applications/staticProps/TetrahedralityParamXYZ.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/TetrahedralityParamXYZ.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 {
  TetrahedralityParamXYZ::TetrahedralityParamXYZ(SimInfo* info,  
                                                 const std::string& filename, 
                                                 const std::string& sele1,
                                                 const std::string& sele2,
                                                 RealType rCut, RealType voxelSize,
                                                 RealType gaussWidth) 
    : StaticAnalyser(info, filename), selectionScript1_(sele1), 
      evaluator1_(info), seleMan1_(info), selectionScript2_(sele2), 
      evaluator2_(info), seleMan2_(info), rCut_(rCut), voxelSize_(voxelSize),
      gaussWidth_(gaussWidth) {
    
    evaluator1_.loadScriptString(sele1);
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
    evaluator2_.loadScriptString(sele2);
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }
    
    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();

    nBins_(0) = int(hmat(0,0) / voxelSize);
    nBins_(1) = int(hmat(1,1) / voxelSize);
    nBins_(2) = int(hmat(2,2) / voxelSize);

    hist_.resize(nBins_(0));
    count_.resize(nBins_(0));
    for (int i = 0 ; i < nBins_(0); ++i) {
      hist_[i].resize(nBins_(1));
      count_[i].resize(nBins_(1));
      for(int j = 0; j < nBins_(1); ++j) {
        hist_[i][j].resize(nBins_(2));
        count_[i][j].resize(nBins_(2));
        std::fill(hist_[i][j].begin(), hist_[i][j].end(), 0.0);
        std::fill(count_[i][j].begin(), count_[i][j].end(), 0.0);

      }
    }   
    
    setOutputName(getPrefix(filename) + ".Qxyz");
  }
  
  TetrahedralityParamXYZ::~TetrahedralityParamXYZ() {
  }
    
  void TetrahedralityParamXYZ::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;
    std::vector<std::pair<Vector3d, RealType> > qvals;
    std::vector<std::pair<Vector3d, RealType> >::iterator qiter;
    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();
      Vector3d halfBox = Vector3d(hmat(0,0), hmat(1,1), 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();
        }
      }
      
      qvals.clear();

      // 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);
          qvals.push_back(std::make_pair(rk, Qk));
        }  
      }

      for (int i = 0; i < nBins_(0); ++i) {
        for(int j = 0; j < nBins_(1); ++j) {
          for(int k = 0; k < nBins_(2); ++k) {
            Vector3d pos = Vector3d(i, j, k) * voxelSize_ - halfBox;
            for(qiter = qvals.begin(); qiter != qvals.end(); ++qiter) {
              Vector3d d = pos - (*qiter).first;
              currentSnapshot_->wrapVector(d);
              RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3);
              RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2);
              RealType weight = exp(exponent) / denom;
              count_[i][j][k] += weight;
              hist_[i][j][k] += weight * (*qiter).second;
            }
          }
        }
      }
    }
    writeQxyz();
  }
  
  void TetrahedralityParamXYZ::writeQxyz() {

    Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();

    // normalize by total weight in voxel:
    for (unsigned int i = 0; i < hist_.size(); ++i) { 
      for(unsigned int j = 0; j < hist_[i].size(); ++j) { 
        for(unsigned int k = 0;k < hist_[i][j].size(); ++k) {
          hist_[i][j][k] = hist_[i][j][k] / count_[i][j][k];
        }
      }
    }

    std::ofstream qXYZstream(outputFilename_.c_str());
    if (qXYZstream.is_open()) {
      qXYZstream <<  "# AmiraMesh ASCII 1.0\n\n";
      qXYZstream <<  "# Dimensions in x-, y-, and z-direction\n";
      qXYZstream <<  "  define Lattice " << hist_.size() << " " << hist_[0].size() << " " << hist_[0][0].size() << "\n";
      
      qXYZstream <<  "Parameters {\n";
      qXYZstream <<  "    CoordType \"uniform\",\n";
      qXYZstream <<  "    # BoundingBox is xmin xmax ymin ymax zmin zmax\n";
      qXYZstream <<  "    BoundingBox 0.0 " << hmat(0,0) << 
        " 0.0 " << hmat(1,1) << 
        " 0.0 " << hmat(2,2) << "\n";
      qXYZstream <<  "}\n";
      
      qXYZstream <<  "Lattice { double ScalarField } = @1\n";
      
      qXYZstream <<  "@1\n";

      int xsize = hist_.size();
      int ysize = hist_[0].size();
      int zsize = hist_[0][0].size();
      
      for (unsigned int k = 0; k < zsize; ++k) { 
        for(unsigned int j = 0; j < ysize; ++j) { 
          for(unsigned int i = 0; i < xsize; ++i) {
            qXYZstream << hist_[i][j][k] << " ";

