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#define _LARGEFILE_SOURCE64 |
2 |
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#define _FILE_OFFSET_BITS 64 |
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|
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#include <sys/types.h> |
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#include <sys/stat.h> |
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|
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#include <iostream> |
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#include <math.h> |
9 |
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|
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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|
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|
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#include "io/ReadWrite.hpp" |
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#include "utils/simError.h" |
17 |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
20 |
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#include "brains/mpiSimulation.hpp" |
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#define TAKE_THIS_TAG_CHAR 0 |
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#define TAKE_THIS_TAG_INT 1 |
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#endif // is_mpi |
24 |
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|
25 |
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|
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DumpReader :: DumpReader(const char *in_name ){ |
27 |
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|
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isScanned = false; |
29 |
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
33 |
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|
34 |
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inFile = fopen(in_name, "r"); |
35 |
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if(inFile == NULL){ |
36 |
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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; |
39 |
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simError(); |
40 |
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} |
1 |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
19 |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
23 |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
28 |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
|
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inFileName = in_name; |
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#ifdef IS_MPI |
44 |
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} |
45 |
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strcpy( checkPointMsg, "Dump file opened for reading successfully." ); |
46 |
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MPIcheckPoint(); |
47 |
< |
#endif |
48 |
< |
return; |
49 |
< |
} |
50 |
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|
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DumpReader :: ~DumpReader( ){ |
52 |
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#ifdef IS_MPI |
53 |
< |
if (worldRank == 0) { |
54 |
< |
#endif |
55 |
< |
vector<fpos_t*>::iterator i; |
56 |
< |
|
57 |
< |
int error; |
58 |
< |
error = fclose( inFile ); |
59 |
< |
if( error ){ |
60 |
< |
sprintf( painCave.errMsg, |
61 |
< |
"Error closing %s\n", inFileName.c_str()); |
62 |
< |
simError(); |
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< |
} |
64 |
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|
65 |
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for(i = framePos.begin(); i != framePos.end(); ++i) |
66 |
< |
delete *i; |
67 |
< |
framePos.clear(); |
68 |
< |
|
69 |
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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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#endif |
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|
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return; |
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} |
77 |
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|
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int DumpReader::getNframes( void ){ |
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|
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if( !isScanned ) |
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scanFile(); |
82 |
< |
return framePos.size(); |
83 |
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} |
84 |
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|
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void DumpReader::scanFile( void ){ |
86 |
< |
|
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int i, j; |
88 |
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int lineNum = 0; |
89 |
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char readBuffer[2000]; |
90 |
< |
fpos_t *currPos; |
91 |
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|
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#ifdef IS_MPI |
93 |
< |
if( worldRank == 0 ){ |
94 |
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#endif // is_mpi |
95 |
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|
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rewind( inFile ); |
97 |
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|
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currPos = new fpos_t; |
