PositiveInfinity);
lScale.Add(1.0);
}
//for the origin
if (input.FitOrigin == true)
{
xList.Add(0.0);
bndL.Add(double.NegativeInfinity);
bndU.Add(double.PositiveInfinity);
lScale.Add(50.0);//changed from 200
}
//for each mode
for (int i = 0; i < input.nModes; i++)
{
//for Omega
if (Modes[i].fitOmega == true)
{
xList.Add(Modes[i].modeOmega);
bndL.Add(0.0);
bndU.Add(double.PositiveInfinity);
lScale.Add(50.0);//changed from 100
}
//for D
if (Modes[i].fitD == true)
{
xList.Add(Modes[i].D);
bndL.Add(0.0);
bndU.Add(double.PositiveInfinity);
lScale.Add(3.0);//changed from 10
}
//for K
if (Modes[i].fitK == true)
{
xList.Add(Modes[i].K);
bndL.Add(double.NegativeInfinity);
bndU.Add(double.PositiveInfinity);
lScale.Add(0.5);//changed from 1
}
//for wexe
if (Modes[i].fitWEXE == true)
{
xList.Add(Modes[i].wExe);
bndL.Add(double.NegativeInfinity);
bndU.Add(double.PositiveInfinity);
lScale.Add(10.0);//change from 50
}
}
//then for cross-terms
if (input.IncludeCrossTerms == true)
{
for (int i = 0; i < input.nModes; i++)
{
for (int j = 0; j < input.nModes; j++)
{
if (input.CrossTermFit[i, j] == true)
{
xList.Add(input.CrossTermMatrix[i, j]);
bndL.Add(double.NegativeInfinity);
bndU.Add(double.PositiveInfinity);
if (j > i)
{
lScale.Add(500.0);//scale for bilinear coupling + cross quadratic, changed from 100
}
if (j == i)
{
lScale.Add(50.0);//change from 250
}
else
{
lScale.Add(50.0);//scale for cross anharmonic, change from 250
}
}
}
}
}
//xVec for minLM optimizer
double[] xVec = xList.ToArray();
//Upper/lower boundary arrays for minLM optimizer
double[] lowBound = bndL.ToArray();
double[] upBound = bndU.ToArray();
//scaling array for minLM optimizer
double[] scale = lScale.ToArray();
//Generate new Master Object
//this is an ugly solution to the problem of using the ALGLIB routines since I need to pass a large amount of information
//to this routine but can only include one object in the arguments. Therefore, I created the MasterObject just to store
//this information which I pass to the ALGLIB routine. Where it's used, it is cast from object to a MasterObject.
SOCJT run = new SOCJT();
MasterObject Masterly = new MasterObject();
//here, if using simple lanczos and wanting evecs, set pVector to false so that they are not calculated each step of the fit
bool evecs = false;
if (input.PrintVector && !input.BlockLanczos)
{
evecs = true;
input.PrintVector = false;
}
Masterly.Initialize(run, input, Modes, inputFile, isQuad, userInput);
//initialize and run MinLM algorithm
double epsg = input.GTol;
double epsf = input.FTol;
double epsx = input.XTol;
int maxits = input.MaxOptimizerSteps;
alglib.minlmstate state;
alglib.minlmreport rep;
//alglib.ndimensional_func func;
//alglib.ndimensional_grad gradient;
//alglib.ndimensional_hess hessian;
alglib.minlmcreatev(userInput.Length, xVec, input.Factor, out state);
//if (input.calcHessian)
//{
// state.needfgh = true;
// //alglib.ndimensional_func func;
// //alglib.ndimensional_grad grad;
// //alglib.ndimensional_hess HessianMat;
// //alglib.minlmoptimize(state, function, null, null, state.repnhess, Masterly);
//}
alglib.minlmsetbc(state, lowBound, upBound);
alglib.minlmsetscale(state, scale);
alglib.minlmsetcond(state, epsg, epsf, epsx, maxits);
alglib.minlmsetxrep(state, true);
//acc = 1, meaning it's on by default. Just leave that.
