11 |
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#include <stdlib.h> |
12 |
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#include <string.h> |
13 |
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|
14 |
< |
|
15 |
< |
#include "ReadWrite.hpp" |
16 |
< |
#include "simError.h" |
17 |
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|
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#include "io/DumpReader.hpp" |
15 |
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#include "utils/simError.h" |
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#include "utils/MemoryUtils" |
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#ifdef IS_MPI |
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|
19 |
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#include <mpi.h> |
20 |
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#include "mpiSimulation.hpp" |
20 |
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#define TAKE_THIS_TAG_CHAR 0 |
21 |
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#define TAKE_THIS_TAG_INT 1 |
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|
23 |
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#endif // is_mpi |
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|
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|
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< |
DumpReader :: DumpReader(const char *in_name ){ |
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namespace oopse { |
27 |
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|
28 |
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isScanned = false; |
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> |
DumpReader::DumpReader(SimInfo* info, const std::string& filename) |
29 |
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: info_(info), filename_(filename), isScanned_(false){ |
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|
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#ifdef IS_MPI |
32 |
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if (worldRank == 0) { |
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|
33 |
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if (worldRank == 0) { |
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#endif |
35 |
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|
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inFile = fopen(in_name, "r"); |
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if(inFile == NULL){ |
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< |
sprintf(painCave.errMsg, |
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< |
"Cannot open file: %s\n", in_name); |
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painCave.isFatal = 1; |
41 |
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simError(); |
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} |
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|
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inFileName = in_name; |
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inFile_ = fopen(filename_.c_str(), "r"); |
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|
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if (inFile_ == NULL) { |
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sprintf(painCave.errMsg, "Cannot open file: %s\n", in_name); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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#ifdef IS_MPI |
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} |
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strcpy( checkPointMsg, "Dump file opened for reading successfully." ); |
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MPIcheckPoint(); |
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|
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} |
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|
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strcpy(checkPointMsg, "Dump file opened for reading successfully."); |
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MPIcheckPoint(); |
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|
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#endif |
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return; |
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|
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return; |
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} |
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|
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DumpReader :: ~DumpReader( ){ |
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DumpReader::~DumpReader() { |
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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|
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if (worldRank == 0) { |
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#endif |
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vector<fpos_t*>::iterator i; |
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|
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int error; |
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error = fclose( inFile ); |
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if( error ){ |
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sprintf( painCave.errMsg, |
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"Error closing %s\n", inFileName.c_str()); |
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simError(); |
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} |
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int error; |
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error = fclose(inFile_); |
