| 1 |
< |
#include "ZConsReader.hpp" |
| 2 |
< |
#include "simError.h" |
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
| 4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
| 8 |
> |
* |
| 9 |
> |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
> |
* publication of scientific results based in part on use of the |
| 11 |
> |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
> |
* the article in which the program was described (Matthew |
| 13 |
> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
> |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
> |
* |
| 18 |
> |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
> |
* notice, this list of conditions and the following disclaimer. |
| 20 |
> |
* |
| 21 |
> |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
> |
* documentation and/or other materials provided with the |
| 24 |
> |
* distribution. |
| 25 |
> |
* |
| 26 |
> |
* This software is provided "AS IS," without a warranty of any |
| 27 |
> |
* kind. All express or implied conditions, representations and |
| 28 |
> |
* warranties, including any implied warranty of merchantability, |
| 29 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
> |
* be liable for any damages suffered by licensee as a result of |
| 32 |
> |
* using, modifying or distributing the software or its |
| 33 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
> |
* damages, however caused and regardless of the theory of liability, |
| 37 |
> |
* arising out of the use of or inability to use software, even if the |
| 38 |
> |
* University of Notre Dame has been advised of the possibility of |
| 39 |
> |
* such damages. |
| 40 |
> |
*/ |
| 41 |
> |
|
| 42 |
> |
#include "io/ZConsReader.hpp" |
| 43 |
> |
#include "utils/simError.h" |
| 44 |
> |
#include "utils/StringUtils.hpp" |
| 45 |
> |
namespace oopse { |
| 46 |
|
|
| 47 |
< |
ZConsReader::ZConsReader(SimInfo* info) |
| 5 |
< |
:istream(NULL){ |
| 47 |
> |
ZConsReader::ZConsReader(SimInfo* info) : info_(info){ |
| 48 |
|
|
| 49 |
< |
GenericData* data; |
| 50 |
< |
StringData* filename; |
| 9 |
< |
this->info = info; |
| 49 |
> |
std::string zconsFileName_ = getPrefix(info_->getFinalConfigFileName()) + ".fz"; |
| 50 |
> |
istream_.open(zconsFileName_.c_str()); |
| 51 |
|
|
| 52 |
< |
//retrieve output filename of z force |
| 53 |
< |
data = info->getProperty(ZCONSFILENAME_ID); |
| 54 |
< |
if(!data) { |
| 14 |
< |
|
| 15 |
< |
|
| 16 |
< |
sprintf( painCave.errMsg, |
| 17 |
< |
"ZConsReader error: If you use an ZConstraint\n" |
| 18 |
< |
" , you must set output filename of z-force.\n"); |
| 19 |
< |
painCave.isFatal = 1; |
| 20 |
< |
simError(); |
| 21 |
< |
|
| 22 |
< |
} |
| 23 |
< |
else{ |
| 24 |
< |
|
| 25 |
< |
filename = dynamic_cast<StringData*>(data); |
| 26 |
< |
|
| 27 |
< |
if(!filename){ |
| 28 |
< |
|
| 29 |
< |
sprintf( painCave.errMsg, |
| 30 |
< |
"ZConsReader error: Can not get property from SimInfo\n"); |
| 31 |
< |
painCave.isFatal = 1; |
| 32 |
< |
simError(); |
| 33 |
< |
|
| 52 |
> |
if (!istream_){ |
| 53 |
> |
std::cerr << "open " << zconsFileName_ << "error" << std::endl; |
| 54 |
> |
exit(1); |
