applications/staticProps/TetrahedralityParamZ.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).
 * [6]  Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 */
 
#include "applications/staticProps/TetrahedralityParamZ.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
#include <vector>
#include <algorithm>
#include <fstream>

using namespace std;
namespace OpenMD {
  TetrahedralityParamZ::TetrahedralityParamZ(SimInfo* info,  
                                             const std::string& filename, 
                                             const std::string& sele1,
                                             const std::string& sele2,
                                             double rCut, int nzbins) 
    : StaticAnalyser(info, filename), selectionScript1_(sele1), 
      evaluator1_(info), seleMan1_(info), selectionScript2_(sele2), 
      evaluator2_(info), seleMan2_(info), nZBins_(nzbins) {
    
    evaluator1_.loadScriptString(sele1);
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
    evaluator2_.loadScriptString(sele2);
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }
    
    // Set up cutoff radius:    
    rCut_ = rCut;

    // fixed number of bins
    sliceQ_.resize(nZBins_);
    sliceCount_.resize(nZBins_);    
    std::fill(sliceQ_.begin(), sliceQ_.end(), 0.0);
    std::fill(sliceCount_.begin(), sliceCount_.end(), 0);
    
    setOutputName(getPrefix(filename) + ".Qz");
  }
  
  TetrahedralityParamZ::~TetrahedralityParamZ() {
    sliceQ_.clear();
    sliceCount_.clear();
    zBox_.clear();
  }
    
  void TetrahedralityParamZ::process() {
    Molecule* mol;
    StuntDouble* sd;
    StuntDouble* sd2;
    StuntDouble* sdi;
    StuntDouble* sdj;
    RigidBody* rb;
    int myIndex;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Vector3d vec;
    Vector3d ri, rj, rk, rik, rkj;
    RealType r;
    RealType cospsi;
    RealType Qk;
    std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
    int isd1;
    int isd2;

    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();

    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      
      Mat3x3d hmat = currentSnapshot_->getHmat();
      zBox_.push_back(hmat(2,2));
      
      RealType halfBoxZ_ = hmat(2,2) / 2.0;      

      if (evaluator1_.isDynamic()) {
        seleMan1_.setSelectionSet(evaluator1_.evaluate());
      }
      
      if (evaluator2_.isDynamic()) {
        seleMan2_.setSelectionSet(evaluator2_.evaluate());
      }
      
      // update the positions of atoms which belong to the rigidbodies
      for (mol = info_->beginMolecule(mi); mol != NULL;
           mol = info_->nextMolecule(mi)) {
        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
             rb = mol->nextRigidBody(rbIter)) {
          rb->updateAtoms();
        }
      }
      
      // outer loop is over the selected StuntDoubles:
      for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
           sd = seleMan1_.nextSelected(isd1)) {
        
        myIndex = sd->getGlobalIndex();
        
        Qk = 1.0;         
        myNeighbors.clear();       

        for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL;
             sd2 = seleMan2_.nextSelected(isd2)) {
          
          if (sd2->getGlobalIndex() != myIndex) {
            
            vec = sd->getPos() - sd2->getPos();       
            
            if (usePeriodicBoundaryConditions_) 
              currentSnapshot_->wrapVector(vec);
            
            r = vec.length();             
            
            // Check to see if neighbor is in bond cutoff 
            
            if (r < rCut_) {                
              myNeighbors.push_back(std::make_pair(r,sd2));
            }
          }
        }
        
        // Sort the vector using predicate and std::sort
        std::sort(myNeighbors.begin(), myNeighbors.end());
        
        // Use only the 4 closest neighbors to do the rest of the work:
        
        int nbors =  myNeighbors.size()> 4 ? 4 : myNeighbors.size();
        int nang = int (0.5 * (nbors * (nbors - 1)));
        
        rk = sd->getPos();
        
        for (int i = 0; i < nbors-1; i++) {       
          
          sdi = myNeighbors[i].second;
          ri = sdi->getPos();
          rik = rk - ri;
          if (usePeriodicBoundaryConditions_) 
            currentSnapshot_->wrapVector(rik);
          
          rik.normalize();
          
          for (int j = i+1; j < nbors; j++) {       
            
            sdj = myNeighbors[j].second;
            rj = sdj->getPos();
            rkj = rk - rj;
            if (usePeriodicBoundaryConditions_) 
              currentSnapshot_->wrapVector(rkj);
            rkj.normalize();
            
            cospsi = dot(rik,rkj);           
            
            // Calculates scaled Qk for each molecule using calculated
            // angles from 4 or fewer nearest neighbors.
            Qk -=  (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);            
          }
        }
        
        if (nang > 0) {
          if (usePeriodicBoundaryConditions_)
            currentSnapshot_->wrapVector(rk);
          
          int binNo = int(nZBins_ * (halfBoxZ_ + rk.z()) / hmat(2,2));
          sliceQ_[binNo] += Qk;
          sliceCount_[binNo] += 1;
        }  
      }
    }
    writeQz();
  }
  
  void TetrahedralityParamZ::writeQz() {

    // compute average box length:
    
