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 (19 years, 8 months ago) by tim
File size:	6109 byte(s)
Log Message:	oopse get built
#	Content
1	#include <iostream>
2	#include <fstream>
3	#include <string>
4
5	#include "applications/dump2Xyz/Dump2XYZCmd.h"
6	#include "brains/SimCreator.hpp"
7	#include "io/DumpReader.hpp"
8	#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	using namespace oopse;
16
17	int main(int argc, char* argv[]){
18	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
28	//get the dumpfile name and meta-data file name
29	if (args_info.input_given){
30	dumpFileName = args_info.input_arg;
31	} 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
39	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
46	//parse md file and set up the system
47	SimCreator creator;
48	SimInfo* info = creator.createSim(mdFileName);
49
50
51
52	//creat visitor list
53	CompositeVisitor* compositeVisitor = new CompositeVisitor();
54
55	//creat ignore visitor
56	if(args_info.ignore_given \|\|args_info.water_flag){
57
58	IgnoreVisitor* ignoreVisitor = new IgnoreVisitor();
59
60	for(int i = 0; i < args_info.ignore_given; i++)
61	ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
62
63	//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
76	compositeVisitor->addVisitor(ignoreVisitor, 1000);
77	}
78
79	//creat RigidBody Visitor
80	if(args_info.rigidbody_flag){
81	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
82	compositeVisitor->addVisitor(rbCOMVisitor, 900);
83	}
84
85	//compositeVisitor->addVisitor(lipidVisitor, 900);
86
87	//creat SSD atom visitor
88	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
89	compositeVisitor->addVisitor(ssdVisitor, 800);
90
91	//creat default atom visitor
92	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
93	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
94
95	//creat waterType visitor
96	if(args_info.watertype_flag){
97	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
98	compositeVisitor->addVisitor(waterTypeVisitor, 600);
99	}
100
101	//create ZconsVisitor
102	if(args_info.zconstraint_flag){
103
104	ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
105
106	if(zconsVisitor->haveZconsMol()) {
107	compositeVisitor->addVisitor(zconsVisitor, 500);
108	} else {
109	delete zconsVisitor;
110	}
111	}
112
113	//creat wrapping visitor
114
115	if(args_info.periodicBox_flag){
116	WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
117	compositeVisitor->addVisitor(wrappingVisitor, 400);
118	}
119
120	//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
127	//creat xyzVisitor
128	XYZVisitor* xyzVisitor = new XYZVisitor(info);
129	compositeVisitor->addVisitor(xyzVisitor, 200);
130
131	std::cout << compositeVisitor->toString();
132
133	//creat prepareVisitor
134	PrepareVisitor* prepareVisitor = new PrepareVisitor();
135
136	//open dump file
137	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
138	int nframes = dumpReader->getNFrames();
139
140
141	std::ofstream xyzStream;
142	xyzStream .open(xyzFileName.c_str());
143
144
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
155	//update atoms of rigidbody
156	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
157
158	//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
164	//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
172	//update visitor
173	compositeVisitor->update();
174
175	//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
183	xyzVisitor->writeFrame(xyzStream);
184	xyzVisitor->clear();
185
186	}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
187
188	xyzStream.close();
189
190
191	delete compositeVisitor;
192	delete info;
193
194
195	}