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#define _LARGEFILE_SOURCE64 |
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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> |
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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" |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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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 |
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|
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|
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DumpReader :: DumpReader(const char *in_name ){ |
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|
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isScanned = false; |
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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|
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inFile = fopen(in_name, "r"); |
35 |
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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; |
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simError(); |
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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 |
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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 |
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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 |
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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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#endif |
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return; |
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} |
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|
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DumpReader :: ~DumpReader( ){ |
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#ifdef IS_MPI |
53 |
< |
if (worldRank == 0) { |
54 |
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#endif |
55 |
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vector<fpos_t*>::iterator i; |
56 |
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|
57 |
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int error; |
58 |
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error = fclose( inFile ); |
59 |
< |
if( error ){ |
60 |
< |
sprintf( painCave.errMsg, |
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"Error closing %s\n", inFileName.c_str()); |
62 |
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simError(); |
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} |
64 |
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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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#define _LARGEFILE_SOURCE64 |
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#define _FILE_OFFSET_BITS 64 |
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|
45 |
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#include <sys/types.h> |
46 |
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#include <sys/stat.h> |
47 |
> |
|
48 |
> |
#include <iostream> |
49 |
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#include <math.h> |
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|
51 |
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#include <stdio.h> |
52 |
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#include <stdlib.h> |
53 |
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#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 |
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#define TAKE_THIS_TAG_INT 1 |
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|
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#endif // is_mpi |
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|
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|
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namespace oopse { |
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|
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DumpReader::DumpReader(SimInfo* info, const std::string& filename) |
