--- trunk/OOPSE/libmdtools/DumpReader.cpp	2003/10/16 19:16:24	804
+++ trunk/OOPSE/libmdtools/DumpReader.cpp	2004/04/12 20:32:20	1097
@@ -1,10 +1,11 @@
+#define _LARGEFILE_SOURCE64
 #define _FILE_OFFSET_BITS 64
 
 #include <sys/types.h>
 #include <sys/stat.h>
 
 #include <iostream>
-#include <cmath>
+#include <math.h>
 
 #include <stdio.h>
 #include <stdlib.h>
@@ -33,7 +34,7 @@ DumpReader :: DumpReader( char *in_name ){
 using namespace dumpRead;
 
 
-DumpReader :: DumpReader( char *in_name ){
+DumpReader :: DumpReader(const char *in_name ){
 
   isScanned = false;
   headFP = new FilePos;
@@ -221,14 +222,13 @@ void DumpReader :: readSet( int whichFrame ){
   double time;
 
   fpos_t *framePos;
+  framePos = frameStart[whichFrame]->getPos();
   
 #ifndef IS_MPI
   
-  framePos = frameStart[whichFrame]->getPos();
-
+  fsetpos(inFile, framePos);
   
 
-
   eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
   if( eof_test == NULL ){
     sprintf( painCave.errMsg,
@@ -316,7 +316,7 @@ void DumpReader :: readSet( int whichFrame ){
   
   haveError = 0;
   if (worldRank == 0) {
-
+    fsetpos(inFile, framePos);
     eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
     if( eof_test == NULL ){
       sprintf( painCave.errMsg,
@@ -465,10 +465,10 @@ char* DumpReader::parseDumpLine(char* readLine, int gl
 
   char *foo; // the pointer to the current string token 
   
-  double pos[3]; // position place holders
-  double vel[3]; // velocity placeholders
-  double q[4]; // the quaternions
-  double jx, jy, jz; // angular velocity placeholders;
+  double pos[3];        // position place holders
+  double vel[3];        // velocity placeholders
+  double q[4];          // the quaternions
+  double ji[3];         // angular velocity placeholders;
   double qSqr, qLength; // needed to normalize the quaternion vector.
   
   Atom **atoms = simnfo->atoms;
@@ -497,17 +497,17 @@ char* DumpReader::parseDumpLine(char* readLine, int gl
   // set the string tokenizer
   
   foo = strtok(readLine, " ,;\t");
-  
+  atoms[atomIndex]->setType(foo);
   // check the atom name to the current atom
   
-  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
-    sprintf( painCave.errMsg,
-	     "Initialize from file error. Atom %s at index %d "
-	     "in file %s does not"
-	     " match the BASS atom %s.\n",
-	     foo, atomIndex, inName, atoms[atomIndex]->getType() );
-    return strdup( painCave.errMsg );
-  }
+  //if( strcmp( foo, atoms[atomIndex]->getType() ) ){
+  //  sprintf( painCave.errMsg,
+  //    "Initialize from file error. Atom %s at index %d "
+  //     "in file %s does not"
+  //     " match the BASS atom %s.\n",
+  //     foo, atomIndex, inName, atoms[atomIndex]->getType() );
+  //  return strdup( painCave.errMsg );
+  //}
     
   // get the positions
 
@@ -629,7 +629,7 @@ char* DumpReader::parseDumpLine(char* readLine, int gl
 	       inName, n_atoms, atomIndex );
       return strdup( painCave.errMsg );
     }
-    jx = atof( foo );
+    ji[0] = atof( foo );
       
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
@@ -639,7 +639,7 @@ char* DumpReader::parseDumpLine(char* readLine, int gl
 	       inName, n_atoms, atomIndex );
       return strdup( painCave.errMsg );
     }
-    jy = atof(foo );
+    ji[1] = atof(foo );
       
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
@@ -649,7 +649,7 @@ char* DumpReader::parseDumpLine(char* readLine, int gl
 	       inName, n_atoms, atomIndex );
       return strdup( painCave.errMsg );
     }
-    jz = atof( foo );
+    ji[2] = atof( foo );
       
     dAtom = ( DirectionalAtom* )atoms[atomIndex];
 
@@ -667,9 +667,7 @@ char* DumpReader::parseDumpLine(char* readLine, int gl
       
     // add the angular velocities
 
-    dAtom->setJx( jx );
-    dAtom->setJy( jy );
-    dAtom->setJz( jz );
+    dAtom->setJ( ji );
   }
     
   // add the positions and velocities to the atom
@@ -686,6 +684,8 @@ char* DumpReader::parseCommentLine(char* readLine, dou
 
   char *foo; // the pointer to the current string token 
   int j;
+  double chi, integralOfChidt;
+  double eta[9];
 
   // set the string tokenizer
   
@@ -784,8 +784,62 @@ char* DumpReader::parseCommentLine(char* readLine, dou
     return strdup( painCave.errMsg );
   }
   boxMat[8] = atof( foo );    
+
+  return NULL;
 
+  //get chi and integralOfChidt, they should appear by pair
+  foo = strtok(NULL, " ,;\t\n");
+  if(foo != NULL){
+    chi = atof(foo);
+    
+    foo = strtok(NULL, " ,;\t\n");
+    if(foo == NULL){
+      sprintf( painCave.errMsg,
+               "chi and integralOfChidt should appear by pair in %s\n", inName );
+      return strdup( painCave.errMsg );
+    }
+    integralOfChidt = atof( foo );
+    
+    //push chi and integralOfChidt into SimInfo::properties which can be
+    //retrieved by integrator later
+    DoubleData* chiValue = new DoubleData();
+    chiValue->setID(CHIVALUE_ID);
+    chiValue->setData(chi);
+    simnfo->addProperty(chiValue);
+    
+    DoubleData* integralOfChidtValue = new DoubleData();
+    integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
+    integralOfChidtValue->setData(integralOfChidt);
+    simnfo->addProperty(integralOfChidtValue);
+    
+  }
+  else
+    return NULL;
+  
+  //get eta
+  for(int i = 0 ; i < 9; i++){
+    foo = strtok(NULL, " ,;\t");
+    if(foo == NULL){
+      sprintf( painCave.errMsg,
+               "error in reading eta[%d] from %s\n", i, inName );
+      return strdup( painCave.errMsg );
+    }
+    eta[i] = atof( foo );
+  }
+  
+  //push eta into SimInfo::properties which can be
+  //retrieved by integrator later
+  //simnfo->setBoxM( theBoxMat3 );
+  DoubleArrayData* etaValue = new DoubleArrayData();
+  etaValue->setID(ETAVALUE_ID);
+  etaValue->setData(eta, 9);
+  simnfo->addProperty(etaValue);
+  
+  
   return NULL;
+  
+  
+
 }