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root/group/trunk/OOPSE/libmdtools/DumpReader.cpp
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Comparing trunk/OOPSE/libmdtools/DumpReader.cpp (file contents):
Revision 804 by mmeineke, Thu Oct 16 19:16:24 2003 UTC vs.
Revision 1074 by tim, Mon Mar 1 20:01:50 2004 UTC

# Line 4 | Line 4
4   #include <sys/stat.h>
5  
6   #include <iostream>
7 < #include <cmath>
7 > #include <math.h>
8  
9   #include <stdio.h>
10   #include <stdlib.h>
# Line 33 | Line 33 | using namespace dumpRead;
33   using namespace dumpRead;
34  
35  
36 < DumpReader :: DumpReader( char *in_name ){
36 > DumpReader :: DumpReader(const char *in_name ){
37  
38    isScanned = false;
39    headFP = new FilePos;
# Line 226 | Line 226 | void DumpReader :: readSet( int whichFrame ){
226    
227    framePos = frameStart[whichFrame]->getPos();
228  
229 +  fsetpos(inFile, framePos);
230    
231  
231 –
232    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
233    if( eof_test == NULL ){
234      sprintf( painCave.errMsg,
# Line 316 | Line 316 | void DumpReader :: readSet( int whichFrame ){
316    
317    haveError = 0;
318    if (worldRank == 0) {
319 <
319 >    fsetpos(inFile, framePos);
320      eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
321      if( eof_test == NULL ){
322        sprintf( painCave.errMsg,
# Line 497 | Line 497 | char* DumpReader::parseDumpLine(char* readLine, int gl
497    // set the string tokenizer
498    
499    foo = strtok(readLine, " ,;\t");
500 <  
500 >  atoms[atomIndex]->setType(foo);
501    // check the atom name to the current atom
502    
503 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
504 <    sprintf( painCave.errMsg,
505 <             "Initialize from file error. Atom %s at index %d "
506 <             "in file %s does not"
507 <             " match the BASS atom %s.\n",
508 <             foo, atomIndex, inName, atoms[atomIndex]->getType() );
509 <    return strdup( painCave.errMsg );
510 <  }
503 >  //if( strcmp( foo, atoms[atomIndex]->getType() ) ){
504 >  //  sprintf( painCave.errMsg,
505 >  //    "Initialize from file error. Atom %s at index %d "
506 >  //     "in file %s does not"
507 >  //     " match the BASS atom %s.\n",
508 >  //     foo, atomIndex, inName, atoms[atomIndex]->getType() );
509 >  //  return strdup( painCave.errMsg );
510 >  //}
511      
512    // get the positions
513  
# Line 686 | Line 686 | char* DumpReader::parseCommentLine(char* readLine, dou
686  
687    char *foo; // the pointer to the current string token
688    int j;
689 +  double chi, integralOfChidt;
690 +  double eta[9];
691  
692    // set the string tokenizer
693    
# Line 785 | Line 787 | char* DumpReader::parseCommentLine(char* readLine, dou
787    }
788    boxMat[8] = atof( foo );    
789  
790 +  return NULL;
791 +
792 +  //get chi and integralOfChidt, they should appear by pair
793 +  foo = strtok(NULL, " ,;\t\n");
794 +  if(foo != NULL){
795 +    chi = atof(foo);
796 +    
797 +    foo = strtok(NULL, " ,;\t\n");
798 +    if(foo == NULL){
799 +      sprintf( painCave.errMsg,
800 +               "chi and integralOfChidt should appear by pair in %s\n", inName );
801 +      return strdup( painCave.errMsg );
802 +    }
803 +    integralOfChidt = atof( foo );
804 +    
805 +    //push chi and integralOfChidt into SimInfo::properties which can be
806 +    //retrieved by integrator later
807 +    DoubleData* chiValue = new DoubleData();
808 +    chiValue->setID(CHIVALUE_ID);
809 +    chiValue->setData(chi);
810 +    simnfo->addProperty(chiValue);
811 +    
812 +    DoubleData* integralOfChidtValue = new DoubleData();
813 +    integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
814 +    integralOfChidtValue->setData(integralOfChidt);
815 +    simnfo->addProperty(integralOfChidtValue);
816 +    
817 +  }
818 +  else
819 +    return NULL;
820 +  
821 +  //get eta
822 +  for(int i = 0 ; i < 9; i++){
823 +    foo = strtok(NULL, " ,;\t");
824 +    if(foo == NULL){
825 +      sprintf( painCave.errMsg,
826 +               "error in reading eta[%d] from %s\n", i, inName );
827 +      return strdup( painCave.errMsg );
828 +    }
829 +    eta[i] = atof( foo );
830 +  }
831 +  
832 +  //push eta into SimInfo::properties which can be
833 +  //retrieved by integrator later
834 +  //simnfo->setBoxM( theBoxMat3 );
835 +  DoubleArrayData* etaValue = new DoubleArrayData();
836 +  etaValue->setID(ETAVALUE_ID);
837 +  etaValue->setData(eta, 9);
838 +  simnfo->addProperty(etaValue);
839 +  
840 +  
841    return NULL;
842 +  
843 +  
844 +
845   }
846  
847  

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