99 |
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fgetpos( inFile, currPos ); |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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lineNum++; |
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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(), |
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lineNum ); |
107 |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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while( !feof( inFile ) ){ |
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|
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framePos.push_back(currPos); |
114 |
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|
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i = atoi(readBuffer); |
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|
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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lineNum++; |
119 |
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if( feof( inFile ) ){ |
120 |
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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(), |
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lineNum ); |
124 |
< |
painCave.isFatal = 1; |
125 |
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simError(); |
126 |
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} |
127 |
< |
|
128 |
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for(j=0; j<i; j++){ |
129 |
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|
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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lineNum++; |
132 |
< |
if( feof( inFile ) ){ |
133 |
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sprintf( painCave.errMsg, |
134 |
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"File \"%s\" ended unexpectedly at line %d," |
135 |
< |
" with atom %d\n", |
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< |
inFileName.c_str(), |
137 |
< |
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 ); |
42 |
> |
#define _LARGEFILE_SOURCE64 |
43 |
> |
#define _FILE_OFFSET_BITS 64 |
44 |
> |
|
45 |
> |
#include <sys/types.h> |
46 |
> |
#include <sys/stat.h> |
47 |
> |
|
48 |
> |
#include <iostream> |
49 |
> |
#include <math.h> |
50 |
> |
|
51 |
> |
#include <stdio.h> |
52 |
> |
#include <stdlib.h> |
53 |
> |
#include <string.h> |
54 |
> |
|
55 |
> |
#include "io/DumpReader.hpp" |
56 |
> |
#include "primitives/Molecule.hpp" |
57 |
> |
#include "utils/simError.h" |
58 |
> |
#include "utils/MemoryUtils.hpp" |
59 |
> |
#include "utils/StringTokenizer.hpp" |
60 |
> |
|
61 |
> |
#ifdef IS_MPI |
62 |
> |
|
63 |
> |
#include <mpi.h> |
64 |
> |
#define TAKE_THIS_TAG_CHAR 0 |
65 |
> |
#define TAKE_THIS_TAG_INT 1 |
66 |
> |
|
67 |
> |
#endif // is_mpi |
68 |
> |
|
69 |
> |
|
70 |
> |
namespace oopse { |
71 |
> |
|
72 |
> |
DumpReader::DumpReader(SimInfo* info, const std::string& filename) |
73 |
> |
: info_(info), filename_(filename), isScanned_(false), nframes_(0) { |
74 |
|
|
75 |
< |
isScanned = true; |
76 |
< |
|
77 |
< |
#ifdef IS_MPI |
78 |
< |
} |
79 |
< |
strcpy( checkPointMsg, "Successfully scanned DumpFile\n" ); |
80 |
< |
MPIcheckPoint(); |
81 |
< |
#endif // is_mpi |
82 |
< |
} |
83 |
< |
|
84 |
< |
void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){ |
85 |
< |
|
86 |
< |
simnfo = the_simnfo; |
87 |
< |
|
88 |
< |
this->readSet( whichFrame ); |
89 |
< |
} |
90 |
< |
|
91 |
< |
|
92 |
< |
|
93 |
< |
void DumpReader :: readSet( int whichFrame ){ |
94 |
< |
|
95 |
< |
int i; |
96 |
< |
unsigned int j; |
97 |
< |
|
98 |
< |
#ifdef IS_MPI |
99 |
< |
int done, which_node, which_atom; // loop counter |
100 |
< |
#endif //is_mpi |
101 |
< |
|
102 |
< |
const int BUFFERSIZE = 2000; // size of the read buffer |
103 |
< |
int nTotObjs; // the number of atoms |
104 |
< |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
105 |
< |
|
106 |
< |
char *eof_test; // ptr to see when we reach the end of the file |
107 |
< |
char *parseErr; |
108 |
< |
|
109 |
< |
vector<StuntDouble*> integrableObjects; |
110 |
< |
|
111 |
< |
|
112 |
< |
#ifndef IS_MPI |
113 |
< |
|
114 |
< |
fsetpos(inFile, framePos[whichFrame]); |
115 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
116 |
< |
if( eof_test == NULL ){ |
117 |
< |
sprintf( painCave.errMsg, |
118 |
< |
"DumpReader error: error reading 1st line of \"%s\"\n", |
119 |
< |
inFileName.c_str() ); |
120 |
< |
painCave.isFatal = 1; |
121 |
< |
simError(); |
122 |
< |
} |
123 |
< |
|
124 |
< |
nTotObjs = atoi( read_buffer ); |
125 |
< |
|
126 |
< |
if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
127 |
< |
sprintf( painCave.errMsg, |
128 |
< |
"DumpReader error. %s nIntegrable, %d, " |
129 |
< |
"does not match the meta-data file's nIntegrable, %d.\n", |
130 |
< |
inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
131 |
< |
painCave.isFatal = 1; |
132 |
< |
simError(); |
133 |
< |
} |
134 |
< |
|
135 |
< |
//read the box mat from the comment line |
136 |
< |
|
137 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
138 |
< |
if(eof_test == NULL){ |
139 |
< |
sprintf( painCave.errMsg, |
140 |
< |
"error in reading commment in %s\n", inFileName.c_str()); |
141 |
< |
painCave.isFatal = 1; |
142 |
< |
simError(); |
143 |
< |
} |
144 |
< |
|
145 |
< |
parseErr = parseCommentLine( read_buffer, simnfo); |
146 |
< |
if( parseErr != NULL ){ |
147 |
< |
strcpy( painCave.errMsg, parseErr ); |
