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;
  vector<RigidBody*> myRigidBodies;
  vector<RigidBody*>::iterator rbIter;
  
  CompositeVisitor* compositeVisitor;
  SSDAtomVisitor* ssdVisitor;
  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 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
  if(args_info.rigidbody_flag){
    rbCOMVisitor = new RBCOMVisitor(info);
    compositeVisitor->addVisitor(rbCOMVisitor, 900);
  }
  //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(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:	1126
Committed:	Tue Apr 20 05:39:38 2004 UTC (20 years, 5 months ago) by tim
File size:	5867 byte(s)
Log Message:	DUMP2XYZ 0.99 version
#	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	tim	1119	vector<RigidBody*> myRigidBodies;
29			vector<RigidBody*>::iterator rbIter;
30	tim	1118
31			CompositeVisitor* compositeVisitor;
32			SSDAtomVisitor* ssdVisitor;
33			DefaultAtomVisitor* defaultAtomVisitor;
34			LipidHeadVisitor* lipidVisitor;
35	tim	1126	RBCOMVisitor* rbCOMVisitor;
36	tim	1118	ReplicateVisitor* replicateVisitor;
37			WrappingVisitor* wrappingVisitor;
38			IgnoreVisitor* ignoreVisitor;
39			XYZVisitor* xyzVisitor;
40			ZConsVisitor* zconsVisitor;
41			PrepareVisitor* prepareVisitor;
42	tim	1126	WaterTypeVisitor* waterTypeVisitor;
43	tim	1118
44			//parse the command line option
45			if (cmdline_parser (argc, argv, &args_info) != 0)
46			exit(1) ;
47
48
49			//get the dumpfile name and bass file name
50			if (args_info.input_given){
51			dumpFileName = args_info.input_arg;
52			}
53			else{
54			cerr << "Does not have input file name" << endl;
55			exit(1);
56			}
57			bassFileName = dumpFileName;
58			bassFileName = bassFileName.substr(0, bassFileName.rfind(".")) + ".bass";
59
60			if (args_info.output_given){
61			xyzFileName = args_info.output_arg;
62			}
63			else{
64			xyzFileName = dumpFileName;
65			xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
66			}
67
68			//parse bass file and set up the system
69			info = new SimInfo();
70			startMe.setSimInfo(info );
71
72			startMe.parseFile( bassFileName.c_str());
73
74			startMe.createSim();
75
76
77			//creat visitor list
78			compositeVisitor = new CompositeVisitor();
79
80			//creat ignore visitor
81			if(args_info.ignore_given \|\|args_info.water_flag){
82
83			ignoreVisitor = new IgnoreVisitor();
84
85			for(int i = 0; i < args_info.ignore_given; i++)
86			ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
87
88			//ignore water
89			if(args_info.water_flag){
90			ignoreVisitor->addIgnoreType("SSD");
91			ignoreVisitor->addIgnoreType("SSD1");
92			ignoreVisitor->addIgnoreType("SSD_E");
93			ignoreVisitor->addIgnoreType("SSD_RF");
94			ignoreVisitor->addIgnoreType("TIP3P_RB_0");
95			ignoreVisitor->addIgnoreType("TIP4P_RB_0");
96			ignoreVisitor->addIgnoreType("TIP5P_RB_0");
97			ignoreVisitor->addIgnoreType("SPCE_RB_0");
98			ignoreVisitor->addIgnoreType("DPD_RB_0");
99			}
100
101			compositeVisitor->addVisitor(ignoreVisitor, 1000);
102			}
103
104			//creat RigidBody Visitor
105	tim	1126	if(args_info.rigidbody_flag){
106			rbCOMVisitor = new RBCOMVisitor(info);
107			compositeVisitor->addVisitor(rbCOMVisitor, 900);
108			}
109			//creat RigidBody Visitor
110	tim	1119	//lipidVisitor = new LipidHeadVisitor(info);
111	tim	1118
112			//adding names of lipid head group
113	tim	1119	//lipidVisitor->addLipidHeadName("PC_RB_0");
114			//lipidVisitor->addLipidHeadName("PE_RB_0");
115	tim	1118
116	tim	1119	//compositeVisitor->addVisitor(lipidVisitor, 900);
117	tim	1118
118			//creat SSD atom visitor
119	tim	1126	ssdVisitor = new SSDAtomVisitor(info);
120			compositeVisitor->addVisitor(ssdVisitor, 800);
121	tim	1118
122			//creat default atom visitor
123			defaultAtomVisitor = new DefaultAtomVisitor(info);
124	tim	1119	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
125	tim	1118
126	tim	1126	//creat waterType visitor
127			if(args_info.watertype_flag){
128			waterTypeVisitor = new WaterTypeVisitor;
129			compositeVisitor->addVisitor(waterTypeVisitor, 600);
130			}
131
132	tim	1118	//create ZconsVisitor
133	tim	1126	if(args_info.zconstraint_flag){
134	tim	1118
135			zconsVisitor = new ZConsVisitor(info);
136
137			if(zconsVisitor->haveZconsMol())
138	tim	1126	compositeVisitor->addVisitor(zconsVisitor, 500);
139	tim	1118	else
140			delete zconsVisitor;
141			}
142
143			//creat wrapping visitor
144
145			if(args_info.periodicBox_flag){
146			wrappingVisitor = new WrappingVisitor(info);
147	tim	1126	compositeVisitor->addVisitor(wrappingVisitor, 400);
148	tim	1118	}
149
150			//creat replicate visitor
151			if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
152			IntVec3 replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
153			replicateVisitor = new ReplicateVisitor(info, replicateOpt);
154	tim	1126	compositeVisitor->addVisitor(replicateVisitor, 300);
155	tim	1118	}
156
157			//creat xyzVisitor
158			xyzVisitor = new XYZVisitor(info);
159	tim	1126	compositeVisitor->addVisitor(xyzVisitor, 200);
160	tim	1118
161	tim	1119	cout << compositeVisitor->toString();
162	tim	1118
163			//creat prepareVisitor
164			prepareVisitor = new PrepareVisitor();
165
166			//open dump file
167			dumpReader = new DumpReader(dumpFileName.c_str());
168			nframes = dumpReader->getNframes();
169
170			xyzStream .open(xyzFileName.c_str());
171
172			for (int i = 0; i < nframes; i += args_info.frame_arg){
173			dumpReader->readFrame(info, i);
174
175			mol = info->molecules;
176	tim	1119
177			//update atoms of rigidbody
178			for(int j = 0; j < info->n_mol; j++){
179			myRigidBodies = mol[j].getMyRigidBodies();
180
181			for(rbIter = myRigidBodies.begin(); rbIter != myRigidBodies.end(); ++rbIter)
182			(*rbIter)->updateAtoms();
183			}
184
185	tim	1118
186			//prepare visit
187			for(int j = 0; j < info->n_mol; j++){
188	tim	1119	integrableObjects = mol[j].getIntegrableObjects();
189	tim	1118
190			for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
191			(*iter)->accept(prepareVisitor);
192			}
193
194			//update visitor
195			compositeVisitor->update();
196
197			//visit stuntdouble
198			for(int j = 0; j < info->n_mol; j++){
199	tim	1119	integrableObjects = mol[j].getIntegrableObjects();
200	tim	1118
201			for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
202			(*iter)->accept(compositeVisitor);
203			}
204
205			xyzVisitor->writeFrame(xyzStream);
206			xyzVisitor->clear();
207
208			}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
209
210			xyzStream.close();
211
212
213			delete compositeVisitor;
214			delete info;
215
216
217			}