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|
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for(i = framePos.begin(); i != framePos.end(); ++i) |
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delete *i; |
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framePos.clear(); |
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|
66 |
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if (error) { |
67 |
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sprintf(painCave.errMsg, "Error closing %s\n", filename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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MemoryUtils::deleteVectorOfPointer(framePos_); |
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|
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#ifdef IS_MPI |
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} |
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strcpy( checkPointMsg, "Dump file closed successfully." ); |
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MPIcheckPoint(); |
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|
76 |
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} |
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|
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strcpy(checkPointMsg, "Dump file closed successfully."); |
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MPIcheckPoint(); |
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|
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#endif |
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|
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return; |
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return; |
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} |
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|
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int DumpReader::getNframes( void ){ |
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int DumpReader::getNFrames(void) { |
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if (!isScanned_) |
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scanFile(); |
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|
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if( !isScanned ) |
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scanFile(); |
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return framePos.size(); |
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return framePos_.size(); |
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} |
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|
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void DumpReader::scanFile( void ){ |
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|
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void DumpReader::scanFile(void) { |
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int i, j; |
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int lineNum = 0; |
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char readBuffer[2000]; |
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fpos_t *currPos; |
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char readBuffer[maxBufferSize]; |
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fpos_t * currPos; |
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|
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#ifdef IS_MPI |
100 |
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if( worldRank == 0 ){ |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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rewind( inFile ); |
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|
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currPos = new fpos_t; |
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fgetpos( inFile, currPos ); |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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lineNum++; |
102 |
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if( feof( inFile ) ){ |
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sprintf( painCave.errMsg, |
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"File \"%s\" ended unexpectedly at line %d\n", |
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inFileName.c_str(), |
106 |
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lineNum ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
103 |
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|
104 |
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while( !feof( inFile ) ){ |
112 |
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|
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framePos.push_back(currPos); |
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rewind(inFile_); |
105 |
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|
106 |
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i = atoi(readBuffer); |
107 |
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|
108 |
< |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
109 |
< |
lineNum++; |
119 |
< |
if( feof( inFile ) ){ |
120 |
< |
sprintf( painCave.errMsg, |
121 |
< |
"File \"%s\" ended unexpectedly at line %d\n", |
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inFileName.c_str(), |
123 |
< |
lineNum ); |
124 |
< |
painCave.isFatal = 1; |
125 |
< |
simError(); |
126 |
< |
} |
127 |
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|
128 |
< |
for(j=0; j<i; j++){ |
129 |
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|
130 |
< |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
131 |
< |
lineNum++; |
132 |
< |
if( feof( inFile ) ){ |
133 |
< |
sprintf( painCave.errMsg, |