148 |
< |
painCave.isFatal = 1; |
149 |
< |
simError(); |
150 |
< |
} |
151 |
< |
|
152 |
< |
//parse dump lines |
153 |
< |
|
154 |
< |
for( i=0; i < simnfo->n_mol; i++){ |
155 |
< |
|
156 |
< |
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
157 |
< |
|
158 |
< |
for(j = 0; j < integrableObjects.size(); j++){ |
159 |
< |
|
160 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
161 |
< |
if(eof_test == NULL){ |
162 |
< |
sprintf(painCave.errMsg, |
163 |
< |
"error in reading file %s\n" |
164 |
< |
"natoms = %d; index = %d\n" |
165 |
< |
"error reading the line from the file.\n", |
166 |
< |
inFileName.c_str(), nTotObjs, i ); |
167 |
< |
painCave.isFatal = 1; |
168 |
< |
simError(); |
169 |
< |
} |
170 |
< |
|
171 |
< |
parseErr = parseDumpLine( read_buffer, integrableObjects[j]); |
172 |
< |
if( parseErr != NULL ){ |
173 |
< |
strcpy( painCave.errMsg, parseErr ); |
174 |
< |
painCave.isFatal = 1; |
175 |
< |
simError(); |
255 |
< |
} |
256 |
< |
} |
257 |
< |
} |
258 |
< |
|
259 |
< |
// MPI Section of code.......... |
260 |
< |
#else //IS_MPI |
261 |
< |
|
262 |
< |
// first thing first, suspend fatalities. |
263 |
< |
painCave.isEventLoop = 1; |
264 |
< |
|
265 |
< |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
266 |
< |
int haveError; |
267 |
< |
|
268 |
< |
MPI_Status istatus; |
269 |
< |
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(); |
285 |
< |
} |
286 |
< |
|
287 |
< |
nitems = atoi( read_buffer ); |
288 |
< |
|
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( 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 |
< |
} |
301 |
< |
|
302 |
< |
//read the boxMat from the comment line |
303 |
< |
|
304 |
< |
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 |
< |
} |
311 |
< |
|
312 |
< |
//Every single processor will parse the comment line by itself |
313 |
< |
//By using this way, we might lose some efficiency, but if we want to add |
314 |
< |
//more parameters into comment line, we only need to modify function |
315 |
< |
//parseCommentLine |
316 |
< |
|
317 |
< |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
318 |
< |
|
319 |
< |
parseErr = parseCommentLine( read_buffer, simnfo); |
320 |
< |
|
321 |
< |
if( parseErr != NULL ){ |
322 |
< |
strcpy( painCave.errMsg, parseErr ); |
323 |
< |
haveError = 1; |
324 |
< |
simError(); |
325 |
< |
} |
326 |
< |
|
327 |
< |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
328 |
< |
which_node = MolToProcMap[i]; |
329 |
< |
if(which_node == 0){ |
330 |
< |
//molecules belong to master node |
331 |
< |
|
332 |
< |
localIndex = mpiSim->getGlobalToLocalMol(i); |
333 |
< |
|
334 |
< |
if(localIndex == -1) { |
335 |
< |
strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
336 |
< |
haveError = 1; |
337 |
< |
simError(); |
338 |
< |
} |
339 |
< |
|
340 |
< |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
341 |
< |
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(); |
355 |
< |
|
356 |
< |
parseDumpLine(read_buffer, integrableObjects[j]); |
75 |
> |
#ifdef IS_MPI |
76 |
> |
|
77 |
> |
if (worldRank == 0) { |
78 |
> |
#endif |
79 |
> |
|
80 |
> |
inFile_ = new std::ifstream(filename_.c_str()); |
81 |
> |
|
82 |
> |
if (inFile_->fail()) { |
83 |
> |
sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str()); |
84 |
> |
painCave.isFatal = 1; |
85 |
> |
simError(); |
86 |
> |
} |
87 |
> |
|
88 |
> |
#ifdef IS_MPI |
89 |
> |
|
90 |
> |
} |
91 |
> |
|
92 |
> |
strcpy(checkPointMsg, "Dump file opened for reading successfully."); |
93 |
> |
MPIcheckPoint(); |
94 |
> |
|
95 |
> |
#endif |
96 |
> |
|
97 |
> |
return; |
98 |
> |
} |
99 |
> |
|
100 |
> |
DumpReader::~DumpReader() { |
101 |
> |
|
102 |
> |
#ifdef IS_MPI |
103 |
> |
|
104 |
> |
if (worldRank == 0) { |
105 |
> |
#endif |
106 |
> |
|
107 |
> |
delete inFile_; |
108 |
> |
|
109 |
> |
#ifdef IS_MPI |
110 |
> |
|
111 |
> |
} |
112 |
> |
|
113 |
> |
strcpy(checkPointMsg, "Dump file closed successfully."); |
114 |
> |
MPIcheckPoint(); |
115 |
> |
|
116 |
> |
#endif |
117 |
> |
|
118 |
> |
return; |
119 |
> |
} |
120 |
> |
|
121 |
> |
int DumpReader::getNFrames(void) { |
122 |
> |
|
123 |
> |
if (!isScanned_) |
124 |
> |
scanFile(); |
125 |
> |
|
126 |
> |
return nframes_; |
127 |
> |
} |
128 |
> |
|
129 |
> |
void DumpReader::scanFile(void) { |
130 |
> |
int i, j; |
131 |
> |
int lineNum = 0; |
132 |
> |
char readBuffer[maxBufferSize]; |
133 |
> |
std::streampos currPos; |
134 |
> |
|
135 |
> |
#ifdef IS_MPI |
136 |
> |
|
137 |
> |
if (worldRank == 0) { |
138 |
> |
#endif // is_mpi |
139 |
> |
|
140 |
> |
inFile_->seekg (0, std::ios::beg); |
141 |
> |
|
142 |
> |
|
143 |
> |
currPos = inFile_->tellg(); |
144 |
> |
inFile_->getline(readBuffer, sizeof(readBuffer)); |
145 |
> |
lineNum++; |
146 |
> |
|
147 |
> |
if (inFile_->eof()) { |
148 |
> |
sprintf(painCave.errMsg, |
149 |
> |
"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
150 |
> |
filename_.c_str(), |
151 |
> |
lineNum); |
152 |
> |
painCave.isFatal = 1; |
153 |
> |
simError(); |
154 |
> |
} |
155 |
> |
|
156 |
> |
while (!inFile_->eof()) { |
157 |
> |
framePos_.push_back(currPos); |
158 |
> |
|
159 |
> |
i = atoi(readBuffer); |
160 |
> |
|
161 |
> |
inFile_->getline(readBuffer, sizeof(readBuffer)); |
162 |
> |
lineNum++; |
163 |
> |
|
164 |
> |
if (inFile_->eof()) { |
165 |
> |
sprintf(painCave.errMsg, |
166 |
> |
"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", |
167 |
> |
filename_.c_str(), |
168 |
> |
lineNum); |
169 |
> |
painCave.isFatal = 1; |