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: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) { |
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|
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#ifdef IS_MPI |
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|
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> |
if (worldRank == 0) { |
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#endif |
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|
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inFile_ = new std::ifstream(filename_.c_str()); |
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|
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if (inFile_->fail()) { |
83 |
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sprintf(painCave.errMsg, |
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"DumpReader: Cannot open file: %s\n", |
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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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#ifdef IS_MPI |
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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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|
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return; |
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} |
101 |
|
|
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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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} |
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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(); |
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return framePos.size(); |
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} |
84 |
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|
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void DumpReader::scanFile( void ){ |
86 |
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|
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int i, j; |
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int lineNum = 0; |
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char readBuffer[2000]; |
90 |
< |
fpos_t *currPos; |
91 |
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|
92 |
< |
#ifdef IS_MPI |
93 |
< |
if( worldRank == 0 ){ |
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< |
#endif // is_mpi |
102 |
> |
DumpReader::~DumpReader() { |
103 |
|
|
104 |
< |
rewind( inFile ); |
104 |
> |
#ifdef IS_MPI |
105 |
|
|
106 |
< |
currPos = new fpos_t; |
107 |
< |
fgetpos( inFile, currPos ); |
100 |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
101 |
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lineNum++; |
102 |
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if( feof( inFile ) ){ |
103 |
< |
sprintf( painCave.errMsg, |
104 |
< |
"File \"%s\" ended unexpectedly at line %d\n", |
105 |
< |
inFileName.c_str(), |
106 |
< |
lineNum ); |
107 |
< |
painCave.isFatal = 1; |
108 |
< |
simError(); |
109 |
< |
} |
110 |
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|
111 |
< |
while( !feof( inFile ) ){ |
106 |
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if (worldRank == 0) { |
107 |
> |
#endif |
108 |
|
|
109 |
< |
framePos.push_back(currPos); |
114 |
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|
115 |
< |
i = atoi(readBuffer); |
109 |
> |
delete inFile_; |
110 |
|
|
111 |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
118 |
< |
lineNum++; |
119 |
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if( feof( inFile ) ){ |
120 |
< |
sprintf( painCave.errMsg, |
121 |
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"File \"%s\" ended unexpectedly at line %d\n", |
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< |
inFileName.c_str(), |
123 |
< |
lineNum ); |
124 |
< |
painCave.isFatal = 1; |
125 |
< |
simError(); |
126 |
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} |
127 |
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|
128 |
< |
for(j=0; j<i; j++){ |
129 |
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|
130 |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
131 |
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lineNum++; |
132 |
< |
if( feof( inFile ) ){ |
133 |
