applications/dump2Xyz/Dump2XYZ.cpp

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

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


using namespace oopse;

int main(int argc, char* argv[]){
    gengetopt_args_info args_info;
    std::string dumpFileName;
    std::string mdFileName;
    std::string xyzFileName;
    
    //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 {
        std::cerr << "Does not have input file name" << std::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
    SimCreator creator;
    SimInfo* info = creator.createSim(mdFileName);
    

    //creat visitor list
    CompositeVisitor* compositeVisitor = new CompositeVisitor();

    //creat ignore visitor
    if(args_info.ignore_given ||args_info.water_flag){

        IgnoreVisitor* 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* rbCOMVisitor = new RBCOMVisitor(info);
        compositeVisitor->addVisitor(rbCOMVisitor, 900);
    }

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

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

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

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

    //create ZconsVisitor
    if(args_info.zconstraint_flag){

        ZConsVisitor* zconsVisitor = new ZConsVisitor(info);

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

    //creat wrapping visitor

    if(args_info.periodicBox_flag){
        WrappingVisitor* 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){
        Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
        ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
        compositeVisitor->addVisitor(replicateVisitor, 300);
    }

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

    std::cout << compositeVisitor->toString();

    //creat prepareVisitor
    PrepareVisitor* prepareVisitor = new PrepareVisitor();

    //open dump file
    DumpReader* dumpReader = new DumpReader(info, dumpFileName);
    int nframes = dumpReader->getNFrames();

    
    std::ofstream xyzStream;    
    xyzStream .open(xyzFileName.c_str());

      
    SimInfo::MoleculeIterator miter;
    Molecule::IntegrableObjectIterator  iiter;
    Molecule::RigidBodyIterator rbIter;
    Molecule* mol;
    StuntDouble* integrableObject;
    RigidBody* rb;
    
    for (int i = 0; i < nframes; i += args_info.frame_arg){
        dumpReader->readFrame(i);

        //update atoms of rigidbody
        for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {

            //change the positions of atoms which belong to the rigidbodies
            for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
                rb->updateAtoms();
            }
        }

        //prepare visit
        for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
            for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
                   integrableObject = mol->nextIntegrableObject(iiter)) {
                integrableObject->accept(prepareVisitor);
            }
        }

        //update visitor
        compositeVisitor->update();