134 |
< |
"File \"%s\" ended unexpectedly at line %d," |
135 |
< |
" with atom %d\n", |
136 |
< |
inFileName.c_str(), |
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< |
lineNum, |
138 |
< |
j ); |
139 |
< |
painCave.isFatal = 1; |
140 |
< |
simError(); |
141 |
< |
} |
142 |
< |
|
143 |
< |
} |
144 |
< |
|
145 |
< |
currPos = new fpos_t; |
146 |
< |
fgetpos( inFile, currPos ); |
147 |
< |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
148 |
< |
lineNum++; |
149 |
< |
} |
150 |
< |
|
151 |
< |
delete currPos; |
152 |
< |
rewind( inFile ); |
153 |
< |
|
154 |
< |
isScanned = true; |
106 |
> |
currPos = new fpos_t; |
107 |
> |
fgetpos(inFile_, currPos); |
108 |
> |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
109 |
> |
lineNum++; |
110 |
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|
111 |
< |
#ifdef IS_MPI |
112 |
< |
} |
113 |
< |
strcpy( checkPointMsg, "Successfully scanned DumpFile\n" ); |
114 |
< |
MPIcheckPoint(); |
115 |
< |
#endif // is_mpi |
116 |
< |
} |
111 |
> |
if (feof(inFile_)) { |
112 |
> |
sprintf(painCave.errMsg, |
113 |
> |
"File \"%s\" ended unexpectedly at line %d\n", |
114 |
> |
filename_.c_str(), |
115 |
> |
lineNum); |
116 |
> |
painCave.isFatal = 1; |
117 |
> |
simError(); |
118 |
> |
} |
119 |
|
|
120 |
< |
void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){ |
120 |
> |
while (!feof(inFile_)) { |
121 |
> |
framePos_.push_back(currPos); |
122 |
|
|
123 |
< |
simnfo = the_simnfo; |
123 |
> |
i = atoi(readBuffer); |
124 |
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|
125 |
< |
this->readSet( whichFrame ); |
126 |
< |
} |
125 |
> |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
126 |
> |
lineNum++; |
127 |
|
|
128 |
+ |
if (feof(inFile_)) { |
129 |
+ |
sprintf(painCave.errMsg, |
130 |
+ |
"File \"%s\" ended unexpectedly at line %d\n", |
131 |
+ |
filename_.c_str(), |
132 |
+ |
lineNum); |
133 |
+ |
painCave.isFatal = 1; |
134 |
+ |
simError(); |
135 |
+ |
} |
136 |
|
|
137 |
+ |
for(j = 0; j < i; j++) { |
138 |
+ |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
139 |
+ |
lineNum++; |
140 |
|
|
141 |
< |
void DumpReader :: readSet( int whichFrame ){ |
141 |
> |
if (feof(inFile_)) { |
142 |
> |
sprintf(painCave.errMsg, |
143 |
> |
"File \"%s\" ended unexpectedly at line %d," |
144 |
> |
" with atom %d\n", filename_.c_str(), |
145 |
> |
lineNum, |
146 |
> |
j); |
147 |
|
|
148 |
< |
int i; |
149 |
< |
unsigned int j; |
148 |
> |
painCave.isFatal = 1; |
149 |
> |
simError(); |
150 |
> |
} |
151 |
> |
} |
152 |
|
|
153 |
< |
#ifdef IS_MPI |
154 |
< |
int done, which_node, which_atom; // loop counter |
155 |
< |
#endif //is_mpi |
153 |
> |
currPos = new fpos_t; |
154 |
> |
fgetpos(inFile_, currPos); |
155 |
> |
fgets(readBuffer, sizeof(readBuffer), inFile_); |
156 |
> |
lineNum++; |
157 |
> |
} |
158 |
|
|
159 |
< |
const int BUFFERSIZE = 2000; // size of the read buffer |
160 |
< |
int nTotObjs; // the number of atoms |
183 |
< |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
159 |
> |
delete currPos; |
160 |
> |
rewind(inFile_); |
161 |
|
|
162 |
< |
char *eof_test; // ptr to see when we reach the end of the file |
186 |
< |
char *parseErr; |
162 |
> |
isScanned = true; |
163 |
|
|
164 |
< |
vector<StuntDouble*> integrableObjects; |
164 |
> |
#ifdef IS_MPI |
165 |
|
|
166 |
+ |
} |
167 |
|
|
168 |
< |
#ifndef IS_MPI |
168 |
> |
strcpy(checkPointMsg, "Successfully scanned DumpFile\n"); |
169 |
> |
MPIcheckPoint(); |
170 |
|
|
171 |
< |
fsetpos(inFile, framePos[whichFrame]); |
194 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
195 |
< |
if( eof_test == NULL ){ |
196 |
< |
sprintf( painCave.errMsg, |
197 |
< |
"DumpReader error: error reading 1st line of \"%s\"\n", |
198 |
< |
inFileName.c_str() ); |
199 |
< |
painCave.isFatal = 1; |
200 |
< |
simError(); |
201 |
< |
} |
171 |
> |
#endif // is_mpi |
172 |
|
|
173 |
< |
nTotObjs = atoi( read_buffer ); |
173 |
> |
} |
174 |
|
|
175 |
< |
if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
176 |
< |
sprintf( painCave.errMsg, |
177 |
< |
"DumpReader error. %s nIntegrable, %d, " |
208 |
< |
"does not match the meta-data file's nIntegrable, %d.\n", |
209 |
< |
inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
210 |
< |
painCave.isFatal = 1; |
211 |
< |
simError(); |
212 |
< |
} |
175 |
> |
void DumpReader::readFrame(int whichFrame) { |
176 |
> |
readSet(whichFrame); |
177 |
> |
} |
178 |
|
|
179 |
< |
//read the box mat from the comment line |
179 |
> |
void DumpReader::readSet(int whichFrame) { |
180 |
> |
int i; |
181 |
> |
int nTotObjs; // the number of atoms |
182 |
> |
char read_buffer[maxBufferSize]; //the line buffer for reading |
183 |
> |
char * eof_test; // ptr to see when we reach the end of the file |
184 |
|
|
185 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
186 |
< |
if(eof_test == NULL){ |
187 |
< |
sprintf( painCave.errMsg, |
188 |
< |
"error in reading commment in %s\n", inFileName.c_str()); |
220 |
< |
painCave.isFatal = 1; |
221 |
< |
simError(); |
222 |
< |
} |
185 |
> |
Molecule* mol; |
186 |
> |
StuntDouble* integrableObject; |
187 |
> |
typename SimInfo::MoleculeIterator mi; |
188 |
> |
typename Molecule::IntegrableObjectIterator ii; |
189 |
|
|
190 |
< |
parseErr = parseCommentLine( read_buffer, simnfo); |
225 |
< |
if( parseErr != NULL ){ |
226 |
< |
strcpy( painCave.errMsg, parseErr ); |
227 |
< |
painCave.isFatal = 1; |
228 |
< |
simError(); |
229 |
< |
} |
190 |
> |
#ifndef IS_MPI |
191 |
|
|
192 |
< |
//parse dump lines |
192 |
> |
fsetpos(inFile_, framePos_[whichFrame]); |
193 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
194 |
|
|
195 |
< |
for( i=0; i < simnfo->n_mol; i++){ |
195 |
> |
if (eof_test == NULL) { |
196 |
> |
