# | 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 226 | Line 227 | void DumpReader :: readSet( int whichFrame ){ | |
227 | ||
228 | framePos = frameStart[whichFrame]->getPos(); | |
229 | ||
230 | + | fsetpos(inFile, framePos); |
231 | ||
232 | ||
231 | – | |
233 | eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); | |
234 | if( eof_test == NULL ){ | |
235 | sprintf( painCave.errMsg, | |
# | Line 316 | Line 317 | void DumpReader :: readSet( int whichFrame ){ | |
317 | ||
318 | haveError = 0; | |
319 | if (worldRank == 0) { | |
320 | < | |
320 | > | fsetpos(inFile, framePos); |
321 | eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); | |
322 | if( eof_test == NULL ){ | |
323 | sprintf( painCave.errMsg, | |
# | Line 497 | Line 498 | char* DumpReader::parseDumpLine(char* readLine, int gl | |
498 | // set the string tokenizer | |
499 | ||
500 | foo = strtok(readLine, " ,;\t"); | |
501 | < | |
501 | > | atoms[atomIndex]->setType(foo); |
502 | // check the atom name to the current atom | |
503 | ||
504 | < | if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
505 | < | sprintf( painCave.errMsg, |
506 | < | "Initialize from file error. Atom %s at index %d " |
507 | < | "in file %s does not" |
508 | < | " match the BASS atom %s.\n", |
509 | < | foo, atomIndex, inName, atoms[atomIndex]->getType() ); |
510 | < | return strdup( painCave.errMsg ); |
511 | < | } |
504 | > | //if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
505 | > | // sprintf( painCave.errMsg, |
506 | > | // "Initialize from file error. Atom %s at index %d " |
507 | > | // "in file %s does not" |
508 | > | // " match the BASS atom %s.\n", |
509 | > | // foo, atomIndex, inName, atoms[atomIndex]->getType() ); |
510 | > | // return strdup( painCave.errMsg ); |
511 | > | //} |
512 | ||
513 | // get the positions | |
514 | ||
# | Line 686 | Line 687 | char* DumpReader::parseCommentLine(char* readLine, dou | |
687 | ||
688 | char *foo; // the pointer to the current string token | |
689 | int j; | |
690 | + | double chi, integralOfChidt; |
691 | + | double eta[9]; |
692 | ||
693 | // set the string tokenizer | |
694 | ||
# | Line 786 | Line 789 | char* DumpReader::parseCommentLine(char* readLine, dou | |
789 | boxMat[8] = atof( foo ); | |
790 | ||
791 | return NULL; | |
792 | + | |
793 | + | //get chi and integralOfChidt, they should appear by pair |
794 | + | foo = strtok(NULL, " ,;\t\n"); |
795 | + | if(foo != NULL){ |
796 | + | chi = atof(foo); |
797 | + | |
798 | + | foo = strtok(NULL, " ,;\t\n"); |
799 | + | if(foo == NULL){ |
800 | + | sprintf( painCave.errMsg, |
801 | + | "chi and integralOfChidt should appear by pair in %s\n", inName ); |
802 | + | return strdup( painCave.errMsg ); |
803 | + | } |
804 | + | integralOfChidt = atof( foo ); |
805 | + | |
806 | + | //push chi and integralOfChidt into SimInfo::properties which can be |
807 | + | //retrieved by integrator later |
808 | + | DoubleData* chiValue = new DoubleData(); |
809 | + | chiValue->setID(CHIVALUE_ID); |
810 | + | chiValue->setData(chi); |
811 | + | simnfo->addProperty(chiValue); |
812 | + | |
813 | + | DoubleData* integralOfChidtValue = new DoubleData(); |
814 | + | integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
815 | + | integralOfChidtValue->setData(integralOfChidt); |
816 | + | simnfo->addProperty(integralOfChidtValue); |
817 | + | |
818 | + | } |
819 | + | else |
820 | + | return NULL; |
821 | + | |
822 | + | //get eta |
823 | + | for(int i = 0 ; i < 9; i++){ |
824 | + | foo = strtok(NULL, " ,;\t"); |
825 | + | if(foo == NULL){ |
826 | + | sprintf( painCave.errMsg, |
827 | + | "error in reading eta[%d] from %s\n", i, inName ); |
828 | + | return strdup( painCave.errMsg ); |
829 | + | } |
830 | + | eta[i] = atof( foo ); |
831 | + | } |
832 | + | |
833 | + | //push eta into SimInfo::properties which can be |
834 | + | //retrieved by integrator later |
835 | + | //simnfo->setBoxM( theBoxMat3 ); |
836 | + | DoubleArrayData* etaValue = new DoubleArrayData(); |
837 | + | etaValue->setID(ETAVALUE_ID); |
838 | + | etaValue->setData(eta, 9); |
839 | + | simnfo->addProperty(etaValue); |
840 | + | |
841 | + | |
842 | + | return NULL; |
843 | + | |
844 | + | |
845 | + | |
846 | } | |
847 | ||
848 |
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