Regularized the utilities in Resources/Utils so that their usage is m…

…ore uniform. E.g. called via the command line with a configuration file specified, where needed.

Resources/Utils/calculateDEM/config.cfg

@@ -1,9 +1,11 @@
+Results
 40
 0.1
 4.0	4.1	4.2	4.3	4.4	4.5	4.6	4.7	4.8	4.9	5.0	5.1	5.2	5.3	5.4	5.5	5.6	5.7	5.8	5.9	6.0	6.1	6.2	6.3	6.4	6.5	6.6	6.7	6.8	6.9	7.0	7.1	7.2	7.3	7.4	7.5	7.6	7.7	7.8	7.9	8.0
 1
-0	0
+0	600
 
+// Results directory
 // Number of temperature bins
 // Width of temperature bin (dex)
 // Temperature bins

Resources/Utils/calculateDEM/source/main.cpp

@@ -5,7 +5,7 @@
 // *
 // * (c) Dr. Stephen J. Bradshaw
 // *
-// * Date last modified: 10/20/2021
+// * Date last modified: 01/04/2023
 // *
 // ****
 
@@ -22,8 +22,8 @@
 
 int main( int argc, char **argv )
 {
-FILE *pCONFIGFile, *pAMRFile, *pPHYFile, *pDEMFile;
-char szAMRFilename[256], szPHYFilename[256], szDEMFilename[256];
+FILE *pCFGFile, *pAMRFile, *pPHYFile, *pDEMFile;
+char szResultsDirectory[256], szAMRFilename[256], szPHYFilename[256], szDEMFilename[256];
 double *pflog10T, *pfDEM;
 double fdexStep, fds, fne, fTe, flog10Te;
 double fBuffer;
@@ -33,31 +33,33 @@ int i, j, k, m;
 int iBuffer;
 
 if( argc == 1 ) {
-	printf( "\nERROR! No configuration file specified.\n" );
-	exit(EXIT_SUCCESS);
+	printf( "\nA configuration file must be specified. E.g. calculateDEM config.cfg\n");
+	exit( EXIT_SUCCESS );
 }
 
 // Open the configuration file
 printf( "\nUsing: %s\n", argv[1] );
-pCONFIGFile = fopen( argv[1], "r" );
+pCFGFile = fopen( argv[1], "r" );
+	// Get the directory containing the numerical results
+	fscanf( pCFGFile, "%s", szResultsDirectory );
 	// Get the number of temperature bins
-	fscanf( pCONFIGFile, "%i", &iNumBins );
+	fscanf( pCFGFile, "%i", &iNumBins );
 	// Get the bin width (dex)
-	ReadDouble( pCONFIGFile, &fdexStep );
+	ReadDouble( pCFGFile, &fdexStep );
 	// Allocate memory for the temperature intervals which define each bin
 	pflog10T = (double*)malloc( sizeof(double*) * ( iNumBins + 1 ) );
 	// Read the temperature intervals from the configuration file
 	for( i=0; i<(iNumBins+1); i++ ) {
-		ReadDouble( pCONFIGFile, &(pflog10T[i]) );
+		ReadDouble( pCFGFile, &(pflog10T[i]) );
 	}
 	// Get the number of output files to write 
 	// (the specified range is split into this number and summed over to calculate each DEM(T))
-	fscanf( pCONFIGFile, "%i", &iNumOutputFiles );
+	fscanf( pCFGFile, "%i", &iNumOutputFiles );
 	// Get the input file range
-	fscanf( pCONFIGFile, "%i", &iFileRangeStart );
-	fscanf( pCONFIGFile, "%i", &iFileRangeEnd );
+	fscanf( pCFGFile, "%i", &iFileRangeStart );
+	fscanf( pCFGFile, "%i", &iFileRangeEnd );
 // Close the configuration file
-fclose( pCONFIGFile );
+fclose( pCFGFile );
 