//alglib.minlmsetacctype(state, 0);
//if (input.calcHessian)
//{
// alglib.minlmoptimize(state, func, gradient, hessian, null, Masterly);
//}
alglib.minlmoptimize(state, function, null, Masterly);
alglib.minlmresults(state, out xVec, out rep);
int report = rep.terminationtype;
int iter = rep.iterationscount;
//this calculates the covariance matrix from the Jacobian using cov[,] = {J^T * J}^-1
//initialize covariance matrix
double[,] resultM = new double[state.x.Length, state.x.Length];
for (int u = 0; u < state.x.Length; u++)
{
for (int uu = 0; uu < state.x.Length; uu++)
{
resultM[u, uu] = 0.0;
}
}
//calculate J^T * J and store in resultM
alglib.rmatrixgemm(state.j.GetLength(1), state.j.GetLength(1), state.j.GetLength(0), 1.0, state.j, 0, 0, 1, state.j, 0, 0, 0, 0.0, ref resultM, 0, 0);
//take inverse of resultM, replaces resultM
int invInfo;
alglib.matinvreport invReport = new alglib.matinvreport();
alglib.rmatrixinverse(ref resultM, out invInfo, out invReport);
//now make correlation coefficient matrix
double[,] corMat = new double[resultM.GetLength(0), resultM.GetLength(0)];
for (int i = 0; i < resultM.GetLength(0); i++)
{
for (int j = 0; j < resultM.GetLength(0); j++)
{
corMat[i, j] = resultM[i, j] / (Math.Sqrt(resultM[i, i] * resultM[j, j]));
}
}
//if eigenvectors are needed when using naive lanczos, run SOCJT routine one more time to calculate them.
if (evecs && !input.BlockLanczos)
{
Console.WriteLine("Calculating eigenvectors.");
Masterly.nInput.PrintVector = true;
Masterly.nSoc.SOCJTroutine(Masterly.nModes, Masterly.nIsQuad, Masterly.nInputFile, Masterly.nInput);
//now assign the lanczosEVectors to those from the SOCJT routine
lanczosEVectors = Masterly.nSoc.lanczosEVectors;
basisSet = Masterly.nSoc.basisSet;
}
//make output
soc = Masterly.nSoc;
output = Masterly.nSoc.outp;
//add something showing RMS error and parameters for each JT mode
double[] error = ComparerVec(userInput, Masterly.nSoc.finalList, Masterly.nInput.Origin, true);
StringBuilder file = new StringBuilder();
file.AppendLine("Fit report below...");
file.AppendLine("Termination Type: ");
if (report == -9)
{
file.Append("Derivative correctness check failed");
}
if (report == 1)
{
file.Append("Relative function improvement is no more than EpsF");
}
if (report == 2)
{
file.Append("Relative step is no more than EpsX");
}
if (report == 4)
{
file.Append("Gradient is no more than EpsG");
}
if (report == 5)
{
file.Append("Maximum number of iterations was exceeded");
}
if (report == 7)
{
file.Append("Stopping conditions are too stringent, further improvement is impossible");
}
file.AppendLine(" ");
file.AppendLine("Number of iterations: " + Convert.ToString(iter));
file.AppendLine("Number of times the eigenvalues were calculated: " + Convert.ToString(rep.nfunc));
file.AppendLine(" ");
file.AppendLine("A * zeta e = " + Convert.ToString(Masterly.nInput.Azeta));
/* This is written for data analysis with the NFG program */
if (input.useNFG == true)
{
file.Append("\n" + "NFG_OUTPUT" + "\t");
for (int ii = 0; ii < Masterly.nInput.nModes; ii++)
