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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#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::initializeHistogram() {
    //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 (unsigned int i = 0; i < histogram_.size(); ++i) { 
        for(unsigned int j = 0; j < histogram_[i].size(); ++j) { 
          for(unsigned 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:	1785
Committed:	Wed Aug 22 18:43:27 2012 UTC (12 years, 8 months ago) by jmichalk
File size:	6535 byte(s)
Log Message:	Trunk: The changes in this commit are confined to applications/staticProps and for the most part deal with a misspelling of initialize. The one other change took place in StaticProps.cpp and deals with the default treatment of sele2. It had previously been set to 'select all' which seems to go against what would be desired by not specifying it with regard to proper operations of many of the analysis programs ( g of r's especially)
#	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	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	310	*/
42
43			#include <algorithm>
44			#include <fstream>
45			#include "applications/staticProps/GofXyz.hpp"
46			#include "utils/simError.h"
47	tim	361	#include "primitives/Molecule.hpp"
48	gezelter	1390	namespace OpenMD {
49	tim	310
50	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)
51	tim	369	: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
52	gezelter	507	setOutputName(getPrefix(filename) + ".gxyz");
53	tim	310
54	gezelter	507	evaluator3_.loadScriptString(sele3);
55			if (!evaluator3_.isDynamic()) {
56	tim	369	seleMan3_.setSelectionSet(evaluator3_.evaluate());
57	gezelter	507	}
58	tim	369
59	gezelter	507	deltaR_ = len_ / nRBins_;
60	tim	354
61	gezelter	507	histogram_.resize(nRBins_);
62			for (int i = 0 ; i < nRBins_; ++i) {
63	tim	354	histogram_[i].resize(nRBins_);
64			for(int j = 0; j < nRBins_; ++j) {
65	gezelter	507	histogram_[i][j].resize(nRBins_);
66	tim	354	}
67	gezelter	507	}
68	tim	369
69	gezelter	507	}
70	tim	310
71
72	gezelter	507	void GofXyz::preProcess() {
73	tim	361	for (int i = 0 ; i < nRBins_; ++i) {
74	gezelter	507	histogram_[i].resize(nRBins_);
75			for(int j = 0; j < nRBins_; ++j) {
76			std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
77			}
78	tim	361	}
79	gezelter	507	}
80	tim	310
81	tim	361
82	jmichalk	1785	void GofXyz::initializeHistogram() {
83	tim	361	//calculate the center of mass of the molecule of selected stuntdouble in selection1
84	tim	310
85	tim	369	if (!evaluator3_.isDynamic()) {
86	gezelter	507	seleMan3_.setSelectionSet(evaluator3_.evaluate());
87	tim	369	}
88
89			assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
90
91			//dipole direction of selection3 and position of selection3 will be used to determine the y-z plane
92			//v1 = s3 -s1,
93			//z = origin.dipole
94	tim	361	//x = v1 X z
95			//y = z X x
96	tim	369	rotMats_.clear();
97	tim	310
98	tim	361	int i;
99	tim	369	int j;
100			StuntDouble* sd1;
101			StuntDouble* sd3;
102
103			for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
104	gezelter	1693	sd1 != NULL \|\| sd3 != NULL;
105	gezelter	507	sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
106	tim	369
107	gezelter	507	Vector3d r3 =sd3->getPos();
108			Vector3d r1 = sd1->getPos();
109			Vector3d v1 = r3 - r1;
110	gezelter	1078	if (usePeriodicBoundaryConditions_)
111			info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
112	gezelter	507	Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
113			Vector3d xaxis = cross(v1, zaxis);
114			Vector3d yaxis = cross(zaxis, xaxis);
115	tim	369
116	gezelter	507	xaxis.normalize();
117			yaxis.normalize();
118			zaxis.normalize();
119	tim	369
120	gezelter	507	RotMat3x3d rotMat;
121			rotMat.setRow(0, xaxis);
122			rotMat.setRow(1, yaxis);
123			rotMat.setRow(2, zaxis);
124	tim	369
125	gezelter	507	rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
126	tim	361	}
127	tim	310
128	gezelter	507	}
129	tim	310
130	gezelter	507	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
131	tim	310
132			Vector3d pos1 = sd1->getPos();
133			Vector3d pos2 = sd2->getPos();
134	tim	361	Vector3d r12 = pos2 - pos1;
135	gezelter	1078	if (usePeriodicBoundaryConditions_)
136			currentSnapshot_->wrapVector(r12);
137	tim	310
138	tim	369	std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
139			assert(i != rotMats_.end());
140	tim	361
141	tim	369	Vector3d newR12 = i->second * r12;
142	tim	364	// x, y and z's possible values range -halfLen_ to halfLen_
143	gezelter	1782	int xbin = (newR12.x() + halfLen_) / deltaR_;
144	tim	369	int ybin = (newR12.y() + halfLen_) / deltaR_;
145			int zbin = (newR12.z() + halfLen_) / deltaR_;
146	tim	361
147	tim	365	if (xbin < nRBins_ && xbin >=0 &&
148			ybin < nRBins_ && ybin >= 0 &&
149			zbin < nRBins_ && zbin >=0 ) {
150	gezelter	507	++histogram_[xbin][ybin][zbin];
151	tim	361	}
152	tim	310
153	gezelter	507	}
154	tim	310
155	gezelter	507	void GofXyz::writeRdf() {
156	tim	362	std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
157	tim	310	if (rdfStream.is_open()) {
158	gezelter	507	//rdfStream << "#g(x, y, z)\n";
159			//rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
160			//rdfStream << "selection2: (" << selectionScript2_ << ")\n";
161			//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
162	gezelter	1782	for (unsigned int i = 0; i < histogram_.size(); ++i) {
163			for(unsigned int j = 0; j < histogram_[i].size(); ++j) {
164			for(unsigned int k = 0;k < histogram_[i][j].size(); ++k) {
165			rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ),
166			sizeof(histogram_[i][j][k] ));
167	gezelter	507	}
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			}