applications/staticProps/TetrahedralityParam.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]  Vardeman & Gezelter, in progress (2009).                        
 *
 *  Created by J. Daniel Gezelter on 09/26/06.
 *  @author  J. Daniel Gezelter
 *  @version $Id: BondOrderParameter.cpp 1442 2010-05-10 17:28:26Z gezelter $
 *
 */
 
#include "applications/staticProps/TetrahedralityParam.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
#include <vector>

namespace OpenMD {

  TetrahedralityParam::TetrahedralityParam(SimInfo* info, 
                                           const std::string& filename, 
                                           const std::string& sele,
                                           double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
    
    setOutputName(getPrefix(filename) + ".q");

    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }

    // Set up cutoff radius:

    rCut_ = rCut;
    nBins_ = nbins;

    Q_histogram_.resize(nBins_);

    // Q can take values from 0 to 1

    MinQ_ = 0.0;
    MaxQ_ = 1.1;
    deltaQ_ = (MaxQ_ - MinQ_) / nbins;

  }

  TetrahedralityParam::~TetrahedralityParam() {
    Q_histogram_.clear(); 
  }
  
  void TetrahedralityParam::initalizeHistogram() {
    std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
  }
  
  void TetrahedralityParam::process() {
    Molecule* mol;
    StuntDouble* sd;
    StuntDouble* sd2;
    StuntDouble* sdi;
    StuntDouble* sdj;
    StuntDouble* sdk;
    RigidBody* rb;
    int myIndex;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::IntegrableObjectIterator ioi;
    Vector3d vec;
    Vector3d ri, rj, rk, rik, rkj, dposition, tposition;
    RealType r;
    RealType dist;
    RealType cospsi;
    RealType Qk;
    std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
    int isd;

    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    frameCounter_ = 0;

    Distorted_.clear();
    Tetrahedral_.clear();

    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      frameCounter_++;
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      
      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());

        std::cerr << myNeighbors.size() <<  " neighbors within " << rCut_  << " A" << " \n";
        
        // 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);

            //std::cerr << "cos(psi) = " << cospsi << " \n";

            // Calculates scaled Qk for each molecule using calculated angles from 4 or fewer nearest neighbors.
            Qk = Qk - (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);
           
          }
        }

        if (nang > 0) {
          collectHistogram(Qk);

        // Saves positions of StuntDoubles & neighbors with distorted coordination (low Qk value)
        if ((Qk < 0.55) && (Qk > 0.45)) {

          Distorted_.push_back(sd);

          dposition = sd->getPos();
          //std::cerr << "distorted position \t" << dposition << "\n";
        }

        // Saves positions of StuntDoubles & neighbors with tetrahedral coordination (high Qk value)
        if (Qk > 0.95) { 

          Tetrahedral_.push_back(sd);

          tposition = sd->getPos();
          //std::cerr << "tetrahedral position \t" << tposition << "\n";
        }

        }

      }
    }
    
    writeOrderParameter();
    std::cerr << "number of distorted StuntDoubles = " << Distorted_.size() << "\n";
    std::cerr << "number of tetrahedral StuntDoubles = " << Tetrahedral_.size() << "\n";
  }
        
  void TetrahedralityParam::collectHistogram(RealType Qk) {

    if (Qk > MinQ_ && Qk < MaxQ_) {
     
      int whichBin = int((Qk - MinQ_) / deltaQ_);
      Q_histogram_[whichBin] += 1;
    }
  }    


  void TetrahedralityParam::writeOrderParameter() {
    
    int nSelected = 0;

    for (int i = 0; i < nBins_; ++i) {
      nSelected = nSelected + Q_histogram_[i]*deltaQ_;
    }

    std::ofstream osq((getOutputFileName() + "Q").c_str());

    if (osq.is_open()) {
      
      osq << "# Tetrahedrality Parameters\n";
      osq << "# selection: (" << selectionScript_ << ")\n";
      osq << "# \n";
      // Normalize by number of frames and write it out:
      for (int i = 0; i < nBins_; ++i) {
        RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;               
        osq << Qval;
        osq << "\t" << (RealType) (Q_histogram_[i]/deltaQ_)/nSelected;        
        osq << "\n";
      }

      osq.close();
      
