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, const std::string& sele3, double len, int nrbins)
    : RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
    setOutputName(getPrefix(filename) + ".gxyz");

    evaluator3_.loadScriptString(sele3);
    if (!evaluator3_.isDynamic()) {
        seleMan3_.setSelectionSet(evaluator3_.evaluate());
    }    

    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_);
        }
    }   
   
}


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

    if (!evaluator3_.isDynamic()) {
        seleMan3_.setSelectionSet(evaluator3_.evaluate());
    }    

    assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
    
    //dipole direction of selection3 and position of selection3 will be used to determine the y-z plane
    //v1 = s3 -s1, 
    //z = origin.dipole
    //x = v1 X z
    //y = z X x 
    rotMats_.clear();

    int i;
    int j;
    StuntDouble* sd1;
    StuntDouble* sd3;
    
    for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j); 
        sd1 != NULL, sd3 != NULL;
        sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {

        Vector3d r3 =sd3->getPos();
        Vector3d r1 = sd1->getPos();
        Vector3d v1 =  r3 - r1;
        info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
        Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
        Vector3d xaxis = cross(v1, zaxis);
        Vector3d yaxis = cross(zaxis, xaxis);

        xaxis.normalize();
        yaxis.normalize();
        zaxis.normalize();

        RotMat3x3d rotMat;
        rotMat.setRow(0, xaxis);
        rotMat.setRow(1, yaxis);
        rotMat.setRow(2, zaxis);
        
        rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
    }

}

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, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
    assert(i != rotMats_.end());
    
    Vector3d newR12 = i->second * r12;
    // x, y and z's possible values range -halfLen_ to halfLen_
    int xbin = (newR12.x()+ halfLen_) / deltaR_;
    int ybin = (newR12.y() + halfLen_) / deltaR_;
    int zbin = (newR12.z() + halfLen_) / deltaR_;

    if (xbin < nRBins_ && xbin >=0 &&
        ybin < nRBins_ && ybin >= 0 &&
        zbin < nRBins_ && zbin >=0 ) {
        ++histogram_[xbin][ybin][zbin];
    }
    
}

void GofXyz::writeRdf() {
    std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
    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][j].size(); ++k) {
                    rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
                }
            }
        }
        
    } else {

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

    rdfStream.close();
}

}
Revision:	2135
Committed:	Mon Mar 28 15:54:04 2005 UTC (19 years, 3 months ago) by tim
File size:	6397 byte(s)
Log Message:	fix a bug in getting the dimension of histogram
#	Content
1	/*
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	#include "primitives/Molecule.hpp"
47	namespace oopse {
48
49	GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, double len, int nrbins)
50	: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
51	setOutputName(getPrefix(filename) + ".gxyz");
52
53	evaluator3_.loadScriptString(sele3);
54	if (!evaluator3_.isDynamic()) {
55	seleMan3_.setSelectionSet(evaluator3_.evaluate());
56	}
57
58	deltaR_ = len_ / nRBins_;
59
60	histogram_.resize(nRBins_);
61	for (int i = 0 ; i < nRBins_; ++i) {
62	histogram_[i].resize(nRBins_);
63	for(int j = 0; j < nRBins_; ++j) {
64	histogram_[i][j].resize(nRBins_);
65	}
66	}
67
68	}
69
70
71	void GofXyz::preProcess() {
72	for (int i = 0 ; i < nRBins_; ++i) {
73	histogram_[i].resize(nRBins_);
74	for(int j = 0; j < nRBins_; ++j) {
75	std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
76	}
77	}
78	}
79
80
81	void GofXyz::initalizeHistogram() {
82	//calculate the center of mass of the molecule of selected stuntdouble in selection1
83
84	if (!evaluator3_.isDynamic()) {
85	seleMan3_.setSelectionSet(evaluator3_.evaluate());
86	}
87
88	assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
89
90	//dipole direction of selection3 and position of selection3 will be used to determine the y-z plane
91	//v1 = s3 -s1,
92	//z = origin.dipole
93	//x = v1 X z
94	//y = z X x
95	rotMats_.clear();
96
97	int i;
98	int j;
99	StuntDouble* sd1;
100	StuntDouble* sd3;
101
102	for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
103	sd1 != NULL, sd3 != NULL;
104	sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
105
106	Vector3d r3 =sd3->getPos();
107	Vector3d r1 = sd1->getPos();
108	Vector3d v1 = r3 - r1;
109	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
110	Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
111	Vector3d xaxis = cross(v1, zaxis);
112	Vector3d yaxis = cross(zaxis, xaxis);
113
114	xaxis.normalize();
115	yaxis.normalize();
116	zaxis.normalize();
117
118	RotMat3x3d rotMat;
119	rotMat.setRow(0, xaxis);
120	rotMat.setRow(1, yaxis);
121	rotMat.setRow(2, zaxis);
122
123	rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
124	}
125
126	}
127
128	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
129
130	Vector3d pos1 = sd1->getPos();
131	Vector3d pos2 = sd2->getPos();
132	Vector3d r12 = pos2 - pos1;
133	currentSnapshot_->wrapVector(r12);
134
135	std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
136	assert(i != rotMats_.end());
137
138	Vector3d newR12 = i->second * r12;
139	// x, y and z's possible values range -halfLen_ to halfLen_
140	int xbin = (newR12.x()+ halfLen_) / deltaR_;
141	int ybin = (newR12.y() + halfLen_) / deltaR_;
142	int zbin = (newR12.z() + halfLen_) / deltaR_;
143
144	if (xbin < nRBins_ && xbin >=0 &&
145	ybin < nRBins_ && ybin >= 0 &&
146	zbin < nRBins_ && zbin >=0 ) {
147	++histogram_[xbin][ybin][zbin];
148	}
149
150	}
151
152	void GofXyz::writeRdf() {
153	std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
154	if (rdfStream.is_open()) {
155	//rdfStream << "#g(x, y, z)\n";
156	//rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
157	//rdfStream << "selection2: (" << selectionScript2_ << ")\n";
158	//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
159	for (int i = 0; i < histogram_.size(); ++i) {
160
161	for(int j = 0; j < histogram_[i].size(); ++j) {
162
163	for(int k = 0;k < histogram_[i][j].size(); ++k) {
164	rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
165	}
166	}
167	}
168
169	} else {
170
171	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
172	painCave.isFatal = 1;
173	simError();
174	}
175
176	rdfStream.close();
177	}
178
179	}