4 |
|
#include <iostream> |
5 |
|
#include <fstream> |
6 |
|
|
7 |
< |
#include <cstring> |
8 |
< |
#include <cstdio> |
9 |
< |
#include <cstdlib> |
7 |
> |
#include <string.h> |
8 |
> |
#include <stdio.h> |
9 |
> |
#include <stdlib.h> |
10 |
> |
#include <unistd.h> |
11 |
> |
#include <sys/types.h> |
12 |
> |
#include <sys/stat.h> |
13 |
|
|
14 |
+ |
|
15 |
|
#include "Atom.hpp" |
16 |
|
#include "SimInfo.hpp" |
17 |
|
#include "Thermo.hpp" |
18 |
|
|
19 |
|
using namespace std; |
20 |
|
|
21 |
+ |
class FilePos{ |
22 |
+ |
|
23 |
+ |
public: |
24 |
+ |
FilePos(){ |
25 |
+ |
myPos = NULL; |
26 |
+ |
next = NULL; |
27 |
+ |
} |
28 |
+ |
FilePos( fpos_t* thePos ) { |
29 |
+ |
myPos = thePos; |
30 |
+ |
next = NULL; |
31 |
+ |
} |
32 |
+ |
~FilePos(){ |
33 |
+ |
if( next != NULL ) delete next; |
34 |
+ |
if( myPos != NULL ) delete myPos; |
35 |
+ |
} |
36 |
+ |
|
37 |
+ |
void add( fpos_t *thePos ){ |
38 |
+ |
if( next != NULL ) |
39 |
+ |
next->add( thePos ); |
40 |
+ |
else |
41 |
+ |
next = new FilePos( thePos ); |
42 |
+ |
} |
43 |
+ |
|
44 |
+ |
FilePos &operator=(fpos_t *thePos){ myPos = thePos; return *this; } |
45 |
+ |
|
46 |
+ |
void setPos( fpos_t *thePos ){ myPos = thePos; } |
47 |
+ |
fpos_t *getPos( void ){ return myPos; } |
48 |
+ |
|
49 |
+ |
FilePos* getNext( void ) { return next; } |
50 |
+ |
private: |
51 |
+ |
|
52 |
+ |
fpos_t *myPos; |
53 |
+ |
FilePos* next; |
54 |
+ |
|
55 |
+ |
}; |
56 |
+ |
|
57 |
|
class DumpWriter{ |
58 |
|
|
59 |
|
public: |
61 |
|
~DumpWriter(); |
62 |
|
|
63 |
|
void writeDump( double currentTime ); |
64 |
< |
void writeFinal( double finalTime ); |
64 |
> |
void writeFinal( double currentTime); |
65 |
> |
void writeFrame( vector<ofstream*>& outFile, double finalTime ); |
66 |
|
|
67 |
+ |
#ifdef IS_MPI |
68 |
+ |
void update(); |
69 |
+ |
#endif |
70 |
+ |
|
71 |
|
private: |
72 |
+ |
|
73 |
+ |
#ifdef IS_MPI |
74 |
+ |
void sortByGlobalIndex(); |
75 |
+ |
#endif |
76 |
+ |
|
77 |
|
SimInfo* entry_plug; |
78 |
< |
ofstream outFile; |
79 |
< |
char outName[500]; |
78 |
> |
ofstream dumpFile; |
79 |
> |
ofstream finalOut; |
80 |
> |
|
81 |
> |
#ifdef IS_MPI |
82 |
> |
vector<pair<int, int> > indexArray; |
83 |
> |
#endif |
84 |
|
}; |
85 |
|
|
86 |
|
class StatWriter{ |
90 |
|
~StatWriter(); |
91 |
|
|
92 |
|
void writeStat( double currentTime ); |
93 |
< |
|
93 |
> |
|
94 |
|
private: |
95 |
< |
|
95 |
> |
|
96 |
|
SimInfo* entry_plug; |
97 |
|
ofstream outFile; |
98 |
|
char outName[500]; |
106 |
|
InitializeFromFile( char *in_name ); |
107 |
|
~InitializeFromFile(); |
108 |
|
|
109 |
< |
void read_xyz( SimInfo* the_entry_plug ); |
110 |
< |
|
109 |
> |
void readInit( SimInfo* the_entry_plug ); |
110 |
> |
|
111 |
|
private: |
112 |
|
char* parseDumpLine(char* line, int atomIndex); |
113 |
+ |
char* parseCommentLine(char* line, SimInfo* entry_plug); |
114 |
|
FILE *c_in_file; |
115 |
|
char c_in_name[500]; |
116 |
< |
SimInfo* entry_plug; |
116 |
> |
SimInfo* simnfo; |
117 |
|
}; |
118 |
|
|
119 |
+ |
class DumpReader{ |
120 |
|
|
121 |
+ |
public: |
122 |
+ |
DumpReader( char *in_name ); |
123 |
+ |
~DumpReader(); |
124 |
|
|
125 |
+ |
int getNframes(); |
126 |
+ |
void scanFile( void ); |
127 |
+ |
|
128 |
+ |
void getNextFrame() {} |
129 |
+ |
void readFrame(SimInfo* the_simnfo, int whichFrame); |
130 |
+ |
|
131 |
+ |
private: |
132 |
+ |
|
133 |
+ |
void readSet( int whichFrame ); |
134 |
+ |
char* parseDumpLine(char* line, int atomIndex); |
135 |
+ |
char* parseCommentLine(char* line, double &time, double boxMat[9] ); |
136 |
+ |
FILE *inFile; |
137 |
+ |
char inName[500]; |
138 |
+ |
bool isScanned; |
139 |
+ |
int nFrames; |
140 |
+ |
|
141 |
+ |
FilePos** frameStart; |
142 |
+ |
FilePos* headFP; |
143 |
+ |
|
144 |
+ |
SimInfo *simnfo; |
145 |
+ |
}; |
146 |
+ |
|
147 |
+ |
|
148 |
+ |
|
149 |
|
#endif |