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sprintf( painCave.errMsg, |
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"File \"%s\" ended unexpectedly at line %d," |
135 |
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" with atom %d\n", |
136 |
< |
inFileName.c_str(), |
137 |
< |
lineNum, |
138 |
< |
j ); |
139 |
< |
painCave.isFatal = 1; |
140 |
< |
simError(); |
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} |
142 |
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|
143 |
< |
} |
111 |
> |
#ifdef IS_MPI |
112 |
|
|
113 |
< |
currPos = new fpos_t; |
146 |
< |
fgetpos( inFile, currPos ); |
147 |
< |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
148 |
< |
lineNum++; |
149 |
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} |
113 |
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} |
114 |
|
|
115 |
< |
delete currPos; |
116 |
< |
rewind( inFile ); |
115 |
> |
strcpy(checkPointMsg, "Dump file closed successfully."); |
116 |
> |
MPIcheckPoint(); |
117 |
> |
|
118 |
> |
#endif |
119 |
> |
|
120 |
> |
return; |
121 |
> |
} |
122 |
> |
|
123 |
> |
int DumpReader::getNFrames(void) { |
124 |
|
|
125 |
< |
isScanned = true; |
126 |
< |
|
127 |
< |
#ifdef IS_MPI |
128 |
< |
} |
129 |
< |
strcpy( checkPointMsg, "Successfully scanned DumpFile\n" ); |
130 |
< |
MPIcheckPoint(); |
131 |
< |
#endif // is_mpi |
132 |
< |
} |
133 |
< |
|
134 |
< |
void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){ |
135 |
< |
|
136 |
< |
simnfo = the_simnfo; |
137 |
< |
|
138 |
< |
this->readSet( whichFrame ); |
139 |
< |
} |
125 |
> |
if (!isScanned_) |
126 |
> |
scanFile(); |
127 |
> |
|
128 |
> |
return nframes_; |
129 |
> |
} |
130 |
> |
|
131 |
> |
void DumpReader::scanFile(void) { |
132 |
> |
int lineNo = 0; |
133 |
> |
std::streampos prevPos; |
134 |
> |
std::streampos currPos; |
135 |
> |
|
136 |
> |
#ifdef IS_MPI |
137 |
> |
|
138 |
> |
if (worldRank == 0) { |
139 |
> |
#endif // is_mpi |
140 |
> |
|
141 |
> |
currPos = inFile_->tellg(); |
142 |
> |
prevPos = currPos; |
143 |
> |
bool foundOpenSnapshotTag = false; |
144 |
> |
bool foundClosedSnapshotTag = false; |
145 |
> |
while(inFile_->getline(buffer, bufferSize)) { |
146 |
> |
++lineNo; |
147 |
> |
|
148 |
> |
std::string line = buffer; |
149 |
> |
currPos = inFile_->tellg(); |
150 |
> |
if (line.find("<Snapshot>")!= std::string::npos) { |
151 |
> |
if (foundOpenSnapshotTag) { |
152 |
> |
sprintf(painCave.errMsg, |
153 |
> |
"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo, |
154 |
> |
filename_.c_str()); |
155 |
> |
painCave.isFatal = 1; |
156 |
> |
simError(); |
157 |
> |
} |
158 |
> |
foundOpenSnapshotTag = true; |
159 |
> |
foundClosedSnapshotTag = false; |
160 |
> |
framePos_.push_back(prevPos); |
161 |
> |
|
162 |
> |
} else if (line.find("</Snapshot>") != std::string::npos){ |
163 |
> |
if (!foundOpenSnapshotTag) { |
164 |
> |
sprintf(painCave.errMsg, |
165 |
> |
"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo, |
166 |
> |
filename_.c_str()); |
167 |
> |
painCave.isFatal = 1; |
168 |
> |
simError(); |
169 |
> |
} |
170 |
> |
|
171 |
> |
if (foundClosedSnapshotTag) { |
172 |
> |
sprintf(painCave.errMsg, |
173 |
> |
"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo, |
174 |
> |
filename_.c_str()); |
175 |
> |
painCave.isFatal = 1; |
176 |
> |
simError(); |
177 |
> |
} |
178 |
> |
foundClosedSnapshotTag = true; |
179 |
> |
foundOpenSnapshotTag = false; |
180 |
> |
} |
181 |
> |
prevPos = currPos; |
182 |
> |
} |
183 |
> |
|
184 |
> |
// only found <Snapshot> for the last frame means the file is corrupted, we should discard |
185 |
> |
// it and give a warning message |
186 |
> |
if (foundOpenSnapshotTag) { |
187 |
> |
sprintf(painCave.errMsg, |
188 |
> |
"DumpReader: last frame in %s is invalid\n", filename_.c_str()); |
189 |
> |
painCave.isFatal = 0; |
190 |
> |
simError(); |
191 |
> |
framePos_.pop_back(); |
192 |
> |
} |
193 |
> |
|
194 |
> |
nframes_ = framePos_.size(); |
195 |
> |
|
196 |
> |
if (nframes_ == 0) { |
197 |
> |
sprintf(painCave.errMsg, |
198 |
> |
"DumpReader: %s does not contain a valid frame\n", filename_.c_str()); |
199 |
> |
painCave.isFatal = 1; |
200 |
> |
simError(); |
201 |
> |
} |
202 |
> |
#ifdef IS_MPI |
203 |
> |
} |
204 |
> |
|
205 |
> |
MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); |
206 |
> |
|
207 |
> |
#endif // is_mpi |
208 |
> |
|
209 |
> |
isScanned_ = true; |
210 |
> |
} |
211 |
> |
|
212 |
> |
void DumpReader::readFrame(int whichFrame) { |
213 |
> |
if (!isScanned_) |
214 |
> |
scanFile(); |
215 |
> |
|
216 |
> |
int storageLayout = info_->getSnapshotManager()->getStorageLayout(); |
217 |
> |
|
218 |
> |
if (storageLayout & DataStorage::dslPosition) { |
219 |
> |
needPos_ = true; |
220 |
> |
} else { |
221 |
> |
needPos_ = false; |
222 |
> |
} |
223 |
> |
|
224 |
> |
if (storageLayout & DataStorage::dslVelocity) { |
225 |
> |
needVel_ = true; |
226 |
> |
} else { |
227 |
> |
needVel_ = false; |
228 |
> |
} |
229 |
> |
|
230 |
> |
if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { |
231 |
> |
needQuaternion_ = true; |
232 |
> |
} else { |
233 |
> |
needQuaternion_ = false; |
234 |
> |
} |
235 |
> |
|
236 |
> |
if (storageLayout & DataStorage::dslAngularMomentum) { |
237 |
> |
needAngMom_ = true; |
238 |
> |
} else { |
239 |
> |
needAngMom_ = false; |
240 |
> |
} |
241 |
> |
|
242 |
> |
readSet(whichFrame); |
243 |
|
|
244 |
+ |
if (needCOMprops_) { |
245 |
+ |
Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); |
246 |
+ |
Vector3d com; |
247 |
+ |
Vector3d comvel; |
248 |
+ |
Vector3d comw; |
249 |
+ |
info_->getComAll(com, comvel); |
250 |
+ |
comw = info_->getAngularMomentum(); |
251 |
+ |
s->setCOMprops(com, comvel, comw); |
252 |
+ |
} |
253 |
|
|
254 |
+ |
} |
255 |
+ |
|
256 |
+ |
void DumpReader::readSet(int whichFrame) { |
257 |
+ |
std::string line; |
258 |
|
|
259 |
< |
void DumpReader :: readSet( int whichFrame ){ |
259 |
> |
#ifndef IS_MPI |
260 |
|
|
261 |
< |
int i; |
262 |
< |
unsigned int j; |
261 |
> |
inFile_->clear(); |
262 |
> |
inFile_->seekg(framePos_[whichFrame]); |
263 |
|
|
264 |
< |
#ifdef IS_MPI |
178 |
< |
int done, which_node, which_atom; // loop counter |
179 |
< |
#endif //is_mpi |
264 |
> |
std::istream& inputStream = *inFile_; |
265 |
|
|
266 |
< |
const int BUFFERSIZE = 2000; // size of the read buffer |
267 |
< |
int nTotObjs; // the number of atoms |
268 |
< |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
266 |
> |
#else |
267 |
> |
int masterNode = 0; |
268 |
> |
std::stringstream sstream; |
269 |
> |
if (worldRank == masterNode) { |
270 |
> |
std::string sendBuffer; |
271 |
|
|
272 |
< |
char *eof_test; // ptr to see when we reach the end of the file |
273 |
< |
char *parseErr; |
272 |
> |
inFile_->clear(); |
273 |
> |
inFile_->seekg(framePos_[whichFrame]); |
274 |
> |
|
275 |
> |
while (inFile_->getline(buffer, bufferSize)) { |
276 |
|
|
277 |
< |
vector<StuntDouble*> integrableObjects; |
277 |
> |
line = buffer; |
278 |
> |
sendBuffer += line; |
279 |
> |
sendBuffer += '\n'; |
280 |
> |
if (line.find("</Snapshot>") != std::string::npos) { |
281 |
> |
break; |
282 |
> |
} |
283 |
> |
} |
284 |
|
|
285 |
+ |
int sendBufferSize = sendBuffer.size(); |
286 |
+ |
MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
287 |
+ |
MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
288 |
+ |
|
289 |
+ |
sstream.str(sendBuffer); |
290 |
+ |
} else { |
291 |
+ |
int sendBufferSize; |
292 |
+ |
MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
293 |
+ |
char * recvBuffer = new char[sendBufferSize+1]; |
294 |
+ |
MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
295 |
+ |
sstream.str(recvBuffer); |
296 |
+ |
} |
297 |
|
|
298 |
< |
#ifndef IS_MPI |
298 |
> |
std::istream& inputStream = sstream; |
299 |
> |
#endif |
300 |
|
|
301 |
< |
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 |
< |
} |
301 |
> |
inputStream.getline(buffer, bufferSize); |
302 |
|
|
303 |
< |
nTotObjs = atoi( read_buffer ); |
303 |
> |
line = buffer; |
304 |
> |
if (line.find("<Snapshot>") == std::string::npos) { |
305 |
> |
sprintf(painCave.errMsg, |
306 |
> |
"DumpReader Error: can not find <Snapshot>\n"); |
307 |
> |
painCave.isFatal = 1; |
308 |
> |
simError(); |
309 |
> |
} |
310 |
> |
|
311 |
> |
//read frameData |
312 |
> |
readFrameProperties(inputStream); |
313 |
|
|
314 |
< |
if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
315 |
< |
sprintf( painCave.errMsg, |
207 |
< |
"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 |
< |
} |
314 |
> |
//read StuntDoubles |
315 |