170 |
> |
simError(); |
171 |
> |
} |
172 |
> |
|
173 |
> |
for(j = 0; j < i; j++) { |
174 |
> |
inFile_->getline(readBuffer, sizeof(readBuffer)); |
175 |
> |
lineNum++; |
176 |
|
|
177 |
< |
} |
178 |
< |
|
179 |
< |
|
180 |
< |
} |
181 |
< |
else{ |
182 |
< |
//molecule belongs to slave nodes |
183 |
< |
|
184 |
< |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
185 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
186 |
< |
|
187 |
< |
for(j=0; j < nCurObj; j++){ |
188 |
< |
|
189 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
190 |
< |
if(eof_test == NULL){ |
191 |
< |
sprintf(painCave.errMsg, |
192 |
< |
"error in reading file %s\n" |
193 |
< |
"natoms = %d; index = %d\n" |
194 |
< |
"error reading the line from the file.\n", |
195 |
< |
inFileName.c_str(), nTotObjs, i ); |
196 |
< |
haveError= 1; |
197 |
< |
simError(); |
198 |
< |
} |
199 |
< |
|
200 |
< |
if(haveError) nodeZeroError(); |
201 |
< |
|
202 |
< |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
203 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
177 |
> |
if (inFile_->eof()) { |
178 |
> |
sprintf(painCave.errMsg, |
179 |
> |
"DumpReader Error: File \"%s\" ended unexpectedly at line %d," |
180 |
> |
" with atom %d\n", filename_.c_str(), |
181 |
> |
lineNum, |
182 |
> |
j); |
183 |
> |
|
184 |
> |
painCave.isFatal = 1; |
185 |
> |
simError(); |
186 |
> |
} |
187 |
> |
} |
188 |
> |
|
189 |
> |
currPos = inFile_->tellg(); |
190 |
> |
inFile_->getline(readBuffer, sizeof(readBuffer)); |
191 |
> |
lineNum++; |
192 |
> |
} |
193 |
> |
|
194 |
> |
inFile_->seekg (0, std::ios::beg); |
195 |
> |
|
196 |
> |
nframes_ = framePos_.size(); |
197 |
> |
#ifdef IS_MPI |
198 |
> |
} |
199 |
> |
|
200 |
> |
MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); |
201 |
> |
|
202 |
> |
strcpy(checkPointMsg, "Successfully scanned DumpFile\n"); |
203 |
> |
MPIcheckPoint(); |
204 |
> |
|
205 |
> |
#endif // is_mpi |
206 |
> |
|
207 |
> |
isScanned_ = true; |
208 |
> |
} |
209 |
> |
|
210 |
> |
void DumpReader::readFrame(int whichFrame) { |
211 |
> |
if (!isScanned_) |
212 |
> |
scanFile(); |
213 |
> |
|
214 |
> |
int storageLayout = info_->getSnapshotManager()->getStorageLayout(); |
215 |
> |
|
216 |
> |
if (storageLayout & DataStorage::dslPosition) { |
217 |
> |
needPos_ = true; |
218 |
> |
} else { |
219 |
> |
needPos_ = false; |
220 |
> |
} |
221 |
> |
|
222 |
> |
if (storageLayout & DataStorage::dslVelocity) { |
223 |
> |
needVel_ = true; |
224 |
> |
} else { |
225 |
> |
needVel_ = false; |
226 |
> |
} |
227 |
> |
|
228 |
> |
if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { |
229 |
> |
needQuaternion_ = true; |
230 |
> |
} else { |
231 |
> |
needQuaternion_ = false; |
232 |
> |
} |
233 |
> |
|
234 |
> |
if (storageLayout & DataStorage::dslAngularMomentum) { |
235 |
> |
needAngMom_ = true; |
236 |
> |
} else { |
237 |
> |
needAngMom_ = false; |
238 |
> |
} |
239 |
> |
|
240 |
> |
readSet(whichFrame); |
241 |
> |
} |
242 |
> |
|
243 |
> |
void DumpReader::readSet(int whichFrame) { |
244 |
> |
int i; |
245 |
> |
int nTotObjs; // the number of atoms |
246 |
> |
char read_buffer[maxBufferSize]; //the line buffer for reading |
247 |
> |
char * eof_test; // ptr to see when we reach the end of the file |
248 |
> |
|
249 |
> |
Molecule* mol; |
250 |
> |
StuntDouble* integrableObject; |
251 |
> |
SimInfo::MoleculeIterator mi; |
252 |
> |
Molecule::IntegrableObjectIterator ii; |
253 |
> |
|
254 |
> |
#ifndef IS_MPI |
255 |
> |
inFile_->clear(); |
256 |
> |
inFile_->seekg(framePos_[whichFrame]); |
257 |
> |
|
258 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
259 |
> |
sprintf(painCave.errMsg, |
260 |
> |
"DumpReader error: error reading 1st line of \"%s\"\n", |
261 |
> |
filename_.c_str()); |
262 |
> |
painCave.isFatal = 1; |
263 |
> |
simError(); |
264 |
> |
} |
265 |
> |
|
266 |
> |
nTotObjs = atoi(read_buffer); |
267 |
> |
|
268 |
> |
if (nTotObjs != info_->getNGlobalIntegrableObjects()) { |
269 |
> |
sprintf(painCave.errMsg, |
270 |
> |
"DumpReader error. %s nIntegrable, %d, " |
271 |
> |
"does not match the meta-data file's nIntegrable, %d.\n", |
272 |
> |
filename_.c_str(), |
273 |
> |
nTotObjs, |
274 |
> |
info_->getNGlobalIntegrableObjects()); |
275 |
> |
|
276 |
> |
painCave.isFatal = 1; |
277 |
> |
simError(); |
278 |
> |
} |
279 |
> |
|
280 |
> |
//read the box mat from the comment line |
281 |
> |
|
282 |
> |
|
283 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
284 |
> |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
285 |
> |
filename_.c_str()); |
286 |
> |
painCave.isFatal = 1; |
287 |
> |
simError(); |
288 |
> |
} |
289 |
> |
|
290 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
291 |
> |
|
292 |
> |
//parse dump lines |
293 |
> |
|
294 |
> |
i = 0; |
295 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
296 |
> |
|
297 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
298 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
299 |
> |
|
300 |
> |
|
301 |
> |
|
302 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
303 |
> |
sprintf(painCave.errMsg, |
304 |
> |
"DumpReader Error: error in reading file %s\n" |
305 |
> |
"natoms = %d; index = %d\n" |
306 |
> |
"error reading the line from the file.\n", |
307 |
> |
filename_.c_str(), |
308 |
> |
nTotObjs, |
309 |
> |
i); |
310 |
|
|
311 |
< |
} |
312 |
< |
|
313 |
< |
} |
314 |
< |
|
315 |
< |
} |
316 |
< |
|
317 |
< |
} |
318 |
< |
else{ |
319 |
< |
//actions taken at slave nodes |
320 |