            //qXYZstream.write(reinterpret_cast<char *>( &hist_[i][j][k] ),
            // sizeof( hist_[i][j][k] ));
          }
        }
      }
      
    } else {      
      sprintf(painCave.errMsg, "TetrahedralityParamXYZ: unable to open %s\n", 
              outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }    
    qXYZstream.close();
  }
}


Revision:	2016
Committed:	Thu Aug 14 19:04:30 2014 UTC (10 years, 8 months ago) by plouden
File size:	10827 byte(s)
Log Message:	changed the output of Tet_Qxyz to Amira Mesh
#	User	Rev	Content
1	gezelter	2015	/*
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/TetrahedralityParamXYZ.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			TetrahedralityParamXYZ::TetrahedralityParamXYZ(SimInfo* info,
56			const std::string& filename,
57			const std::string& sele1,
58			const std::string& sele2,
59			RealType rCut, RealType voxelSize,
60			RealType gaussWidth)
61			: StaticAnalyser(info, filename), selectionScript1_(sele1),
62			evaluator1_(info), seleMan1_(info), selectionScript2_(sele2),
63			evaluator2_(info), seleMan2_(info), rCut_(rCut), voxelSize_(voxelSize),
64			gaussWidth_(gaussWidth) {
65
66			evaluator1_.loadScriptString(sele1);
67			if (!evaluator1_.isDynamic()) {
68			seleMan1_.setSelectionSet(evaluator1_.evaluate());
69			}
70			evaluator2_.loadScriptString(sele2);
71			if (!evaluator2_.isDynamic()) {
72			seleMan2_.setSelectionSet(evaluator2_.evaluate());
73			}
74
75			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
76
77			nBins_(0) = int(hmat(0,0) / voxelSize);
78			nBins_(1) = int(hmat(1,1) / voxelSize);
79			nBins_(2) = int(hmat(2,2) / voxelSize);
80
81			hist_.resize(nBins_(0));
82			count_.resize(nBins_(0));
83			for (int i = 0 ; i < nBins_(0); ++i) {
84			hist_[i].resize(nBins_(1));
85			count_[i].resize(nBins_(1));
86			for(int j = 0; j < nBins_(1); ++j) {
87			hist_[i][j].resize(nBins_(2));
88			count_[i][j].resize(nBins_(2));
89			std::fill(hist_[i][j].begin(), hist_[i][j].end(), 0.0);
90			std::fill(count_[i][j].begin(), count_[i][j].end(), 0.0);
91
92			}
93			}
94
95			setOutputName(getPrefix(filename) + ".Qxyz");
96			}
97
98			TetrahedralityParamXYZ::~TetrahedralityParamXYZ() {
99			}
100
101			void TetrahedralityParamXYZ::process() {
102			Molecule* mol;
103			StuntDouble* sd;
104			StuntDouble* sd2;
105			StuntDouble* sdi;
106			StuntDouble* sdj;
107			RigidBody* rb;
108			int myIndex;
109			SimInfo::MoleculeIterator mi;
110			Molecule::RigidBodyIterator rbIter;
111			Vector3d vec;
112			Vector3d ri, rj, rk, rik, rkj;
113			RealType r;
114			RealType cospsi;
115			RealType Qk;
116			std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
117			std::vector<std::pair<Vector3d, RealType> > qvals;
118			std::vector<std::pair<Vector3d, RealType> >::iterator qiter;
119			int isd1;
120			int isd2;
121
122			DumpReader reader(info_, dumpFilename_);
123			int nFrames = reader.getNFrames();
124
125			for (int istep = 0; istep < nFrames; istep += step_) {
126			reader.readFrame(istep);
127
128	plouden	2016	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
129			Mat3x3d hmat = currentSnapshot_->getHmat();
130			Vector3d halfBox = Vector3d(hmat(0,0), hmat(1,1), hmat(2,2)) / 2.0;
131
132	gezelter	2015	if (evaluator1_.isDynamic()) {
133			seleMan1_.setSelectionSet(evaluator1_.evaluate());
134			}
135
136			if (evaluator2_.isDynamic()) {
137			seleMan2_.setSelectionSet(evaluator2_.evaluate());
