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;
  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(defaultAtomVisitor, 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(xyzVisitor, 300);

  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:	1119
Committed:	Mon Apr 19 17:44:48 2004 UTC (20 years, 5 months ago) by tim
File size:	5473 byte(s)
Log Message:	Dump2XYZ is almost working except atoms in rigidbody are double counted
#	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			ReplicateVisitor* replicateVisitor;
36			WrappingVisitor* wrappingVisitor;
37			IgnoreVisitor* ignoreVisitor;
38			XYZVisitor* xyzVisitor;
39			ZConsVisitor* zconsVisitor;
40			PrepareVisitor* prepareVisitor;
41
42			//parse the command line option
43			if (cmdline_parser (argc, argv, &args_info) != 0)
44			exit(1) ;
45
46
47			//get the dumpfile name and bass file name
48			if (args_info.input_given){
49			dumpFileName = args_info.input_arg;
50			}
51			else{
52			cerr << "Does not have input file name" << endl;
53			exit(1);
54			}
55			bassFileName = dumpFileName;
56			bassFileName = bassFileName.substr(0, bassFileName.rfind(".")) + ".bass";
57
58			if (args_info.output_given){
59			xyzFileName = args_info.output_arg;
60			}
61			else{
62			xyzFileName = dumpFileName;
63			xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
64			}
65
66			//parse bass file and set up the system
67			info = new SimInfo();
68			startMe.setSimInfo(info );
69
70			startMe.parseFile( bassFileName.c_str());
71
72			startMe.createSim();
73
74
75			//creat visitor list
76			compositeVisitor = new CompositeVisitor();
77
78			//creat ignore visitor
79			if(args_info.ignore_given \|\|args_info.water_flag){
80
81			ignoreVisitor = new IgnoreVisitor();
82
83			for(int i = 0; i < args_info.ignore_given; i++)
84			ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
85
86			//ignore water
87			if(args_info.water_flag){
88			ignoreVisitor->addIgnoreType("SSD");
89			ignoreVisitor->addIgnoreType("SSD1");
90			ignoreVisitor->addIgnoreType("SSD_E");
91			ignoreVisitor->addIgnoreType("SSD_RF");
92			ignoreVisitor->addIgnoreType("TIP3P_RB_0");
93			ignoreVisitor->addIgnoreType("TIP4P_RB_0");
94			ignoreVisitor->addIgnoreType("TIP5P_RB_0");
95			ignoreVisitor->addIgnoreType("SPCE_RB_0");
96			ignoreVisitor->addIgnoreType("DPD_RB_0");
97			}
98
99			compositeVisitor->addVisitor(ignoreVisitor, 1000);
100			}
101
102			//creat RigidBody Visitor
103	tim	1119	//lipidVisitor = new LipidHeadVisitor(info);
104	tim	1118
105			//adding names of lipid head group
106	tim	1119	//lipidVisitor->addLipidHeadName("PC_RB_0");
107			//lipidVisitor->addLipidHeadName("PE_RB_0");
108	tim	1118
109	tim	1119	//compositeVisitor->addVisitor(lipidVisitor, 900);
110	tim	1118
111			//creat SSD atom visitor
112	tim	1119	//ssdVisitor = new SSDAtomVisitor(info);
113			//compositeVisitor->addVisitor(ssdVisitor, 800);
114	tim	1118
115			//creat default atom visitor
116			defaultAtomVisitor = new DefaultAtomVisitor(info);
117	tim	1119	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
118	tim	1118
119			//create ZconsVisitor
120			if(args_info.replace_given){
121
122			zconsVisitor = new ZConsVisitor(info);
123
124			if(zconsVisitor->haveZconsMol())
125			compositeVisitor->addVisitor(zconsVisitor, 600);
126			else
127			delete zconsVisitor;
128			}
129
130			//creat wrapping visitor
131
132			if(args_info.periodicBox_flag){
133			wrappingVisitor = new WrappingVisitor(info);
134			compositeVisitor->addVisitor(wrappingVisitor, 500);
135			}
136
137			//creat replicate visitor
138			if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
139			IntVec3 replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
140			replicateVisitor = new ReplicateVisitor(info, replicateOpt);
141			compositeVisitor->addVisitor(replicateVisitor, 400);
142			}
143
144			//creat xyzVisitor
145			xyzVisitor = new XYZVisitor(info);
146	tim	1119	compositeVisitor->addVisitor(xyzVisitor, 300);
147	tim	1118
148	tim	1119	cout << compositeVisitor->toString();
149	tim	1118
150			//creat prepareVisitor
151			prepareVisitor = new PrepareVisitor();
152
153			//open dump file
154			dumpReader = new DumpReader(dumpFileName.c_str());
155			nframes = dumpReader->getNframes();
156
157			xyzStream .open(xyzFileName.c_str());
158
159			for (int i = 0; i < nframes; i += args_info.frame_arg){
160			dumpReader->readFrame(info, i);
161
162			mol = info->molecules;
163	tim	1119
164			//update atoms of rigidbody
165			for(int j = 0; j < info->n_mol; j++){
166			myRigidBodies = mol[j].getMyRigidBodies();
167
168			for(rbIter = myRigidBodies.begin(); rbIter != myRigidBodies.end(); ++rbIter)
169			(*rbIter)->updateAtoms();
170			}
171
172	tim	1118
173			//prepare visit
174			for(int j = 0; j < info->n_mol; j++){
175	tim	1119	integrableObjects = mol[j].getIntegrableObjects();
176	tim	1118
177			for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
178			(*iter)->accept(prepareVisitor);
179			}
180
181			//update visitor
182			compositeVisitor->update();
183
184			//visit stuntdouble
185			for(int j = 0; j < info->n_mol; j++){
186	tim	1119	integrableObjects = mol[j].getIntegrableObjects();
187	tim	1118
188			for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
189			(*iter)->accept(compositeVisitor);
190			}
191
192			xyzVisitor->writeFrame(xyzStream);
193			xyzVisitor->clear();
194
195			}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
196
197			xyzStream.close();
198
199
200			delete compositeVisitor;
201			delete info;
202
203
204			}