sprintf(painCave.errMsg, |
197 |
> |
"DumpReader error: error reading 1st line of \"%s\"\n", |
198 |
> |
filename_.c_str()); |
199 |
> |
painCave.isFatal = 1; |
200 |
> |
simError(); |
201 |
> |
} |
202 |
|
|
203 |
< |
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
203 |
> |
nTotObjs = atoi(read_buffer); |
204 |
|
|
205 |
< |
for(j = 0; j < integrableObjects.size(); j++){ |
238 |
< |
|
239 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
240 |
< |
if(eof_test == NULL){ |
205 |
> |
if (nTotObjs != info_->getNGlobalIntegrableObjects()) { |
206 |
|
sprintf(painCave.errMsg, |
207 |
< |
"error in reading file %s\n" |
208 |
< |
"natoms = %d; index = %d\n" |
209 |
< |
"error reading the line from the file.\n", |
210 |
< |
inFileName.c_str(), nTotObjs, i ); |
207 |
> |
"DumpReader error. %s nIntegrable, %d, " |
208 |
> |
"does not match the meta-data file's nIntegrable, %d.\n", |
209 |
> |
filename_.c_str(), |
210 |
> |
nTotObjs, |
211 |
> |
info_->getNIntegrableObjects()); |
212 |
> |
|
213 |
|
painCave.isFatal = 1; |
214 |
|
simError(); |
248 |
– |
} |
249 |
– |
|
250 |
– |
parseErr = parseDumpLine( read_buffer, integrableObjects[j]); |
251 |
– |
if( parseErr != NULL ){ |
252 |
– |
strcpy( painCave.errMsg, parseErr ); |
253 |
– |
painCave.isFatal = 1; |
254 |
– |
simError(); |
255 |
– |
} |
215 |
|
} |
257 |
– |
} |
216 |
|
|
217 |
< |
// MPI Section of code.......... |
260 |
< |
#else //IS_MPI |
217 |
> |
//read the box mat from the comment line |
218 |
|
|
219 |
< |
// first thing first, suspend fatalities. |
263 |
< |
painCave.isEventLoop = 1; |
219 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
220 |
|
|
221 |
< |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
222 |
< |
int haveError; |
223 |
< |
|
224 |
< |
MPI_Status istatus; |
225 |
< |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
270 |
< |
int localIndex; |
271 |
< |
int nCurObj; |
272 |
< |
int nitems; |
273 |
< |
|
274 |
< |
nTotObjs = simnfo->getTotIntegrableObjects(); |
275 |
< |
haveError = 0; |
276 |
< |
if (worldRank == 0) { |
277 |
< |
fsetpos(inFile, framePos[whichFrame]); |
278 |
< |
|
279 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
280 |
< |
if( eof_test == NULL ){ |
281 |
< |
sprintf( painCave.errMsg, |
282 |
< |
"Error reading 1st line of %s \n ",inFileName.c_str()); |
283 |
< |
haveError = 1; |
284 |
< |
simError(); |
221 |
> |
if (eof_test == NULL) { |
222 |
> |
sprintf(painCave.errMsg, "error in reading commment in %s\n", |
223 |
> |
filename_.c_str()); |
224 |
> |
painCave.isFatal = 1; |
225 |
> |
simError(); |
226 |
|
} |
227 |
|
|
228 |
< |
nitems = atoi( read_buffer ); |
228 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot(), info_->useInitState()); |
229 |
|
|
230 |
< |
// Check to see that the number of integrable objects in the |
290 |
< |
// intial configuration file is the same as derived from the |
291 |
< |
// meta-data file. |
230 |
> |
//parse dump lines |
231 |
|
|
232 |
< |
if( nTotObjs != nitems){ |
294 |
< |
sprintf( painCave.errMsg, |
295 |
< |
"DumpReader Error. %s nIntegrable, %d, " |
296 |
< |
"does not match the meta-data file's nIntegrable, %d.\n", |
297 |
< |
inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
298 |
< |
haveError= 1; |
299 |
< |
simError(); |
300 |
< |
} |
232 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
233 |
|
|
234 |
< |
//read the boxMat from the comment line |
234 |
> |
for (integrableObject = mol->beginIntegrableObject(i); integrableObject != NULL; |
235 |
> |
integrableObject = mol->nextIntegrableObject(i)) { |
236 |
|
|
237 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
305 |
< |
if(eof_test == NULL){ |
306 |
< |
sprintf( painCave.errMsg, |
307 |
< |
"error in reading commment in %s\n", inFileName.c_str()); |
308 |
< |
haveError = 1; |
309 |
< |
simError(); |
310 |
< |
} |
237 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
238 |
|
|
239 |
< |
//Every single processor will parse the comment line by itself |
240 |
< |
//By using this way, we might lose some efficiency, but if we want to add |
241 |
< |
//more parameters into comment line, we only need to modify function |
242 |
< |
//parseCommentLine |
239 |
> |
if (eof_test == NULL) { |
240 |
> |
sprintf(painCave.errMsg, |
241 |
> |
"error in reading file %s\n" |
242 |
> |
"natoms = %d; index = %d\n" |
243 |
> |
"error reading the line from the file.\n", |
244 |
> |
filename_.c_str(), |
245 |
> |
nTotObjs, |
246 |
> |
i); |
247 |
|
|
248 |
< |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
248 |
> |
painCave.isFatal = 1; |
249 |
> |
simError(); |
250 |
> |
} |
251 |
|
|
252 |
< |
parseErr = parseCommentLine( read_buffer, simnfo); |
253 |
< |
|
254 |
< |
if( parseErr != NULL ){ |
322 |
< |
strcpy( painCave.errMsg, parseErr ); |
323 |
< |
haveError = 1; |
324 |
< |
simError(); |
252 |
> |
parseDumpLine(read_buffer, integrableObjects[j]); |
253 |
> |
|
254 |
> |
} |
255 |
|
} |
256 |
|
|
257 |
< |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
328 |
< |
which_node = MolToProcMap[i]; |
329 |
< |
if(which_node == 0){ |
330 |
< |
//molecules belong to master node |
257 |
> |
// MPI Section of code.......... |
258 |
|
|
259 |
< |
localIndex = mpiSim->getGlobalToLocalMol(i); |
259 |
> |
#else //IS_MPI |
260 |
|
|
261 |
< |
if(localIndex == -1) { |
262 |
< |
strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
263 |
< |
haveError = 1; |
264 |
< |
simError(); |
338 |
< |
} |
261 |
> |
// first thing first, suspend fatalities. |
262 |
> |
int masterNode = 0; |
263 |
> |
int nCurObj; |
264 |
> |
painCave.isEventLoop = 1; |
265 |
|
|
266 |
< |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
267 |
< |
for(j=0; j < integrableObjects.size(); j++){ |
342 |
< |
|