{
double JTSE;
if (Masterly.nModes[ii].IsAType == true)
{
JTSE = 0.0;
}
else
{
JTSE = Masterly.nModes[ii].D * Masterly.nModes[ii].modeOmega * (Masterly.nModes[ii].K + 1.0);
}
file.Append(String.Format("{0,7:0.00}", Masterly.nModes[ii].modeOmega) + "\t" + String.Format("{0,4:0.00}", Masterly.nModes[ii].wExe) + "\t" + String.Format("{0,5:0.0000}", Masterly.nModes[ii].D) + "\t" + String.Format("{0,5:0.0000}", Masterly.nModes[ii].K) + "\t" + String.Format("{0,4:0.00}", JTSE) + "\t");
}
if (input.IncludeCrossTerms == true)
{
for (int i = 0; i < input.nModes; i++)
{
for (int j = 0; j < input.nModes; j++)
{
if (input.CrossTermMatrix[i, j] != 0.0 || input.CrossTermFit[i, j] == true)
{
if (i < j)
{
file.Append(String.Format("{0,10:0.0000}", input.CrossTermMatrix[i, j]) + "\t");
}
else
{
file.Append(String.Format("{0,10:0.0000}", input.CrossTermMatrix[i, j]) + "\t");
}
}
}
}
}
for (int ll = 0; ll < resultM.GetLength(0); ll++)
{
file.Append(String.Format("{0,10:0.0000}", Math.Sqrt(resultM[ll, ll])) + "\t");
}
file.Append(String.Format("{0,10:0.000}", (Math.Sqrt(FitSOCJT.Comparer(userInput, Masterly.nSoc.finalList, Masterly.nInput.Origin) / userInput.Length))));
file.Append("\n" + "ELEVEL");
for (int ii = 0; ii < Masterly.nSoc.finalList.Length; ii++)
{
if (Masterly.nSoc.finalList[ii].JBlock == 0.5M)
{
file.Append("\t" + String.Format("{0,9:0.0000}", Masterly.nSoc.finalList[ii].Evalue));
}
}
file.Append("\n" + "A1LEVEL");
for (int ii = 0; ii < Masterly.nSoc.finalList.Length; ii++)
{
if (Masterly.nSoc.finalList[ii].JBlock == 1.5M && Masterly.nSoc.finalList[ii].IsA1 == true)
{
file.Append("\t" + String.Format("{0,9:0.0000}", Masterly.nSoc.finalList[ii].Evalue));
}
}
file.Append("\n" + "A2LEVEL");
for (int ii = 0; ii < Masterly.nSoc.finalList.Length; ii++)
{
if (Masterly.nSoc.finalList[ii].JBlock == 1.5M && Masterly.nSoc.finalList[ii].IsA1 == false)
{
file.Append("\t" + String.Format("{0,9:0.0000}", Masterly.nSoc.finalList[ii].Evalue));
}
}
file.AppendLine("\n");
} // end if useNFG == true
file.AppendLine("Final Parameters for Each Mode:");
file.AppendLine("Mode #" + "\t" + "V(min)" + "\t" + "V(max)" + "\t" + "Omega(E)" + "\t" + "wexe" + "\t" + "D" + "\t" + "K" + "\t" + "JTSE" + "\t" + "Omega(A)" + "\t" + "A Type?");
for (int i = 0; i < Masterly.nInput.nModes; i++)
{
double JTSE;
if (Masterly.nModes[i].IsAType == true)
{
JTSE = 0.0;
}
else
{
JTSE = Masterly.nModes[i].D * Masterly.nModes[i].modeOmega * (Masterly.nModes[i].K + 1.0);
}
file.AppendLine(Convert.ToString(i + 1) + "\t" + String.Format("{0,4:0}", 0) + "\t" + String.Format("{0,4:0}", Masterly.nModes[i].modeVMax) + "\t" + String.Format("{0,7:0.00}", Masterly.nModes[i].modeOmega) + "\t" + "\t" + String.Format("{0,4:0.00}", Masterly.nModes[i].wExe) + "\t" + String.Format("{0,5:0.0000}", Masterly.nModes[i].D) + "\t" + String.Format("{0,5:0.0000}", Masterly.nModes[i].K) + "\t" + String.Format("{0,4:0.00}", JTSE) + "\t" + String.Format("{0,7:0.00}", Masterly.nModes[i].modeAOmega) + "\t" + "\t" + Convert.ToString(Masterly.nModes[i].IsAType));
}
file.AppendLine(" ");
