OOPSE/utils/Dump2XYZ.cpp

#include <iostream>
#include <fstream>
#include <string>

#include "SimSetup.hpp"
#include "Dump2XYZCmd.h"
#include "AtomVisitor.hpp"
#include "CompositeVisitor.hpp"
#include "RigidBodyVisitor.hpp"
#include "OtherVisitor.hpp"
#include "ZconsVisitor.hpp"

using namespace std;

int main(int argc, char* argv[]){
  gengetopt_args_info args_info;
  string dumpFileName;
  string bassFileName;
  string xyzFileName;
  SimInfo* info;
  SimSetup startMe;
  DumpReader* dumpReader;
  ofstream xyzStream;
  int nframes;
  Molecule* mol;  
  vector<StuntDouble*> integrableObjects;
  vector<StuntDouble*>::iterator iter;
  
  CompositeVisitor* compositeVisitor;
  SSDAtomVisitor* ssdVisitor;
  DefaultAtomVisitor* defaultAtomVisitor;
  LipidHeadVisitor* lipidVisitor;
  ReplicateVisitor* replicateVisitor;
  WrappingVisitor* wrappingVisitor;
  IgnoreVisitor* ignoreVisitor;
  XYZVisitor* xyzVisitor;
  ZConsVisitor* zconsVisitor;
  PrepareVisitor* prepareVisitor;
  
  //parse the command line option
    if (cmdline_parser (argc, argv, &args_info) != 0)
      exit(1) ;


  //get the dumpfile name and bass file name
  if (args_info.input_given){
    dumpFileName = args_info.input_arg;
  }
  else{
    cerr << "Does not have input file name" << endl;
    exit(1);
  }
  bassFileName = dumpFileName;
  bassFileName = bassFileName.substr(0, bassFileName.rfind(".")) + ".bass";

  if (args_info.output_given){
    xyzFileName = args_info.output_arg;
  }
  else{
    xyzFileName = dumpFileName;
    xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
  }

  //parse bass file and set up the system
  info = new SimInfo();
  startMe.setSimInfo(info );

  startMe.parseFile( bassFileName.c_str());

  startMe.createSim();

  
  //creat visitor list
  compositeVisitor = new CompositeVisitor();

  //creat ignore visitor
  if(args_info.ignore_given ||args_info.water_flag){
    
    ignoreVisitor = new IgnoreVisitor();

    for(int i = 0; i < args_info.ignore_given; i++)
      ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);

    //ignore water 
    if(args_info.water_flag){
      ignoreVisitor->addIgnoreType("SSD");
      ignoreVisitor->addIgnoreType("SSD1");
      ignoreVisitor->addIgnoreType("SSD_E");
      ignoreVisitor->addIgnoreType("SSD_RF");
      ignoreVisitor->addIgnoreType("TIP3P_RB_0");
      ignoreVisitor->addIgnoreType("TIP4P_RB_0");
      ignoreVisitor->addIgnoreType("TIP5P_RB_0");
      ignoreVisitor->addIgnoreType("SPCE_RB_0");      
      ignoreVisitor->addIgnoreType("DPD_RB_0");
    }

     compositeVisitor->addVisitor(ignoreVisitor, 1000);
  }

  //creat RigidBody Visitor
  lipidVisitor = new LipidHeadVisitor(info);

  //adding names of lipid head group
  lipidVisitor->addLipidHeadName("PC_RB_0");
  lipidVisitor->addLipidHeadName("PE_RB_0");

  compositeVisitor->addVisitor(lipidVisitor, 900);

  //creat SSD atom visitor
  ssdVisitor = new SSDAtomVisitor(info);
  compositeVisitor->addVisitor(ssdVisitor, 800);

  //creat default atom visitor
  defaultAtomVisitor = new DefaultAtomVisitor(info);
  compositeVisitor->addVisitor(ssdVisitor, 700);

  //create ZconsVisitor
  if(args_info.replace_given){
    
    zconsVisitor = new ZConsVisitor(info);

    if(zconsVisitor->haveZconsMol())
      compositeVisitor->addVisitor(zconsVisitor, 600);
    else
      delete zconsVisitor;
  }