343 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
344 |
< |
if(eof_test == NULL){ |
345 |
< |
sprintf(painCave.errMsg, |
346 |
< |
"error in reading file %s\n" |
347 |
< |
"natoms = %d; index = %d\n" |
348 |
< |
"error reading the line from the file.\n", |
349 |
< |
inFileName.c_str(), nTotObjs, i ); |
350 |
< |
haveError= 1; |
351 |
< |
simError(); |
352 |
< |
} |
353 |
< |
|
354 |
< |
if(haveError) nodeZeroError(); |
266 |
> |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
267 |
> |
int haveError; |
268 |
|
|
269 |
< |
parseDumpLine(read_buffer, integrableObjects[j]); |
270 |
< |
|
358 |
< |
} |
269 |
> |
MPI_Status istatus; |
270 |
> |
int nitems; |
271 |
|
|
272 |
+ |
nTotObjs = info_->getNGlobalIntegrableObjects(); |
273 |
+ |
haveError = 0; |
274 |
|
|
275 |
< |
} |
276 |
< |
else{ |
363 |
< |
//molecule belongs to slave nodes |
275 |
> |
if (worldRank == masterNode) { |
276 |
> |
fsetpos(inFile_, framePos_[whichFrame]); |
277 |
|
|
278 |
< |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
366 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
367 |
< |
|
368 |
< |
for(j=0; j < nCurObj; j++){ |
369 |
< |
|
370 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
371 |
< |
if(eof_test == NULL){ |
372 |
< |
sprintf(painCave.errMsg, |
373 |
< |
"error in reading file %s\n" |
374 |
< |
"natoms = %d; index = %d\n" |
375 |
< |
"error reading the line from the file.\n", |
376 |
< |
inFileName.c_str(), nTotObjs, i ); |
377 |
< |
haveError= 1; |
378 |
< |
simError(); |
379 |
< |
} |
380 |
< |
|
381 |
< |
if(haveError) nodeZeroError(); |
278 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
279 |
|
|
280 |
< |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
281 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
282 |
< |
|
283 |
< |
} |
280 |
> |
if (eof_test == NULL) { |
281 |
> |
sprintf(painCave.errMsg, "Error reading 1st line of %s \n ", |
282 |
> |
filename_.c_str()); |
283 |
> |
painCave.isFatal = 1; |
284 |
> |
simError(); |
285 |
> |
} |
286 |
|
|
287 |
< |
} |
389 |
< |
|
390 |
< |
} |
391 |
< |
|
392 |
< |
} |
393 |
< |
else{ |
394 |
< |
//actions taken at slave nodes |
395 |
< |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
287 |
> |
nitems = atoi(read_buffer); |
288 |
|
|
289 |
< |
parseErr = parseCommentLine( read_buffer, simnfo); |
289 |
> |
// Check to see that the number of integrable objects in the |
290 |
> |
// intial configuration file is the same as derived from the |
291 |
> |
// meta-data file. |
292 |
|
|
293 |
< |
if( parseErr != NULL ){ |
294 |
< |
strcpy( painCave.errMsg, parseErr ); |
295 |
< |
haveError = 1; |
296 |
< |
simError(); |
297 |
< |
} |
298 |
< |
|
299 |
< |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
406 |
< |
which_node = MolToProcMap[i]; |
407 |
< |
|
408 |
< |
if(which_node == worldRank){ |
409 |
< |
//molecule with global index i belongs to this processor |
410 |
< |
|
411 |
< |
localIndex = mpiSim->getGlobalToLocalMol(i); |
293 |
> |
if (nTotObjs != nitems) { |
294 |
> |
sprintf(painCave.errMsg, |
295 |
> |
"DumpReader Error. %s nIntegrable, %d, " |
296 |
> |
"does not match the meta-data file's nIntegrable, %d.\n", |
297 |
> |
filename_.c_str(), |
298 |
> |
nTotObjs, |
299 |
> |
info_->getTotIntegrableObjects()); |
300 |
|
|
301 |
< |
if(localIndex == -1) { |
302 |
< |
sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
415 |
< |
haveError = 1; |
416 |
< |
simError(); |
301 |
> |
painCave.isFatal = 1; |
302 |
> |
simError(); |
303 |
|
} |
304 |
|
|
305 |
< |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
305 |
> |
//read the boxMat from the comment line |
306 |
|
|
307 |
< |
nCurObj = integrableObjects.size(); |
422 |
< |
|
423 |
< |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
424 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
307 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
308 |
|
|
309 |
< |
for(j = 0; j < integrableObjects.size(); j++){ |
309 |
> |
if (eof_test == NULL) { |
310 |
> |
sprintf(painCave.errMsg, "error in reading commment in %s\n", |
311 |
> |
filename_.c_str()); |
312 |
> |
painCave.isFatal = 1; |
313 |
> |
simError(); |
314 |
> |
} |
315 |
|
|
316 |
< |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
317 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
316 |
> |
//Every single processor will parse the comment line by itself |
317 |
> |
//By using this way, we might lose some efficiency, but if we want to add |
318 |
> |
//more parameters into comment line, we only need to modify function |
319 |
> |
//parseCommentLine |
320 |
|
|
321 |
< |
parseErr = parseDumpLine(read_buffer, integrableObjects[j]); |
321 |
> |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
322 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot(), info_->useInitState()); |
323 |
|
|
324 |
< |
if( parseErr != NULL ){ |
325 |
< |
strcpy( painCave.errMsg, parseErr ); |
435 |
< |
simError(); |
436 |
< |
} |
324 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
325 |
> |
which_node = info_->getMolToProc(i); |
326 |
|
|
327 |
< |
} |
328 |
< |
|
329 |
< |
} |
330 |
< |
|
442 |
< |
} |
327 |
> |
if (which_node == masterNode) { |
328 |
> |
//molecules belong to master node |
329 |
> |
|
330 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
331 |
|
|
332 |
< |
} |
332 |
> |
if (mol == NULL) { |
333 |
> |
strcpy(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
334 |
> |
painCave.isFatal = 1; |
335 |
> |
simError(); |
336 |
> |
} |
337 |
|
|
338 |
< |
#endif |
339 |
< |
} |
338 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
339 |
> |
integrableObject = mol->nextIntegrableObject(ii)){ |
340 |
> |
|
341 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
342 |
|
|
343 |
< |