> |
readStuntDoubles(inputStream); |
316 |
|
|
317 |
< |
//read the box mat from the comment line |
317 |
> |
inputStream.getline(buffer, bufferSize); |
318 |
> |
line = buffer; |
319 |
> |
if (line.find("</Snapshot>") == std::string::npos) { |
320 |
> |
sprintf(painCave.errMsg, |
321 |
> |
"DumpReader Error: can not find </Snapshot>\n"); |
322 |
> |
painCave.isFatal = 1; |
323 |
> |
simError(); |
324 |
> |
} |
325 |
> |
|
326 |
> |
} |
327 |
> |
|
328 |
> |
void DumpReader::parseDumpLine(const std::string& line) { |
329 |
|
|
330 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
331 |
< |
if(eof_test == NULL){ |
332 |
< |
sprintf( painCave.errMsg, |
333 |
< |
"error in reading commment in %s\n", inFileName.c_str()); |
334 |
< |
painCave.isFatal = 1; |
335 |
< |
simError(); |
336 |
< |
} |
330 |
> |
|
331 |
> |
StringTokenizer tokenizer(line); |
332 |
> |
int nTokens; |
333 |
> |
|
334 |
> |
nTokens = tokenizer.countTokens(); |
335 |
> |
|
336 |
> |
if (nTokens < 2) { |
337 |
> |
sprintf(painCave.errMsg, |
338 |
> |
"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
339 |
> |
painCave.isFatal = 1; |
340 |
> |
simError(); |
341 |
> |
} |
342 |
|
|
343 |
< |
parseErr = parseCommentLine( read_buffer, simnfo); |
344 |
< |
if( parseErr != NULL ){ |
345 |
< |
strcpy( painCave.errMsg, parseErr ); |
227 |
< |
painCave.isFatal = 1; |
228 |
< |
simError(); |
229 |
< |
} |
343 |
> |
int index = tokenizer.nextTokenAsInt(); |
344 |
> |
|
345 |
> |
StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index); |
346 |
|
|
347 |
< |
//parse dump lines |
347 |
> |
if (integrableObject == NULL) { |
348 |
> |
return; |
349 |
> |
} |
350 |
> |
std::string type = tokenizer.nextToken(); |
351 |
> |
int size = type.size(); |
352 |
|
|
353 |
< |
for( i=0; i < simnfo->n_mol; i++){ |
353 |
> |
for(int i = 0; i < size; ++i) { |
354 |
> |
switch(type[i]) { |
355 |
> |
|
356 |
> |
case 'p': { |
357 |
> |
Vector3d pos; |
358 |
> |
pos[0] = tokenizer.nextTokenAsDouble(); |
359 |
> |
pos[1] = tokenizer.nextTokenAsDouble(); |
360 |
> |
pos[2] = tokenizer.nextTokenAsDouble(); |
361 |
> |
if (needPos_) { |
362 |
> |
integrableObject->setPos(pos); |
363 |
> |
} |
364 |
> |
break; |
365 |
> |
} |
366 |
> |
case 'v' : { |
367 |
> |
Vector3d vel; |
368 |
> |
vel[0] = tokenizer.nextTokenAsDouble(); |
369 |
> |
vel[1] = tokenizer.nextTokenAsDouble(); |
370 |
> |
vel[2] = tokenizer.nextTokenAsDouble(); |
371 |
> |
if (needVel_) { |
372 |
> |
integrableObject->setVel(vel); |
373 |
> |
} |
374 |
> |
break; |
375 |
> |
} |
376 |
|
|
377 |
< |
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
377 |
> |
case 'q' : { |
378 |
> |
Quat4d q; |
379 |
> |
if (integrableObject->isDirectional()) { |
380 |
> |
|
381 |
> |
q[0] = tokenizer.nextTokenAsDouble(); |
382 |
> |
q[1] = tokenizer.nextTokenAsDouble(); |
383 |
> |
q[2] = tokenizer.nextTokenAsDouble(); |
384 |
> |
q[3] = tokenizer.nextTokenAsDouble(); |
385 |
> |
|
386 |
> |
RealType qlen = q.length(); |
387 |
> |
if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
388 |
> |
|
389 |
> |
sprintf(painCave.errMsg, |
390 |
> |
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); |
391 |
> |
painCave.isFatal = 1; |
392 |
> |
simError(); |
393 |
> |
|
394 |
> |
} |
395 |
> |
|
396 |
> |
q.normalize(); |
397 |
> |
if (needQuaternion_) { |
398 |
> |
integrableObject->setQ(q); |
399 |
> |
} |
400 |
> |
} |
401 |
> |
break; |
402 |
> |
} |
403 |
> |
case 'j' : { |
404 |
> |
Vector3d ji; |
405 |
> |
if (integrableObject->isDirectional()) { |
406 |
> |
ji[0] = tokenizer.nextTokenAsDouble(); |
407 |
> |
ji[1] = tokenizer.nextTokenAsDouble(); |
408 |
> |
ji[2] = tokenizer.nextTokenAsDouble(); |
409 |
> |
if (needAngMom_) { |
410 |
> |
integrableObject->setJ(ji); |
411 |
> |
} |
412 |
> |
} |
413 |
> |
break; |
414 |
> |
} |
415 |
> |
case 'f': { |
416 |
|
|
417 |
< |
for(j = 0; j < integrableObjects.size(); j++){ |
417 |
> |
Vector3d force; |
418 |
> |
force[0] = tokenizer.nextTokenAsDouble(); |
419 |
> |
force[1] = tokenizer.nextTokenAsDouble(); |
420 |
> |
force[2] = tokenizer.nextTokenAsDouble(); |
421 |
> |
integrableObject->setFrc(force); |
422 |
> |
break; |
423 |
> |
} |
424 |
> |
case 't' : { |
425 |
> |
|
426 |
> |
Vector3d torque; |
427 |
> |
torque[0] = tokenizer.nextTokenAsDouble(); |