    RealType zSum = 0.0;
    for (std::vector<RealType>::iterator j = zBox_.begin(); 
         j != zBox_.end(); ++j) {
      zSum += *j;       
    }
    RealType zAve = zSum / zBox_.size();

    std::ofstream qZstream(outputFilename_.c_str());
    if (qZstream.is_open()) {
      qZstream << "#Tetrahedrality Parameters (z)\n";
      qZstream << "#nFrames:\t" << zBox_.size() << "\n";
      qZstream << "#selection 1: (" << selectionScript1_ << ")\n";
      qZstream << "#selection 2: (" << selectionScript2_ << ")\n";
      qZstream << "#z\tQk\n";
      for (unsigned int i = 0; i < sliceQ_.size(); ++i) {
        RealType z = zAve * (i+0.5) / sliceQ_.size();
        qZstream << z << "\t" << sliceQ_[i] / sliceCount_[i] << "\n";
      }
      
    } else {      
      sprintf(painCave.errMsg, "TetrahedralityParamZ: unable to open %s\n", 
              outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }    
    qZstream.close();
  }
}


Revision:	1846
Committed:	Thu Jan 31 15:55:47 2013 UTC (12 years, 8 months ago) by gezelter
File size:	8780 byte(s)
Log Message:	Bug fix in Tetrahedrality parameter Z exposed another bug in SimInfo.
#	User	Rev	Content
1	plouden	1762	/*
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	gezelter	1843	*
36	plouden	1762	* [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	gezelter	1843	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			* [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
42	plouden	1762	*/
43
44			#include "applications/staticProps/TetrahedralityParamZ.hpp"
45			#include "utils/simError.h"
46			#include "io/DumpReader.hpp"
47			#include "primitives/Molecule.hpp"
48			#include "utils/NumericConstant.hpp"
49			#include <vector>
50			#include <algorithm>
51			#include <fstream>
52
53			using namespace std;
54	gezelter	1843	namespace OpenMD {
55			TetrahedralityParamZ::TetrahedralityParamZ(SimInfo* info,
56			const std::string& filename,
57	gezelter	1846	const std::string& sele1,
58			const std::string& sele2,
59	gezelter	1843	double rCut, int nzbins)
60	gezelter	1846	: StaticAnalyser(info, filename), selectionScript1_(sele1),
61			evaluator1_(info), seleMan1_(info), selectionScript2_(sele2),
62			evaluator2_(info), seleMan2_(info), nZBins_(nzbins) {
63	plouden	1762
64	gezelter	1846	evaluator1_.loadScriptString(sele1);
65			if (!evaluator1_.isDynamic()) {
66			seleMan1_.setSelectionSet(evaluator1_.evaluate());
67	gezelter	1843	}
68	gezelter	1846	evaluator2_.loadScriptString(sele2);
69			if (!evaluator2_.isDynamic()) {
70			seleMan2_.setSelectionSet(evaluator2_.evaluate());
71			}
72	gezelter	1843
73			// Set up cutoff radius:
74	plouden	1762	rCut_ = rCut;
75
76	gezelter	1843	// fixed number of bins
77			sliceQ_.resize(nZBins_);
78			sliceCount_.resize(nZBins_);
79			std::fill(sliceQ_.begin(), sliceQ_.end(), 0.0);
80			std::fill(sliceCount_.begin(), sliceCount_.end(), 0);
81
82			setOutputName(getPrefix(filename) + ".Qz");
83	plouden	1762	}
84
85	gezelter	1843	TetrahedralityParamZ::~TetrahedralityParamZ() {
86			sliceQ_.clear();
87			sliceCount_.clear();
88			zBox_.clear();
89	plouden	1762	}
90	gezelter	1843
91			void TetrahedralityParamZ::process() {
92	plouden	1762	Molecule* mol;
93			StuntDouble* sd;
94			StuntDouble* sd2;
95			StuntDouble* sdi;
96			StuntDouble* sdj;
97			RigidBody* rb;
98			int myIndex;
99			SimInfo::MoleculeIterator mi;
100			Molecule::RigidBodyIterator rbIter;
101			Vector3d vec;
102	gezelter	1843	Vector3d ri, rj, rk, rik, rkj;
103	plouden	1762	RealType r;
104			RealType cospsi;
105			RealType Qk;
106	gezelter	1843	std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
107	gezelter	1846	int isd1;
108			int isd2;
109	gezelter	1767
110	plouden	1762	DumpReader reader(info_, dumpFilename_);
111			int nFrames = reader.getNFrames();
112
113	gezelter	1796	for (int istep = 0; istep < nFrames; istep += step_) {
114			reader.readFrame(istep);
115			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
116
117	gezelter	1843	Mat3x3d hmat = currentSnapshot_->getHmat();
118			zBox_.push_back(hmat(2,2));
119
120			RealType halfBoxZ_ = hmat(2,2) / 2.0;
121
122	gezelter	1846	if (evaluator1_.isDynamic()) {
123			seleMan1_.setSelectionSet(evaluator1_.evaluate());
124	gezelter	1796	}
125	gezelter	1843
