Changeset 375dcf for molecuilder/src/parser.cpp

Timestamp:

Jun 27, 2008, 9:14:58 PM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

74baec

Parents:

d7b1bf

git-author:

Frederik Heber <heber@…> (06/27/08 21:12:52)

git-committer:

Frederik Heber <heber@…> (06/27/08 21:14:58)

Message:

introduced shieldings to analyzer and joiner

both now handle pcp.sigma_all...csv files just as pcp.forces.all. Therefore the data format in pcp/perturbed.c was adapted a bit, as we need a header.
periodentafel.hpp got periodentafel and element class from molecules.hpp

File:

• molecuilder/src/parser.cpp (modified) (10 diffs)

molecuilder/src/parser.cpp

@@ -10 +10 @@
 #include "parser.hpp"
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 // ======================================= FUNCTIONS ==========================================
 
 /** Test if given filename can be opened.
  * \param filename name of file
+ * \param test true - no error message, false - print error
  * \return given file exists
  */
-#ifdef HAVE_INLINE
-inline bool FilePresent(const char *filename)
-#else
-bool FilePresent(const char *filename)
-#endif
+bool FilePresent(const char *filename, bool test)
 {
   ifstream input;
@@ -26 +28 @@
   input.open(filename, ios::in);
   if (input == NULL) {
-    cout << endl << "Unable to open " << filename << ", is the directory correct?" << endl;
+    if (!test)
+      cout << endl << "Unable to open " << filename << ", is the directory correct?" << endl;
     return false;
   }
@@ -44 +47 @@
 
   line << argv[1] << FRAGMENTPREFIX << KEYSETFILE;
-  return FilePresent(line.str().c_str());
+  return FilePresent(line.str().c_str(), false);
 };
 