if (input.FitOrigin == true)
{
file.AppendLine("Origin Shift = " + String.Format("{0,8:0.000}", -1.0 * Masterly.nInput.Origin));
}
file.AppendLine(" ");
if (input.IncludeCrossTerms == true)
{
for (int i = 0; i < input.nModes; i++)
{
for (int j = 0; j < input.nModes; j++)
{
if (input.CrossTermMatrix[i, j] != 0.0 || input.CrossTermFit[i, j] == true)
{
if (i < j)
{
file.AppendLine("Mode " + Convert.ToString(i + 1) + " Mode " + Convert.ToString(j + 1) + " JT cross-term = " + String.Format("{0,10:0.0000}", input.CrossTermMatrix[i, j]));
}
else
{
file.AppendLine("Mode " + Convert.ToString(j + 1) + " Mode " + Convert.ToString(i + 1) + " AT cross-term = " + String.Format("{0,10:0.00}", input.CrossTermMatrix[i, j]));
}
}
}
}
file.AppendLine(" ");
}
file.AppendLine("Fitting Results:");
if (input.FitOrigin == true)
{
file.AppendLine("Experimental values are shifted by " + String.Format("{0,8:0.000}", Masterly.nInput.Origin) + " wavenumbers.");
}
file.AppendLine("FitFile Value" + "\t" + "Calculated Value" + "\t" + "Exp - Calc" + "\t" + "(Exp - Calc)^2");
for (int i = 0; i < error.Length; i++)
{
file.AppendLine(String.Format("{0,13:0.000}", userInput[i].Evalue + Masterly.nInput.Origin) + "\t" + String.Format("{0,13:0.000}", userInput[i].Evalue + Masterly.nInput.Origin - error[i]) + "\t" + "\t" + String.Format("{0,9:0.000}", error[i]) + "\t" + String.Format("{0,11:0.000}", Math.Pow(error[i], 2D)));
}
file.AppendLine(" ");
file.AppendLine("RMS Error = " + String.Format("{0,10:0.000}", (Math.Sqrt(FitSOCJT.Comparer(userInput, Masterly.nSoc.finalList, Masterly.nInput.Origin) / userInput.Length))));
file.AppendLine(" ");
int l = 0;
if (Masterly.nInput.FitAzeta == true)
{
file.AppendLine("Azeta StdDev = " + String.Format("{0,10:0.000000}", Math.Sqrt(resultM[l, l])));
l++;
}
if (Masterly.nInput.FitOrigin == true)
{
file.AppendLine("Origin StdDev = " + String.Format("{0,10:0.00}", Math.Sqrt(resultM[l, l])));
l++;
}
for (int i = 0; i < Masterly.nInput.nModes; i++)
{
if (Masterly.nModes[i].fitOmega == true)
{
file.AppendLine("Mode " + Convert.ToString(i + 1) + " Omega StdDev = " + String.Format("{0,10:0.00}", Math.Sqrt(resultM[l, l])));
l++;
}
if (Masterly.nModes[i].fitD == true)
{
file.AppendLine("Mode " + Convert.ToString(i + 1) + " D StdDev = " + String.Format("{0,10:0.0000}", Math.Sqrt(resultM[l, l])));
l++;
}
if (Masterly.nModes[i].fitK == true)
{
file.AppendLine("Mode " + Convert.ToString(i + 1) + " K StdDev = " + String.Format("{0,10:0.0000}", Math.Sqrt(resultM[l, l])));
l++;
}
if (Masterly.nModes[i].fitWEXE == true)
{
file.AppendLine("Mode " + Convert.ToString(i + 1) + " wexe StdDev = " + String.Format("{0,10:0.00}", Math.Sqrt(resultM[l, l])));
l++;
}
}
if (Masterly.nInput.IncludeCrossTerms == true)
{
for (int i = 0; i < Masterly.nInput.nModes; i++)
{
for (int h = 0; h < Masterly.nInput.nModes; h++)
{
if (Masterly.nInput.CrossTermFit[i, h] == true)
{
if (i < h)
{
file.AppendLine("Mode " + Convert.ToString(i + 1) + " Mode " + Convert.ToString(h + 1) + " JT Term StdDev = " + String.Format("{0,10:0.0000}", Math.Sqrt(resultM[l, l])));
