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::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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	6478 byte(s)
Log Message:	updated copyright notices
#	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, 24107 (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	namespace OpenMD {
49
50	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	: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
52	setOutputName(getPrefix(filename) + ".gxyz");
53
54	evaluator3_.loadScriptString(sele3);
55	if (!evaluator3_.isDynamic()) {
56	seleMan3_.setSelectionSet(evaluator3_.evaluate());
57	}
58
59	deltaR_ = len_ / nRBins_;
60
61	histogram_.resize(nRBins_);
62	for (int i = 0 ; i < nRBins_; ++i) {
63	histogram_[i].resize(nRBins_);
64	for(int j = 0; j < nRBins_; ++j) {
65	histogram_[i][j].resize(nRBins_);
66	}
67	}
68
69	}
70
71
72	void GofXyz::preProcess() {
73	for (int i = 0 ; i < nRBins_; ++i) {
74	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	}
79	}
80
81
82	void GofXyz::initalizeHistogram() {
83	//calculate the center of mass of the molecule of selected stuntdouble in selection1
84
85	if (!evaluator3_.isDynamic()) {
86	seleMan3_.setSelectionSet(evaluator3_.evaluate());
87	}
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	//x = v1 X z
95	//y = z X x
96	rotMats_.clear();
97
98	int i;
99	int j;
100	StuntDouble* sd1;
101	StuntDouble* sd3;
102
103	for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
104	sd1 != NULL, sd3 != NULL;
105	sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
106
107	Vector3d r3 =sd3->getPos();
108	Vector3d r1 = sd1->getPos();
109	Vector3d v1 = r3 - r1;
110	if (usePeriodicBoundaryConditions_)
111	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
112	Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
113	Vector3d xaxis = cross(v1, zaxis);
114	Vector3d yaxis = cross(zaxis, xaxis);
115
116	xaxis.normalize();
117	yaxis.normalize();
118	zaxis.normalize();
119
120	RotMat3x3d rotMat;
121	rotMat.setRow(0, xaxis);
122	rotMat.setRow(1, yaxis);
123	rotMat.setRow(2, zaxis);
124
125	rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
126	}
127
128	}
129
130	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
131
132	Vector3d pos1 = sd1->getPos();
133	Vector3d pos2 = sd2->getPos();
134	Vector3d r12 = pos2 - pos1;
135	if (usePeriodicBoundaryConditions_)
136	currentSnapshot_->wrapVector(r12);
137
138	std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
139	assert(i != rotMats_.end());
140
141	Vector3d newR12 = i->second * r12;
142	// x, y and z's possible values range -halfLen_ to halfLen_
143	int xbin = (newR12.x()+ halfLen_) / deltaR_;
144	int ybin = (newR12.y() + halfLen_) / deltaR_;
145	int zbin = (newR12.z() + halfLen_) / deltaR_;
146
147	if (xbin < nRBins_ && xbin >=0 &&
148	ybin < nRBins_ && ybin >= 0 &&
149	zbin < nRBins_ && zbin >=0 ) {
150	++histogram_[xbin][ybin][zbin];
151	}
152
153	}
154
155	void GofXyz::writeRdf() {
156	std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
157	if (rdfStream.is_open()) {
158	//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	for (int i = 0; i < histogram_.size(); ++i) {
163
164	for(int j = 0; j < histogram_[i].size(); ++j) {
165
166	for(int k = 0;k < histogram_[i][j].size(); ++k) {
167	rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
168	}
169	}
170	}
171
172	} else {
173
174	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
175	painCave.isFatal = 1;
176	simError();
177	}
178
179	rdfStream.close();
180	}
181
182	}