428 |
> |
torque[1] = tokenizer.nextTokenAsDouble(); |
429 |
> |
torque[2] = tokenizer.nextTokenAsDouble(); |
430 |
> |
integrableObject->setTrq(torque); |
431 |
> |
break; |
432 |
> |
} |
433 |
> |
default: { |
434 |
> |
sprintf(painCave.errMsg, |
435 |
> |
"DumpReader Error: %s is an unrecognized type\n", type.c_str()); |
436 |
> |
painCave.isFatal = 1; |
437 |
> |
simError(); |
438 |
> |
break; |
439 |
> |
} |
440 |
|
|
239 |
– |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
240 |
– |
if(eof_test == NULL){ |
241 |
– |
sprintf(painCave.errMsg, |
242 |
– |
"error in reading file %s\n" |
243 |
– |
"natoms = %d; index = %d\n" |
244 |
– |
"error reading the line from the file.\n", |
245 |
– |
inFileName.c_str(), nTotObjs, i ); |
246 |
– |
painCave.isFatal = 1; |
247 |
– |
simError(); |
441 |
|
} |
249 |
– |
|
250 |
– |
parseErr = parseDumpLine( read_buffer, integrableObjects[j]); |
251 |
– |
if( parseErr != NULL ){ |
252 |
– |
strcpy( painCave.errMsg, parseErr ); |
253 |
– |
painCave.isFatal = 1; |
254 |
– |
simError(); |
255 |
– |
} |
442 |
|
} |
443 |
< |
} |
443 |
> |
|
444 |
> |
} |
445 |
> |
|
446 |
|
|
447 |
< |
// MPI Section of code.......... |
260 |
< |
#else //IS_MPI |
447 |
> |
void DumpReader::readStuntDoubles(std::istream& inputStream) { |
448 |
|
|
449 |
< |
// first thing first, suspend fatalities. |
450 |
< |
painCave.isEventLoop = 1; |
451 |
< |
|
452 |
< |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
453 |
< |
int haveError; |
454 |
< |
|
455 |
< |
MPI_Status istatus; |
456 |
< |
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(); |
449 |
> |
inputStream.getline(buffer, bufferSize); |
450 |
> |
std::string line(buffer); |
451 |
> |
|
452 |
> |
if (line.find("<StuntDoubles>") == std::string::npos) { |
453 |
> |
sprintf(painCave.errMsg, |
454 |
> |
"DumpReader Error: Missing <StuntDoubles>\n"); |
455 |
> |
painCave.isFatal = 1; |
456 |
> |
simError(); |
457 |
|
} |
458 |
|
|
459 |
< |
nitems = atoi( read_buffer ); |
460 |
< |
|
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]); |
357 |
< |
|
358 |
< |
} |
359 |
< |
|
360 |
< |
|
361 |
< |
} |
362 |
< |
else{ |
363 |
< |
//molecule belongs to slave nodes |
364 |
< |
|
365 |
< |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
366 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
459 |
> |
while(inputStream.getline(buffer, bufferSize)) { |
460 |
> |
line = buffer; |
461 |
|
|
462 |
< |
for(j=0; j < nCurObj; j++){ |
463 |
< |
|
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(); |
382 |
< |
|
383 |
< |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
384 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
385 |
< |
|
386 |
< |
} |
387 |
< |
|
462 |
> |
if(line.find("</StuntDoubles>") != std::string::npos) { |
463 |
> |
break; |
464 |
|
} |
389 |
– |
|
390 |
– |
} |
391 |
– |
|
392 |
– |
} |
393 |
– |
else{ |
394 |
– |
//actions taken at slave nodes |
395 |
– |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
465 |
|
|
466 |
< |
parseErr = parseCommentLine( read_buffer, simnfo); |
398 |
< |
|
399 |
< |
if( parseErr != NULL ){ |
400 |
< |
strcpy( painCave.errMsg, parseErr ); |
401 |
< |
haveError = 1; |
402 |
< |
simError(); |
466 |
> |
parseDumpLine(line); |
467 |
|
} |
468 |
|
|
469 |
< |
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); |
469 |
> |
} |
470 |
|
|
471 |
< |
if(localIndex == -1) { |
414 |
< |
sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
415 |
< |
haveError = 1; |
416 |
< |
simError(); |
417 |
< |
} |
471 |
> |
void DumpReader::readFrameProperties(std::istream& inputStream) { |
472 |
|
|
473 |
< |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
473 |
> |
Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); |
474 |
> |
inputStream.getline(buffer, bufferSize); |
475 |
> |
std::string line(buffer); |
476 |
|
|
477 |
< |
nCurObj = integrableObjects.size(); |
478 |
< |
|
479 |
< |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
480 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
477 |
> |
if (line.find("<FrameData>") == std::string::npos) { |
478 |
> |
sprintf(painCave.errMsg, |
479 |
> |
"DumpReader Error: Missing <FrameData>\n"); |
480 |
> |
painCave.isFatal = 1; |
481 |
> |
simError(); |
482 |
> |
} |
483 |
|
|
484 |
