| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 47 |
|
#ifndef IO_RESTREADER_HPP |
| 48 |
|
#define IO_RESTREADER_HPP |
| 49 |
|
|
| 50 |
< |
#include "io/DumpReader.hpp" |
| 50 |
> |
#include <cstdio> |
| 51 |
> |
#include <string> |
| 52 |
> |
#include "brains/SimInfo.hpp" |
| 53 |
> |
#include "primitives/StuntDouble.hpp" |
| 54 |
|
|
| 55 |
|
namespace OpenMD { |
| 56 |
|
|
| 57 |
|
/** |
| 58 |
|
* @class RestReader RestReader.hpp "io/RestReader.hpp" |
| 59 |
|
*/ |
| 60 |
< |
class RestReader : public DumpReader { |
| 60 |
> |
class RestReader { |
| 61 |
|
public: |
| 62 |
< |
RestReader(SimInfo* info, const std::string &filename) : DumpReader(info, filename){} |
| 63 |
< |
void readReferenceStructure(); |
| 62 |
> |
RestReader(SimInfo* info, const std::string &filename, |
| 63 |
> |
std::vector<int> stuntDoubleIndex) |
| 64 |
> |
: info_(info), filename_(filename), stuntDoubleIndex_(stuntDoubleIndex) { |
| 65 |
> |
#ifdef IS_MPI |
| 66 |
> |
|
| 67 |
> |
if (worldRank == 0) { |
| 68 |
> |
#endif |
| 69 |
> |
|
| 70 |
> |
inFile_ = new std::ifstream(filename_.c_str(), |
| 71 |
> |
ifstream::in | ifstream::binary); |
| 72 |
> |
|
| 73 |
> |
if (inFile_->fail()) { |
| 74 |
> |
sprintf(painCave.errMsg, |
| 75 |
> |
"RestReader: Cannot open file: %s\n", |
| 76 |
> |
filename_.c_str()); |
| 77 |
> |
painCave.isFatal = 1; |
| 78 |
> |
simError(); |
| 79 |
> |
} |
| 80 |
> |
|
| 81 |
> |
#ifdef IS_MPI |
| 82 |
> |
|
| 83 |
> |
} |
| 84 |
> |
|
| 85 |
> |
strcpy(checkPointMsg, "Reference file opened for reading successfully."); |
| 86 |
> |
errorCheckPoint(); |
| 87 |
> |
|
| 88 |
> |
#endif |
| 89 |
> |
|
| 90 |
> |
return; |
| 91 |
> |
} |
| 92 |
> |
|
| 93 |
> |
void readReferenceStructure(void); |
| 94 |
> |
|
| 95 |
> |
~RestReader(){ |
| 96 |
> |
#ifdef IS_MPI |
| 97 |
> |
if (worldRank == 0){ |
| 98 |
> |
#endif |
| 99 |
> |
|
| 100 |
> |
delete inFile_; |
| 101 |
> |
|
| 102 |
> |
#ifdef IS_MPI |
| 103 |
> |
} |
| 104 |
> |
|
| 105 |
> |
strcpy(checkPointMsg, "Reference file closed successfully."); |
| 106 |
> |
errorCheckPoint(); |
| 107 |
> |
#endif |
| 108 |
> |
} |
| 109 |
> |
|
| 110 |
|
protected: |
| 111 |
< |
virtual void parseDumpLine(const std::string&); |
| 112 |
< |
virtual void readFrameProperties(std::istream& inputStream); |
| 111 |
> |
void parseDumpLine(const std::string& line); |
| 112 |
> |
void readStuntDoubles(std::istream& inpuStream); |
| 113 |
> |
void readFrameProperties(std::istream& inputStream); |
| 114 |
> |
void scanFile(void); |
| 115 |
> |
void readSet(void); |
| 116 |
|
private: |
| 117 |
+ |
|
| 118 |
+ |
SimInfo* info_; |
| 119 |
+ |
|
| 120 |
|
std::vector<Vector3d> all_pos_; |
| 121 |
+ |
std::vector<int> stuntDoubleIndex_; |
| 122 |
+ |
|
| 123 |
+ |
std::istream* inFile_; |
| 124 |
+ |
std::string filename_; |
| 125 |
+ |
|
| 126 |
+ |
std::streampos framePos_; |
| 127 |
+ |
|
| 128 |
+ |
const static int bufferSize = 4096; |
| 129 |
+ |
char buffer[bufferSize]; |
| 130 |
|
}; |
| 131 |
|
|
| 132 |
|
} //end namespace OpenMD |
