applications/dump2Xyz/Dump2XYZ.cpp

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

#include "brains/SimSetup.hpp"
#include "applications/dump2Xyz/Dump2XYZCmd.h"
#include "visitors/AtomVisitor.hpp"
#include "visitors/CompositeVisitor.hpp"
#include "visitors/RigidBodyVisitor.hpp"
#include "visitors/OtherVisitor.hpp"
#include "visitors/ZconsVisitor.hpp"

using namespace std;

int main(int argc, char* argv[]){
  gengetopt_args_info args_info;
  string dumpFileName;
  string mdFileName;
  char inFileName[2002];
  string xyzFileName;
  SimInfo* info;
  SimSetup startMe;
  DumpReader* dumpReader;
  ofstream xyzStream;
  int nframes;
  Molecule* mol;  
  vector<StuntDouble*> integrableObjects;
  vector<StuntDouble*>::iterator iter;
  vector<RigidBody*> myRigidBodies;
  vector<RigidBody*>::iterator rbIter;
  
  CompositeVisitor* compositeVisitor;
  SSDAtomVisitor* ssdVisitor;
  LinearAtomVisitor* linearVisitor;
  DefaultAtomVisitor* defaultAtomVisitor;
  LipidHeadVisitor* lipidVisitor;
  RBCOMVisitor* rbCOMVisitor;
  ReplicateVisitor* replicateVisitor;
  WrappingVisitor* wrappingVisitor;
  IgnoreVisitor* ignoreVisitor;
  XYZVisitor* xyzVisitor;
  ZConsVisitor* zconsVisitor;
  PrepareVisitor* prepareVisitor;
  WaterTypeVisitor* waterTypeVisitor;
  
  //parse the command line option
    if (cmdline_parser (argc, argv, &args_info) != 0)
      exit(1) ;


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

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

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

  strcpy(inFileName, mdFileName.c_str() );
  startMe.parseFile( inFileName );

  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
  if(args_info.rigidbody_flag){
    rbCOMVisitor = new RBCOMVisitor(info);
    compositeVisitor->addVisitor(rbCOMVisitor, 900);
  }

  //compositeVisitor->addVisitor(lipidVisitor, 900);

  //creat SSD atom visitor
  ssdVisitor = new SSDAtomVisitor(info);
  compositeVisitor->addVisitor(ssdVisitor, 800);
  linearVisitor = new LinearAtomVisitor(info);
  compositeVisitor->addVisitor(linearVisitor, 750);

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

  //creat waterType visitor
  if(args_info.watertype_flag){
    waterTypeVisitor = new WaterTypeVisitor;
    compositeVisitor->addVisitor(waterTypeVisitor, 600);
  }

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

    if(zconsVisitor->haveZconsMol())
      compositeVisitor->addVisitor(zconsVisitor, 500);
    else
      delete zconsVisitor;
  }

  //creat wrapping visitor

  if(args_info.periodicBox_flag){
    wrappingVisitor = new WrappingVisitor(info);
    compositeVisitor->addVisitor(wrappingVisitor, 400);
  }
  
  //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, 300);
  }

  //creat xyzVisitor
  xyzVisitor = new XYZVisitor(info);
  compositeVisitor->addVisitor(xyzVisitor, 200);

  cout << compositeVisitor->toString();

  //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;

    //update atoms of rigidbody
    for(int j = 0; j < info->n_mol; j++){
      myRigidBodies = mol[j].getMyRigidBodies();

      for(rbIter = myRigidBodies.begin(); rbIter != myRigidBodies.end(); ++rbIter)
        (*rbIter)->updateAtoms();
    }    

