OOPSE-1.0/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;
  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;
  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 );

  strcpy(inFileName, bassFileName.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);
  }
  //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:	1334
Committed:	Fri Jul 16 18:58:03 2004 UTC (19 years, 11 months ago) by gezelter
File size:	5928 byte(s)
Log Message:	Initial import of OOPSE-1.0 source tree
#	User	Rev	Content
1	gezelter	1334	#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			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			DefaultAtomVisitor* defaultAtomVisitor;
35			LipidHeadVisitor* lipidVisitor;
36			RBCOMVisitor* rbCOMVisitor;
37			ReplicateVisitor* replicateVisitor;
38			WrappingVisitor* wrappingVisitor;
39			IgnoreVisitor* ignoreVisitor;
40			XYZVisitor* xyzVisitor;
41			ZConsVisitor* zconsVisitor;
42			PrepareVisitor* prepareVisitor;
43			WaterTypeVisitor* waterTypeVisitor;
44
45			//parse the command line option
46			if (cmdline_parser (argc, argv, &args_info) != 0)
47			exit(1) ;
48
49
50			//get the dumpfile name and bass file name
51			if (args_info.input_given){
52			dumpFileName = args_info.input_arg;
53			}
54			else{
55			cerr << "Does not have input file name" << endl;
56			exit(1);
57			}
58			bassFileName = dumpFileName;
59			bassFileName = bassFileName.substr(0, bassFileName.rfind(".")) + ".bass";
60
61			if (args_info.output_given){
62			xyzFileName = args_info.output_arg;
63			}
64			else{
65			xyzFileName = dumpFileName;
66			xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
67			}
68
69			//parse bass file and set up the system
70			info = new SimInfo();
71			startMe.setSimInfo(info );
72
73			strcpy(inFileName, bassFileName.c_str() );
74			startMe.parseFile( inFileName );
75
76			startMe.createSim();
77
78
79			//creat visitor list
80			compositeVisitor = new CompositeVisitor();
81
82			//creat ignore visitor
83			if(args_info.ignore_given \|\|args_info.water_flag){
84
85			ignoreVisitor = new IgnoreVisitor();
86
87			for(int i = 0; i < args_info.ignore_given; i++)
88			ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
89
90			//ignore water
91			if(args_info.water_flag){
92			ignoreVisitor->addIgnoreType("SSD");
93			ignoreVisitor->addIgnoreType("SSD1");
94			ignoreVisitor->addIgnoreType("SSD_E");
95			ignoreVisitor->addIgnoreType("SSD_RF");
96			ignoreVisitor->addIgnoreType("TIP3P_RB_0");
97			ignoreVisitor->addIgnoreType("TIP4P_RB_0");
98			ignoreVisitor->addIgnoreType("TIP5P_RB_0");
99			ignoreVisitor->addIgnoreType("SPCE_RB_0");
100			ignoreVisitor->addIgnoreType("DPD_RB_0");
101			}
102
103			compositeVisitor->addVisitor(ignoreVisitor, 1000);
104			}
105
106			//creat RigidBody Visitor
107			if(args_info.rigidbody_flag){
108			rbCOMVisitor = new RBCOMVisitor(info);
109			compositeVisitor->addVisitor(rbCOMVisitor, 900);
110			}
111			//creat RigidBody Visitor
112			//lipidVisitor = new LipidHeadVisitor(info);
113
114			//adding names of lipid head group
115			//lipidVisitor->addLipidHeadName("PC_RB_0");
116			//lipidVisitor->addLipidHeadName("PE_RB_0");
117
118			//compositeVisitor->addVisitor(lipidVisitor, 900);
119
120			//creat SSD atom visitor
121			ssdVisitor = new SSDAtomVisitor(info);
122			compositeVisitor->addVisitor(ssdVisitor, 800);
123
124			//creat default atom visitor
125			defaultAtomVisitor = new DefaultAtomVisitor(info);
126			compositeVisitor->addVisitor(defaultAtomVisitor, 700);
127
128			//creat waterType visitor
129			if(args_info.watertype_flag){
130			waterTypeVisitor = new WaterTypeVisitor;
131			compositeVisitor->addVisitor(waterTypeVisitor, 600);
132			}
133
134			//create ZconsVisitor
135			if(args_info.zconstraint_flag){
136
137			zconsVisitor = new ZConsVisitor(info);
138
139			if(zconsVisitor->haveZconsMol())
140			compositeVisitor->addVisitor(zconsVisitor, 500);
141			else
142			delete zconsVisitor;
143			}
144
145			//creat wrapping visitor
146
147			if(args_info.periodicBox_flag){
148			wrappingVisitor = new WrappingVisitor(info);
149			compositeVisitor->addVisitor(wrappingVisitor, 400);
150			}
151
152			//creat replicate visitor
153			if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
154			IntVec3 replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
155			replicateVisitor = new ReplicateVisitor(info, replicateOpt);
156			compositeVisitor->addVisitor(replicateVisitor, 300);
157			}
158
159			//creat xyzVisitor
160			xyzVisitor = new XYZVisitor(info);
161			compositeVisitor->addVisitor(xyzVisitor, 200);
162
163			cout << compositeVisitor->toString();
164
165			//creat prepareVisitor
166			prepareVisitor = new PrepareVisitor();
167
168			//open dump file
169			dumpReader = new DumpReader(dumpFileName.c_str());
170			nframes = dumpReader->getNframes();
171
172			xyzStream .open(xyzFileName.c_str());
173
174			for (int i = 0; i < nframes; i += args_info.frame_arg){
175			dumpReader->readFrame(info, i);
176
177			mol = info->molecules;
178
179			//update atoms of rigidbody
180			for(int j = 0; j < info->n_mol; j++){
181			myRigidBodies = mol[j].getMyRigidBodies();
182
183			for(rbIter = myRigidBodies.begin(); rbIter != myRigidBodies.end(); ++rbIter)
184			(*rbIter)->updateAtoms();
185			}
186
187
188			//prepare visit
189			for(int j = 0; j < info->n_mol; j++){
190			integrableObjects = mol[j].getIntegrableObjects();
191
192			for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
193			(*iter)->accept(prepareVisitor);
194			}
195
196			//update visitor
197			compositeVisitor->update();
198
199			//visit stuntdouble
200			for(int j = 0; j < info->n_mol; j++){
201			integrableObjects = mol[j].getIntegrableObjects();
202
203			for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
204			(*iter)->accept(compositeVisitor);
205			}
206
207			xyzVisitor->writeFrame(xyzStream);
208			xyzVisitor->clear();
209
210			}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
211
212			xyzStream.close();
213
214
215			delete compositeVisitor;
216			delete info;
217
218
219			}