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
#	Content
1	#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	LinearAtomVisitor* linearVisitor;
35	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	linearVisitor = new LinearAtomVisitor(info);
119	compositeVisitor->addVisitor(linearVisitor, 750);
120
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	}