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"
#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:	1832
Committed:	Thu Jan 10 18:15:02 2013 UTC (12 years, 3 months ago) by gezelter
File size:	6797 byte(s)
Log Message:	More careful with casts, fixed windows compilation issues
#	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	#include "types/MultipoleAdapter.hpp"
49
50	namespace OpenMD {
51
52	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	: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
54	setOutputName(getPrefix(filename) + ".gxyz");
55
56	evaluator3_.loadScriptString(sele3);
57	if (!evaluator3_.isDynamic()) {
58	seleMan3_.setSelectionSet(evaluator3_.evaluate());
59	}
60
61	deltaR_ = len_ / nRBins_;
62
63	histogram_.resize(nRBins_);
64	for (int i = 0 ; i < nRBins_; ++i) {
65	histogram_[i].resize(nRBins_);
66	for(int j = 0; j < nRBins_; ++j) {
67	histogram_[i][j].resize(nRBins_);
68	}
69	}
70
71	}
72
73
74	void GofXyz::preProcess() {
75	for (int i = 0 ; i < nRBins_; ++i) {
76	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	}
81	}
82
83
84	void GofXyz::initializeHistogram() {
85	//calculate the center of mass of the molecule of selected stuntdouble in selection1
86
87	if (!evaluator3_.isDynamic()) {
88	seleMan3_.setSelectionSet(evaluator3_.evaluate());
89	}
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	//x = v1 X z
97	//y = z X x
98	rotMats_.clear();
99
100	int i;
101	int j;
102	StuntDouble* sd1;
103	StuntDouble* sd3;
104
105	for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
106	sd1 != NULL \|\| sd3 != NULL;
107	sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
108
109	Vector3d r3 = sd3->getPos();
110	Vector3d r1 = sd1->getPos();
111	Vector3d v1 = r3 - r1;
112	if (usePeriodicBoundaryConditions_)
113	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
114
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	Vector3d xaxis = cross(v1, zaxis);
125	Vector3d yaxis = cross(zaxis, xaxis);
126
127	xaxis.normalize();
128	yaxis.normalize();
129	zaxis.normalize();
130
131	RotMat3x3d rotMat;
132	rotMat.setRow(0, xaxis);
133	rotMat.setRow(1, yaxis);
134	rotMat.setRow(2, zaxis);
135
136	rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
137	}
138
139	}
140
141	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
142
143	Vector3d pos1 = sd1->getPos();
144	Vector3d pos2 = sd2->getPos();
145	Vector3d r12 = pos2 - pos1;
146	if (usePeriodicBoundaryConditions_)
147	currentSnapshot_->wrapVector(r12);
148
149	std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
150	assert(i != rotMats_.end());
151
152	Vector3d newR12 = i->second * r12;
153	// x, y and z's possible values range -halfLen_ to halfLen_
154	int xbin = int( (newR12.x() + halfLen_) / deltaR_);
155	int ybin = int( (newR12.y() + halfLen_) / deltaR_);
156	int zbin = int( (newR12.z() + halfLen_) / deltaR_);
157
158	if (xbin < nRBins_ && xbin >=0 &&
159	ybin < nRBins_ && ybin >= 0 &&
160	zbin < nRBins_ && zbin >=0 ) {
161	++histogram_[xbin][ybin][zbin];
162	}
163
164	}
165
166	void GofXyz::writeRdf() {
167	std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
168	if (rdfStream.is_open()) {
169	//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	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	}
179	}
180	}
181
182	} else {
183
184	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
185	painCave.isFatal = 1;
186	simError();
187	}
188
189	rdfStream.close();
190	}
191
192	}