        //visit stuntdouble
        for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
            for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
                   integrableObject = mol->nextIntegrableObject(iiter)) {
                integrableObject->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:	1833
Committed:	Thu Dec 2 16:53:56 2004 UTC (21 years, 2 months ago) by tim
File size:	6109 byte(s)
Log Message:	oopse get built
#	User	Rev	Content
1	tim	1501	#include <iostream>
2			#include <fstream>
3			#include <string>
4
5			#include "applications/dump2Xyz/Dump2XYZCmd.h"
6	tim	1833	#include "brains/SimCreator.hpp"
7			#include "io/DumpReader.hpp"
8	tim	1501	#include "visitors/AtomVisitor.hpp"
9			#include "visitors/CompositeVisitor.hpp"
10			#include "visitors/RigidBodyVisitor.hpp"
11			#include "visitors/OtherVisitor.hpp"
12			#include "visitors/ZconsVisitor.hpp"
13
14
15	tim	1833	using namespace oopse;
16	tim	1827
17	tim	1501	int main(int argc, char* argv[]){
18	tim	1833	gengetopt_args_info args_info;
19			std::string dumpFileName;
20			std::string mdFileName;
21			std::string xyzFileName;
22
23			//parse the command line option
24			if (cmdline_parser (argc, argv, &args_info) != 0) {
25			exit(1) ;
26			}
27	tim	1501
28	tim	1833	//get the dumpfile name and meta-data file name
29			if (args_info.input_given){
30	tim	1501	dumpFileName = args_info.input_arg;
31	tim	1833	} else {
32			std::cerr << "Does not have input file name" << std::endl;
33			exit(1);
34			}
35
36			mdFileName = dumpFileName;
37			mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
38	tim	1501
39	tim	1833	if (args_info.output_given){
40			xyzFileName = args_info.output_arg;
41			} else {
42			xyzFileName = dumpFileName;
43			xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
44			}
45	tim	1501
46			//parse md file and set up the system
47	tim	1833	SimCreator creator;
48			SimInfo* info = creator.createSim(mdFileName);
49
50	tim	1501
51	tim	1833
52			//creat visitor list
53			CompositeVisitor* compositeVisitor = new CompositeVisitor();
54	tim	1501
55	tim	1833	//creat ignore visitor
56			if(args_info.ignore_given \|\|args_info.water_flag){
57	tim	1501
58	tim	1833	IgnoreVisitor* ignoreVisitor = new IgnoreVisitor();
59	tim	1501
60	tim	1833	for(int i = 0; i < args_info.ignore_given; i++)
61			ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
62	tim	1501
63	tim	1833	//ignore water
64			if(args_info.water_flag){
65			ignoreVisitor->addIgnoreType("SSD");
66			ignoreVisitor->addIgnoreType("SSD1");
67			ignoreVisitor->addIgnoreType("SSD_E");
68			ignoreVisitor->addIgnoreType("SSD_RF");
69			ignoreVisitor->addIgnoreType("TIP3P_RB_0");
70			ignoreVisitor->addIgnoreType("TIP4P_RB_0");
71			ignoreVisitor->addIgnoreType("TIP5P_RB_0");
72			ignoreVisitor->addIgnoreType("SPCE_RB_0");
73			ignoreVisitor->addIgnoreType("DPD_RB_0");
74			}
75	tim	1501
76	tim	1833	compositeVisitor->addVisitor(ignoreVisitor, 1000);
77	tim	1501	}
78
79	tim	1833	//creat RigidBody Visitor
80			if(args_info.rigidbody_flag){
81			RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
82			compositeVisitor->addVisitor(rbCOMVisitor, 900);
83			}
84	tim	1501
85			//compositeVisitor->addVisitor(lipidVisitor, 900);
86
87	tim	1833	//creat SSD atom visitor
88			SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
89			compositeVisitor->addVisitor(ssdVisitor, 800);
90	tim	1501
91	tim	1833	//creat default atom visitor
92			DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
93			compositeVisitor->addVisitor(defaultAtomVisitor, 700);
94	tim	1501
95	tim	1833	//creat waterType visitor
96			if(args_info.watertype_flag){
97			WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
98			compositeVisitor->addVisitor(waterTypeVisitor, 600);
99			}
100	tim	1501
101	tim	1833	//create ZconsVisitor
102			if(args_info.zconstraint_flag){
103	tim	1501
104	tim	1833	ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
105	tim	1501
106	tim	1833	if(zconsVisitor->haveZconsMol()) {
107			compositeVisitor->addVisitor(zconsVisitor, 500);
108			} else {
109			delete zconsVisitor;
110			}
111			}
112	tim	1501
113	tim	1833	//creat wrapping visitor
114
115			if(args_info.periodicBox_flag){
116			WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
117			compositeVisitor->addVisitor(wrappingVisitor, 400);
118			}
119	tim	1501
120	tim	1833	//creat replicate visitor
121			if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
122			Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
123			ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
124			compositeVisitor->addVisitor(replicateVisitor, 300);
125			}
126	tim	1501
127	tim	1833	//creat xyzVisitor
128			XYZVisitor* xyzVisitor = new XYZVisitor(info);
129			compositeVisitor->addVisitor(xyzVisitor, 200);
130	tim	1501
131	tim	1833	std::cout << compositeVisitor->toString();
132	tim	1501
133	tim	1833	//creat prepareVisitor
134			PrepareVisitor* prepareVisitor = new PrepareVisitor();
135	tim	1501
136	tim	1833	//open dump file
137			DumpReader* dumpReader = new DumpReader(info, dumpFileName);
138			int nframes = dumpReader->getNFrames();
139	tim	1501
140	tim	1833
141			std::ofstream xyzStream;
142			xyzStream .open(xyzFileName.c_str());
143	tim	1501
144	tim	1833
145			SimInfo::MoleculeIterator miter;
146			Molecule::IntegrableObjectIterator iiter;
147			Molecule::RigidBodyIterator rbIter;
148			Molecule* mol;
149			StuntDouble* integrableObject;
150			RigidBody* rb;
151
152			for (int i = 0; i < nframes; i += args_info.frame_arg){
153			dumpReader->readFrame(i);
154	tim	1501
155	tim	1833	//update atoms of rigidbody
156			for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
157	tim	1501
158	tim	1833	//change the positions of atoms which belong to the rigidbodies
159			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
160			rb->updateAtoms();
161			}
162			}
163	tim	1501
164	tim	1833	//prepare visit
165			for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
166			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
167			integrableObject = mol->nextIntegrableObject(iiter)) {
168			integrableObject->accept(prepareVisitor);
169			}
170			}
171	tim	1501
172	tim	1833	//update visitor
173			compositeVisitor->update();
174	tim	1501
175	tim	1833	//visit stuntdouble
176			for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
177			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
178			integrableObject = mol->nextIntegrableObject(iiter)) {
179			integrableObject->accept(compositeVisitor);
180			}
181			}
182	tim	1501
183	tim	1833	xyzVisitor->writeFrame(xyzStream);
184			xyzVisitor->clear();
185	tim	1501
186	tim	1833	}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
187	tim	1501
188	tim	1833	xyzStream.close();
189	tim	1501
190
191	tim	1833	delete compositeVisitor;
192			delete info;
193	tim	1501
194
195			}