< |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
321 |
< |
|
322 |
< |
parseErr = parseCommentLine( read_buffer, simnfo); |
323 |
< |
|
324 |
< |
if( parseErr != NULL ){ |
325 |
< |
strcpy( painCave.errMsg, parseErr ); |
326 |
< |
haveError = 1; |
327 |
< |
simError(); |
328 |
< |
} |
329 |
< |
|
330 |
< |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
331 |
< |
which_node = MolToProcMap[i]; |
332 |
< |
|
333 |
< |
if(which_node == worldRank){ |
334 |
< |
//molecule with global index i belongs to this processor |
335 |
< |
|
336 |
< |
localIndex = mpiSim->getGlobalToLocalMol(i); |
337 |
< |
|
338 |
< |
if(localIndex == -1) { |
339 |
< |
sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
340 |
< |
haveError = 1; |
341 |
< |
simError(); |
342 |
< |
} |
343 |
< |
|
344 |
< |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
345 |
< |
|
346 |
< |
nCurObj = integrableObjects.size(); |
347 |
< |
|
348 |
< |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
349 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
350 |
< |
|
351 |
< |
for(j = 0; j < integrableObjects.size(); j++){ |
352 |
< |
|
353 |
< |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
354 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
355 |
< |
|
356 |
< |
parseErr = parseDumpLine(read_buffer, integrableObjects[j]); |
357 |
< |
|
358 |
< |
if( parseErr != NULL ){ |
359 |
< |
strcpy( painCave.errMsg, parseErr ); |
360 |
< |
simError(); |
361 |
< |
} |
362 |
< |
|
363 |
< |
} |
364 |
< |
|
365 |
< |
} |
366 |
< |
|
367 |
< |
} |
368 |
< |
|
369 |
< |
} |
370 |
< |
|
371 |
< |
#endif |
372 |
< |
} |
373 |
< |
|
374 |
< |
char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){ |
375 |
< |
|
376 |
< |
char *foo; // the pointer to the current string token |
377 |
< |
|
378 |
< |
double pos[3]; // position place holders |
379 |
< |
double vel[3]; // velocity placeholders |
380 |
< |
double q[4]; // the quaternions |
381 |
< |
double ji[3]; // angular velocity placeholders; |
382 |
< |
double qSqr, qLength; // needed to normalize the quaternion vector. |
383 |
< |
|
384 |
< |
|
385 |
< |
// set the string tokenizer |
386 |
< |
|
387 |
< |
foo = strtok(readLine, " ,;\t"); |
388 |
< |
|
389 |
< |
// check the atom name to the current atom |
390 |
< |
|
391 |
< |
if( strcmp( foo, sd->getType() ) ){ |
392 |
< |
sprintf( painCave.errMsg, |
393 |
< |
"DumpReader error. Does not" |
394 |
< |
" match the meta-data atom %s.\n", |
395 |
< |
sd->getType() ); |
396 |
< |
return strdup( painCave.errMsg ); |
397 |
< |
} |
398 |
< |
|
399 |
< |
// get the positions |
400 |
< |
|
401 |
< |
foo = strtok(NULL, " ,;\t"); |
402 |
< |
if(foo == NULL){ |
403 |
< |
sprintf( painCave.errMsg, |
404 |
< |
"error in reading postition x from %s\n", |
405 |
< |
inFileName.c_str()); |
406 |
< |
return strdup( painCave.errMsg ); |
407 |
< |
} |
408 |
< |
pos[0] = atof( foo ); |
409 |
< |
|
410 |
< |
foo = strtok(NULL, " ,;\t"); |
411 |
< |
if(foo == NULL){ |
412 |
< |
sprintf( painCave.errMsg, |
413 |
< |
"error in reading postition y from %s\n", |
414 |
< |
inFileName.c_str()); |
415 |
< |
return strdup( painCave.errMsg ); |
416 |
< |
} |
417 |
< |
pos[1] = atof( foo ); |
418 |
< |
|
419 |
< |
foo = strtok(NULL, " ,;\t"); |
420 |
< |
if(foo == NULL){ |
421 |
< |
sprintf( painCave.errMsg, |
422 |
< |
"error in reading postition z from %s\n", |
423 |
< |
inFileName.c_str()); |
424 |
< |
return strdup( painCave.errMsg ); |
425 |
< |
} |
426 |
< |
pos[2] = atof( foo ); |
427 |
< |
|
428 |
< |
|
429 |
< |
// get the velocities |
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[0] = atof( foo ); |
439 |
< |
|
440 |
< |
foo = strtok(NULL, " ,;\t"); |
441 |
< |
if(foo == NULL){ |
442 |
< |
sprintf( painCave.errMsg, |
443 |
< |
"error in reading velocity x from %s\n", |
444 |
< |
inFileName.c_str() ); |
445 |
< |
return strdup( painCave.errMsg ); |
446 |
< |
} |
447 |
< |
vel[1] = atof( foo ); |
448 |
< |
|
449 |
< |
foo = strtok(NULL, " ,;\t"); |
450 |
< |
if(foo == NULL){ |
451 |
< |
sprintf( painCave.errMsg, |
452 |
< |
"error in reading velocity x from %s\n", |
453 |
< |
inFileName.c_str() ); |
454 |
< |
return strdup( painCave.errMsg ); |
455 |
< |
} |
456 |
< |
vel[2] = atof( foo ); |
457 |
< |
|
458 |
< |
|
459 |
< |
// add the positions and velocities to the atom |
460 |
< |
|
461 |
< |
sd->setPos( pos ); |
462 |
< |
sd->setVel( vel ); |
463 |
< |
|
464 |
< |
if (!sd->isDirectional()) |
465 |
< |
return NULL; |
466 |
< |
|
467 |
< |
// get the quaternions |
468 |
< |
|
469 |
< |
if( sd->isDirectional() ){ |
470 |
< |
|
471 |
< |
foo = strtok(NULL, " ,;\t"); |
472 |
< |
if(foo == NULL){ |
473 |
< |
sprintf( painCave.errMsg, |
474 |
< |
"error in reading velocity x from %s\n", |
475 |
< |
inFileName.c_str() ); |
476 |
< |
return strdup( painCave.errMsg ); |
477 |
< |
} |
478 |
< |
q[0] = atof( foo ); |
479 |
< |
|
480 |
< |
foo = strtok(NULL, " ,;\t"); |
481 |
< |
if(foo == NULL){ |
482 |
< |
sprintf( painCave.errMsg, |
483 |
< |
"error in reading velocity x from %s\n", |
484 |
< |
inFileName.c_str() ); |
485 |
< |
return strdup( painCave.errMsg ); |
486 |
< |
} |
487 |
< |
q[1] = atof( foo ); |
488 |
< |
|
489 |
< |
foo = strtok(NULL, " ,;\t"); |
490 |
< |
if(foo == NULL){ |
491 |
< |
sprintf( painCave.errMsg, |
492 |
< |
"error in reading velocity x from %s\n", |
493 |
< |
inFileName.c_str() ); |
494 |
< |
return strdup( painCave.errMsg ); |
495 |
< |
} |
496 |
< |
q[2] = atof( foo ); |
497 |
< |
|
498 |
< |
