applications/staticProps/GofXyz.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */

#include <algorithm>
#include <fstream>
#include "applications/staticProps/GofXyz.hpp"
#include "utils/simError.h"
#include "primitives/Molecule.hpp"
namespace oopse {

GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins)
    : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins) {
    setOutputName(getPrefix(filename) + ".gxyz");

    deltaR_ = len_ / nRBins_;
    
    histogram_.resize(nRBins_);
    for (int i = 0 ; i < nRBins_; ++i) {
        histogram_[i].resize(nRBins_);
        for(int j = 0; j < nRBins_; ++j) {
            histogram_[i][j].resize(nRBins_);
        }
    }   

    //create atom2Mol mapping (should be other class' responsibility)
    atom2Mol_.insert(atom2Mol_.begin(), info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(), static_cast<Molecule*>(NULL));
    
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    
    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
        
        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
            atom2Mol_[atom->getGlobalIndex()] = mol;
        }

        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
            atom2Mol_[rb->getGlobalIndex()] = mol;
        }
        
    }       
}


void GofXyz::preProcess() {
    for (int i = 0 ; i < nRBins_; ++i) {
        histogram_[i].resize(nRBins_);
        for(int j = 0; j < nRBins_; ++j) {
            std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
        }
    }   
}


void GofXyz::initalizeHistogram() {
    //calculate the center of mass of the molecule of selected stuntdouble in selection1

    //determine the new coordinate set of selection1
    //v1 = Rs1 -Rcom, 
    //z = Rs1.dipole
    //x = v1 X z
    //y = z X x 
    coorSets_.clear();

    int i;
    StuntDouble* sd;
    for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) {
        Vector3d rcom = getMolCom(sd);
        Vector3d rs1 = sd->getPos();
        Vector3d v1 =  rcom - rs1;
        CoorSet currCoorSet;
        currCoorSet.zaxis = sd->getElectroFrame().getColumn(2);
        v1.normalize();
        currCoorSet.zaxis.normalize();
        currCoorSet.xaxis = cross(v1, currCoorSet.zaxis);
        currCoorSet.yaxis = cross(currCoorSet.zaxis, currCoorSet.xaxis);
        coorSets_.insert(std::map<int, CoorSet>::value_type(sd->getGlobalIndex(), currCoorSet));
    }

}

void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {

    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12 = pos2 - pos1;
    currentSnapshot_->wrapVector(r12);

    std::map<int, CoorSet>::iterator i = coorSets_.find(sd1->getGlobalIndex());
    assert(i != coorSets_.end());
    
    double x = dot(r12, i->second.xaxis);
    double y = dot(r12, i->second.yaxis);
    double z = dot(r12, i->second.zaxis);

    int xbin = x / deltaR_;
    int ybin = y / deltaR_;
    int zbin = z / deltaR_;

    if (xbin < nRBins_ && ybin < nRBins_ && zbin < nRBins_) {
        ++histogram_[x][y][z];
    }
    
}

void GofXyz::writeRdf() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
        rdfStream << "#g(x, y, z)\n";
        rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
        rdfStream << "selection2: (" << selectionScript2_ << ")\n";
        rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
        for (int i = 0; i < histogram_.size(); ++i) {
 
            for(int j = 0; j < histogram_[i].size(); ++j) {
 
                for(int k = 0;k < histogram_[i].size(); ++k) {
 
                    rdfStream << histogram_[i][j][k]/nProcessed_ << "\t";
                }
                rdfStream << "\n";                
            }
        }
        
    } else {

        sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
        painCave.isFatal = 1;
        simError();  
    }

    rdfStream.close();
}

Vector3d GofXyz::getMolCom(StuntDouble* sd){
    Molecule* mol = atom2Mol_[sd->getGlobalIndex()];
    assert(mol);
    return mol->getCom();
}