< |
for(j = 0; j < integrableObjects.size(); j++){ |
485 |
< |
|
486 |
< |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
487 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
488 |
< |
|
431 |
< |
parseErr = parseDumpLine(read_buffer, integrableObjects[j]); |
432 |
< |
|
433 |
< |
if( parseErr != NULL ){ |
434 |
< |
strcpy( painCave.errMsg, parseErr ); |
435 |
< |
simError(); |
436 |
< |
} |
437 |
< |
|
438 |
< |
} |
439 |
< |
|
484 |
> |
while(inputStream.getline(buffer, bufferSize)) { |
485 |
> |
line = buffer; |
486 |
> |
|
487 |
> |
if(line.find("</FrameData>") != std::string::npos) { |
488 |
> |
break; |
489 |
|
} |
490 |
|
|
491 |
< |
} |
491 |
> |
StringTokenizer tokenizer(line, " ;\t\n\r{}:,"); |
492 |
> |
if (!tokenizer.hasMoreTokens()) { |
493 |
> |
sprintf(painCave.errMsg, |
494 |
> |
"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
495 |
> |
painCave.isFatal = 1; |
496 |
> |
simError(); |
497 |
> |
} |
498 |
|
|
499 |
< |
} |
500 |
< |
|
501 |
< |
#endif |
502 |
< |
} |
503 |
< |
|
504 |
< |
char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){ |
505 |
< |
|
506 |
< |
char *foo; // the pointer to the current string token |
507 |
< |
|
508 |
< |
double pos[3]; // position place holders |
509 |
< |
double vel[3]; // velocity placeholders |
510 |
< |
double q[4]; // the quaternions |
511 |
< |
double ji[3]; // angular velocity placeholders; |
512 |
< |
double qSqr, qLength; // needed to normalize the quaternion vector. |
513 |
< |
|
514 |
< |
|
515 |
< |
// set the string tokenizer |
516 |
< |
|
517 |
< |
foo = strtok(readLine, " ,;\t"); |
518 |
< |
|
519 |
< |
// check the atom name to the current atom |
520 |
< |
|
521 |
< |
if( strcmp( foo, sd->getType() ) ){ |
522 |
< |
sprintf( painCave.errMsg, |
523 |
< |
"DumpReader error. Does not" |
524 |
< |
" match the meta-data atom %s.\n", |
525 |
< |
sd->getType() ); |
526 |
< |
return strdup( painCave.errMsg ); |
527 |
< |
} |
528 |
< |
|
529 |
< |
// get the positions |
530 |
< |
|
531 |
< |
foo = strtok(NULL, " ,;\t"); |
532 |
< |
if(foo == NULL){ |
533 |
< |
sprintf( painCave.errMsg, |
534 |
< |
"error in reading postition x from %s\n", |
535 |
< |
inFileName.c_str()); |
536 |
< |
return strdup( painCave.errMsg ); |
482 |
< |
} |
483 |
< |
pos[0] = atof( foo ); |
484 |
< |
|
485 |
< |
foo = strtok(NULL, " ,;\t"); |
486 |
< |
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 ); |
493 |
< |
|
494 |
< |
foo = strtok(NULL, " ,;\t"); |
495 |
< |
if(foo == NULL){ |
496 |
< |
sprintf( painCave.errMsg, |
497 |
< |
"error in reading postition z from %s\n", |
498 |
< |
inFileName.c_str()); |
499 |
< |
return strdup( painCave.errMsg ); |
500 |
< |
} |
501 |
< |
pos[2] = atof( foo ); |
502 |
< |
|
503 |
< |
|
504 |
< |
// get the velocities |
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 ); |
512 |
< |
} |
513 |
< |
vel[0] = atof( foo ); |
514 |
< |
|
515 |
< |
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 ); |
523 |
< |
|
524 |
< |
foo = strtok(NULL, " ,;\t"); |
525 |
< |
if(foo == NULL){ |
526 |
< |
sprintf( painCave.errMsg, |
527 |
< |
"error in reading velocity x from %s\n", |
528 |
< |
inFileName.c_str() ); |
529 |
< |
return strdup( painCave.errMsg ); |
530 |
< |
} |
531 |
< |
vel[2] = atof( foo ); |
532 |
< |
|
533 |
< |
|
534 |
< |
// add the positions and velocities to the atom |
535 |
< |
|
536 |
< |
sd->setPos( pos ); |
537 |
< |
sd->setVel( vel ); |
538 |
< |
|
539 |
< |
if (!sd->isDirectional()) |
540 |
< |
return NULL; |
541 |
< |
|
542 |
< |
// get the quaternions |
543 |
< |
|
544 |
< |
if( sd->isDirectional() ){ |
545 |
< |
|
546 |
< |
foo = strtok(NULL, " ,;\t"); |
547 |
< |
if(foo == NULL){ |
548 |
< |
sprintf( painCave.errMsg, |
549 |
< |
"error in reading velocity x from %s\n", |
550 |
< |
inFileName.c_str() ); |
551 |
< |
return strdup( painCave.errMsg ); |
552 |
< |
} |
553 |
< |
q[0] = atof( foo ); |
554 |
< |
|
555 |
< |
foo = strtok(NULL, " ,;\t"); |
556 |
< |
if(foo == NULL){ |
557 |
< |
sprintf( painCave.errMsg, |
558 |
< |
"error in reading velocity x from %s\n", |
559 |
< |
inFileName.c_str() ); |
560 |
< |
return strdup( painCave.errMsg ); |
561 |
< |
} |
562 |
< |
q[1] = atof( foo ); |
563 |
< |
|
564 |
< |
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 ); |