    }else {
      sprintf(painCave.errMsg, "TetrahedralityParam: unable to open %s\n", 
              (getOutputFileName() + "q").c_str());
      painCave.isFatal = 1;
      simError();  
    }

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

    if (nFrames == 1) {

    std::vector<StuntDouble*>::iterator iter;
    std::ofstream osd((getOutputFileName() + "dxyz").c_str());

    if (osd.is_open()) {

      osd << Distorted_.size() << "\n";

      osd << "1000000.00000000;    34.52893134     0.00000000     0.00000000;     0.00000000    34.52893134     0.00000000;     0.00000000     0.00000000    34.52893134" << "\n";
      
      for (iter = Distorted_.begin(); iter != Distorted_.end(); ++iter) {

        Vector3d position;

        position = (*iter)->getPos();

        osd << "O  " << "\t";

          for (int z=0; z<position.size(); z++) {

            osd << position[z] << "  " << "\t";
          }

          osd << "\n";

      }

      osd.close();
    }


    std::ofstream ost((getOutputFileName() + "txyz").c_str());
    
    if (ost.is_open()) {

      ost << Tetrahedral_.size() << "\n";

      ost << "1000000.00000000;    34.52893134     0.00000000     0.00000000;     0.00000000    34.52893134     0.00000000;     0.00000000     0.00000000    34.52893134" << "\n";
      
      for (iter = Tetrahedral_.begin(); iter != Tetrahedral_.end(); ++iter) {

        Vector3d position;

        position = (*iter)->getPos();

        ost << "O  " << "\t";

          for (int z=0; z<position.size(); z++) {

            ost << position[z] << "  " << "\t";
          }

          ost << "\n";