| 55 |
|
} |
| 35 |
– |
else{ |
| 36 |
– |
zconsFileName = filename->getData(); |
| 37 |
– |
} |
| 38 |
– |
|
| 39 |
– |
} |
| 56 |
|
|
| 57 |
< |
istream = new ifstream(zconsFileName.c_str()); |
| 58 |
< |
|
| 59 |
< |
if (!istream){ |
| 60 |
< |
cerr << "open " << filename << "error" << endl; |
| 61 |
< |
exit(1); |
| 62 |
< |
} |
| 47 |
< |
|
| 48 |
< |
readHeader(); |
| 57 |
> |
Globals* simParam = info_->getSimParams(); |
| 58 |
> |
int nZconstraints = simParam->getNzConstraints(); |
| 59 |
> |
ZconStamp** stamp = simParam->getZconStamp(); |
| 60 |
> |
for (int i = 0; i < nZconstraints; i++){ |
| 61 |
> |
allZmols_.push_back(stamp[i]->getMolIndex()); |
| 62 |
> |
} |
| 63 |
|
} |
| 64 |
|
|
| 51 |
– |
ZConsReader::ZConsReader(const string& filename){ |
| 52 |
– |
istream = new ifstream(zconsFileName.c_str()); |
| 53 |
– |
|
| 54 |
– |
if (!istream){ |
| 55 |
– |
cerr << "open " << filename << "error" << endl; |
| 56 |
– |
exit(1); |
| 57 |
– |
} |
| 58 |
– |
|
| 59 |
– |
readHeader(); |
| 60 |
– |
} |
| 61 |
– |
|
| 65 |
|
ZConsReader::~ZConsReader(){ |
| 66 |
< |
istream->close(); |
| 66 |
> |
istream_.close(); |
| 67 |
|
} |
| 68 |
|
|
| 69 |
< |
int ZConsReader::getNumZMol(){ |
| 70 |
< |
return nZMol; |
| 71 |
< |
} |
| 69 |
> |
void ZConsReader::readNextFrame(){ |
| 70 |
> |
char line[MAXBUFFERSIZE]; |
| 71 |
> |
int nFixedZmol; |
| 72 |
> |
int sscanfCount; |
| 73 |
|
|
| 74 |
< |
vector<int> ZConsReader::getZConsIndex(){ |
| 71 |
< |
return index; |
| 72 |
< |
} |
| 74 |
> |
fixedZmolData_.clear(); |
| 75 |
|
|
| 76 |
< |
vector<double> ZConsReader::getZConsPos(){ |
| 77 |
< |
return zconsPos; |
| 78 |
< |
} |
| 76 |
> |
while(istream_.getline(line, MAXBUFFERSIZE) && line[0] == '/' && line[1] == '/'); |
| 77 |
> |
sscanfCount = sscanf(line, "%lf", &curTime_); |
| 78 |
> |
if (sscanfCount != 1){ |
| 79 |
> |
std::cerr << "ZConsReader Error : reading file error" << std::endl; |
| 80 |
> |
exit(1); |
| 81 |
> |
} |
| 82 |
|
|
| 83 |
< |
//double ZConsReader::getKRatio(){ |
| 84 |
< |
// return kRatio; |
| 85 |
< |
//} |
| 86 |
< |
|
| 87 |
< |
double ZConsReader::getCurTime(){ |
| 83 |
< |
return curTime; |
| 84 |
< |
} |
| 85 |
< |
|
| 86 |
< |
vector<double> ZConsReader::getCurZPos(){ |
| 87 |
< |
return curZPos; |
| 88 |
< |
} |
| 89 |
< |
|
| 90 |
< |
vector<double> ZConsReader::getCurFZ(){ |
| 91 |
< |
return curFZ; |
| 92 |
< |
} |
| 93 |
< |
|
| 94 |
< |
void ZConsReader::readHeader(){ |
| 95 |
< |
const int MAXBUFFERSIZE = 2000; |
| 96 |
< |
char line[MAXBUFFERSIZE]; |
| 97 |
< |
int zmolIndex; |
| 98 |
< |
float zmolPos; |
| 99 |
< |
int sscanfCount; |
| 100 |
< |
|
| 101 |
< |
istream->getline(line, MAXBUFFERSIZE); |
| 102 |
< |
|
| 103 |
< |
cout << line << endl; |
| 104 |
< |
//skip the comment lines |
| 105 |
< |
while(line[0] == '#') |
| 106 |
< |
istream->getline(line, MAXBUFFERSIZE); |
| 107 |
< |
|
| 108 |
< |
sscanfCount = sscanf(line, "%d", &nZMol); |
| 109 |
< |
|
| 110 |
< |
if (sscanfCount != 1){ |
| 111 |
< |
cerr << "ZConsReader Error : reading file error" << endl; |
| 112 |
< |
exit(1); |
| 113 |
< |
} |
| 114 |
< |
|
| 115 |
< |
