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, 234107 (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();
        if (sliceCount_[i] != 0) {
          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:	2025
Committed:	Tue Oct 21 00:38:44 2014 UTC (10 years, 6 months ago) by gezelter
File size:	8828 byte(s)
Log Message:	Only print out lines in TetrahedralityParamZ if there are actually observations in that Z bin
#	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, 234107 (2008).
39	* [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	*/
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	namespace OpenMD {
55	TetrahedralityParamZ::TetrahedralityParamZ(SimInfo* info,
56	const std::string& filename,
57	const std::string& sele1,
58	const std::string& sele2,
59	double rCut, int nzbins)
60	: StaticAnalyser(info, filename), selectionScript1_(sele1),
61	evaluator1_(info), seleMan1_(info), selectionScript2_(sele2),
62	evaluator2_(info), seleMan2_(info), nZBins_(nzbins) {
63
64	evaluator1_.loadScriptString(sele1);
65	if (!evaluator1_.isDynamic()) {
66	seleMan1_.setSelectionSet(evaluator1_.evaluate());
67	}
68	evaluator2_.loadScriptString(sele2);
69	if (!evaluator2_.isDynamic()) {
70	seleMan2_.setSelectionSet(evaluator2_.evaluate());
71	}
72
73	// Set up cutoff radius:
74	rCut_ = rCut;
75
76	// 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	}
84
85	TetrahedralityParamZ::~TetrahedralityParamZ() {
86	sliceQ_.clear();
87	sliceCount_.clear();
88	zBox_.clear();
89	}
90
91	void TetrahedralityParamZ::process() {
92	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	Vector3d ri, rj, rk, rik, rkj;
103	RealType r;
104	RealType cospsi;
105	RealType Qk;
106	std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
107	int isd1;
108	int isd2;
109
110	DumpReader reader(info_, dumpFilename_);
111	int nFrames = reader.getNFrames();
112
113	for (int istep = 0; istep < nFrames; istep += step_) {
114	reader.readFrame(istep);
115	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
116
117	Mat3x3d hmat = currentSnapshot_->getHmat();
118	zBox_.push_back(hmat(2,2));
119
120	RealType halfBoxZ_ = hmat(2,2) / 2.0;
121
122	if (evaluator1_.isDynamic()) {
123	seleMan1_.setSelectionSet(evaluator1_.evaluate());
124	}
125
126	if (evaluator2_.isDynamic()) {
127	seleMan2_.setSelectionSet(evaluator2_.evaluate());
128	}
129
130	// update the positions of atoms which belong to the rigidbodies
131	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	}
137	}
138
139	// outer loop is over the selected StuntDoubles:
140	for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
141	sd = seleMan1_.nextSelected(isd1)) {
142
143	myIndex = sd->getGlobalIndex();
144
145	Qk = 1.0;
146	myNeighbors.clear();
147
148	for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL;
149	sd2 = seleMan2_.nextSelected(isd2)) {
150
151	if (sd2->getGlobalIndex() != myIndex) {
152
153	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	}
165	}
166	}
167
168	// Sort the vector using predicate and std::sort
169	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	int nang = int (0.5 * (nbors * (nbors - 1)));
175
176	rk = sd->getPos();
177
178	for (int i = 0; i < nbors-1; i++) {
179
180	sdi = myNeighbors[i].second;
181	ri = sdi->getPos();
182	rik = rk - ri;
183	if (usePeriodicBoundaryConditions_)
184	currentSnapshot_->wrapVector(rik);
185
186	rik.normalize();
187
188	for (int j = i+1; j < nbors; j++) {
189
190	sdj = myNeighbors[j].second;
191	rj = sdj->getPos();
192	rkj = rk - rj;
193	if (usePeriodicBoundaryConditions_)
194	currentSnapshot_->wrapVector(rkj);
195	rkj.normalize();
196
197	cospsi = dot(rik,rkj);
198
199	// Calculates scaled Qk for each molecule using calculated
200	// angles from 4 or fewer nearest neighbors.
201	Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);
202	}
203	}
204
205	if (nang > 0) {
206	if (usePeriodicBoundaryConditions_)
207	currentSnapshot_->wrapVector(rk);
208
209	int binNo = int(nZBins_ * (halfBoxZ_ + rk.z()) / hmat(2,2));
210	sliceQ_[binNo] += Qk;
211	sliceCount_[binNo] += 1;
212	}
213	}
214	}
215	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	}
227	RealType zAve = zSum / zBox_.size();
228
229	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	qZstream << "#selection 1: (" << selectionScript1_ << ")\n";
234	qZstream << "#selection 2: (" << selectionScript2_ << ")\n";
235	qZstream << "#z\tQk\n";
236	for (unsigned int i = 0; i < sliceQ_.size(); ++i) {
237	RealType z = zAve * (i+0.5) / sliceQ_.size();
238	if (sliceCount_[i] != 0) {
239	qZstream << z << "\t" << sliceQ_[i] / sliceCount_[i] << "\n";
240	}
241	}
242
243	} else {
244	sprintf(painCave.errMsg, "TetrahedralityParamZ: unable to open %s\n",
245	outputFilename_.c_str());
246	painCave.isFatal = 1;
247	simError();
248	}
249	qZstream.close();
250	}
251	}
252
253
254