    
    //prepare visit
    for(int j = 0; j < info->n_mol; j++){
      integrableObjects = mol[j].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[j].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:	1718
Committed:	Fri Nov 5 21:45:14 2004 UTC (19 years, 8 months ago) by chrisfen
File size:	5919 byte(s)
Log Message:	Added the linear visitor
#	User	Rev	Content
1	tim	1501	#include <iostream>
2			#include <fstream>
3			#include <string>
4
5			#include "brains/SimSetup.hpp"
6			#include "applications/dump2Xyz/Dump2XYZCmd.h"
7			#include "visitors/AtomVisitor.hpp"
8			#include "visitors/CompositeVisitor.hpp"
9			#include "visitors/RigidBodyVisitor.hpp"
10			#include "visitors/OtherVisitor.hpp"
11			#include "visitors/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 mdFileName;
19			char inFileName[2002];
20			string xyzFileName;
21			SimInfo* info;
22			SimSetup startMe;
23			DumpReader* dumpReader;
24			ofstream xyzStream;
25			int nframes;
26			Molecule* mol;
27			vector<StuntDouble*> integrableObjects;
28			vector<StuntDouble*>::iterator iter;
29			vector<RigidBody*> myRigidBodies;
30			vector<RigidBody*>::iterator rbIter;
31
32			CompositeVisitor* compositeVisitor;
33			SSDAtomVisitor* ssdVisitor;
34	chrisfen	1718	LinearAtomVisitor* linearVisitor;
35	tim	1501	DefaultAtomVisitor* defaultAtomVisitor;
36			LipidHeadVisitor* lipidVisitor;
37			RBCOMVisitor* rbCOMVisitor;
38			ReplicateVisitor* replicateVisitor;
39			WrappingVisitor* wrappingVisitor;
40			IgnoreVisitor* ignoreVisitor;
41			XYZVisitor* xyzVisitor;
42			ZConsVisitor* zconsVisitor;
43			PrepareVisitor* prepareVisitor;
44			WaterTypeVisitor* waterTypeVisitor;
45
46			//parse the command line option
47			if (cmdline_parser (argc, argv, &args_info) != 0)
48			exit(1) ;
49
50
51			//get the dumpfile name and meta-data file name
52			if (args_info.input_given){
53			dumpFileName = args_info.input_arg;
54			}
55			else{
56			cerr << "Does not have input file name" << endl;
57			exit(1);
58			}
59			mdFileName = dumpFileName;
60			mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
61
62			if (args_info.output_given){
63			xyzFileName = args_info.output_arg;
64			}
65			else{
66			xyzFileName = dumpFileName;
67			xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
68			}
69
70			//parse md file and set up the system
71			info = new SimInfo();
72			startMe.setSimInfo(info );
73
74			strcpy(inFileName, mdFileName.c_str() );
75			startMe.parseFile( inFileName );
76
77			startMe.createSim();
78
79
80			//creat visitor list
81			compositeVisitor = new CompositeVisitor();
82
83			//creat ignore visitor
84			if(args_info.ignore_given \|\|args_info.water_flag){
85
86			ignoreVisitor = new IgnoreVisitor();
87
88			for(int i = 0; i < args_info.ignore_given; i++)
89			ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
90
91			//ignore water
92			if(args_info.water_flag){
93			ignoreVisitor->addIgnoreType("SSD");
94			ignoreVisitor->addIgnoreType("SSD1");
95			ignoreVisitor->addIgnoreType("SSD_E");
96			ignoreVisitor->addIgnoreType("SSD_RF");
97			ignoreVisitor->addIgnoreType("TIP3P_RB_0");
98			ignoreVisitor->addIgnoreType("TIP4P_RB_0");
99			ignoreVisitor->addIgnoreType("TIP5P_RB_0");
100			ignoreVisitor->addIgnoreType("SPCE_RB_0");
101			ignoreVisitor->addIgnoreType("DPD_RB_0");
102			}
103
104			compositeVisitor->addVisitor(ignoreVisitor, 1000);
105			}
106
107			//creat RigidBody Visitor
108			if(args_info.rigidbody_flag){
109			rbCOMVisitor = new RBCOMVisitor(info);
110			compositeVisitor->addVisitor(rbCOMVisitor, 900);
111			}
112
113			//compositeVisitor->addVisitor(lipidVisitor, 900);
114
115			//creat SSD atom visitor
116			ssdVisitor = new SSDAtomVisitor(info);
117			compositeVisitor->addVisitor(ssdVisitor, 800);
118	chrisfen	1718	linearVisitor = new LinearAtomVisitor(info);
119			compositeVisitor->addVisitor(linearVisitor, 750);
120	tim	1501
121			//creat default atom visitor
122			defaultAtomVisitor = new DefaultAtomVisitor(info);
123			compositeVisitor->addVisitor(defaultAtomVisitor, 700);
124
125			//creat waterType visitor
126			if(args_info.watertype_flag){
127			waterTypeVisitor = new WaterTypeVisitor;
128			compositeVisitor->addVisitor(waterTypeVisitor, 600);
129			}
130
131			//create ZconsVisitor
132			if(args_info.zconstraint_flag){
133
134			zconsVisitor = new ZConsVisitor(info);
135
136			if(zconsVisitor->haveZconsMol())
137			compositeVisitor->addVisitor(zconsVisitor, 500);
138			else
139			delete zconsVisitor;
140			}
141
142			//creat wrapping visitor
143
144			if(args_info.periodicBox_flag){
145			wrappingVisitor = new WrappingVisitor(info);
146			compositeVisitor->addVisitor(wrappingVisitor, 400);
147			}
148
149			//creat replicate visitor
150			if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
151			IntVec3 replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
152			replicateVisitor = new ReplicateVisitor(info, replicateOpt);
153			compositeVisitor->addVisitor(replicateVisitor, 300);
154			}
155
156			//creat xyzVisitor
157			xyzVisitor = new XYZVisitor(info);
158			compositeVisitor->addVisitor(xyzVisitor, 200);
159
160			cout << compositeVisitor->toString();
161
162			//creat prepareVisitor
163			prepareVisitor = new PrepareVisitor();
164
165			//open dump file
166			dumpReader = new DumpReader(dumpFileName.c_str());
167			nframes = dumpReader->getNframes();
168
169			xyzStream .open(xyzFileName.c_str());
170
171			for (int i = 0; i < nframes; i += args_info.frame_arg){
172			dumpReader->readFrame(info, i);
173
174			mol = info->molecules;
175
176			//update atoms of rigidbody
177			for(int j = 0; j < info->n_mol; j++){
178			myRigidBodies = mol[j].getMyRigidBodies();
179
180			for(rbIter = myRigidBodies.begin(); rbIter != myRigidBodies.end(); ++rbIter)
181			(*rbIter)->updateAtoms();
182			}
183
184
185			//prepare visit
186			for(int j = 0; j < info->n_mol; j++){
187			integrableObjects = mol[j].getIntegrableObjects();
188
189			for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
190			(*iter)->accept(prepareVisitor);
191			}
192
193			//update visitor
194			compositeVisitor->update();
195
196			//visit stuntdouble
197			for(int j = 0; j < info->n_mol; j++){
198			integrableObjects = mol[j].getIntegrableObjects();
199
200			for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
201			(*iter)->accept(compositeVisitor);
202			}
203
204			xyzVisitor->writeFrame(xyzStream);
205			xyzVisitor->clear();
206
207			}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
208
209			xyzStream.close();
210
211
212			delete compositeVisitor;
213			delete info;
214
215
216			}