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& sele,
                                             double rCut, int nzbins) 
    : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), 
      seleMan_(info), nZBins_(nzbins) {
    
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.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::IntegrableObjectIterator ioi;
    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 isd;

    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 (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.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 = seleMan_.beginSelected(isd); sd != NULL;
           sd = seleMan_.nextSelected(isd)) {
        
        myIndex = sd->getGlobalIndex();

        Qk = 1.0;         
        myNeighbors.clear();
        
        // inner loop is over all StuntDoubles in the system:
        
        for (mol = info_->beginMolecule(mi); mol != NULL; 
             mol = info_->nextMolecule(mi)) {

          for (sd2 = mol->beginIntegrableObject(ioi); sd2 != NULL; 
               sd2 = mol->nextIntegrableObject(ioi)) {
            
            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: (" << selectionScript_ << ")\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:	1843
Committed:	Tue Jan 29 20:58:08 2013 UTC (12 years, 3 months ago) by gezelter
File size:	8480 byte(s)
Log Message:	Simplified the Tetrahedrality [Qk(z)] analysis code.
#	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			const std::string& sele,
58			double rCut, int nzbins)
59			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info),
60			seleMan_(info), nZBins_(nzbins) {
61	plouden	1762
62			evaluator_.loadScriptString(sele);
63	gezelter	1843	if (!evaluator_.isDynamic()) {
64			seleMan_.setSelectionSet(evaluator_.evaluate());
65			}
66
67			// Set up cutoff radius:
68	plouden	1762	rCut_ = rCut;
69
70	gezelter	1843	// fixed number of bins
71			sliceQ_.resize(nZBins_);
72			sliceCount_.resize(nZBins_);
73			std::fill(sliceQ_.begin(), sliceQ_.end(), 0.0);
74			std::fill(sliceCount_.begin(), sliceCount_.end(), 0);
75
76			setOutputName(getPrefix(filename) + ".Qz");
77	plouden	1762	}
78
79	gezelter	1843	TetrahedralityParamZ::~TetrahedralityParamZ() {
80			sliceQ_.clear();
81			sliceCount_.clear();
82			zBox_.clear();
83	plouden	1762	}
84	gezelter	1843
85			void TetrahedralityParamZ::process() {
86	plouden	1762	Molecule* mol;
87			StuntDouble* sd;
88			StuntDouble* sd2;
89			StuntDouble* sdi;
90			StuntDouble* sdj;
91			RigidBody* rb;
92			int myIndex;
93			SimInfo::MoleculeIterator mi;
94	gezelter	1843	Molecule::IntegrableObjectIterator ioi;
95	plouden	1762	Molecule::RigidBodyIterator rbIter;
96			Vector3d vec;
97	gezelter	1843	Vector3d ri, rj, rk, rik, rkj;
98	plouden	1762	RealType r;
99			RealType cospsi;
100			RealType Qk;
101	gezelter	1843	std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
102			int isd;
103	gezelter	1767
104	plouden	1762	DumpReader reader(info_, dumpFilename_);
105			int nFrames = reader.getNFrames();
106
107	gezelter	1796	for (int istep = 0; istep < nFrames; istep += step_) {
108			reader.readFrame(istep);
109			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
110
111	gezelter	1843	Mat3x3d hmat = currentSnapshot_->getHmat();
112			zBox_.push_back(hmat(2,2));
113
114			RealType halfBoxZ_ = hmat(2,2) / 2.0;
115
116	gezelter	1796	if (evaluator_.isDynamic()) {
117	gezelter	1843	seleMan_.setSelectionSet(evaluator_.evaluate());
118	gezelter	1796	}
119	gezelter	1843
120	plouden	1762	// update the positions of atoms which belong to the rigidbodies
121	gezelter	1796	for (mol = info_->beginMolecule(mi); mol != NULL;
122			mol = info_->nextMolecule(mi)) {
123			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
124			rb = mol->nextRigidBody(rbIter)) {