foo = strtok(NULL, " ,;\t"); |
499 |
< |
if(foo == NULL){ |
500 |
< |
sprintf( painCave.errMsg, |
501 |
< |
"error in reading velocity x from %s\n", |
502 |
< |
inFileName.c_str() ); |
503 |
< |
return strdup( painCave.errMsg ); |
504 |
< |
} |
505 |
< |
q[3] = atof( foo ); |
506 |
< |
|
507 |
< |
// get the angular velocities |
508 |
< |
|
509 |
< |
foo = strtok(NULL, " ,;\t"); |
510 |
< |
if(foo == NULL){ |
511 |
< |
sprintf( painCave.errMsg, |
512 |
< |
"error in reading velocity x from %s\n", |
513 |
< |
inFileName.c_str() ); |
514 |
< |
return strdup( painCave.errMsg ); |
515 |
< |
} |
516 |
< |
ji[0] = atof( foo ); |
517 |
< |
|
518 |
< |
foo = strtok(NULL, " ,;\t"); |
519 |
< |
if(foo == NULL){ |
520 |
< |
sprintf( painCave.errMsg, |
521 |
< |
"error in reading velocity x from %s\n", |
522 |
< |
inFileName.c_str() ); |
523 |
< |
return strdup( painCave.errMsg ); |
524 |
< |
} |
525 |
< |
ji[1] = atof(foo ); |
526 |
< |
|
527 |
< |
foo = strtok(NULL, " ,;\t"); |
528 |
< |
if(foo == NULL){ |
529 |
< |
sprintf( painCave.errMsg, |
530 |
< |
"error in reading velocity x from %s\n", |
531 |
< |
inFileName.c_str() ); |
532 |
< |
return strdup( painCave.errMsg ); |
533 |
< |
} |
534 |
< |
ji[2] = atof( foo ); |
535 |
< |
|
536 |
< |
|
537 |
< |
// check that the quaternion vector is normalized |
538 |
< |
|
539 |
< |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
540 |
< |
|
541 |
< |
if (fabs(qSqr) < 1e-6) { |
542 |
< |
sprintf(painCave.errMsg, |
543 |
< |
"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n"); |
544 |
< |
return strdup(painCave.errMsg); |
545 |
< |
} |
546 |
< |
|
547 |
< |
qLength = sqrt( qSqr ); |
548 |
< |
q[0] = q[0] / qLength; |
549 |
< |
q[1] = q[1] / qLength; |
550 |
< |
q[2] = q[2] / qLength; |
551 |
< |
q[3] = q[3] / qLength; |
552 |
< |
|
553 |
< |
// add quaternion and angular velocities |
554 |
< |
|
555 |
< |
sd->setQ( q ); |
556 |
< |
sd->setJ( ji ); |
557 |
< |
} |
558 |
< |
|
559 |
< |
|
560 |
< |
|
561 |
< |
return NULL; |
562 |
< |
} |
563 |
< |
|
564 |
< |
|
565 |
< |
char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
566 |
< |
|
567 |
< |
double currTime; |
568 |
< |
double boxMat[9]; |
569 |
< |
double theBoxMat3[3][3]; |
570 |
< |
double chi; |
571 |
< |
double integralOfChidt; |
572 |
< |
double eta[9]; |
573 |
< |
|
574 |
< |
char *foo; // the pointer to the current string token |
575 |
< |
|
576 |
< |
// set the string tokenizer |
577 |
< |
|
578 |
< |
foo = strtok(readLine, " ,;\t"); |
579 |
< |
// set the timeToken. |
580 |
< |
|
581 |
< |
if(foo == NULL){ |
582 |
< |
sprintf( painCave.errMsg, |
583 |
< |
"error in reading Time from %s\n", |
584 |
< |
inFileName.c_str() ); |
585 |
< |
return strdup( painCave.errMsg ); |
586 |
< |
} |
587 |
< |
|
588 |
< |
currTime = atof( foo ); |
589 |
< |
entry_plug->setTime( currTime ); |
590 |
< |
|
591 |
< |
//get H-Matrix |
592 |
< |
|
593 |
< |
for(int i = 0 ; i < 9; i++){ |
594 |
< |
foo = strtok(NULL, " ,;\t"); |
595 |
< |
if(foo == NULL){ |
596 |
< |
sprintf( painCave.errMsg, |
597 |
< |
"error in reading H[%d] from %s\n", i, inFileName.c_str() ); |
598 |
< |
return strdup( painCave.errMsg ); |
599 |
< |
} |
600 |
< |
boxMat[i] = atof( foo ); |
601 |
< |
} |
602 |
< |
|
603 |
< |
for(int i=0;i<3;i++) |
604 |
< |
for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
605 |
< |
|
606 |
< |
//set H-Matrix |
607 |
< |
entry_plug->setBoxM( theBoxMat3 ); |
608 |
< |
|
609 |
< |
//get chi and integralOfChidt, they should appear by pair |
610 |
< |
|
611 |
< |
if( entry_plug->useInitXSstate ){ |
612 |
< |
foo = strtok(NULL, " ,;\t\n"); |
613 |
< |
if(foo != NULL){ |
614 |
< |
chi = atof(foo); |
615 |
< |
|
616 |
< |
foo = strtok(NULL, " ,;\t\n"); |
617 |
< |
if(foo == NULL){ |
618 |
< |
sprintf( painCave.errMsg, |
619 |
< |
"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() ); |
620 |
< |
return strdup( painCave.errMsg ); |
621 |
< |
} |
622 |
< |
integralOfChidt = atof( foo ); |
623 |
< |
|
624 |
< |
//push chi and integralOfChidt into SimInfo::properties which can be |
625 |
< |
//retrieved by integrator later |
626 |
< |
DoubleGenericData* chiValue = new DoubleGenericData(); |
627 |
< |
chiValue->setID(CHIVALUE_ID); |
628 |
< |
chiValue->setData(chi); |
629 |
< |
entry_plug->addProperty(chiValue); |
630 |
< |
|
706 |
< |
DoubleGenericData* integralOfChidtValue = new DoubleGenericData(); |
707 |
< |
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
708 |
< |
integralOfChidtValue->setData(integralOfChidt); |
709 |
< |
entry_plug->addProperty(integralOfChidtValue); |
710 |
< |
|
711 |
< |
} |
712 |
< |
else |
713 |
< |
return NULL; |
714 |
< |
|
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 |
< |
DoubleVectorGenericData* etaValue = new DoubleVectorGenericData(ETAVALUE_ID); |
737 |
< |
etaValue->insert(etaValue->end(), eta, eta+9); |
738 |
< |
entry_plug->addProperty(etaValue); |
739 |
< |
} |
740 |
< |
|
741 |
< |
return NULL; |
742 |
< |
} |
743 |
< |
|
744 |
< |
#ifdef IS_MPI |
745 |
< |
void DumpReader::nodeZeroError( void ){ |
746 |
< |
int j, myStatus; |
747 |
< |
|
748 |
< |
myStatus = 0; |
749 |
< |
for (j = 0; j < mpiSim->getNProcessors(); j++) { |
750 |
< |
MPI_Send( &myStatus, 1, MPI_INT, j, |
751 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
752 |
< |
} |
753 |
< |
|
754 |
< |
|
755 |
< |
MPI_Finalize(); |
756 |
< |
exit (0); |
757 |
< |
|
758 |
< |
} |
759 |
< |
|
760 |
< |
void DumpReader::anonymousNodeDie( void ){ |
761 |
< |
|
762 |
< |
MPI_Finalize(); |