572 |
< |
|
573 |
< |
foo = strtok(NULL, " ,;\t"); |
574 |
< |
if(foo == NULL){ |
575 |
< |
sprintf( painCave.errMsg, |
576 |
< |
"error in reading velocity x from %s\n", |
577 |
< |
inFileName.c_str() ); |
578 |
< |
return strdup( painCave.errMsg ); |
579 |
< |
} |
580 |
< |
q[3] = atof( foo ); |
581 |
< |
|
582 |
< |
// get the angular velocities |
583 |
< |
|
584 |
< |
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 ); |
592 |
< |
|
593 |
< |
foo = strtok(NULL, " ,;\t"); |
594 |
< |
if(foo == NULL){ |
595 |
< |
sprintf( painCave.errMsg, |
596 |
< |
"error in reading velocity x from %s\n", |
597 |
< |
inFileName.c_str() ); |
598 |
< |
return strdup( painCave.errMsg ); |
599 |
< |
} |
600 |
< |
ji[1] = atof(foo ); |
601 |
< |
|
602 |
< |
foo = strtok(NULL, " ,;\t"); |
603 |
< |
if(foo == NULL){ |
604 |
< |
sprintf( painCave.errMsg, |
605 |
< |
"error in reading velocity x from %s\n", |
606 |
< |
inFileName.c_str() ); |
607 |
< |
return strdup( painCave.errMsg ); |
608 |
< |
} |
609 |
< |
ji[2] = atof( foo ); |
610 |
< |
|
611 |
< |
|
612 |
< |
// check that the quaternion vector is normalized |
613 |
< |
|
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); |
620 |
< |
} |
621 |
< |
|
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 ); |
499 |
> |
std::string propertyName = tokenizer.nextToken(); |
500 |
> |
if (propertyName == "Time") { |
501 |
> |
RealType currTime = tokenizer.nextTokenAsDouble(); |
502 |
> |
s->setTime(currTime); |
503 |
> |
} else if (propertyName == "Hmat"){ |
504 |
> |
Mat3x3d hmat; |
505 |
> |
hmat(0, 0) = tokenizer.nextTokenAsDouble(); |
506 |
> |
hmat(0, 1) = tokenizer.nextTokenAsDouble(); |
507 |
> |
hmat(0, 2) = tokenizer.nextTokenAsDouble(); |
508 |
> |
hmat(1, 0) = tokenizer.nextTokenAsDouble(); |
509 |
> |
hmat(1, 1) = tokenizer.nextTokenAsDouble(); |
510 |
> |
hmat(1, 2) = tokenizer.nextTokenAsDouble(); |
511 |
> |
hmat(2, 0) = tokenizer.nextTokenAsDouble(); |
512 |
> |
hmat(2, 1) = tokenizer.nextTokenAsDouble(); |
513 |
> |
hmat(2, 2) = tokenizer.nextTokenAsDouble(); |
514 |
> |
s->setHmat(hmat); |
515 |
> |
} else if (propertyName == "Thermostat") { |
516 |
> |
RealType chi = tokenizer.nextTokenAsDouble(); |
517 |
> |
RealType integralOfChiDt = tokenizer.nextTokenAsDouble(); |
518 |
> |
s->setChi(chi); |
519 |
> |
s->setIntegralOfChiDt(integralOfChiDt); |
520 |
> |
} else if (propertyName == "Barostat") { |
521 |
> |
Mat3x3d eta; |
522 |
> |
eta(0, 0) = tokenizer.nextTokenAsDouble(); |
523 |
> |
eta(0, 1) = tokenizer.nextTokenAsDouble(); |
524 |
> |
eta(0, 2) = tokenizer.nextTokenAsDouble(); |
525 |
> |
eta(1, 0) = tokenizer.nextTokenAsDouble(); |
526 |
> |
eta(1, 1) = tokenizer.nextTokenAsDouble(); |
527 |
> |
eta(1, 2) = tokenizer.nextTokenAsDouble(); |
528 |
> |
eta(2, 0) = tokenizer.nextTokenAsDouble(); |
529 |
> |
eta(2, 1) = tokenizer.nextTokenAsDouble(); |
530 |
> |
eta(2, 2) = tokenizer.nextTokenAsDouble(); |
531 |
> |
s->setEta(eta); |
532 |
> |
} else { |
533 |
> |
sprintf(painCave.errMsg, |
534 |
> |
"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str()); |
535 |
> |
painCave.isFatal = 0; |
536 |
> |
simError(); |
537 |
|
} |
697 |
– |
integralOfChidt = atof( foo ); |
538 |
|
|
699 |
– |
//push chi and integralOfChidt into SimInfo::properties which can be |
700 |
– |
//retrieved by integrator later |
701 |
– |
DoubleGenericData* chiValue = new DoubleGenericData(); |
702 |
– |
chiValue->setID(CHIVALUE_ID); |
703 |
– |
chiValue->setData(chi); |
704 |
– |
entry_plug->addProperty(chiValue); |
705 |
– |
|
706 |
– |
DoubleGenericData* integralOfChidtValue = new DoubleGenericData(); |
707 |
– |
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
708 |
– |
integralOfChidtValue->setData(integralOfChidt); |
709 |
– |
entry_plug->addProperty(integralOfChidtValue); |
710 |
– |
|
539 |
|
} |
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 |
– |
} |
540 |
|
|
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); |
541 |
|
} |
542 |
|
|
543 |
< |
|
544 |
< |
MPI_Finalize(); |
756 |
< |
exit (0); |
757 |
< |
|
758 |
< |
} |
759 |
< |
|
760 |
< |
void DumpReader::anonymousNodeDie( void ){ |
761 |
< |
|
762 |
< |
MPI_Finalize(); |
763 |
< |
exit (0); |
764 |
< |
} |
765 |
< |
#endif |
543 |
> |
|
544 |
> |
}//end namespace oopse |