126	gezelter	1846	if (evaluator2_.isDynamic()) {
127			seleMan2_.setSelectionSet(evaluator2_.evaluate());
128			}
129
130	plouden	1762	// update the positions of atoms which belong to the rigidbodies
131	gezelter	1796	for (mol = info_->beginMolecule(mi); mol != NULL;
132			mol = info_->nextMolecule(mi)) {
133			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
134			rb = mol->nextRigidBody(rbIter)) {
135			rb->updateAtoms();
136	gezelter	1843	}
137			}
138
139	gezelter	1796	// outer loop is over the selected StuntDoubles:
140	gezelter	1846	for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
141			sd = seleMan1_.nextSelected(isd1)) {
142	gezelter	1843
143	gezelter	1796	myIndex = sd->getGlobalIndex();
144	gezelter	1846
145	gezelter	1796	Qk = 1.0;
146	gezelter	1846	myNeighbors.clear();
147	gezelter	1843
148	gezelter	1846	for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL;
149			sd2 = seleMan2_.nextSelected(isd2)) {
150
151			if (sd2->getGlobalIndex() != myIndex) {
152	gezelter	1796
153	gezelter	1846	vec = sd->getPos() - sd2->getPos();
154
155			if (usePeriodicBoundaryConditions_)
156			currentSnapshot_->wrapVector(vec);
157
158			r = vec.length();
159
160			// Check to see if neighbor is in bond cutoff
161
162			if (r < rCut_) {
163			myNeighbors.push_back(std::make_pair(r,sd2));
164	gezelter	1796	}
165			}
166			}
167
168			// Sort the vector using predicate and std::sort
169	gezelter	1843	std::sort(myNeighbors.begin(), myNeighbors.end());
170
171			// Use only the 4 closest neighbors to do the rest of the work:
172
173			int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size();
174	gezelter	1796	int nang = int (0.5 * (nbors * (nbors - 1)));
175	gezelter	1843
176	gezelter	1796	rk = sd->getPos();
177	gezelter	1846
178	gezelter	1843	for (int i = 0; i < nbors-1; i++) {
179	gezelter	1846
180	gezelter	1796	sdi = myNeighbors[i].second;
181			ri = sdi->getPos();
182			rik = rk - ri;
183			if (usePeriodicBoundaryConditions_)
184	gezelter	1843	currentSnapshot_->wrapVector(rik);
185
186	gezelter	1796	rik.normalize();
187	gezelter	1846
188	gezelter	1843	for (int j = i+1; j < nbors; j++) {
189	gezelter	1846
190	gezelter	1796	sdj = myNeighbors[j].second;
191			rj = sdj->getPos();
192			rkj = rk - rj;
193			if (usePeriodicBoundaryConditions_)
194			currentSnapshot_->wrapVector(rkj);
195			rkj.normalize();
196
197	gezelter	1843	cospsi = dot(rik,rkj);
198	gezelter	1846
199	gezelter	1796	// Calculates scaled Qk for each molecule using calculated
200			// angles from 4 or fewer nearest neighbors.
201	gezelter	1843	Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);
202	gezelter	1796	}
203			}
204	gezelter	1846
205	gezelter	1796	if (nang > 0) {
206	gezelter	1843	if (usePeriodicBoundaryConditions_)
207			currentSnapshot_->wrapVector(rk);
208	gezelter	1796
209	gezelter	1843	int binNo = int(nZBins_ * (halfBoxZ_ + rk.z()) / hmat(2,2));
210			sliceQ_[binNo] += Qk;
211			sliceCount_[binNo] += 1;
212			}
213	plouden	1762	}
214	gezelter	1796	}
215	gezelter	1843	writeQz();
216			}
217
218			void TetrahedralityParamZ::writeQz() {
219
220			// compute average box length:
221
222			RealType zSum = 0.0;
223			for (std::vector<RealType>::iterator j = zBox_.begin();
224			j != zBox_.end(); ++j) {
225			zSum += *j;
226	gezelter	1796	}
227	gezelter	1843	RealType zAve = zSum / zBox_.size();
228	plouden	1762
229	gezelter	1843	std::ofstream qZstream(outputFilename_.c_str());
230			if (qZstream.is_open()) {
231			qZstream << "#Tetrahedrality Parameters (z)\n";
232			qZstream << "#nFrames:\t" << zBox_.size() << "\n";
233	gezelter	1846	qZstream << "#selection 1: (" << selectionScript1_ << ")\n";
234			qZstream << "#selection 2: (" << selectionScript2_ << ")\n";
235	gezelter	1843	qZstream << "#z\tQk\n";
236			for (unsigned int i = 0; i < sliceQ_.size(); ++i) {
237			RealType z = zAve * (i+0.5) / sliceQ_.size();
238			qZstream << z << "\t" << sliceQ_[i] / sliceCount_[i] << "\n";
239			}
240
241			} else {
242	gezelter	1796	sprintf(painCave.errMsg, "TetrahedralityParamZ: unable to open %s\n",
243	gezelter	1843	outputFilename_.c_str());
244	gezelter	1796	painCave.isFatal = 1;
245			simError();
246	gezelter	1843	}
247			qZstream.close();
248	plouden	1762	}
249			}
250
251
252