763 |
< |
exit (0); |
764 |
< |
} |
765 |
< |
#endif |
311 |
> |
painCave.isFatal = 1; |
312 |
> |
simError(); |
313 |
> |
} |
314 |
> |
|
315 |
> |
parseDumpLine(read_buffer, integrableObject); |
316 |
> |
i++; |
317 |
> |
} |
318 |
> |
} |
319 |
> |
|
320 |
> |
// MPI Section of code.......... |
321 |
> |
|
322 |
> |
#else //IS_MPI |
323 |
> |
|
324 |
> |
// first thing first, suspend fatalities. |
325 |
> |
int masterNode = 0; |
326 |
> |
int nCurObj; |
327 |
> |
painCave.isEventLoop = 1; |
328 |
> |
|
329 |
> |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
330 |
> |
int haveError; |
331 |
> |
|
332 |
> |
MPI_Status istatus; |
333 |
> |
int nitems; |
334 |
> |
|
335 |
> |
nTotObjs = info_->getNGlobalIntegrableObjects(); |
336 |
> |
haveError = 0; |
337 |
> |
|
338 |
> |
if (worldRank == masterNode) { |
339 |
> |
inFile_->clear(); |
340 |
> |
inFile_->seekg(framePos_[whichFrame]); |
341 |
> |
|
342 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
343 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ", |
344 |
> |
filename_.c_str()); |
345 |
> |
painCave.isFatal = 1; |
346 |
> |
simError(); |
347 |
> |
} |
348 |
> |
|
349 |
> |
nitems = atoi(read_buffer); |
350 |
> |
|
351 |
> |
// Check to see that the number of integrable objects in the |
352 |
> |
// intial configuration file is the same as derived from the |
353 |
> |
// meta-data file. |
354 |
> |
|
355 |
> |
if (nTotObjs != nitems) { |
356 |
> |
sprintf(painCave.errMsg, |
357 |
> |
"DumpReader Error. %s nIntegrable, %d, " |
358 |
> |
"does not match the meta-data file's nIntegrable, %d.\n", |
359 |
> |
filename_.c_str(), |
360 |
> |
nTotObjs, |
361 |
> |
info_->getNGlobalIntegrableObjects()); |
362 |
> |
|
363 |
> |
painCave.isFatal = 1; |
364 |
> |
simError(); |
365 |
> |
} |
366 |
> |
|
367 |
> |
//read the boxMat from the comment line |
368 |
> |
|
369 |
> |
|
370 |
> |
|
371 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
372 |
> |
sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n", |
373 |
> |
filename_.c_str()); |
374 |
> |
painCave.isFatal = 1; |
375 |
> |
simError(); |
376 |
> |
} |
377 |
> |
|
378 |
> |
//Every single processor will parse the comment line by itself |
379 |
> |
//By using this way, we might lose some efficiency, but if we want to add |
380 |
> |
//more parameters into comment line, we only need to modify function |
381 |
> |
//parseCommentLine |
382 |
> |
|
383 |
> |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
384 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
385 |
> |
|
386 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
387 |
> |
int which_node = info_->getMolToProc(i); |
388 |
> |
|
389 |
> |
if (which_node == masterNode) { |
390 |
> |
//molecules belong to master node |
391 |
> |
|
392 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
393 |
> |
|
394 |
> |
if (mol == NULL) { |
395 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
396 |
> |
painCave.isFatal = 1; |
397 |
> |
simError(); |
398 |
> |
} |
399 |
> |
|
400 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
401 |
> |
integrableObject = mol->nextIntegrableObject(ii)){ |
402 |
> |
|
403 |
> |
|
404 |
> |
|
405 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
406 |
> |
sprintf(painCave.errMsg, |
407 |
> |
"DumpReader Error: error in reading file %s\n" |
408 |
> |
"natoms = %d; index = %d\n" |
409 |
> |
"error reading the line from the file.\n", |
410 |
> |
filename_.c_str(), |
411 |
> |
nTotObjs, |
412 |
> |
i); |
413 |
> |
|
414 |
> |
painCave.isFatal = 1; |
415 |
> |
simError(); |
416 |
> |
} |
417 |
> |
|
418 |
> |
parseDumpLine(read_buffer, integrableObject); |
419 |
> |
} |
420 |
> |
} else { |
421 |
> |
//molecule belongs to slave nodes |
422 |
> |
|
423 |
> |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
424 |
> |
MPI_COMM_WORLD, &istatus); |
425 |
> |
|
426 |
> |
for(int j = 0; j < nCurObj; j++) { |
427 |
> |
|
428 |
> |
|
429 |
> |
if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { |
430 |
> |
sprintf(painCave.errMsg, |
431 |
> |
"DumpReader Error: error in reading file %s\n" |
432 |
> |
"natoms = %d; index = %d\n" |
433 |
> |
"error reading the line from the file.\n", |
434 |
> |
filename_.c_str(), |
435 |
> |
nTotObjs, |
436 |
> |
i); |
437 |
> |
|
438 |
> |
painCave.isFatal = 1; |
439 |
> |
simError(); |
440 |
> |
} |
441 |
> |
|
442 |
> |
MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node, |
443 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
444 |
> |
} |
445 |
> |
} |
446 |
> |
} |
447 |
> |
} else { |
448 |
> |
//actions taken at slave nodes |
449 |
> |
MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
450 |
> |
|
451 |
> |
/**@todo*/ |
452 |
> |
parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot()); |
453 |
> |
|
454 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
455 |
> |
int which_node = info_->getMolToProc(i); |
456 |
> |
|
457 |
> |
if (which_node == worldRank) { |
458 |
> |
//molecule with global index i belongs to this processor |
459 |
> |
|
460 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
461 |
> |
if (mol == NULL) { |
462 |
> |
sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank); |
463 |
> |
painCave.isFatal = 1; |
464 |
> |
simError(); |
465 |
> |
} |
466 |
> |
|
467 |
> |
nCurObj = mol->getNIntegrableObjects(); |
468 |
> |
|
469 |
> |
MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT, |
470 |
> |
MPI_COMM_WORLD); |
471 |
> |
|
472 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