char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){ |
343 |
> |
if (eof_test == NULL) { |
344 |
> |
sprintf(painCave.errMsg, |
345 |
> |
"error in reading file %s\n" |
346 |
> |
"natoms = %d; index = %d\n" |
347 |
> |
"error reading the line from the file.\n", |
348 |
> |
filename_.c_str(), |
349 |
> |
nTotObjs, |
350 |
> |
i); |
351 |
|
|
352 |
< |
char *foo; // the pointer to the current string token |
352 |
> |
painCave.isFatal = 1; |
353 |
> |
simError(); |
354 |
> |
} |
355 |
|
|
356 |
< |
double pos[3]; // position place holders |
357 |
< |
double vel[3]; // velocity placeholders |
358 |
< |
double q[4]; // the quaternions |
359 |
< |
double ji[3]; // angular velocity placeholders; |
457 |
< |
double qSqr, qLength; // needed to normalize the quaternion vector. |
356 |
> |
parseDumpLine(read_buffer, integrableObject); |
357 |
> |
} |
358 |
> |
} else { |
359 |
> |
//molecule belongs to slave nodes |
360 |
|
|
361 |
+ |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
362 |
+ |
MPI_COMM_WORLD, &istatus); |
363 |
|
|
364 |
< |
// set the string tokenizer |
364 |
> |
for(int j = 0; j < nCurObj; j++) { |
365 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_); |
366 |
|
|
367 |
< |
foo = strtok(readLine, " ,;\t"); |
367 |
> |
if (eof_test == NULL) { |
368 |
> |
sprintf(painCave.errMsg, |
369 |
> |
"error in reading file %s\n" |
370 |
> |
"natoms = %d; index = %d\n" |
371 |
> |
"error reading the line from the file.\n", |
372 |
> |
filename_.c_str(), |
373 |
> |
nTotObjs, |
374 |
> |
i); |
375 |
|
|
376 |
< |
// check the atom name to the current atom |
376 |
> |
painCave.isFatal = 1; |
377 |
> |
simError(); |
378 |
> |
} |
379 |
> |
|
380 |
> |
MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, |
381 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
382 |
> |
} |
383 |
> |
} |
384 |
> |
} |
385 |
> |
} else { |
386 |
> |
//actions taken at slave nodes |
387 |
> |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
388 |
|
|
389 |
< |
if( strcmp( foo, sd->getType() ) ){ |
390 |
< |
sprintf( painCave.errMsg, |
468 |
< |
"DumpReader error. Does not" |
469 |
< |
" match the meta-data atom %s.\n", |
470 |
< |
sd->getType() ); |
471 |
< |
return strdup( painCave.errMsg ); |
472 |
< |
} |
389 |
> |
/**@todo*/ |
390 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot(), info_->useInitState()); |
391 |
|
|
392 |
< |
// get the positions |
392 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
393 |
> |
which_node = info_->getMolToProc(i); |
394 |
|
|
395 |
< |
foo = strtok(NULL, " ,;\t"); |
396 |
< |
if(foo == NULL){ |
397 |
< |
sprintf( painCave.errMsg, |
398 |
< |
"error in reading postition x from %s\n", |
399 |
< |
inFileName.c_str()); |
400 |
< |
return strdup( painCave.errMsg ); |
401 |
< |
} |
402 |
< |
pos[0] = atof( foo ); |
395 |
> |
if (which_node == worldRank) { |
396 |
> |
//molecule with global index i belongs to this processor |
397 |
> |
|
398 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
399 |
> |
if (mol == NULL) { |
400 |
> |
strcpy(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
401 |
> |
painCave.isFatal = 1; |
402 |
> |
simError(); |
403 |
> |
} |
404 |
> |
|
405 |
> |
nCurObj = mol->getNIntegrableObjects(); |
406 |
|
|
407 |
< |
foo = strtok(NULL, " ,;\t"); |
408 |
< |
if(foo == NULL){ |
487 |
< |
sprintf( painCave.errMsg, |
488 |
< |
"error in reading postition y from %s\n", |
489 |
< |
inFileName.c_str()); |
490 |
< |
return strdup( painCave.errMsg ); |
491 |
< |
} |
492 |
< |
pos[1] = atof( foo ); |
407 |
> |
MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, |
408 |
> |
MPI_COMM_WORLD); |
409 |
|
|
410 |
< |
foo = strtok(NULL, " ,;\t"); |
411 |
< |
if(foo == NULL){ |
412 |
< |
sprintf( painCave.errMsg, |
413 |
< |
"error in reading postition z from %s\n", |
414 |
< |
inFileName.c_str()); |
499 |
< |
return strdup( painCave.errMsg ); |
500 |
< |
} |
501 |
< |
pos[2] = atof( foo ); |
410 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
411 |
> |
integrableObject = mol->nextIntegrableObject(ii)){ |
412 |
> |
|
413 |
> |
MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, |
414 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
415 |
|
|
416 |
+ |
parseDumpLine(read_buffer, integrableObject); |
417 |
+ |
} |
418 |
+ |
|
419 |
+ |
} |
420 |
+ |
|
421 |
+ |
} |
422 |
+ |
|
423 |
+ |
} |
424 |
|
|
425 |
< |
// get the velocities |
425 |
> |
#endif |
426 |
|
|
427 |
< |
foo = strtok(NULL, " ,;\t"); |
507 |
< |
if(foo == NULL){ |
508 |
< |
sprintf( painCave.errMsg, |
509 |
< |
"error in reading velocity x from %s\n", |
510 |
< |
inFileName.c_str() ); |
511 |
< |
return strdup( painCave.errMsg ); |
512 |
< |
} |
513 |
< |
vel[0] = atof( foo ); |
427 |
> |
} |
428 |
|
|
429 |
< |
foo = strtok(NULL, " ,;\t"); |
516 |
< |
if(foo == NULL){ |
517 |
< |
sprintf( painCave.errMsg, |
518 |
< |
"error in reading velocity x from %s\n", |
519 |
< |
inFileName.c_str() ); |
520 |
< |
return strdup( painCave.errMsg ); |
521 |
< |
} |
522 |
< |
vel[1] = atof( foo ); |
429 |
> |
void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { |
430 |
|
|
431 |
< |
foo = strtok(NULL, " ,;\t"); |
432 |
< |
if(foo == NULL){ |
433 |
< |
sprintf( painCave.errMsg, |
434 |
< |
"error in reading velocity x from %s\n", |
435 |
< |
inFileName.c_str() ); |
436 |
< |
return strdup( painCave.errMsg ); |
437 |
< |
} |
438 |
< |
vel[2] = atof( foo ); |
431 |
> |
Vector3d pos; // position place holders |
432 |
> |
Vector3d vel; // velocity placeholders |
433 |
> |
Quat4d q; // the quaternions |
434 |
> |
Vector3d ji; // angular velocity placeholders; |
435 |
> |
StringTokenizer tokenizer(line); |
436 |
> |
int nTokens; |
437 |
> |
|
438 |
> |
nTokens = tokenizer.countTokens(); |