 // Split the input file range to produce the specified number of output files
 iSubRangeStep = ( iFileRangeEnd - iFileRangeStart ) / iNumOutputFiles;
@@ -100,8 +102,8 @@ for( i=0; i<iNumOutputFiles; i++ ) {
 	memset( pfDEM, '\0', iNumBins*sizeof(double) );
 	for( j=ppiFileSubRange[LOWER][i]; j<=ppiFileSubRange[UPPER][i]; j++ ) {
 		// Construct the .amr and .phy filenames
-		sprintf( szAMRFilename, "profile%i.amr", j );
-		sprintf( szPHYFilename, "profile%i.phy", j );
+		sprintf( szAMRFilename, "%s/profile%i.amr", szResultsDirectory, j );
+		sprintf( szPHYFilename, "%s/profile%i.phy", szResultsDirectory, j );
 		// Open the .amr file and read the header information
 		pAMRFile = fopen( szAMRFilename, "r" );
 			// Read the header
@@ -155,7 +157,7 @@ for( i=0; i<iNumOutputFiles; i++ ) {
 		fclose( pAMRFile );
 	}
 	// Construct the output filename
-	sprintf( szDEMFilename, "DEM(%ito%i).txt", ppiFileSubRange[LOWER][i], ppiFileSubRange[UPPER][i] );
+	sprintf( szDEMFilename, "%s/DEM(%ito%i).txt", szResultsDirectory, ppiFileSubRange[LOWER][i], ppiFileSubRange[UPPER][i] );
 	// Write the DEM(T) profile to the output file
 	pDEMFile = fopen( szDEMFilename, "w" );
 		fprintf( pDEMFile, "%i\n", iNumBins );

Resources/Utils/calculateIonizationTemperature/build_scripts/build_calculateIonizationTemperature.bat

@@ -1 +1 @@
-g++ -O3 -flto -Wall ../source/main.cpp ../../../../Radiation_Model/source/ionfrac.cpp ../../../../Radiation_Model/source/radiation.cpp ../../../../Radiation_Model/source/element.cpp ../../../source/fitpoly.cpp ../../../source/file.cpp -o ../../../../calculateIonizationTemperature.exe
+g++ -O3 -flto -Wall ../source/main.cpp ../../../../Radiation_Model/source/ionfrac.cpp ../../../../Radiation_Model/source/radiation.cpp ../../../../Radiation_Model/source/element.cpp ../../../source/fitpoly.cpp ../../../source/file.cpp -o ../calculateIonizationTemperature.exe

Resources/Utils/calculateIonizationTemperature/config.cfg

@@ -1,6 +1,6 @@
 Results
 4.0 8.0 0.01
-0   0
+0   600
 
 // Results directory
 // (log10) temperature range and increment (dex)

Resources/Utils/calculateIonizationTemperature/source/main.cpp

@@ -4,7 +4,7 @@
 // *
 // * (c) Dr. Stephen J. Bradshaw
 // *
-// * Date last modified: 01/03/2023
+// * Date last modified: 01/04/2023
 // *
 // ****
 
@@ -29,23 +29,23 @@ double fBuffer;
 int iFrom, iTo, iNumCells;
 int iBuffer, i, j;
 
-if( argc > 1 ) {
-	// Open and read the configuration file
-	pCFGFile = fopen( argv[1], "r" );
-		// Get the directory containing the numerical results
-		fscanf( pCFGFile, "%s", szResultsDirectory );
-		// Get the (log) temperature range and increment (dex) over which to calculate the (effective) ionization temperature
-		for( i=0; i<3; i++ )
-			ReadDouble( pCFGFile, &(flogTRange[i]) );
-		// Get the range of output files over which to calculate the (effective) ionization temperature
-		fscanf( pCFGFile, "%i", &iFrom );
-		fscanf( pCFGFile, "%i", &iTo );
-	fclose( pCFGFile );
-} else {
+if( argc == 1 ) {
 	printf( "\nA configuration file must be specified. E.g. calculateIonizationTemperature config.cfg\n");
 	exit( EXIT_SUCCESS );
 }
 