l++;
}
else
{
file.AppendLine("Mode " + Convert.ToString(h + 1) + " Mode " + Convert.ToString(i + 1) + " AT Term StdDev = " + String.Format("{0,10:0.00}", Math.Sqrt(resultM[l, l])));
l++;
}
}
}
}
}
file.AppendLine(" ");
file.AppendLine("Correlation coefficient matrix:");
for (int i = 0; i < resultM.GetLength(0); i++)
{
file.AppendLine("");
file.Append("(");
for (int j = 0; j < resultM.GetLength(0); j++)
{
if (j != 0)
{
file.Append(", ");
}
file.Append(String.Format("{0,8:0.000}", corMat[i, j]));
}
file.Append(")");
}
file.AppendLine(" ");
file.AppendLine(" ");
output.Add(file.ToString());
output.AddRange(OutputFile.inputFileMaker(Masterly.nInput, Masterly.nModes));
return output;
}
static void Main(string[] args)
{
try
{
string fileDirectory;
#if DEBUG
//prompt user for input directory. Default value is C:\SOCJT 2
Console.WriteLine("Enter file directory or press enter to use C:\\SOCJT 2");
fileDirectory = Console.ReadLine();
if (fileDirectory == "")
{
fileDirectory = "C:\\SOCJT 2\\";
}
if (Directory.Exists(fileDirectory) == false)
{
throw new DirectoryNotFoundException();
}
#else
fileDirectory = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
#endif
Directory.SetCurrentDirectory(fileDirectory);
string inFileName;
string outFile;
if (args == null || args.Length == 0)
{
Console.WriteLine("Enter file name including extension:");
inFileName = Console.ReadLine();
//obtain output file name. If blank, default value of input + .out is used
Console.WriteLine("Enter output file name or press enter to use " + inFileName + ".out:");
outFile = Console.ReadLine();
if (outFile == "" || outFile == " ")
{
outFile = string.Concat(inFileName, ".out");
}
}
else
{
inFileName = args[0];
outFile = args[1];
}
//Original Input
//prompt user to enter input file name
/*Console.WriteLine("Enter file name including extension:");
string inFileName = Console.ReadLine();
//obtain output file name. If blank, default value of input + .out is used
Console.WriteLine("Enter output file name or press enter to use " + inFileName + ".out:");
string outFile = Console.ReadLine();
if (outFile == "" || outFile == " ")
{
outFile = string.Concat(inFileName, ".out");
}*/
//start timer for overall program execution
Stopwatch totalTime = new Stopwatch();
totalTime.Start();
//set input, output, and fit file values.
string filepath = string.Concat(fileDirectory);
//filepath += "/"; // FOR THE CLUSTER
filepath += "\\";
string filepathIN = string.Copy(filepath);
string filepathOUT = string.Copy(filepath);
string filepathFIT = string.Copy(filepath);
filepathIN += inFileName;
filepathOUT += outFile;
if (filepathOUT == filepathIN)
{
throw new FileNameError("outFile");
}
//read and parse input file, then initialize FileInfo object
string[] inputFile = FileInfo.FileRead(filepathIN);
FileInfo input = new FileInfo();
input.SetFileInfo(inputFile, filepath);
input.FilePath = filepath;
//make the fitfile point to something
filepathFIT = string.Concat(input.FitFile);
//see if matFile is true, and if so if the matfile exists or not.