}
Revision:	361
Committed:	Thu Feb 17 18:30:54 2005 UTC (20 years, 8 months ago) by tim
File size:	6449 byte(s)
Log Message:	finish GofXyz
#	User	Rev	Content
1	tim	310	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include <algorithm>
43			#include <fstream>
44			#include "applications/staticProps/GofXyz.hpp"
45			#include "utils/simError.h"
46	tim	361	#include "primitives/Molecule.hpp"
47	tim	310	namespace oopse {
48
49	tim	354	GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins)
50			: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins) {
51	tim	311	setOutputName(getPrefix(filename) + ".gxyz");
52	tim	310
53	tim	354	deltaR_ = len_ / nRBins_;
54
55			histogram_.resize(nRBins_);
56			for (int i = 0 ; i < nRBins_; ++i) {
57			histogram_[i].resize(nRBins_);
58			for(int j = 0; j < nRBins_; ++j) {
59			histogram_[i][j].resize(nRBins_);
60			}
61			}
62	tim	361
63			//create atom2Mol mapping (should be other class' responsibility)
64			atom2Mol_.insert(atom2Mol_.begin(), info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(), static_cast<Molecule*>(NULL));
65
66			SimInfo::MoleculeIterator mi;
67			Molecule* mol;
68			Molecule::AtomIterator ai;
69			Atom* atom;
70			Molecule::RigidBodyIterator rbIter;
71			RigidBody* rb;
72
73			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
74
75			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
76			atom2Mol_[atom->getGlobalIndex()] = mol;
77			}
78
79			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
80			atom2Mol_[rb->getGlobalIndex()] = mol;
81			}
82
83			}
84	tim	310	}
85
86
87			void GofXyz::preProcess() {
88	tim	361	for (int i = 0 ; i < nRBins_; ++i) {
89			histogram_[i].resize(nRBins_);
90			for(int j = 0; j < nRBins_; ++j) {
91			std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
92			}
93			}
94	tim	310	}
95
96	tim	361
97	tim	310	void GofXyz::initalizeHistogram() {
98	tim	361	//calculate the center of mass of the molecule of selected stuntdouble in selection1
99	tim	310
100	tim	361	//determine the new coordinate set of selection1
101			//v1 = Rs1 -Rcom,
102			//z = Rs1.dipole
103			//x = v1 X z
104			//y = z X x
105			coorSets_.clear();
106	tim	310
107	tim	361	int i;
108			StuntDouble* sd;
109			for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) {
110			Vector3d rcom = getMolCom(sd);
111			Vector3d rs1 = sd->getPos();
112			Vector3d v1 = rcom - rs1;
113			CoorSet currCoorSet;
114			currCoorSet.zaxis = sd->getElectroFrame().getColumn(2);
115			v1.normalize();
116			currCoorSet.zaxis.normalize();
117			currCoorSet.xaxis = cross(v1, currCoorSet.zaxis);
118			currCoorSet.yaxis = cross(currCoorSet.zaxis, currCoorSet.xaxis);
119			coorSets_.insert(std::map<int, CoorSet>::value_type(sd->getGlobalIndex(), currCoorSet));
120			}
121	tim	310
122			}
123
124			void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
125
126			Vector3d pos1 = sd1->getPos();
127			Vector3d pos2 = sd2->getPos();
128	tim	361	Vector3d r12 = pos2 - pos1;
129	tim	310	currentSnapshot_->wrapVector(r12);
130
131	tim	361	std::map<int, CoorSet>::iterator i = coorSets_.find(sd1->getGlobalIndex());
132			assert(i != coorSets_.end());
133
134			double x = dot(r12, i->second.xaxis);
135			double y = dot(r12, i->second.yaxis);
136			double z = dot(r12, i->second.zaxis);
137	tim	310
138	tim	361	int xbin = x / deltaR_;
139			int ybin = y / deltaR_;
140			int zbin = z / deltaR_;
141
142			if (xbin < nRBins_ && ybin < nRBins_ && zbin < nRBins_) {
143			++histogram_[x][y][z];
144			}
145	tim	310
146			}
147
148			void GofXyz::writeRdf() {
149			std::ofstream rdfStream(outputFilename_.c_str());
150			if (rdfStream.is_open()) {
151	tim	361	rdfStream << "#g(x, y, z)\n";
152	tim	310	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
153			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
154	tim	361	rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
155	tim	310	for (int i = 0; i < histogram_.size(); ++i) {
156	tim	361
157	tim	310	for(int j = 0; j < histogram_[i].size(); ++j) {
158	tim	361
159	tim	310	for(int k = 0;k < histogram_[i].size(); ++k) {
160	tim	361
161			rdfStream << histogram_[i][j][k]/nProcessed_ << "\t";
162	tim	311	}
163	tim	361	rdfStream << "\n";
164	tim	310	}
165			}
166
167			} else {
168
169	tim	360	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
170			painCave.isFatal = 1;
171			simError();
172	tim	310	}
173
174			rdfStream.close();
175			}
176
177	tim	361	Vector3d GofXyz::getMolCom(StuntDouble* sd){
178			Molecule* mol = atom2Mol_[sd->getGlobalIndex()];
179			assert(mol);
180			return mol->getCom();
181	tim	310	}
182
183	tim	361	}