+// Open and read the configuration file
+pCFGFile = fopen( argv[1], "r" );
+	// Get the directory containing the numerical results
+	fscanf( pCFGFile, "%s", szResultsDirectory );
+	// Get the (log) temperature range and increment (dex) over which to calculate the (effective) ionization temperature
+	for( i=0; i<3; i++ )
+		ReadDouble( pCFGFile, &(flogTRange[i]) );
+	// Get the range of output files over which to calculate the (effective) ionization temperature
+	fscanf( pCFGFile, "%i", &iFrom );
+	fscanf( pCFGFile, "%i", &iTo );
+fclose( pCFGFile );
+
 pRadiation = new CRadiation( (char *)"Radiation_Model/config/elements_neq.cfg" );
 pIonFrac = new CIonFrac( NULL, (char *)"Radiation_Model/config/elements_neq.cfg", pRadiation );
 

Resources/Utils/calculateVALheating/build_scripts/build_calculateVALheating.bat

@@ -1 +1 @@
-g++ -O3 -flto -Wall ../source/main.cpp ../../../../Radiation_Model/source/radiation.cpp ../../../../Radiation_Model/source/element.cpp ../../../../Radiation_Model/source/OpticallyThick/OpticallyThickIon.cpp ../../../source/fitpoly.cpp ../../../source/file.cpp -o ../../../../calculateVALheating.exe
+g++ -O3 -flto -Wall ../source/main.cpp ../../../../Radiation_Model/source/radiation.cpp ../../../../Radiation_Model/source/element.cpp ../../../../Radiation_Model/source/OpticallyThick/OpticallyThickIon.cpp ../../../source/fitpoly.cpp ../../../source/file.cpp -o ../calculateVALheating.exe

Resources/Utils/calculateVALheating/source/main.cpp

@@ -1,10 +1,10 @@
 //
-//  updateVAL.cpp
+//  main.cpp
 //
 //  Updates the VAL heating profile in the case that the initial
 //  density profile has been altered.
 //
-//  Created by Jeffrey Reep on 7/27/15.
+//  Created by Jeffrey Reep on 07/27/2015
 //
 //
 
@@ -21,10 +21,10 @@
 
 using namespace std;
 
-int main()
+int main( void )
 {
-
-    /*ifstream fin("Radiation_Model/atomic_data/OpticallyThick/VAL_atmospheres/VAL.heat");
+    /*
+    ifstream fin("Radiation_Model/atomic_data/OpticallyThick/VAL_atmospheres/VAL.heat");
     int heat_num_lines,i;
     double **heat_rows;
     fin >> heat_num_lines;
@@ -198,4 +198,4 @@ int main()
     outfile.close();
 
     return 0;
-}
+}

Resources/Utils/extractQuantities/config.cfg

@@ -1,3 +1,4 @@
+Results
 profile	ine
 2
 1	f

Resources/Utils/extractQuantities/source/main.cpp

@@ -5,30 +5,36 @@
 // *
 // * (c) Dr. Stephen J. Bradshaw
 // *
-// * Date last modified: 01/21/2021
+// * Date last modified: 01/04/2023
 // *
 // ****
 
 #include <stdio.h>
-#include <malloc.h>
+#include <stdlib.h>
 
 #include "../../../source/file.h"
 
-
-int main(void)
+int main( int argc, char **argv )
 {
 FILE *pCONFIGFile, *pINPUTFile, *pOUTPUTFile;
 char **ppcDataType;
-char szRoot[256], szExtension[32], szINPUTFilename[256], szOUTPUTFilename[256];
+char szResultsDirectory[256], szRoot[256], szExtension[32], szINPUTFilename[256], szOUTPUTFilename[256];
 char cBuffer;
 double fBuffer;
 int *piNumColumns, *piRow, *piColumn, iRange[2];
 int iNumRows, iNumEntries, iEntry, iNumRecords;
 int i, j, m, n;
 int iBuffer;
 
