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, 3 months ago) by gezelter
File size:	6859 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include <algorithm>
44	#include <fstream>
45	#include "applications/staticProps/GofXyz.hpp"
46	#include "utils/simError.h"
47	#include "primitives/Molecule.hpp"
48	#include "types/MultipoleAdapter.hpp"
49
50	namespace OpenMD {
51
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
58	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	void GofXyz::preProcess() {
77	for (int i = 0 ; i < nRBins_; ++i) {
78	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	}
83	}
84
85
86	void GofXyz::initializeHistogram() {
87	// Calculate the center of mass of the molecule of selected
88	// StuntDouble in selection1
89
90	if (!evaluator3_.isDynamic()) {
91	seleMan3_.setSelectionSet(evaluator3_.evaluate());
92	}
93
94	assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
95
96	// 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	rotMats_.clear();
103
104	int i;
105	int j;
106	StuntDouble* sd1;
107	StuntDouble* sd3;
108
109	for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
110	sd1 != NULL \|\| sd3 != NULL;
111	sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
112
113	Vector3d r3 = sd3->getPos();
114	Vector3d r1 = sd1->getPos();
115	Vector3d v1 = r3 - r1;
116	if (usePeriodicBoundaryConditions_)
117	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
118
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	Vector3d xaxis = cross(v1, zaxis);
129	Vector3d yaxis = cross(zaxis, xaxis);
130
131	xaxis.normalize();
132	yaxis.normalize();
133	zaxis.normalize();
134
135	RotMat3x3d rotMat;
136	rotMat.setRow(0, xaxis);
137	rotMat.setRow(1, yaxis);
138	rotMat.setRow(2, zaxis);
139
140	rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
141	}
142
143	}
144
145	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
146
147	Vector3d pos1 = sd1->getPos();
148	Vector3d pos2 = sd2->getPos();
149	Vector3d r12 = pos2 - pos1;
150	if (usePeriodicBoundaryConditions_)
151	currentSnapshot_->wrapVector(r12);
152
153	std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
154	assert(i != rotMats_.end());
155
156	Vector3d newR12 = i->second * r12;
157	// x, y and z's possible values range -halfLen_ to halfLen_
158	int xbin = int( (newR12.x() + halfLen_) / deltaR_);
159	int ybin = int( (newR12.y() + halfLen_) / deltaR_);
160	int zbin = int( (newR12.z() + halfLen_) / deltaR_);
161
162	if (xbin < nRBins_ && xbin >=0 &&
163	ybin < nRBins_ && ybin >= 0 &&
164	zbin < nRBins_ && zbin >=0 ) {
165	++histogram_[xbin][ybin][zbin];
166	}
167
168	}
169
170	void GofXyz::writeRdf() {
171	std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
172	if (rdfStream.is_open()) {
173	//rdfStream << "#g(x, y, z)\n";
174	//rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
175	//rdfStream << "selection2: (" << selectionScript2_ << ")\n";
176	//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = "
177	// << len_ << "deltaR = " << deltaR_ <<"\n";
178	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	rdfStream.write(reinterpret_cast<char *>( &histogram_[i][j][k] ),
182	sizeof( histogram_[i][j][k] ));
183	}
184	}
185	}
186
187	} else {
188
189	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n",
190	outputFilename_.c_str());
191	painCave.isFatal = 1;
192	simError();
193	}
194
195	rdfStream.close();
196	}
197
198	}