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, 234107 (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"
#include "types/MultipoleAdapter.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);

      AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
      MultipoleAdapter ma1 = MultipoleAdapter(atype1);

      Vector3d zaxis;
      if (ma1.isDipole()) 
        zaxis = sd1->getDipole();
      else
        zaxis = sd1->getA().transpose() * V3Z;

      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 = int( (newR12.x() + halfLen_) / deltaR_);
    int ybin = int( (newR12.y() + halfLen_) / deltaR_);
    int zbin = int( (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:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	6798 byte(s)
Log Message:	Fixed a widespread typo in the license
#	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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [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	1787	#include "types/MultipoleAdapter.hpp"
49
50	gezelter	1390	namespace OpenMD {
51	tim	310
52	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)
53	tim	369	: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
54	gezelter	507	setOutputName(getPrefix(filename) + ".gxyz");
55	tim	310
56	gezelter	507	evaluator3_.loadScriptString(sele3);
57			if (!evaluator3_.isDynamic()) {
58	tim	369	seleMan3_.setSelectionSet(evaluator3_.evaluate());
59	gezelter	507	}
60	tim	369
61	gezelter	507	deltaR_ = len_ / nRBins_;
62	tim	354
63	gezelter	507	histogram_.resize(nRBins_);
64			for (int i = 0 ; i < nRBins_; ++i) {
65	tim	354	histogram_[i].resize(nRBins_);
66			for(int j = 0; j < nRBins_; ++j) {
67	gezelter	507	histogram_[i][j].resize(nRBins_);
68	tim	354	}
69	gezelter	507	}
70	tim	369
71	gezelter	507	}
72	tim	310
73
74	gezelter	507	void GofXyz::preProcess() {
75	tim	361	for (int i = 0 ; i < nRBins_; ++i) {
76	gezelter	507	histogram_[i].resize(nRBins_);
77			for(int j = 0; j < nRBins_; ++j) {
78			std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
79			}
80	tim	361	}
81	gezelter	507	}
82	tim	310
83	tim	361
84	gezelter	1794	void GofXyz::initializeHistogram() {
85	tim	361	//calculate the center of mass of the molecule of selected stuntdouble in selection1
86	tim	310
87	tim	369	if (!evaluator3_.isDynamic()) {
88	gezelter	507	seleMan3_.setSelectionSet(evaluator3_.evaluate());
89	tim	369	}
90
91			assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
92
93			//dipole direction of selection3 and position of selection3 will be used to determine the y-z plane
94			//v1 = s3 -s1,
95			//z = origin.dipole
96	tim	361	//x = v1 X z
97			//y = z X x
98	tim	369	rotMats_.clear();
99	tim	310
100	tim	361	int i;
101	tim	369	int j;
102			StuntDouble* sd1;
103			StuntDouble* sd3;
104
105			for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
106	gezelter	1692	sd1 != NULL \|\| sd3 != NULL;
107	gezelter	507	sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
108	tim	369
109	gezelter	1787	Vector3d r3 = sd3->getPos();
110	gezelter	507	Vector3d r1 = sd1->getPos();
111			Vector3d v1 = r3 - r1;
112	gezelter	1078	if (usePeriodicBoundaryConditions_)
113			info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
114	gezelter	1787
115			AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
116			MultipoleAdapter ma1 = MultipoleAdapter(atype1);
117
118			Vector3d zaxis;
119			if (ma1.isDipole())
120			zaxis = sd1->getDipole();
121			else
122			zaxis = sd1->getA().transpose() * V3Z;
123
124	gezelter	507	Vector3d xaxis = cross(v1, zaxis);
125			Vector3d yaxis = cross(zaxis, xaxis);
126	tim	369
127	gezelter	507	xaxis.normalize();
128			yaxis.normalize();
129			zaxis.normalize();
130	tim	369
131	gezelter	507	RotMat3x3d rotMat;
132			rotMat.setRow(0, xaxis);
133			rotMat.setRow(1, yaxis);
134			rotMat.setRow(2, zaxis);
135	tim	369
136	gezelter	507	rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
137	tim	361	}
138	tim	310
139	gezelter	507	}
140	tim	310
141	gezelter	507	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
142	tim	310
143			Vector3d pos1 = sd1->getPos();
144			Vector3d pos2 = sd2->getPos();
145	tim	361	Vector3d r12 = pos2 - pos1;
146	gezelter	1078	if (usePeriodicBoundaryConditions_)
147			currentSnapshot_->wrapVector(r12);
148	tim	310
149	tim	369	std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
150			assert(i != rotMats_.end());
151	tim	361
152	tim	369	Vector3d newR12 = i->second * r12;
153	tim	364	// x, y and z's possible values range -halfLen_ to halfLen_
154	gezelter	1832	int xbin = int( (newR12.x() + halfLen_) / deltaR_);
155			int ybin = int( (newR12.y() + halfLen_) / deltaR_);
156			int zbin = int( (newR12.z() + halfLen_) / deltaR_);
157	tim	361
158	tim	365	if (xbin < nRBins_ && xbin >=0 &&
159			ybin < nRBins_ && ybin >= 0 &&
160			zbin < nRBins_ && zbin >=0 ) {
161	gezelter	507	++histogram_[xbin][ybin][zbin];
162	tim	361	}
163	tim	310
164	gezelter	507	}
165	tim	310
166	gezelter	507	void GofXyz::writeRdf() {
167	tim	362	std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
168	tim	310	if (rdfStream.is_open()) {
169	gezelter	507	//rdfStream << "#g(x, y, z)\n";
170			//rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
171			//rdfStream << "selection2: (" << selectionScript2_ << ")\n";
172			//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
173	gezelter	1767	for (unsigned int i = 0; i < histogram_.size(); ++i) {
174			for(unsigned int j = 0; j < histogram_[i].size(); ++j) {
175			for(unsigned int k = 0;k < histogram_[i][j].size(); ++k) {
176			rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ),
177			sizeof(histogram_[i][j][k] ));
178	gezelter	507	}
179			}
180			}
181	tim	310
182			} else {
183
184	gezelter	507	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
185			painCave.isFatal = 1;
186			simError();
187	tim	310	}
188
189			rdfStream.close();
190	gezelter	507	}
191	tim	310
192			}