+if( argc == 1 ) {
+	printf( "\nA configuration file must be specified. E.g. extractQuantities config.cfg\n");
+	exit( EXIT_SUCCESS );
+}
+
 // Open the configuration file
-pCONFIGFile = fopen( "config.cfg", "r" );
+pCONFIGFile = fopen( argv[1], "r" );
+	// Get the directory containing the numerical results
+	fscanf( pCONFIGFile, "%s", szResultsDirectory );
 	// Get the filename structure of the files containing the data to be extracted
 	fscanf(pCONFIGFile, "%s", szRoot );
 	fscanf(pCONFIGFile, "%s", szExtension );
@@ -48,7 +54,7 @@ pCONFIGFile = fopen( "config.cfg", "r" );
 				}
 		}
 	// Get the number of entries to extract from each record
-	fscanf(pCONFIGFile, "%i", &iNumEntries );
+	fscanf( pCONFIGFile, "%i", &iNumEntries );
 		// Allocate memory to store the row and column number for each entry
 		piRow = (int*)malloc( sizeof(int) * iNumEntries );
 		piColumn = (int*)malloc( sizeof(int) * iNumEntries );	
@@ -63,7 +69,7 @@ pCONFIGFile = fopen( "config.cfg", "r" );
 // Close the configuration file
 fclose( pCONFIGFile );
 
-printf( "\n%s.%s\n", szRoot, szExtension );
+printf( "\n%s/%s.%s\n", szResultsDirectory, szRoot, szExtension );
 printf( "\niNumber of Rows = %i\n", iNumRows );
 for( i=0; i<iNumRows; i++ ) {
 	printf( "Number of Columns in Row %i = %i\n", i+1, piNumColumns[i] );
@@ -86,7 +92,7 @@ for( i=iRange[0]; i<=iRange[1]; i++ ) {
 
 	// Get the number of records from the .amr file
 	// Construct the .amr filename and open the file
-	sprintf( szINPUTFilename, "profile%i.amr", i );
+	sprintf( szINPUTFilename, "%s/profile%i.amr", szResultsDirectory, i );
 	pINPUTFile = fopen( szINPUTFilename, "r" );
 		// Get the timestamp from the .amr file
 		ReadDouble( pINPUTFile, &fBuffer );
@@ -99,10 +105,10 @@ for( i=iRange[0]; i<=iRange[1]; i++ ) {
 	fclose( pINPUTFile );
 
 	// Construct the output filename and open the file
-	sprintf( szOUTPUTFilename, "profile%i.qts", i );
+	sprintf( szOUTPUTFilename, "%s/profile%i.qts", szResultsDirectory, i );
 	pOUTPUTFile = fopen( szOUTPUTFilename, "w" );
 		// Construct the input filename and open the file
-		sprintf( szINPUTFilename, "%s%i.%s", szRoot, i, szExtension );
+		sprintf( szINPUTFilename, "%s/%s%i.%s", szResultsDirectory, szRoot, i, szExtension );
 		pINPUTFile = fopen( szINPUTFilename, "r" );
 			// Extract the specified entries from each record and write them to a new file
 			for( j=0; j<iNumRecords; j++ ) {

Resources/Utils/extractSpatialAverages/config.cfg

@@ -1,3 +1,4 @@
+Results
 profile	phy
 11
 3
@@ -7,6 +8,7 @@ profile	phy
 1
 0	600
 
+// Results directory
 // Filename and Extension
 // # Columns
 // # Columns to Average

Resources/Utils/extractSpatialAverages/source/main.cpp

@@ -5,24 +5,22 @@
 // *
 // * (c) Dr. Stephen J. Bradshaw
 // *
-// * Date last modified: 01/21/2021
+// * Date last modified: 01/04/2023
 // *
 // ****
 
 #include <stdio.h>
-#include <malloc.h>
+#include <stdlib.h>
 
 #include "../../../../HYDRAD/source/config.h"
 #include "../../../source/file.h"
 
-
 // #define READ_ELECTRON_MASS_DENSITY		// Required for runs using the optically-thick chromosphere model
 
