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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

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

  GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType 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;
      if (usePeriodicBoundaryConditions_)
        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;
    if (usePeriodicBoundaryConditions_)
      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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 11 months ago) by gezelter
File size:	6412 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	310	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	310	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	310	*/
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	gezelter	1390	namespace OpenMD {
48	tim	310
49	tim	963	GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins)
50	tim	369	: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
51	gezelter	507	setOutputName(getPrefix(filename) + ".gxyz");
52	tim	310
53	gezelter	507	evaluator3_.loadScriptString(sele3);
54			if (!evaluator3_.isDynamic()) {
55	tim	369	seleMan3_.setSelectionSet(evaluator3_.evaluate());
56	gezelter	507	}
57	tim	369
58	gezelter	507	deltaR_ = len_ / nRBins_;
59	tim	354
60	gezelter	507	histogram_.resize(nRBins_);
61			for (int i = 0 ; i < nRBins_; ++i) {
62	tim	354	histogram_[i].resize(nRBins_);
63			for(int j = 0; j < nRBins_; ++j) {
64	gezelter	507	histogram_[i][j].resize(nRBins_);
65	tim	354	}
66	gezelter	507	}
67	tim	369
68	gezelter	507	}
69	tim	310
70
71	gezelter	507	void GofXyz::preProcess() {
72	tim	361	for (int i = 0 ; i < nRBins_; ++i) {
73	gezelter	507	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	tim	361	}
78	gezelter	507	}
79	tim	310
80	tim	361
81	gezelter	507	void GofXyz::initalizeHistogram() {
82	tim	361	//calculate the center of mass of the molecule of selected stuntdouble in selection1
83	tim	310
84	tim	369	if (!evaluator3_.isDynamic()) {
85	gezelter	507	seleMan3_.setSelectionSet(evaluator3_.evaluate());
86	tim	369	}
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	tim	361	//x = v1 X z
94			//y = z X x
95	tim	369	rotMats_.clear();
96	tim	310
97	tim	361	int i;
98	tim	369	int j;
99			StuntDouble* sd1;
100			StuntDouble* sd3;
101
102			for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
103	gezelter	507	sd1 != NULL, sd3 != NULL;
104			sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
105	tim	369
106	gezelter	507	Vector3d r3 =sd3->getPos();
107			Vector3d r1 = sd1->getPos();
108			Vector3d v1 = r3 - r1;
109	gezelter	1078	if (usePeriodicBoundaryConditions_)
110			info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
111	gezelter	507	Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
112			Vector3d xaxis = cross(v1, zaxis);
113			Vector3d yaxis = cross(zaxis, xaxis);
114	tim	369
115	gezelter	507	xaxis.normalize();
116			yaxis.normalize();
117			zaxis.normalize();
118	tim	369
119	gezelter	507	RotMat3x3d rotMat;
120			rotMat.setRow(0, xaxis);
121			rotMat.setRow(1, yaxis);
122			rotMat.setRow(2, zaxis);
123	tim	369
124	gezelter	507	rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
125	tim	361	}
126	tim	310
127	gezelter	507	}
128	tim	310
129	gezelter	507	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
130	tim	310
131			Vector3d pos1 = sd1->getPos();
132			Vector3d pos2 = sd2->getPos();
133	tim	361	Vector3d r12 = pos2 - pos1;
134	gezelter	1078	if (usePeriodicBoundaryConditions_)
135			currentSnapshot_->wrapVector(r12);
136	tim	310
137	tim	369	std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
138			assert(i != rotMats_.end());
139	tim	361
140	tim	369	Vector3d newR12 = i->second * r12;
141	tim	364	// x, y and z's possible values range -halfLen_ to halfLen_
142	tim	369	int xbin = (newR12.x()+ halfLen_) / deltaR_;
143			int ybin = (newR12.y() + halfLen_) / deltaR_;
144			int zbin = (newR12.z() + halfLen_) / deltaR_;
145	tim	361
146	tim	365	if (xbin < nRBins_ && xbin >=0 &&
147			ybin < nRBins_ && ybin >= 0 &&
148			zbin < nRBins_ && zbin >=0 ) {
149	gezelter	507	++histogram_[xbin][ybin][zbin];
150	tim	361	}
151	tim	310
152	gezelter	507	}
153	tim	310
154	gezelter	507	void GofXyz::writeRdf() {
155	tim	362	std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
156	tim	310	if (rdfStream.is_open()) {
157	gezelter	507	//rdfStream << "#g(x, y, z)\n";
158			//rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
159			//rdfStream << "selection2: (" << selectionScript2_ << ")\n";
160			//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
161			for (int i = 0; i < histogram_.size(); ++i) {
162	tim	361
163	gezelter	507	for(int j = 0; j < histogram_[i].size(); ++j) {
164	tim	361
165	gezelter	507	for(int k = 0;k < histogram_[i][j].size(); ++k) {
166			rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
167			}
168			}
169			}
170	tim	310
171			} else {
172
173	gezelter	507	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
174			painCave.isFatal = 1;
175			simError();
176	tim	310	}
177
178			rdfStream.close();
179	gezelter	507	}
180	tim	310
181			}