  //creat wrapping visitor

  if(args_info.periodicBox_flag){
    wrappingVisitor = new WrappingVisitor(info);
    compositeVisitor->addVisitor(wrappingVisitor, 500);
  }
  
  //creat replicate visitor
  if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
    IntVec3 replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
    replicateVisitor = new ReplicateVisitor(info, replicateOpt);
    compositeVisitor->addVisitor(replicateVisitor, 400);
  }

  //creat xyzVisitor
  xyzVisitor = new XYZVisitor(info);
  compositeVisitor->addVisitor(wrappingVisitor, 300);


  //creat prepareVisitor
  prepareVisitor = new PrepareVisitor();

  //open dump file
  dumpReader = new DumpReader(dumpFileName.c_str());
  nframes = dumpReader->getNframes();

  xyzStream .open(xyzFileName.c_str());
  
  for (int i = 0; i < nframes; i += args_info.frame_arg){
    dumpReader->readFrame(info, i);

    mol = info->molecules;
    
    //prepare visit
    for(int j = 0; j < info->n_mol; j++){
      integrableObjects = mol[i].getIntegrableObjects();

      for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
        (*iter)->accept(prepareVisitor);
    }    

    //update visitor
    compositeVisitor->update();
    
    //visit stuntdouble
    for(int j = 0; j < info->n_mol; j++){
      integrableObjects = mol[i].getIntegrableObjects();

      for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
        (*iter)->accept(compositeVisitor);
    }

    xyzVisitor->writeFrame(xyzStream);
    xyzVisitor->clear();
    
  }//end for (int i = 0; i < nframes; i += args_info.frame_arg)

  xyzStream.close();


  delete compositeVisitor;
  delete info;