125			rb->updateAtoms();
126	gezelter	1843	}
127			}
128
129	gezelter	1796	// outer loop is over the selected StuntDoubles:
130	gezelter	1843	for (sd = seleMan_.beginSelected(isd); sd != NULL;
131			sd = seleMan_.nextSelected(isd)) {
132
133	gezelter	1796	myIndex = sd->getGlobalIndex();
134	gezelter	1843
135	gezelter	1796	Qk = 1.0;
136			myNeighbors.clear();
137	gezelter	1843
138			// inner loop is over all StuntDoubles in the system:
139
140			for (mol = info_->beginMolecule(mi); mol != NULL;
141			mol = info_->nextMolecule(mi)) {
142
143			for (sd2 = mol->beginIntegrableObject(ioi); sd2 != NULL;
144			sd2 = mol->nextIntegrableObject(ioi)) {
145	gezelter	1796
146	gezelter	1843	if (sd2->getGlobalIndex() != myIndex) {
147
148			vec = sd->getPos() - sd2->getPos();
149
150			if (usePeriodicBoundaryConditions_)
151			currentSnapshot_->wrapVector(vec);
152
153			r = vec.length();
154
155			// Check to see if neighbor is in bond cutoff
156
157			if (r < rCut_) {
158			myNeighbors.push_back(std::make_pair(r,sd2));
159			}
160	gezelter	1796	}
161			}
162			}
163
164			// Sort the vector using predicate and std::sort
165	gezelter	1843	std::sort(myNeighbors.begin(), myNeighbors.end());
166
167			// Use only the 4 closest neighbors to do the rest of the work:
168
169			int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size();
170	gezelter	1796	int nang = int (0.5 * (nbors * (nbors - 1)));
171	gezelter	1843
172	gezelter	1796	rk = sd->getPos();
173	gezelter	1843
174			for (int i = 0; i < nbors-1; i++) {
175
176	gezelter	1796	sdi = myNeighbors[i].second;
177			ri = sdi->getPos();
178			rik = rk - ri;
179			if (usePeriodicBoundaryConditions_)
180	gezelter	1843	currentSnapshot_->wrapVector(rik);
181
182	gezelter	1796	rik.normalize();
183	gezelter	1843
184			for (int j = i+1; j < nbors; j++) {
185
186	gezelter	1796	sdj = myNeighbors[j].second;
187			rj = sdj->getPos();
188			rkj = rk - rj;
189			if (usePeriodicBoundaryConditions_)
190			currentSnapshot_->wrapVector(rkj);
191			rkj.normalize();
192
193	gezelter	1843	cospsi = dot(rik,rkj);
194
195	gezelter	1796	// Calculates scaled Qk for each molecule using calculated
196			// angles from 4 or fewer nearest neighbors.
197	gezelter	1843	Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);
198	gezelter	1796	}
199			}
200	gezelter	1843
201	gezelter	1796	if (nang > 0) {
202	gezelter	1843	if (usePeriodicBoundaryConditions_)
203			currentSnapshot_->wrapVector(rk);
204	gezelter	1796
205	gezelter	1843	int binNo = int(nZBins_ * (halfBoxZ_ + rk.z()) / hmat(2,2));
206			sliceQ_[binNo] += Qk;
207			sliceCount_[binNo] += 1;
208			}
209	plouden	1762	}
210	gezelter	1796	}
211	gezelter	1843	writeQz();
212			}
213
214			void TetrahedralityParamZ::writeQz() {
215
216			// compute average box length:
217
218			RealType zSum = 0.0;
219			for (std::vector<RealType>::iterator j = zBox_.begin();
220			j != zBox_.end(); ++j) {
221			zSum += *j;
222	gezelter	1796	}
223	gezelter	1843	RealType zAve = zSum / zBox_.size();
224	plouden	1762
225	gezelter	1843	std::ofstream qZstream(outputFilename_.c_str());
226			if (qZstream.is_open()) {
227			qZstream << "#Tetrahedrality Parameters (z)\n";
228			qZstream << "#nFrames:\t" << zBox_.size() << "\n";
229			qZstream << "#selection: (" << selectionScript_ << ")\n";
230			qZstream << "#z\tQk\n";
231			for (unsigned int i = 0; i < sliceQ_.size(); ++i) {
232			RealType z = zAve * (i+0.5) / sliceQ_.size();
233			qZstream << z << "\t" << sliceQ_[i] / sliceCount_[i] << "\n";
234			}
235
236			} else {
237	gezelter	1796	sprintf(painCave.errMsg, "TetrahedralityParamZ: unable to open %s\n",
238	gezelter	1843	outputFilename_.c_str());
239	gezelter	1796	painCave.isFatal = 1;
240			simError();
241	gezelter	1843	}
242			qZstream.close();
243	plouden	1762	}
244			}
245
246
247