if (input.UseMatrixFile)
{
input.MatrixFilePath = string.Copy(filepath);
input.MatrixFilePath += input.MatrixFile;
//check that the mat file has a valid path
if (input.MatrixFilePath == filepathIN || input.MatrixFilePath == filepathOUT || input.MatrixFilePath == filepathFIT)
{
throw new FileNameError("matFile");
}
//if this file already exists, then use it for the matrix generation
if (File.Exists(input.MatrixFilePath))
{
input.MatrixMade = true;
}
}
//initialize the modes
List<ModeInfo> Modes = ModeInitialization(inputFile, input);
//Determines if the quadratic basis set should be used
bool isQuad = IsQuad(input, Modes);
//Determines if any values are being fit
bool fit = IsFit(input, Modes);
//main subroutine execution when not running a scan
if (input.Scan == false)
{
List<string> linesToWrite = new List<string>();
linesToWrite = OutputFile.inputFileMaker(input, Modes);
if (!fit)
{
SOCJT runner = new SOCJT();
linesToWrite.AddRange(runner.SOCJTroutine(Modes, isQuad, inputFile, input));
WriteOutputFile(totalTime, filepathOUT, linesToWrite);
//Here, if necessary, the eigenvectors for very large matrices are calculated after the rest of the calculations have been done.
//This is done because this process may take a large amount of time
if (runner.lanczosEVectors != null)
{
CalcLargeEvecs(filepath, input, runner.lanczosEVectors, runner.basisSet);
}
}
else
{
FitSOCJT fitt = new FitSOCJT();
linesToWrite.AddRange(fitt.fit(Modes, isQuad, inputFile, input, filepathFIT));
WriteOutputFile(totalTime, filepathOUT, linesToWrite);
if (fitt.lanczosEVectors != null)
{
CalcLargeEvecs(filepath, input, fitt.lanczosEVectors, fitt.basisSet);
}
}
//WriteOutputFile(totalTime, filepathOUT, linesToWrite);
}//end no scan
else//means a scan is being run
{
#region SCAN
SOCJT runner = new SOCJT();
List<Eigenvalue[]> scanList = new List<Eigenvalue[]>();
List<string> finalOut = new List<string>();
for (int h = 0; h < input.ScanSteps; h++)
{
List<string> linesToWrite = new List<string>();
//run loop over each variable to be scanned and increment by step size times loop iteration.
for (int n = 0; n < input.ScanList.Count; n++)
{
if (input.ScanList[n].varToFit.ToUpper() == "OMEGA")
{
Modes[input.ScanList[n].Mode - 1].modeOmega = input.ScanList[n].Start + input.ScanList[n].Step * (double)h;
}
if (input.ScanList[n].varToFit.ToUpper() == "WEXE")
{
Modes[input.ScanList[n].Mode - 1].wExe = input.ScanList[n].Start + input.ScanList[n].Step * (double)h;
}
if (input.ScanList[n].varToFit.ToUpper() == "D")
{
Modes[input.ScanList[n].Mode - 1].D = input.ScanList[n].Start + input.ScanList[n].Step * (double)h;
}
if (input.ScanList[n].varToFit.ToUpper() == "K")
{
Modes[input.ScanList[n].Mode - 1].K = input.ScanList[n].Start + input.ScanList[n].Step * (double)h;
}
if (input.ScanList[n].varToFit.ToUpper() == "B" || input.ScanList[n].varToFit.ToUpper() == "C")
{
int tRow = input.ScanList[n].Mode;
int tCol = input.ScanList[n].Cross;
int temp;
if (tRow > tCol)
{
temp = tRow;
tRow = tCol;
tCol = temp;
}
input.CrossTermMatrix[tRow - 1, tCol - 1] = input.ScanList[n].Start + input.ScanList[n].Step * (double)h;
}
if (input.ScanList[n].varToFit.ToUpper() == "SPECIAL")
{
input.CrossTermMatrix[0, 0] = input.ScanList[n].Start + input.ScanList[n].Step * (double)h;
}
if (input.ScanList[n].varToFit.ToUpper() == "AT")
{
int tRow = input.ScanList[n].Mode;
int tCol = input.ScanList[n].Cross;
int temp;
if (tRow < tCol)
{
temp = tRow;
tRow = tCol;
