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), len_(len), 
      halfLen_(len/2), nRBins_(nrbins), evaluator3_(info), seleMan3_(info) {
    
    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());
    
    // The 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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 2 months ago) by gezelter
File size:	6859 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	1879	#include "types/MultipoleAdapter.hpp"
49
50	gezelter	1390	namespace OpenMD {
51	gezelter	2071
52			GofXyz::GofXyz(SimInfo* info, const std::string& filename,
53			const std::string& sele1, const std::string& sele2,
54			const std::string& sele3, RealType len, int nrbins)
55			: RadialDistrFunc(info, filename, sele1, sele2), len_(len),
56			halfLen_(len/2), nRBins_(nrbins), evaluator3_(info), seleMan3_(info) {
57	tim	354
58	gezelter	2071	setOutputName(getPrefix(filename) + ".gxyz");
59
60			evaluator3_.loadScriptString(sele3);
61			if (!evaluator3_.isDynamic()) {
62			seleMan3_.setSelectionSet(evaluator3_.evaluate());
63			}
64
65			deltaR_ = len_ / nRBins_;
66
67			histogram_.resize(nRBins_);
68			for (int i = 0 ; i < nRBins_; ++i) {
69			histogram_[i].resize(nRBins_);
70			for(int j = 0; j < nRBins_; ++j) {
71			histogram_[i][j].resize(nRBins_);
72			}
73			}
74			}
75
76	gezelter	507	void GofXyz::preProcess() {
77	tim	361	for (int i = 0 ; i < nRBins_; ++i) {
78	gezelter	507	histogram_[i].resize(nRBins_);
79			for(int j = 0; j < nRBins_; ++j) {
80			std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
81			}
82	tim	361	}
83	gezelter	507	}
84	gezelter	2071
85
86	jmichalk	1785	void GofXyz::initializeHistogram() {
87	gezelter	2071	// Calculate the center of mass of the molecule of selected
88			// StuntDouble in selection1
89
90	tim	369	if (!evaluator3_.isDynamic()) {
91	gezelter	507	seleMan3_.setSelectionSet(evaluator3_.evaluate());
92	tim	369	}
93
94			assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
95
96	gezelter	2071	// The Dipole direction of selection3 and position of selection3 will
97			// be used to determine the y-z plane
98			// v1 = s3 -s1,
99			// z = origin.dipole
100			// x = v1 X z
101			// y = z X x
102	tim	369	rotMats_.clear();
103	tim	310
104	tim	361	int i;
105	tim	369	int j;
106			StuntDouble* sd1;
107			StuntDouble* sd3;
108
109			for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
110	gezelter	1693	sd1 != NULL \|\| sd3 != NULL;
111	gezelter	507	sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
112	tim	369
113	gezelter	1879	Vector3d r3 = sd3->getPos();
114	gezelter	507	Vector3d r1 = sd1->getPos();
115			Vector3d v1 = r3 - r1;
116	gezelter	1078	if (usePeriodicBoundaryConditions_)
117			info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
118	gezelter	1879
119			AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
120			MultipoleAdapter ma1 = MultipoleAdapter(atype1);
121
122			Vector3d zaxis;
123			if (ma1.isDipole())
124			zaxis = sd1->getDipole();
125			else
126			zaxis = sd1->getA().transpose() * V3Z;
127
128	gezelter	507	Vector3d xaxis = cross(v1, zaxis);
129			Vector3d yaxis = cross(zaxis, xaxis);
130	tim	369
131	gezelter	507	xaxis.normalize();
132			yaxis.normalize();
133			zaxis.normalize();
134	tim	369
135	gezelter	507	RotMat3x3d rotMat;
136			rotMat.setRow(0, xaxis);
137			rotMat.setRow(1, yaxis);
138			rotMat.setRow(2, zaxis);
139	tim	369
140	gezelter	507	rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
141	tim	361	}
142	tim	310
143	gezelter	507	}
144	tim	310
145	gezelter	507	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
146	tim	310
147			Vector3d pos1 = sd1->getPos();
148			Vector3d pos2 = sd2->getPos();
149	tim	361	Vector3d r12 = pos2 - pos1;
150	gezelter	1078	if (usePeriodicBoundaryConditions_)
151			currentSnapshot_->wrapVector(r12);
152	tim	310
153	tim	369	std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
154			assert(i != rotMats_.end());
155	tim	361
156	tim	369	Vector3d newR12 = i->second * r12;
157	tim	364	// x, y and z's possible values range -halfLen_ to halfLen_
158	gezelter	1879	int xbin = int( (newR12.x() + halfLen_) / deltaR_);
159			int ybin = int( (newR12.y() + halfLen_) / deltaR_);
160			int zbin = int( (newR12.z() + halfLen_) / deltaR_);
161	tim	361
162	tim	365	if (xbin < nRBins_ && xbin >=0 &&
163			ybin < nRBins_ && ybin >= 0 &&
164			zbin < nRBins_ && zbin >=0 ) {
165	gezelter	507	++histogram_[xbin][ybin][zbin];
166	tim	361	}
167	tim	310
168	gezelter	507	}
169	tim	310
170	gezelter	507	void GofXyz::writeRdf() {
171	tim	362	std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
172	tim	310	if (rdfStream.is_open()) {
173	gezelter	507	//rdfStream << "#g(x, y, z)\n";
174			//rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
175			//rdfStream << "selection2: (" << selectionScript2_ << ")\n";
176	gezelter	2071	//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = "
177			// << len_ << "deltaR = " << deltaR_ <<"\n";
178	gezelter	1782	for (unsigned int i = 0; i < histogram_.size(); ++i) {
179			for(unsigned int j = 0; j < histogram_[i].size(); ++j) {
180			for(unsigned int k = 0;k < histogram_[i][j].size(); ++k) {
181	gezelter	2071	rdfStream.write(reinterpret_cast<char *>( &histogram_[i][j][k] ),
182			sizeof( histogram_[i][j][k] ));
183	gezelter	507	}
184			}
185			}
186	tim	310
187			} else {
188
189	gezelter	2071	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n",
190			outputFilename_.c_str());
191	gezelter	507	painCave.isFatal = 1;
192			simError();
193	tim	310	}
194
195			rdfStream.close();
196	gezelter	507	}
197	tim	310
198			}