-
-int main(void)
+int main( int argc, char **argv )
 {
 FILE *pCONFIGFile, *pAMRFile, *pEXTFile, *pOUTPUTFile;
-char szRoot[256], szExtension[32], szAMRFilename[256], szEXTFilename[256], szOUTPUTFilename[256];
+char szResultsDirectory[256], szRoot[256], szExtension[32], szAMRFilename[256], szEXTFilename[256], szOUTPUTFilename[256];
 double *pfSum;
 double fLLp, fULp, fLL, fUL;
 double fTimeStamp, fL, fs, fds;
@@ -32,9 +30,15 @@ int iNumColumns, iNumAverages, iNumFiles, iNumCells;
 int i, j, k, l, m, n;
 int iBuffer;
 
-// Open the configuration file
-pCONFIGFile = fopen( "config.cfg", "r" );
+if( argc == 1 ) {
+	printf( "\nA configuration file must be specified. E.g. extractSpatialAverages config.cfg\n");
+	exit( EXIT_SUCCESS );
+}
 
+// Open the configuration file
+pCONFIGFile = fopen( argv[1], "r" );
+	// Get the directory containing the numerical results
+	fscanf( pCONFIGFile, "%s", szResultsDirectory );
 	// Get the filename structure of the files containing the data to be spatially averaged
 	fscanf(pCONFIGFile, "%s", szRoot );
 	fscanf(pCONFIGFile, "%s", szExtension );
@@ -55,9 +59,9 @@ pCONFIGFile = fopen( "config.cfg", "r" );
 	fLLp /= 100.0; fULp /= 100.0;
 
 	// Get the number of spatial average files to write
-	fscanf(pCONFIGFile, "%i", &iNumFiles );
+	fscanf( pCONFIGFile, "%i", &iNumFiles );
 
-	printf( "\n%s.%s\n", szRoot, szExtension );
+	printf( "\n%s/%s.%s\n", szResultsDirectory, szRoot, szExtension );
 	printf( "\nNumber of Columns = %i\n", iNumColumns );
 	printf( "\nNumber of Columns to Average = %i\n", iNumAverages );	
 	printf( "\tColumns:");
@@ -78,7 +82,7 @@ pCONFIGFile = fopen( "config.cfg", "r" );
 		printf( " [%i,%i]", iRange[0], iRange[1] );
 
 		// Construct the output filename and open the file
-		sprintf( szOUTPUTFilename, "f(t)(%ito%i).txt", iRange[0], iRange[1] );
+		sprintf( szOUTPUTFilename, "%s/f(t)(%ito%i).txt", szResultsDirectory, iRange[0], iRange[1] );
 		pOUTPUTFile = fopen( szOUTPUTFilename, "w" );
 			// Write the number of rows to the output file
 			fprintf( pOUTPUTFile, "%i\n", (iRange[1]-iRange[0])+1 );
@@ -89,7 +93,7 @@ pCONFIGFile = fopen( "config.cfg", "r" );
 					pfSum[k] = 0.0;
 
 				// Construct the .amr filename and open the file
-				sprintf( szAMRFilename, "profile%i.amr", j );
+				sprintf( szAMRFilename, "%s/profile%i.amr", szResultsDirectory, j );
 				pAMRFile = fopen( szAMRFilename, "r" );
 					// Get the timestamp from the .amr file
 					ReadDouble( pAMRFile, &fTimeStamp );
@@ -102,7 +106,7 @@ pCONFIGFile = fopen( "config.cfg", "r" );
 					fscanf( pAMRFile, "%i", &iNumCells );
 
 					// Construct the .ext filename and open the file
-					sprintf( szEXTFilename, "%s%i.%s", szRoot, j, szExtension );
+					sprintf( szEXTFilename, "%s/%s%i.%s", szResultsDirectory, szRoot, j, szExtension );
 					pEXTFile = fopen( szEXTFilename, "r" );
 						for( k=0; k<iNumCells; k++ )
 						{

Resources/Utils/generatePieceWiseFit/fits/B(closed).txt

@@ -103,3 +103,9 @@
 0.98	26.91035506
 0.99	28.13762816
 1	29.40254167
+
+// Order of polynomial fit
+// Number of domains to fit
+// Domain boundaries. E.g. 0 1 (one domain) or 0 0.5 1 (two domains)
+// Number of tabulated data points
+// Normalized spatial coordinate [0,1] and quantity to fit to