      }

      ost.close();
    }
    
  }
}
}
      

Revision:	1524
Committed:	Fri Nov 19 20:48:18 2010 UTC (14 years, 5 months ago) by kstocke1
File size:	10301 byte(s)
Log Message:	added missing files
#	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] Vardeman & Gezelter, in progress (2009).
40	*
41	* Created by J. Daniel Gezelter on 09/26/06.
42	* @author J. Daniel Gezelter
43	* @version $Id: BondOrderParameter.cpp 1442 2010-05-10 17:28:26Z gezelter $
44	*
45	*/
46
47	#include "applications/staticProps/TetrahedralityParam.hpp"
48	#include "utils/simError.h"
49	#include "io/DumpReader.hpp"
50	#include "primitives/Molecule.hpp"
51	#include "utils/NumericConstant.hpp"
52	#include <vector>
53
54	namespace OpenMD {
55
56	TetrahedralityParam::TetrahedralityParam(SimInfo* info,
57	const std::string& filename,
58	const std::string& sele,
59	double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){
60
61	setOutputName(getPrefix(filename) + ".q");
62
63	evaluator_.loadScriptString(sele);
64	if (!evaluator_.isDynamic()) {
65	seleMan_.setSelectionSet(evaluator_.evaluate());
66	}
67
68	// Set up cutoff radius:
69
70	rCut_ = rCut;
71	nBins_ = nbins;
72
73	Q_histogram_.resize(nBins_);
74
75	// Q can take values from 0 to 1
76
77	MinQ_ = 0.0;
78	MaxQ_ = 1.1;
79	deltaQ_ = (MaxQ_ - MinQ_) / nbins;
80
81	}
82
83	TetrahedralityParam::~TetrahedralityParam() {
84	Q_histogram_.clear();
85	}
86
87	void TetrahedralityParam::initalizeHistogram() {
88	std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0);
89	}
90
91	void TetrahedralityParam::process() {
92	Molecule* mol;
93	StuntDouble* sd;
94	StuntDouble* sd2;
95	StuntDouble* sdi;
96	StuntDouble* sdj;
97	StuntDouble* sdk;
98	RigidBody* rb;
99	int myIndex;
100	SimInfo::MoleculeIterator mi;
101	Molecule::RigidBodyIterator rbIter;
102	Molecule::IntegrableObjectIterator ioi;
103	Vector3d vec;
104	Vector3d ri, rj, rk, rik, rkj, dposition, tposition;
105	RealType r;
106	RealType dist;
107	RealType cospsi;
108	RealType Qk;
109	std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
110	int isd;
111
112	DumpReader reader(info_, dumpFilename_);
113	int nFrames = reader.getNFrames();
114	frameCounter_ = 0;
115
116	Distorted_.clear();
117	Tetrahedral_.clear();
118
119	for (int istep = 0; istep < nFrames; istep += step_) {
120	reader.readFrame(istep);
121	frameCounter_++;
122	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
123
124	if (evaluator_.isDynamic()) {
125	seleMan_.setSelectionSet(evaluator_.evaluate());
126	}
127
128	// update the positions of atoms which belong to the rigidbodies
129
130	for (mol = info_->beginMolecule(mi); mol != NULL;
131	mol = info_->nextMolecule(mi)) {
132	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
133	rb = mol->nextRigidBody(rbIter)) {
134	rb->updateAtoms();
135	}
136	}
137
138
139	// outer loop is over the selected StuntDoubles:
140
141	for (sd = seleMan_.beginSelected(isd); sd != NULL;
142	sd = seleMan_.nextSelected(isd)) {
143
144	myIndex = sd->getGlobalIndex();
145	Qk = 1.0;
146
147	myNeighbors.clear();
148
149	// inner loop is over all StuntDoubles in the system:
150
151	for (mol = info_->beginMolecule(mi); mol != NULL;
152	mol = info_->nextMolecule(mi)) {
153
154	for (sd2 = mol->beginIntegrableObject(ioi); sd2 != NULL;
155	sd2 = mol->nextIntegrableObject(ioi)) {
156
157	if (sd2->getGlobalIndex() != myIndex) {
158
159	vec = sd->getPos() - sd2->getPos();
160
161	if (usePeriodicBoundaryConditions_)
162	currentSnapshot_->wrapVector(vec);
163
164	r = vec.length();
165
166	// Check to see if neighbor is in bond cutoff
167
168	if (r < rCut_) {
169
170	myNeighbors.push_back(std::make_pair(r,sd2));
171	}
172	}
173	}
174	}
175
176	// Sort the vector using predicate and std::sort
177	std::sort(myNeighbors.begin(), myNeighbors.end());
178
179	std::cerr << myNeighbors.size() << " neighbors within " << rCut_ << " A" << " \n";
180
181	// Use only the 4 closest neighbors to do the rest of the work:
182
183	int nbors = myNeighbors.size();
184	// > 4 ? 4 : myNeighbors.size();
185	int nang = int (0.5 * (nbors * (nbors - 1)));
186