439 |
|
|
440 |
+ |
if (nTokens < ) { |
441 |
|
|
534 |
– |
// add the positions and velocities to the atom |
442 |
|
|
443 |
< |
sd->setPos( pos ); |
537 |
< |
sd->setVel( vel ); |
443 |
> |
} |
444 |
|
|
445 |
< |
if (!sd->isDirectional()) |
540 |
< |
return NULL; |
445 |
> |
std::string name = tokenizer.nextToken(); |
446 |
|
|
447 |
< |
// get the quaternions |
447 |
> |
if (name != integrableObject->getType()) { |
448 |
> |
|
449 |
> |
} |
450 |
|
|
451 |
< |
if( sd->isDirectional() ){ |
451 |
> |
pos[0] = tokenizer.nextTokenAsFloat(); |
452 |
> |
pos[1] = tokenizer.nextTokenAsFloat(); |
453 |
> |
pos[2] = tokenizer.nextTokenAsFloat(); |
454 |
> |
integrableObject->setPos(pos); |
455 |
> |
|
456 |
> |
vel[0] = tokenizer.nextTokenAsFloat(); |
457 |
> |
vel[1] = tokenizer.nextTokenAsFloat(); |
458 |
> |
vel[2] = tokenizer.nextTokenAsFloat(); |
459 |
> |
integrableObject->setVel(vel); |
460 |
|
|
461 |
< |
foo = strtok(NULL, " ,;\t"); |
462 |
< |
if(foo == NULL){ |
463 |
< |
sprintf( painCave.errMsg, |
464 |
< |
"error in reading velocity x from %s\n", |
465 |
< |
inFileName.c_str() ); |
551 |
< |
return strdup( painCave.errMsg ); |
552 |
< |
} |
553 |
< |
q[0] = atof( foo ); |
461 |
> |
if (integrableObject->isDirectional()) { |
462 |
> |
q[0] = tokenizer.nextTokenAsFloat(); |
463 |
> |
q[1] = tokenizer.nextTokenAsFloat(); |
464 |
> |
q[2] = tokenizer.nextTokenAsFloat(); |
465 |
> |
q[3] = tokenizer.nextTokenAsFloat(); |
466 |
|
|
467 |
< |
foo = strtok(NULL, " ,;\t"); |
468 |
< |
if(foo == NULL){ |
469 |
< |
sprintf( painCave.errMsg, |
470 |
< |
"error in reading velocity x from %s\n", |
471 |
< |
inFileName.c_str() ); |
472 |
< |
return strdup( painCave.errMsg ); |
467 |
> |
double qlen = q.length(); |
468 |
> |
if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
469 |
> |
|
470 |
> |
sprintf(painCave.errMsg, |
471 |
> |
"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
472 |
> |
painCave.isFatal = 1; |
473 |
> |
simError(); |
474 |
> |
|
475 |
> |
} else if (fabs(qlen - 1.0) > oopse::epsilon) { // check that the quaternion vector is normalized |
476 |
> |
sprintf(painCave.errMsg, |
477 |
> |
"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 != 1.0).\n"); |
478 |
> |
painCave.isFatal = 0; |
479 |
> |
simError(); |
480 |
> |
|
481 |
> |
q.normalize(); |
482 |
> |
} |
483 |
> |
integrableObject->setQ(q); |
484 |
> |
|
485 |
> |
ji[0] = tokenizer.nextTokenAsFloat(); |
486 |
> |
ji[1] = tokenizer.nextTokenAsFloat(); |
487 |
> |
ji[2] = tokenizer.nextTokenAsFloat(); |
488 |
> |
integrableObject->setJ(ji); |
489 |
|
} |
562 |
– |
q[1] = atof( foo ); |
490 |
|
|
491 |
< |
foo = strtok(NULL, " ,;\t"); |
565 |
< |
if(foo == NULL){ |
566 |
< |
sprintf( painCave.errMsg, |
567 |
< |
"error in reading velocity x from %s\n", |
568 |
< |
inFileName.c_str() ); |
569 |
< |
return strdup( painCave.errMsg ); |
570 |
< |
} |
571 |
< |
q[2] = atof( foo ); |
491 |
> |
} |
492 |
|
|
493 |
< |
foo = strtok(NULL, " ,;\t"); |
494 |
< |
if(foo == NULL){ |
495 |
< |
sprintf( painCave.errMsg, |
496 |
< |
"error in reading velocity x from %s\n", |
497 |
< |
inFileName.c_str() ); |
498 |
< |
return strdup( painCave.errMsg ); |
499 |
< |
} |
580 |
< |
q[3] = atof( foo ); |
493 |
> |
|
494 |
> |
char *DumpReader::parseCommentLine(char* line, Snapshot* s, bool useInitXSstate) { |
495 |
> |
double currTime; |
496 |
> |
Mat3x3d hmat; |
497 |
> |
double chi; |
498 |
> |
double integralOfChiDt; |
499 |
> |
Mat3x3d eta; |
500 |
|
|
501 |
< |
// get the angular velocities |
501 |
> |
StringTokenizer tokenizer(line); |
502 |
> |
int nTokens; |
503 |
|
|
504 |
< |
foo = strtok(NULL, " ,;\t"); |
585 |
< |
if(foo == NULL){ |
586 |
< |
sprintf( painCave.errMsg, |
587 |
< |
"error in reading velocity x from %s\n", |
588 |
< |
inFileName.c_str() ); |
589 |
< |
return strdup( painCave.errMsg ); |
590 |
< |
} |
591 |
< |
ji[0] = atof( foo ); |
504 |
> |
nTokens = tokenizer.countTokens(); |
505 |
|
|
506 |
< |
foo = strtok(NULL, " ,;\t"); |
507 |
< |
if(foo == NULL){ |
508 |
< |
sprintf( painCave.errMsg, |
509 |
< |
"error in reading velocity x from %s\n", |
510 |
< |
inFileName.c_str() ); |
511 |
< |
return strdup( painCave.errMsg ); |
506 |
> |
//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens) |
507 |
> |
if (nTokens < 10) { |
508 |
> |
sprintf(painCave.errMsg, |
509 |
> |
"Not enough tokens in comment line: %s", line); |
510 |
> |
painCave.isFatal = 1; |
511 |
> |
simError(); |
512 |
|
} |
600 |
– |
ji[1] = atof(foo ); |
513 |
|
|
514 |
< |
foo = strtok(NULL, " ,;\t"); |
515 |
< |
if(foo == NULL){ |
516 |
< |
sprintf( painCave.errMsg, |
517 |
< |
"error in reading velocity x from %s\n", |
606 |
< |
inFileName.c_str() ); |
607 |
< |
return strdup( painCave.errMsg ); |
514 |
> |
//read current time |
515 |
> |
currTime = tokenizer.nextTokenAsFloat(); |
516 |
> |
if (useInitXSstate) { |
517 |
> |
s->setTime(currTime); |
518 |
|
} |
519 |
< |
ji[2] = atof( foo ); |
519 |
> |
|
520 |
> |
//read h-matrix |
521 |
> |
hmat(0, 0) = tokenizer.nextTokenAsFloat(); |
522 |
> |
hmat(0, 1) = tokenizer.nextTokenAsFloat(); |
523 |
> |
hmat(0, 2) = tokenizer.nextTokenAsFloat(); |
524 |
> |
hmat(1, 0) = tokenizer.nextTokenAsFloat(); |
525 |
> |
hmat(1, 1) = tokenizer.nextTokenAsFloat(); |
526 |
> |
hmat(1, 2) = tokenizer.nextTokenAsFloat(); |
527 |
> |
hmat(2, 0) = tokenizer.nextTokenAsFloat(); |
528 |
> |
hmat(2, 1) = tokenizer.nextTokenAsFloat(); |
529 |
> |
hmat(2, 2) = tokenizer.nextTokenAsFloat(); |
530 |
> |
s->setHmat(hmat); |
531 |
> |
|
532 |
> |
if (useInitXSstate) { |
533 |
> |
//read chi and integrablOfChidt, they should apprear in pair |
534 |
> |
if (tokenizer.countTokens() >= 2) { |
535 |
> |
chi = tokenizer.nextTokenAsFloat(); |