for(int i = 0 ; i < nZMol; i++){ |
| 116 |
< |
|
| 117 |
< |
istream->getline(line, MAXBUFFERSIZE); |
| 118 |
< |
|
| 119 |
< |
sscanfCount = sscanf(line, "%d\t%f", &zmolIndex, &zmolPos); |
| 120 |
< |
if (sscanfCount != 2){ |
| 121 |
< |
cerr << "ZConsReader Error : reading file error" << endl; |
| 122 |
< |
exit(1); |
| 83 |
> |
istream_.getline(line, MAXBUFFERSIZE); |
| 84 |
> |
sscanfCount = sscanf(line, "%d", &nFixedZmol); |
| 85 |
> |
if (sscanfCount != 1){ |
| 86 |
> |
std::cerr << "ZConsReader Error : reading file error" << std::endl; |
| 87 |
> |
exit(1); |
| 88 |
|
} |
| 124 |
– |
|
| 125 |
– |
index.push_back(zmolIndex); |
| 126 |
– |
zconsPos.push_back(zmolPos); |
| 127 |
– |
} |
| 89 |
|
|
| 90 |
< |
curZPos.resize(nZMol); |
| 91 |
< |
curFZ.resize(nZMol); |
| 92 |
< |
} |
| 90 |
> |
ZconsData data; |
| 91 |
> |
for(int i = 0; i < nFixedZmol; i++){ |
| 92 |
> |
istream_.getline(line, MAXBUFFERSIZE); |
| 93 |
> |
sscanfCount = sscanf(line, "%d\t%lf\t%lf\t%lf", &data.zmolIndex, &data.zforce, &data.zpos,&data.zconsPos); |
| 94 |
> |
if (sscanfCount != 4){ |
| 95 |
> |
std::cerr << "ZConsReader Error : reading file error" << std::endl; |
| 96 |
> |
exit(1); |
| 97 |
> |
} |
| 98 |
|
|
| 99 |
< |
void ZConsReader::readNextFrame(){ |
| 134 |
< |
const int MAXBUFFERSIZE = 2000; |
| 135 |
< |
char line[MAXBUFFERSIZE]; |
| 136 |
< |
int tempNZMol; |
| 137 |
< |
int sscanfCount; |
| 138 |
< |
int tempIndex; |
| 139 |
< |
float tempCurTime; |
| 140 |
< |
float tempFZ; |
| 141 |
< |
float tempCurZPos; |
| 142 |
< |
float tempZconsPos; |
| 143 |
< |
|
| 144 |
< |
istream->getline(line, MAXBUFFERSIZE); |
| 145 |
< |
sscanfCount = sscanf(line, "%f", &tempCurTime); |
| 146 |
< |
if (sscanfCount != 1){ |
| 147 |
< |
cerr << "ZConsReader Error : reading file error" << endl; |
| 148 |
< |
exit(1); |
| 149 |
< |
} |
| 150 |
< |
curTime = tempCurTime; |
| 151 |
< |
|
| 152 |
< |
istream->getline(line, MAXBUFFERSIZE); |
| 153 |
< |
sscanfCount = sscanf(line, "%d", &tempNZMol); |
| 154 |
< |
if (sscanfCount != 1){ |
| 155 |
< |
cerr << "ZConsReader Error : reading file error" << endl; |
| 156 |
< |
exit(1); |
| 157 |
< |
} |
| 158 |
< |
|
| 159 |
< |
if (tempNZMol != nZMol){ |
| 160 |
< |
cerr << "ZConsReader Error: reading file error" << endl; |
| 161 |
< |
exit(1); |
| 162 |
< |
} |
| 163 |
< |
|
| 164 |
< |
for(int i = 0; i < nZMol; i++){ |
| 165 |
< |
istream->getline(line, MAXBUFFERSIZE); |
| 166 |
< |
sscanfCount = sscanf(line, "%d\t%f\t%f\t%f", &tempIndex, &tempFZ, &tempCurZPos,&tempZconsPos); |
| 167 |
< |
if (sscanfCount != 4){ |
| 168 |
< |
cerr << "ZConsReader Error : reading file error" << endl; |
| 169 |
< |
exit(1); |
| 99 |
> |
fixedZmolData_.push_back(data); |
| 100 |
|
} |
| 101 |
|
|
| 172 |
– |
index[i] = tempIndex; |
| 173 |
– |
curFZ[i] = tempFZ; |
| 174 |
– |
curZPos[i]= tempCurZPos; |
| 175 |
– |
zconsPos[i] = tempZconsPos; |
| 176 |
– |
} |
| 177 |
– |
|
| 102 |
|
} |
| 103 |
|
|
| 104 |
|
bool ZConsReader::hasNextFrame(){ |
| 105 |
< |
return istream->peek() != EOF ? true : false; |
| 105 |
> |
return istream_.peek() != EOF ? true : false; |
| 106 |
|
} |
| 107 |
|
|
| 108 |
+ |
} |