187	rk = sd->getPos();
188
189	for (int i = 0; i < nbors-1; i++) {
190
191	sdi = myNeighbors[i].second;
192	ri = sdi->getPos();
193	rik = rk - ri;
194	if (usePeriodicBoundaryConditions_)
195	currentSnapshot_->wrapVector(rik);
196
197	rik.normalize();
198
199	for (int j = i+1; j < nbors; j++) {
200
201	sdj = myNeighbors[j].second;
202	rj = sdj->getPos();
203	rkj = rk - rj;
204	if (usePeriodicBoundaryConditions_)
205	currentSnapshot_->wrapVector(rkj);
206	rkj.normalize();
207
208	cospsi = dot(rik,rkj);
209
210	//std::cerr << "cos(psi) = " << cospsi << " \n";
211
212	// Calculates scaled Qk for each molecule using calculated angles from 4 or fewer nearest neighbors.
213	Qk = Qk - (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);
214
215	}
216	}
217
218	if (nang > 0) {
219	collectHistogram(Qk);
220
221	// Saves positions of StuntDoubles & neighbors with distorted coordination (low Qk value)
222	if ((Qk < 0.55) && (Qk > 0.45)) {
223
224	Distorted_.push_back(sd);
225
226	dposition = sd->getPos();
227	//std::cerr << "distorted position \t" << dposition << "\n";
228	}
229
230	// Saves positions of StuntDoubles & neighbors with tetrahedral coordination (high Qk value)
231	if (Qk > 0.95) {
232
233	Tetrahedral_.push_back(sd);
234
235	tposition = sd->getPos();
236	//std::cerr << "tetrahedral position \t" << tposition << "\n";
237	}
238
239	}
240
241	}
242	}
243
244	writeOrderParameter();
245	std::cerr << "number of distorted StuntDoubles = " << Distorted_.size() << "\n";
246	std::cerr << "number of tetrahedral StuntDoubles = " << Tetrahedral_.size() << "\n";
247	}
248
249	void TetrahedralityParam::collectHistogram(RealType Qk) {
250
251	if (Qk > MinQ_ && Qk < MaxQ_) {
252
253	int whichBin = int((Qk - MinQ_) / deltaQ_);
254	Q_histogram_[whichBin] += 1;
255	}
256	}
257
258
259	void TetrahedralityParam::writeOrderParameter() {
260
261	int nSelected = 0;
262
263	for (int i = 0; i < nBins_; ++i) {
264	nSelected = nSelected + Q_histogram_[i]*deltaQ_;
265	}
266
267	std::ofstream osq((getOutputFileName() + "Q").c_str());
268
269	if (osq.is_open()) {
270
271	osq << "# Tetrahedrality Parameters\n";
272	osq << "# selection: (" << selectionScript_ << ")\n";
273	osq << "# \n";
274	// Normalize by number of frames and write it out:
275	for (int i = 0; i < nBins_; ++i) {
276	RealType Qval = MinQ_ + (i + 0.5) * deltaQ_;
277	osq << Qval;
278	osq << "\t" << (RealType) (Q_histogram_[i]/deltaQ_)/nSelected;
279	osq << "\n";
280	}
281
282	osq.close();
283
284	}else {
285	sprintf(painCave.errMsg, "TetrahedralityParam: unable to open %s\n",
286	(getOutputFileName() + "q").c_str());
287	painCave.isFatal = 1;
288	simError();
289	}
290
291	DumpReader reader(info_, dumpFilename_);
292	int nFrames = reader.getNFrames();
293
294	if (nFrames == 1) {
295
296	std::vector<StuntDouble*>::iterator iter;
297	std::ofstream osd((getOutputFileName() + "dxyz").c_str());
298
299	if (osd.is_open()) {
300
301	osd << Distorted_.size() << "\n";
302
303	osd << "1000000.00000000; 34.52893134 0.00000000 0.00000000; 0.00000000 34.52893134 0.00000000; 0.00000000 0.00000000 34.52893134" << "\n";
304
305	for (iter = Distorted_.begin(); iter != Distorted_.end(); ++iter) {
306
307	Vector3d position;
308
309	position = (*iter)->getPos();
310
311	osd << "O " << "\t";
312
313	for (int z=0; z<position.size(); z++) {
314
315	osd << position[z] << " " << "\t";
316	}
317
318	osd << "\n";
319
320	}
321
322	osd.close();
323	}
324
325
326	std::ofstream ost((getOutputFileName() + "txyz").c_str());
327
328	if (ost.is_open()) {
329
330	ost << Tetrahedral_.size() << "\n";
331
332	ost << "1000000.00000000; 34.52893134 0.00000000 0.00000000; 0.00000000 34.52893134 0.00000000; 0.00000000 0.00000000 34.52893134" << "\n";
333
334	for (iter = Tetrahedral_.begin(); iter != Tetrahedral_.end(); ++iter) {
335
336	Vector3d position;
337
338	position = (*iter)->getPos();
339
340	ost << "O " << "\t";
341
342	for (int z=0; z<position.size(); z++) {
343
344	ost << position[z] << " " << "\t";
345	}
346
347	ost << "\n";
348
349	}
350
351	ost.close();
352	}
353
354	}
355	}
356	}
357
358
359