tCol = temp;
}
input.CrossTermMatrix[tRow - 1, tCol - 1] = input.ScanList[n].Start + input.ScanList[n].Step * (double)h;
}
if (input.ScanList[n].varToFit.ToUpper() == "JT")
{
int tRow = input.ScanList[n].Mode;
int tCol = input.ScanList[n].Cross;
int temp;
if (tRow > tCol)
{
temp = tRow;
tRow = tCol;
tCol = temp;
}
input.CrossTermMatrix[tRow - 1, tCol - 1] = input.ScanList[n].Start + input.ScanList[n].Step * (double)h;
}
}//end adjust each variable to fit
//now make output file for each step
linesToWrite = OutputFile.inputFileMaker(input, Modes);
linesToWrite.AddRange(runner.SOCJTroutine(Modes, isQuad, inputFile, input));
string stepFile = filepathOUT + "_step_" + Convert.ToString(h + 1) + ".out";
File.WriteAllLines(stepFile, linesToWrite);
//add this steps eigenvalues to the scan output file
scanList.Add(runner.finalList);
linesToWrite = null;
stepFile = null;
}//end of steps loop
//write scan output file including total elapsed time
List<string> scanOut = OutputFile.ScanOutput(scanList);
totalTime.Stop();
double TIME = totalTime.ElapsedMilliseconds / 1000D;
scanOut.Add(" ");
scanOut.Add("SOCJT 2 has completed. Total time elapsed = " + String.Format("{0,11:0.0000}", TIME) + " seconds.");
File.WriteAllLines(filepathOUT, scanOut);
#endregion
}//end else for scan
//Writes the matrix to file if needed
if (input.UseMatrixFile && !input.MatrixMade)
{
OutputFile.writeMatFile(input);
}//end if to write matrix to file
}//end try block
//Exception handling
catch (DirectoryNotFoundException)
{
Console.WriteLine("The directory does not exist");
Console.WriteLine("Press enter to terminate the program.");
Console.ReadLine();
}
catch (FileNotFoundException a)
{
Console.WriteLine(a.Message);
Console.WriteLine("Press enter to terminate the program.");
Console.ReadLine();
}
catch (InvalidInput a)
{
Console.WriteLine(a.EMessage);
Console.WriteLine("Press enter to terminate the program.");
Console.ReadLine();
}
#if !DEBUG
catch (IndexOutOfRangeException)
{
Console.WriteLine("An index out of range exception has occurred");
Console.WriteLine("Check to make sure that NMODES is correct and");
Console.WriteLine("that any CROSS_TERM arguments are correct.");
Console.WriteLine("Press enter to terminate the program.");
Console.ReadLine();
}
catch (BasisSetTooSmallException a)
{
Console.Write(a.EMessage);
Console.ReadLine();
}
catch (AEAnharmonicTermException)
{
Console.WriteLine("Cross anharmonic terms can only be included between two A modes.");
Console.WriteLine("Take out any cross anharmonic terms between A and E modes.");
Console.WriteLine("Press enter to terminate the program.");
Console.ReadLine();
}
catch (RepeaterError)
{
Console.WriteLine("NaN Error in Naive Lanczos routine.");
Console.WriteLine("Try decreasing NOITS or using Block Lanczos instead.");
Console.WriteLine("Press enter to terminate the program.");
Console.ReadLine();
}
catch (FileNameError err)
{
Console.WriteLine(err.EMessage);
Console.ReadLine();
}
catch (MatrixFileError)
{
Console.WriteLine("The basis sets of the input file and matrix file are different sizes.");
Console.WriteLine("Try regenerating the matrix.");
Console.WriteLine("Press enter to terminate the program.");
Console.ReadLine();
}
catch (Exception ex)
{
Console.WriteLine("An exception has occurred: " + ex.Message);
Console.WriteLine("Check your input file and try again.");
Console.WriteLine("Press enter to terminate the program.");
Console.ReadLine();
}
#endif
}