applications/dump2Xyz/Dump2XYZ.cpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */
 
#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"

#include "UseTheForce/DUFF.hpp"
#include "UseTheForce/ForceFieldCreator.hpp"

using namespace oopse;

int main(int argc, char* argv[]){

    static ForceFieldBuilder<DUFF>* DUFFCreator = new ForceFieldBuilder<DUFF>("DUFF");

    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:	1890
Committed:	Wed Dec 15 21:07:48 2004 UTC (19 years, 7 months ago) by tim
File size:	7423 byte(s)
Log Message:	add EAM Force Field
#	Content
1	/*
2	* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3	*
4	* Contact: oopse@oopse.org
5	*
6	* This program is free software; you can redistribute it and/or
7	* modify it under the terms of the GNU Lesser General Public License
8	* as published by the Free Software Foundation; either version 2.1
9	* of the License, or (at your option) any later version.
10	* All we ask is that proper credit is given for our work, which includes
11	* - but is not limited to - adding the above copyright notice to the beginning
12	* of your source code files, and to any copyright notice that you may distribute
13	* with programs based on this work.
14	*
15	* This program is distributed in the hope that it will be useful,
16	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18	* GNU Lesser General Public License for more details.
19	*
20	* You should have received a copy of the GNU Lesser General Public License
21	* along with this program; if not, write to the Free Software
22	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23	*
24	*/
25
26	#include <iostream>
27	#include <fstream>
28	#include <string>
29
30	#include "applications/dump2Xyz/Dump2XYZCmd.h"
31	#include "brains/SimCreator.hpp"
32	#include "io/DumpReader.hpp"
33	#include "visitors/AtomVisitor.hpp"
34	#include "visitors/CompositeVisitor.hpp"
35	#include "visitors/RigidBodyVisitor.hpp"
36	#include "visitors/OtherVisitor.hpp"
37	#include "visitors/ZconsVisitor.hpp"
38
39	#include "UseTheForce/DUFF.hpp"
40	#include "UseTheForce/ForceFieldCreator.hpp"
41
42	using namespace oopse;
43
44	int main(int argc, char* argv[]){
45
46	static ForceFieldBuilder<DUFF>* DUFFCreator = new ForceFieldBuilder<DUFF>("DUFF");
47
48	gengetopt_args_info args_info;
49	std::string dumpFileName;
50	std::string mdFileName;
51	std::string xyzFileName;
52
53	//parse the command line option
54	if (cmdline_parser (argc, argv, &args_info) != 0) {
55	exit(1) ;
56	}
57
58	//get the dumpfile name and meta-data file name
59	if (args_info.input_given){
60	dumpFileName = args_info.input_arg;
61	} else {
62	std::cerr << "Does not have input file name" << std::endl;
63	exit(1);
64	}
65
66	mdFileName = dumpFileName;
67	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
68
69	if (args_info.output_given){
70	xyzFileName = args_info.output_arg;
71	} else {
72	xyzFileName = dumpFileName;
73	xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
74	}
75
76	//parse md file and set up the system
77	SimCreator creator;
78	SimInfo* info = creator.createSim(mdFileName);
79
80
81
82	//creat visitor list
83	CompositeVisitor* compositeVisitor = new CompositeVisitor();
84
85	//creat ignore visitor
86	if(args_info.ignore_given \|\|args_info.water_flag){
87
88	IgnoreVisitor* ignoreVisitor = new IgnoreVisitor();
89
90	for(int i = 0; i < args_info.ignore_given; i++)
91	ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
92
93	//ignore water
94	if(args_info.water_flag){
95	ignoreVisitor->addIgnoreType("SSD");
96	ignoreVisitor->addIgnoreType("SSD1");
97	ignoreVisitor->addIgnoreType("SSD_E");
98	ignoreVisitor->addIgnoreType("SSD_RF");
99	ignoreVisitor->addIgnoreType("TIP3P_RB_0");
100	ignoreVisitor->addIgnoreType("TIP4P_RB_0");
101	ignoreVisitor->addIgnoreType("TIP5P_RB_0");
102	ignoreVisitor->addIgnoreType("SPCE_RB_0");
103	ignoreVisitor->addIgnoreType("DPD_RB_0");
104	}
105
106	compositeVisitor->addVisitor(ignoreVisitor, 1000);
107	}
108
109	//creat RigidBody Visitor
110	if(args_info.rigidbody_flag){
111	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
112	compositeVisitor->addVisitor(rbCOMVisitor, 900);
113	}
114
115	//compositeVisitor->addVisitor(lipidVisitor, 900);
116
117	//creat SSD atom visitor
118	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
119	compositeVisitor->addVisitor(ssdVisitor, 800);
120
121	//creat default atom visitor
122	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
123	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
124
125	//creat waterType visitor
126	if(args_info.watertype_flag){
127	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
128	compositeVisitor->addVisitor(waterTypeVisitor, 600);
129	}
130
131	//create ZconsVisitor
132	if(args_info.zconstraint_flag){
133
134	ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
135
136	if(zconsVisitor->haveZconsMol()) {
137	compositeVisitor->addVisitor(zconsVisitor, 500);
138	} else {
139	delete zconsVisitor;
140	}
141	}
142
143	//creat wrapping visitor
144
145	if(args_info.periodicBox_flag){
146	WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
147	compositeVisitor->addVisitor(wrappingVisitor, 400);
148	}
149
150	//creat replicate visitor
151	if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
152	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
153	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
154	compositeVisitor->addVisitor(replicateVisitor, 300);
155	}
156
157	//creat xyzVisitor
158	XYZVisitor* xyzVisitor = new XYZVisitor(info);
159	compositeVisitor->addVisitor(xyzVisitor, 200);
160
161	std::cout << compositeVisitor->toString();
162
163	//creat prepareVisitor
164	PrepareVisitor* prepareVisitor = new PrepareVisitor();
165
166	//open dump file
167	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
168	int nframes = dumpReader->getNFrames();
169
170
171	std::ofstream xyzStream;
172	xyzStream .open(xyzFileName.c_str());
173
174
175	SimInfo::MoleculeIterator miter;
176	Molecule::IntegrableObjectIterator iiter;
177	Molecule::RigidBodyIterator rbIter;
178	Molecule* mol;
179	StuntDouble* integrableObject;
180	RigidBody* rb;
181
182	for (int i = 0; i < nframes; i += args_info.frame_arg){
183	dumpReader->readFrame(i);
184
185	//update atoms of rigidbody
186	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
187
188	//change the positions of atoms which belong to the rigidbodies
189	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
190	rb->updateAtoms();
191	}
192	}
193
194	//prepare visit
195	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
196	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
197	integrableObject = mol->nextIntegrableObject(iiter)) {
198	integrableObject->accept(prepareVisitor);
199	}
200	}
201
202	//update visitor
203	compositeVisitor->update();
204
205	//visit stuntdouble
206	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
207	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
208	integrableObject = mol->nextIntegrableObject(iiter)) {
209	integrableObject->accept(compositeVisitor);
210	}
211	}
212
213	xyzVisitor->writeFrame(xyzStream);
214	xyzVisitor->clear();
215
216	}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
217
218	xyzStream.close();
219
220
221	delete compositeVisitor;
222	delete info;
223
224
225	}