473 |
> |
integrableObject = mol->nextIntegrableObject(ii)){ |
474 |
> |
|
475 |
> |
MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode, |
476 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
477 |
> |
|
478 |
> |
parseDumpLine(read_buffer, integrableObject); |
479 |
> |
} |
480 |
> |
|
481 |
> |
} |
482 |
> |
|
483 |
> |
} |
484 |
> |
|
485 |
> |
} |
486 |
> |
|
487 |
> |
#endif |
488 |
> |
|
489 |
> |
} |
490 |
> |
|
491 |
> |
void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) { |
492 |
> |
|
493 |
> |
Vector3d pos; // position place holders |
494 |
> |
Vector3d vel; // velocity placeholders |
495 |
> |
Quat4d q; // the quaternions |
496 |
> |
Vector3d ji; // angular velocity placeholders; |
497 |
> |
StringTokenizer tokenizer(line); |
498 |
> |
int nTokens; |
499 |
> |
|
500 |
> |
nTokens = tokenizer.countTokens(); |
501 |
> |
|
502 |
> |
if (nTokens < 14) { |
503 |
> |
sprintf(painCave.errMsg, |
504 |
> |
"DumpReader Error: Not enough Tokens.\n%s\n", line); |
505 |
> |
painCave.isFatal = 1; |
506 |
> |
simError(); |
507 |
> |
} |
508 |
> |
|
509 |
> |
std::string name = tokenizer.nextToken(); |
510 |
> |
|
511 |
> |
if (name != integrableObject->getType()) { |
512 |
> |
|
513 |
> |
sprintf(painCave.errMsg, |
514 |
> |
"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n", |
515 |
> |
name.c_str(), filename_.c_str(), integrableObject->getType().c_str()); |
516 |
> |
painCave.isFatal = 1; |
517 |
> |
simError(); |
518 |
> |
} |
519 |
> |
|
520 |
> |
pos[0] = tokenizer.nextTokenAsDouble(); |
521 |
> |
pos[1] = tokenizer.nextTokenAsDouble(); |
522 |
> |
pos[2] = tokenizer.nextTokenAsDouble(); |
523 |
> |
if (needPos_) { |
524 |
> |
integrableObject->setPos(pos); |
525 |
> |
} |
526 |
> |
|
527 |
> |
vel[0] = tokenizer.nextTokenAsDouble(); |
528 |
> |
vel[1] = tokenizer.nextTokenAsDouble(); |
529 |
> |
vel[2] = tokenizer.nextTokenAsDouble(); |
530 |
> |
if (needVel_) { |
531 |
> |
integrableObject->setVel(vel); |
532 |
> |
} |
533 |
> |
|
534 |
> |
if (integrableObject->isDirectional()) { |
535 |
> |
|
536 |
> |
q[0] = tokenizer.nextTokenAsDouble(); |
537 |
> |
q[1] = tokenizer.nextTokenAsDouble(); |
538 |
> |
q[2] = tokenizer.nextTokenAsDouble(); |
539 |
> |
q[3] = tokenizer.nextTokenAsDouble(); |
540 |
> |
|
541 |
> |
double qlen = q.length(); |
542 |
> |
if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
543 |
> |
|
544 |
> |
sprintf(painCave.errMsg, |
545 |
> |
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0\n"); |
546 |
> |
painCave.isFatal = 1; |
547 |
> |
simError(); |
548 |
> |
|
549 |
> |
} |
550 |
> |
|
551 |
> |
q.normalize(); |
552 |
> |
if (needQuaternion_) { |
553 |
> |
integrableObject->setQ(q); |
554 |
> |
} |
555 |
> |
|
556 |
> |
ji[0] = tokenizer.nextTokenAsDouble(); |
557 |
> |
ji[1] = tokenizer.nextTokenAsDouble(); |
558 |
> |
ji[2] = tokenizer.nextTokenAsDouble(); |
559 |
> |
if (needAngMom_) { |
560 |
> |
integrableObject->setJ(ji); |
561 |
> |
} |
562 |
> |
} |
563 |
> |
|
564 |
> |
} |
565 |
> |
|
566 |
> |
|
567 |
> |
void DumpReader::parseCommentLine(char* line, Snapshot* s) { |
568 |
> |
double currTime; |
569 |
> |
Mat3x3d hmat; |
570 |
> |
double chi; |
571 |
> |
double integralOfChiDt; |
572 |
> |
Mat3x3d eta; |
573 |
> |
|
574 |
> |
StringTokenizer tokenizer(line); |
575 |
> |
int nTokens; |
576 |
> |
|
577 |
> |
nTokens = tokenizer.countTokens(); |
578 |
> |
|
579 |
> |
//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens) |
580 |
> |
if (nTokens < 10) { |
581 |
> |
sprintf(painCave.errMsg, |
582 |
> |
"DumpReader Error: Not enough tokens in comment line: %s", line); |
583 |
> |
painCave.isFatal = 1; |
584 |
> |
simError(); |
585 |
> |
} |
586 |
> |
|
587 |
> |
//read current time |
588 |
> |
currTime = tokenizer.nextTokenAsDouble(); |
589 |
> |
s->setTime(currTime); |
590 |
> |
|
591 |
> |
//read h-matrix |
592 |
> |
hmat(0, 0) = tokenizer.nextTokenAsDouble(); |
593 |
> |
hmat(0, 1) = tokenizer.nextTokenAsDouble(); |
594 |
> |
hmat(0, 2) = tokenizer.nextTokenAsDouble(); |
595 |
> |
hmat(1, 0) = tokenizer.nextTokenAsDouble(); |
596 |
> |
hmat(1, 1) = tokenizer.nextTokenAsDouble(); |
597 |
> |
hmat(1, 2) = tokenizer.nextTokenAsDouble(); |
598 |
> |
hmat(2, 0) = tokenizer.nextTokenAsDouble(); |
599 |
> |
hmat(2, 1) = tokenizer.nextTokenAsDouble(); |
600 |
> |
hmat(2, 2) = tokenizer.nextTokenAsDouble(); |
601 |
> |
s->setHmat(hmat); |
602 |
> |
|
603 |
> |
//read chi and integralOfChidt, they should apprear in pair |
604 |
> |
if (tokenizer.countTokens() >= 2) { |
605 |
> |
chi = tokenizer.nextTokenAsDouble(); |
606 |
> |
integralOfChiDt = tokenizer.nextTokenAsDouble(); |
607 |
> |
|
608 |
> |
s->setChi(chi); |
609 |
> |
s->setIntegralOfChiDt(integralOfChiDt); |
610 |
> |
} |
611 |
> |
|
612 |
> |
//read eta (eta is 3x3 matrix) |
613 |
> |
if (tokenizer.countTokens() >= 9) { |
614 |
> |
eta(0, 0) = tokenizer.nextTokenAsDouble(); |
615 |
> |
eta(0, 1) = tokenizer.nextTokenAsDouble(); |
616 |
> |
eta(0, 2) = tokenizer.nextTokenAsDouble(); |
617 |
> |
eta(1, 0) = tokenizer.nextTokenAsDouble(); |
618 |
> |
eta(1, 1) = tokenizer.nextTokenAsDouble(); |
619 |
> |
eta(1, 2) = tokenizer.nextTokenAsDouble(); |
620 |
> |
eta(2, 0) = tokenizer.nextTokenAsDouble(); |
621 |
> |
eta(2, 1) = tokenizer.nextTokenAsDouble(); |
622 |
> |
eta(2, 2) = tokenizer.nextTokenAsDouble(); |
623 |
> |
|
624 |
> |
s->setEta(eta); |
625 |
> |
} |
626 |
> |
|
627 |
> |
|
628 |
> |
} |
629 |
> |
|
630 |
> |
}//end namespace oopse |