@@ -89 +92 @@
 
 /** Parsing a number of matrices.
+ * -# First, count the number of matrices by counting lines in KEYSETFILE
+ * -# Then, 
+ *    -# construct the fragment number
+ *    -# open the matrix file
+ *    -# skip some lines (\a skiplines)
+ *    -# scan header lines for number of columns
+ *    -# scan lines for number of rows
+ *    -# allocate matrix
+ *    -# loop over found column and row counts and parse in each entry
+ * -# Finally, allocate one additional matrix (\a MatrixCounter) containing combined or temporary values 
  * \param *name directory with files
  * \param *prefix prefix of each matrix file
@@ -131 +144 @@
     stringstream line;
     FragmentNumber = FixedDigitNumber(MatrixCounter, i);
+    file.str(" ");
     if (i != MatrixCounter)  
-      line << name << FRAGMENTPREFIX << FragmentNumber << "/" << prefix << suffix;
+      file << name << FRAGMENTPREFIX << FragmentNumber << "/" << prefix << suffix;
     else
-      line << name << prefix << suffix;
+      file << name << prefix << suffix;
     Free((void **)&FragmentNumber, "MatrixContainer::ParseMatrix: *FragmentNumber");
-    input.open(line.str().c_str(), ios::in);
-    //cout << "Opening " << line.str() << " ... "  << input << endl;
+    input.open(file.str().c_str(), ios::in);
+    //cout << "Opening " << file.str() << " ... "  << input << endl;
     if (input == NULL) {
-      cerr << endl << "Unable to open " << line.str() << ", is the directory correct?" << endl;
+      cerr << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl;
       return false;
     }
+    
     // skip some initial lines
     for (int m=skiplines+1;m--;)
       input.getline(Header, 1023);
+    
     // scan header for number of columns
     line.str(Header);
@@ -159 +175 @@
     //cout << line.str() << endl;
     //cout << "ColumnCounter: " << ColumnCounter << endl;
+    
     // scan rest for number of rows/lines
     RowCounter[i]=-1;    // counts one line too much
@@ -169 +186 @@
       }
     }
-    cout << "RowCounter[" << i << "]: " << RowCounter[i] << endl;
-    Matrix[i] = (double **) Malloc(sizeof(double *)*(RowCounter[i]+1), "MatrixContainer::ParseMatrix: **Matrix[]");
-    input.clear();
-    input.seekg(ios::beg);
-    for (int m=skiplines+1;m--;)
-      input.getline(Header, 1023);    // skip header
-    line.str(Header);
-    for(int k=skipcolumns;k--;)  // skip columns in header too
-      line >> filename;
-    strncpy(Header, line.str().c_str(), 1023);  
-    for(int j=0;j<RowCounter[i];j++) {
-      Matrix[i][j] = (double *) Malloc(sizeof(double)*ColumnCounter, "MatrixContainer::ParseMatrix: *Matrix[][]");
-      input.getline(filename, 1023);
-      stringstream lines(filename);
-      //cout << "Matrix at level " << j << ":";// << filename << endl;
-      for(int k=skipcolumns;k--;)
-        lines >> filename;
-      for(int k=0;(k<ColumnCounter) && (!lines.eof());k++) {
-        lines >> Matrix[i][j][k];
-        //cout << " " << setprecision(2) << Matrix[i][j][k];;
+    //cout << "RowCounter[" << i << "]: " << RowCounter[i] << " from file " << file.str() << "." << endl;
+    
+    // allocate matrix if it's not zero dimension in one direction
+    if ((ColumnCounter > 0) && (RowCounter[i] > -1)) {
+      Matrix[i] = (double **) Malloc(sizeof(double *)*(RowCounter[i]+1), "MatrixContainer::ParseMatrix: **Matrix[]");
+    
+      // parse in each entry for this matrix
+      input.clear();
+      input.seekg(ios::beg);
+      for (int m=skiplines+1;m--;)
+        input.getline(Header, 1023);    // skip header
+      line.str(Header);
+      for(int k=skipcolumns;k--;)  // skip columns in header too
+        line >> filename;
+      strncpy(Header, line.str().c_str(), 1023);  
+      for(int j=0;j<RowCounter[i];j++) {
+        Matrix[i][j] = (double *) Malloc(sizeof(double)*ColumnCounter, "MatrixContainer::ParseMatrix: *Matrix[][]");
+        input.getline(filename, 1023);
+        stringstream lines(filename);
+        //cout << "Matrix at level " << j << ":";// << filename << endl;
+        for(int k=skipcolumns;k--;)
+          lines >> filename;
+        for(int k=0;(k<ColumnCounter) && (!lines.eof());k++) {
+          lines >> Matrix[i][j][k];
+          //cout << " " << setprecision(2) << Matrix[i][j][k];;
+        }
+        //cout << endl;
+        Matrix[i][ RowCounter[i] ] = (double *) Malloc(sizeof(double)*ColumnCounter, "MatrixContainer::ParseMatrix: *Matrix[RowCounter[i]][]");
+        for(int j=ColumnCounter;j--;)
+          Matrix[i][ RowCounter[i] ][j] = 0.;
       }
-      //cout << endl;
-    }
-    Matrix[i][ RowCounter[i] ] = (double *) Malloc(sizeof(double)*ColumnCounter, "MatrixContainer::ParseMatrix: *Matrix[RowCounter[i]][]");
-    for(int j=ColumnCounter;j--;)
-      Matrix[i][ RowCounter[i] ][j] = 0.;
+    } else {
+      cerr << "ERROR: Matrix nr. " << i << " has column and row count of (" << ColumnCounter << "," << RowCounter[i] << "), could not allocate nor parse!" << endl; 
+    }
     input.close();
   }
@@ -430 +455 @@
   stringstream line;
   
-  cout << "Parsing force indices." << endl;
+  cout << "Parsing force indices for " << MatrixCounter << " matrices." << endl;
   Indices = (int **) Malloc(sizeof(int *)*(MatrixCounter+1), "ForceMatrix::ParseIndices: **Indices");
   line << name << FRAGMENTPREFIX << FORCESFILE;
@@ -446 +471 @@
     Indices[i] = (int *) Malloc(sizeof(int)*RowCounter[i], "ForceMatrix::ParseIndices: *Indices[]");
     FragmentNumber = FixedDigitNumber(MatrixCounter, i);
-    cout << FRAGMENTPREFIX << FragmentNumber << "[" << RowCounter[i] << "]:";
+    //cout << FRAGMENTPREFIX << FragmentNumber << "[" << RowCounter[i] << "]:";
     Free((void **)&FragmentNumber, "ForceMatrix::ParseIndices: *FragmentNumber");
     for(int j=0;(j<RowCounter[i]) && (!line.eof());j++) {
       line >> Indices[i][j];
-      cout << " " << Indices[i][j];
-    }
-    cout << endl;
+      //cout << " " << Indices[i][j];
+    }
+    //cout << endl;
   }
   Indices[MatrixCounter] = (int *) Malloc(sizeof(int)*RowCounter[MatrixCounter], "ForceMatrix::ParseIndices: *Indices[]");
@@ -568 +593 @@
   
   cout << "Creating Fragment terms." << endl;
-  // scan through all to determine order
+  // scan through all to determine maximum order
   Order=0;
   for(int i=FragmentCounter;i--;) {