}
Revision:	1118
Committed:	Mon Apr 19 03:52:27 2004 UTC (20 years, 5 months ago) by tim
File size:	5090 byte(s)
Log Message:	new implement of quickLate using visitor and composite pattern
#	User	Rev	Content
1	tim	1118	#include <iostream>
2			#include <fstream>
3			#include <string>
4
5			#include "SimSetup.hpp"
6			#include "Dump2XYZCmd.h"
7			#include "AtomVisitor.hpp"
8			#include "CompositeVisitor.hpp"
9			#include "RigidBodyVisitor.hpp"
10			#include "OtherVisitor.hpp"
11			#include "ZconsVisitor.hpp"
12
13			using namespace std;
14
15			int main(int argc, char* argv[]){
16			gengetopt_args_info args_info;
17			string dumpFileName;
18			string bassFileName;
19			string xyzFileName;
20			SimInfo* info;
21			SimSetup startMe;
22			DumpReader* dumpReader;
23			ofstream xyzStream;
24			int nframes;
25			Molecule* mol;
26			vector<StuntDouble*> integrableObjects;
27			vector<StuntDouble*>::iterator iter;
28
29			CompositeVisitor* compositeVisitor;
30			SSDAtomVisitor* ssdVisitor;
31			DefaultAtomVisitor* defaultAtomVisitor;
32			LipidHeadVisitor* lipidVisitor;
33			ReplicateVisitor* replicateVisitor;
34			WrappingVisitor* wrappingVisitor;
35			IgnoreVisitor* ignoreVisitor;
36			XYZVisitor* xyzVisitor;
37			ZConsVisitor* zconsVisitor;
38			PrepareVisitor* prepareVisitor;
39
40			//parse the command line option
41			if (cmdline_parser (argc, argv, &args_info) != 0)
42			exit(1) ;
43
44
45			//get the dumpfile name and bass file name
46			if (args_info.input_given){
47			dumpFileName = args_info.input_arg;
48			}
49			else{
50			cerr << "Does not have input file name" << endl;
51			exit(1);
52			}
53			bassFileName = dumpFileName;
54			bassFileName = bassFileName.substr(0, bassFileName.rfind(".")) + ".bass";
55
56			if (args_info.output_given){
57			xyzFileName = args_info.output_arg;
58			}
59			else{
60			xyzFileName = dumpFileName;
61			xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
62			}
63
64			//parse bass file and set up the system
65			info = new SimInfo();
66			startMe.setSimInfo(info );
67
68			startMe.parseFile( bassFileName.c_str());
69
70			startMe.createSim();
71
72
73			//creat visitor list
74			compositeVisitor = new CompositeVisitor();
75
76			//creat ignore visitor
77			if(args_info.ignore_given \|\|args_info.water_flag){
78
79			ignoreVisitor = new IgnoreVisitor();
80
81			for(int i = 0; i < args_info.ignore_given; i++)
82			ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
83
84			//ignore water
85			if(args_info.water_flag){
86			ignoreVisitor->addIgnoreType("SSD");
87			ignoreVisitor->addIgnoreType("SSD1");
88			ignoreVisitor->addIgnoreType("SSD_E");
89			ignoreVisitor->addIgnoreType("SSD_RF");
90			ignoreVisitor->addIgnoreType("TIP3P_RB_0");
91			ignoreVisitor->addIgnoreType("TIP4P_RB_0");
92			ignoreVisitor->addIgnoreType("TIP5P_RB_0");
93			ignoreVisitor->addIgnoreType("SPCE_RB_0");
94			ignoreVisitor->addIgnoreType("DPD_RB_0");
95			}
96
97			compositeVisitor->addVisitor(ignoreVisitor, 1000);
98			}
99
100			//creat RigidBody Visitor
101			lipidVisitor = new LipidHeadVisitor(info);
102
103			//adding names of lipid head group
104			lipidVisitor->addLipidHeadName("PC_RB_0");
105			lipidVisitor->addLipidHeadName("PE_RB_0");
106
107			compositeVisitor->addVisitor(lipidVisitor, 900);
108
109			//creat SSD atom visitor
110			ssdVisitor = new SSDAtomVisitor(info);
111			compositeVisitor->addVisitor(ssdVisitor, 800);
112
113			//creat default atom visitor
114			defaultAtomVisitor = new DefaultAtomVisitor(info);
115			compositeVisitor->addVisitor(ssdVisitor, 700);
116
117			//create ZconsVisitor
118			if(args_info.replace_given){
119
120			zconsVisitor = new ZConsVisitor(info);
121
122			if(zconsVisitor->haveZconsMol())
123			compositeVisitor->addVisitor(zconsVisitor, 600);
124			else
125			delete zconsVisitor;
126			}
127
128			//creat wrapping visitor
129
130			if(args_info.periodicBox_flag){
131			wrappingVisitor = new WrappingVisitor(info);
132			compositeVisitor->addVisitor(wrappingVisitor, 500);
133			}
134
135			//creat replicate visitor
136			if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
137			IntVec3 replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
138			replicateVisitor = new ReplicateVisitor(info, replicateOpt);
139			compositeVisitor->addVisitor(replicateVisitor, 400);
140			}
141
142			//creat xyzVisitor
143			xyzVisitor = new XYZVisitor(info);
144			compositeVisitor->addVisitor(wrappingVisitor, 300);
145
146
147			//creat prepareVisitor
148			prepareVisitor = new PrepareVisitor();
149
150			//open dump file
151			dumpReader = new DumpReader(dumpFileName.c_str());
152			nframes = dumpReader->getNframes();
153
154			xyzStream .open(xyzFileName.c_str());
155
156			for (int i = 0; i < nframes; i += args_info.frame_arg){
157			dumpReader->readFrame(info, i);
158
159			mol = info->molecules;
160
161			//prepare visit
162			for(int j = 0; j < info->n_mol; j++){
163			integrableObjects = mol[i].getIntegrableObjects();
164
165			for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
166			(*iter)->accept(prepareVisitor);
167			}
168
169			//update visitor
170			compositeVisitor->update();
171
172			//visit stuntdouble
173			for(int j = 0; j < info->n_mol; j++){
174			integrableObjects = mol[i].getIntegrableObjects();
175
176			for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
177			(*iter)->accept(compositeVisitor);
178			}
179
180			xyzVisitor->writeFrame(xyzStream);
181			xyzVisitor->clear();
182
183			}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
184
185			xyzStream.close();
186
187
188			delete compositeVisitor;
189			delete info;
190
191
192			}