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)
#	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::initializeHistogram() {
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 (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	}
168	}
169	}
170
171	} else {
172
173	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
174	painCave.isFatal = 1;
175	simError();
176	}
177
178	rdfStream.close();
179	}
180
181	}