536 |
> |
integralOfChiDt = tokenizer.nextTokenAsFloat(); |
537 |
|
|
538 |
+ |
s->setChi(chi); |
539 |
+ |
s->setIntegralOfChiDt(integralOfChiDt); |
540 |
+ |
} |
541 |
+ |
|
542 |
+ |
//read eta (eta is 3x3 matrix) |
543 |
+ |
if (tokenizer.countTokens() >= 9) { |
544 |
+ |
eta(0, 0) = tokenizer.nextTokenAsFloat(); |
545 |
+ |
eta(0, 1) = tokenizer.nextTokenAsFloat(); |
546 |
+ |
eta(0, 2) = tokenizer.nextTokenAsFloat(); |
547 |
+ |
eta(1, 0) = tokenizer.nextTokenAsFloat(); |
548 |
+ |
eta(1, 1) = tokenizer.nextTokenAsFloat(); |
549 |
+ |
eta(1, 2) = tokenizer.nextTokenAsFloat(); |
550 |
+ |
eta(2, 0) = tokenizer.nextTokenAsFloat(); |
551 |
+ |
eta(2, 1) = tokenizer.nextTokenAsFloat(); |
552 |
+ |
eta(2, 2) = tokenizer.nextTokenAsFloat(); |
553 |
|
|
554 |
< |
// check that the quaternion vector is normalized |
555 |
< |
|
614 |
< |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
615 |
< |
|
616 |
< |
if (fabs(qSqr) < 1e-6) { |
617 |
< |
sprintf(painCave.errMsg, |
618 |
< |
"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
619 |
< |
return strdup(painCave.errMsg); |
554 |
> |
s->setEta(eta); |
555 |
> |
} |
556 |
|
} |
557 |
|
|
622 |
– |
qLength = sqrt( qSqr ); |
623 |
– |
q[0] = q[0] / qLength; |
624 |
– |
q[1] = q[1] / qLength; |
625 |
– |
q[2] = q[2] / qLength; |
626 |
– |
q[3] = q[3] / qLength; |
627 |
– |
|
628 |
– |
// add quaternion and angular velocities |
629 |
– |
|
630 |
– |
sd->setQ( q ); |
631 |
– |
sd->setJ( ji ); |
632 |
– |
} |
633 |
– |
|
634 |
– |
|
635 |
– |
|
636 |
– |
return NULL; |
637 |
– |
} |
638 |
– |
|
639 |
– |
|
640 |
– |
char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
641 |
– |
|
642 |
– |
double currTime; |
643 |
– |
double boxMat[9]; |
644 |
– |
double theBoxMat3[3][3]; |
645 |
– |
double chi; |
646 |
– |
double integralOfChidt; |
647 |
– |
double eta[9]; |
648 |
– |
|
649 |
– |
char *foo; // the pointer to the current string token |
650 |
– |
|
651 |
– |
// set the string tokenizer |
652 |
– |
|
653 |
– |
foo = strtok(readLine, " ,;\t"); |
654 |
– |
// set the timeToken. |
655 |
– |
|
656 |
– |
if(foo == NULL){ |
657 |
– |
sprintf( painCave.errMsg, |
658 |
– |
"error in reading Time from %s\n", |
659 |
– |
inFileName.c_str() ); |
660 |
– |
return strdup( painCave.errMsg ); |
661 |
– |
} |
662 |
– |
|
663 |
– |
currTime = atof( foo ); |
664 |
– |
entry_plug->setTime( currTime ); |
665 |
– |
|
666 |
– |
//get H-Matrix |
667 |
– |
|
668 |
– |
for(int i = 0 ; i < 9; i++){ |
669 |
– |
foo = strtok(NULL, " ,;\t"); |
670 |
– |
if(foo == NULL){ |
671 |
– |
sprintf( painCave.errMsg, |
672 |
– |
"error in reading H[%d] from %s\n", i, inFileName.c_str() ); |
673 |
– |
return strdup( painCave.errMsg ); |
674 |
– |
} |
675 |
– |
boxMat[i] = atof( foo ); |
676 |
– |
} |
677 |
– |
|
678 |
– |
for(int i=0;i<3;i++) |
679 |
– |
for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
680 |
– |
|
681 |
– |
//set H-Matrix |
682 |
– |
entry_plug->setBoxM( theBoxMat3 ); |
683 |
– |
|
684 |
– |
//get chi and integralOfChidt, they should appear by pair |
685 |
– |
|
686 |
– |
if( entry_plug->useInitXSstate ){ |
687 |
– |
foo = strtok(NULL, " ,;\t\n"); |
688 |
– |
if(foo != NULL){ |
689 |
– |
chi = atof(foo); |
690 |
– |
|
691 |
– |
foo = strtok(NULL, " ,;\t\n"); |
692 |
– |
if(foo == NULL){ |
693 |
– |
sprintf( painCave.errMsg, |
694 |
– |
"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() ); |
695 |
– |
return strdup( painCave.errMsg ); |
696 |
– |
} |
697 |
– |
integralOfChidt = atof( foo ); |
698 |
– |
|
699 |
– |
//push chi and integralOfChidt into SimInfo::properties which can be |
700 |
– |
//retrieved by integrator later |
701 |
– |
DoubleData* chiValue = new DoubleData(); |
702 |
– |
chiValue->setID(CHIVALUE_ID); |
703 |
– |
chiValue->setData(chi); |
704 |
– |
entry_plug->addProperty(chiValue); |
705 |
– |
|
706 |
– |
DoubleData* integralOfChidtValue = new DoubleData(); |
707 |
– |
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
708 |
– |
integralOfChidtValue->setData(integralOfChidt); |
709 |
– |
entry_plug->addProperty(integralOfChidtValue); |
710 |
– |
|
711 |
– |
} |
712 |
– |
else |
713 |
– |
return NULL; |
558 |
|
|
715 |
– |
//get eta |
716 |
– |
foo = strtok(NULL, " ,;\t\n"); |
717 |
– |
if(foo != NULL ){ |
718 |
– |
|
719 |
– |
for(int i = 0 ; i < 9; i++){ |
720 |
– |
|
721 |
– |
if(foo == NULL){ |
722 |
– |
sprintf( painCave.errMsg, |
723 |
– |
"error in reading eta[%d] from %s\n", i, inFileName.c_str() ); |
724 |
– |
return strdup( painCave.errMsg ); |
725 |
– |
} |
726 |
– |
eta[i] = atof( foo ); |
727 |
– |
foo = strtok(NULL, " ,;\t\n"); |
728 |
– |
} |
729 |
– |
} |
730 |
– |
else |
731 |
– |
return NULL; |
732 |
– |
|
733 |
– |
//push eta into SimInfo::properties which can be |
734 |
– |
//retrieved by integrator later |
735 |
– |
//entry_plug->setBoxM( theBoxMat3 ); |
736 |
– |
DoubleArrayData* etaValue = new DoubleArrayData(); |
737 |
– |
etaValue->setID(ETAVALUE_ID); |
738 |
– |
etaValue->setData(eta, 9); |
739 |
– |
entry_plug->addProperty(etaValue); |
740 |
– |
} |
741 |
– |
|
742 |
– |
return NULL; |
559 |
|
} |
560 |
|
|
561 |
< |
#ifdef IS_MPI |
746 |
< |
void DumpReader::nodeZeroError( void ){ |
747 |
< |
int j, myStatus; |
748 |
< |
|
749 |
< |
myStatus = 0; |
750 |
< |
for (j = 0; j < mpiSim->getNProcessors(); j++) { |
751 |
< |
MPI_Send( &myStatus, 1, MPI_INT, j, |
752 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
753 |
< |
} |
754 |
< |
|
755 |
< |
|
756 |
< |
MPI_Finalize(); |
757 |
< |
exit (0); |
758 |
< |
|
759 |
< |
} |
760 |
< |
|
761 |
< |
void DumpReader::anonymousNodeDie( void ){ |
762 |
< |
|
763 |
< |
MPI_Finalize(); |
764 |
< |
exit (0); |
765 |
< |
} |
766 |
< |
#endif |
561 |
> |
}//end namespace oopse |