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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 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <sys/types.h>
5   #include <sys/stat.h>
6  
7   #include <iostream>
8 < #include <cmath>
8 > #include <math.h>
9  
10   #include <stdio.h>
11   #include <stdlib.h>
# Line 33 | Line 34 | using namespace dumpRead;
34   using namespace dumpRead;
35  
36  
37 < DumpReader :: DumpReader( char *in_name ){
37 > DumpReader :: DumpReader(const char *in_name ){
38  
39    isScanned = false;
40    headFP = new FilePos;
# Line 221 | Line 222 | void DumpReader :: readSet( int whichFrame ){
222    double time;
223  
224    fpos_t *framePos;
225 +  framePos = frameStart[whichFrame]->getPos();
226    
227   #ifndef IS_MPI
228    
229 <  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 465 | Line 465 | char* DumpReader::parseDumpLine(char* readLine, int gl
465  
466    char *foo; // the pointer to the current string token
467    
468 <  double pos[3]; // position place holders
469 <  double vel[3]; // velocity placeholders
470 <  double q[4]; // the quaternions
471 <  double jx, jy, jz; // angular velocity placeholders;
468 >  double pos[3];        // position place holders
469 >  double vel[3];        // velocity placeholders
470 >  double q[4];          // the quaternions
471 >  double ji[3];         // angular velocity placeholders;
472    double qSqr, qLength; // needed to normalize the quaternion vector.
473    
474    Atom **atoms = simnfo->atoms;
# 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 629 | Line 629 | char* DumpReader::parseDumpLine(char* readLine, int gl
629                 inName, n_atoms, atomIndex );
630        return strdup( painCave.errMsg );
631      }
632 <    jx = atof( foo );
632 >    ji[0] = atof( foo );
633        
634      foo = strtok(NULL, " ,;\t");
635      if(foo == NULL){
# Line 639 | Line 639 | char* DumpReader::parseDumpLine(char* readLine, int gl
639                 inName, n_atoms, atomIndex );
640        return strdup( painCave.errMsg );
641      }
642 <    jy = atof(foo );
642 >    ji[1] = atof(foo );
643        
644      foo = strtok(NULL, " ,;\t");
645      if(foo == NULL){
# Line 649 | Line 649 | char* DumpReader::parseDumpLine(char* readLine, int gl
649                 inName, n_atoms, atomIndex );
650        return strdup( painCave.errMsg );
651      }
652 <    jz = atof( foo );
652 >    ji[2] = atof( foo );
653        
654      dAtom = ( DirectionalAtom* )atoms[atomIndex];
655  
# Line 667 | Line 667 | char* DumpReader::parseDumpLine(char* readLine, int gl
667        
668      // add the angular velocities
669  
670 <    dAtom->setJx( jx );
671 <    dAtom->setJy( jy );
672 <    dAtom->setJz( jz );
670 >    dAtom->setJ( ji );
671    }
672      
673    // add the positions and velocities to the atom
# Line 686 | Line 684 | char* DumpReader::parseCommentLine(char* readLine, dou
684  
685    char *foo; // the pointer to the current string token
686    int j;
687 +  double chi, integralOfChidt;
688 +  double eta[9];
689  
690    // set the string tokenizer
691    
# Line 784 | Line 784 | char* DumpReader::parseCommentLine(char* readLine, dou
784      return strdup( painCave.errMsg );
785    }
786    boxMat[8] = atof( foo );    
787 +
788 +  return NULL;
789  
790 +  //get chi and integralOfChidt, they should appear by pair
791 +  foo = strtok(NULL, " ,;\t\n");
792 +  if(foo != NULL){
793 +    chi = atof(foo);
794 +    
795 +    foo = strtok(NULL, " ,;\t\n");
796 +    if(foo == NULL){
797 +      sprintf( painCave.errMsg,
798 +               "chi and integralOfChidt should appear by pair in %s\n", inName );
799 +      return strdup( painCave.errMsg );
800 +    }
801 +    integralOfChidt = atof( foo );
802 +    
803 +    //push chi and integralOfChidt into SimInfo::properties which can be
804 +    //retrieved by integrator later
805 +    DoubleData* chiValue = new DoubleData();
806 +    chiValue->setID(CHIVALUE_ID);
807 +    chiValue->setData(chi);
808 +    simnfo->addProperty(chiValue);
809 +    
810 +    DoubleData* integralOfChidtValue = new DoubleData();
811 +    integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
812 +    integralOfChidtValue->setData(integralOfChidt);
813 +    simnfo->addProperty(integralOfChidtValue);
814 +    
815 +  }
816 +  else
817 +    return NULL;
818 +  
819 +  //get eta
820 +  for(int i = 0 ; i < 9; i++){
821 +    foo = strtok(NULL, " ,;\t");
822 +    if(foo == NULL){
823 +      sprintf( painCave.errMsg,
824 +               "error in reading eta[%d] from %s\n", i, inName );
825 +      return strdup( painCave.errMsg );
826 +    }
827 +    eta[i] = atof( foo );
828 +  }
829 +  
830 +  //push eta into SimInfo::properties which can be
831 +  //retrieved by integrator later
832 +  //simnfo->setBoxM( theBoxMat3 );
833 +  DoubleArrayData* etaValue = new DoubleArrayData();
834 +  etaValue->setID(ETAVALUE_ID);
835 +  etaValue->setData(eta, 9);
836 +  simnfo->addProperty(etaValue);
837 +  
838 +  
839    return NULL;
840 +  
841 +  
842 +
843   }
844  
845  

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