138			}
139
140			// update the positions of atoms which belong to the rigidbodies
141			for (mol = info_->beginMolecule(mi); mol != NULL;
142			mol = info_->nextMolecule(mi)) {
143			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
144			rb = mol->nextRigidBody(rbIter)) {
145			rb->updateAtoms();
146			}
147			}
148
149			qvals.clear();
150
151			// outer loop is over the selected StuntDoubles:
152			for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
153			sd = seleMan1_.nextSelected(isd1)) {
154
155			myIndex = sd->getGlobalIndex();
156
157			Qk = 1.0;
158			myNeighbors.clear();
159
160			for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL;
161			sd2 = seleMan2_.nextSelected(isd2)) {
162
163			if (sd2->getGlobalIndex() != myIndex) {
164
165			vec = sd->getPos() - sd2->getPos();
166
167			if (usePeriodicBoundaryConditions_)
168			currentSnapshot_->wrapVector(vec);
169
170			r = vec.length();
171
172			// Check to see if neighbor is in bond cutoff
173
174			if (r < rCut_) {
175			myNeighbors.push_back(std::make_pair(r,sd2));
176			}
177			}
178			}
179
180			// Sort the vector using predicate and std::sort
181			std::sort(myNeighbors.begin(), myNeighbors.end());
182
183			// Use only the 4 closest neighbors to do the rest of the work:
184
185			int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size();
186			int nang = int (0.5 * (nbors * (nbors - 1)));
187
188			rk = sd->getPos();
189
190			for (int i = 0; i < nbors-1; i++) {
191
192			sdi = myNeighbors[i].second;
193			ri = sdi->getPos();
194			rik = rk - ri;
195			if (usePeriodicBoundaryConditions_)
196			currentSnapshot_->wrapVector(rik);
197
198			rik.normalize();
199
200			for (int j = i+1; j < nbors; j++) {
201
202			sdj = myNeighbors[j].second;
203			rj = sdj->getPos();
204			rkj = rk - rj;
205			if (usePeriodicBoundaryConditions_)
206			currentSnapshot_->wrapVector(rkj);
207			rkj.normalize();
208
209			cospsi = dot(rik,rkj);
210
211			// Calculates scaled Qk for each molecule using calculated
212			// angles from 4 or fewer nearest neighbors.
213			Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);
214			}
215			}
216
217			if (nang > 0) {
218			if (usePeriodicBoundaryConditions_)
219			currentSnapshot_->wrapVector(rk);
220			qvals.push_back(std::make_pair(rk, Qk));
221			}
222			}
223
224			for (int i = 0; i < nBins_(0); ++i) {
225			for(int j = 0; j < nBins_(1); ++j) {
226			for(int k = 0; k < nBins_(2); ++k) {
227	plouden	2016	Vector3d pos = Vector3d(i, j, k) * voxelSize_ - halfBox;
228	gezelter	2015	for(qiter = qvals.begin(); qiter != qvals.end(); ++qiter) {
229			Vector3d d = pos - (*qiter).first;
230	plouden	2016	currentSnapshot_->wrapVector(d);
231	gezelter	2015	RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3);
232			RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2);
233			RealType weight = exp(exponent) / denom;
234			count_[i][j][k] += weight;
235			hist_[i][j][k] += weight * (*qiter).second;
236			}
237			}
238			}
239			}
240			}
241			writeQxyz();
242			}
243
244			void TetrahedralityParamXYZ::writeQxyz() {
245	plouden	2016
246			Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
247
248	gezelter	2015	// normalize by total weight in voxel:
249			for (unsigned int i = 0; i < hist_.size(); ++i) {
250			for(unsigned int j = 0; j < hist_[i].size(); ++j) {
251			for(unsigned int k = 0;k < hist_[i][j].size(); ++k) {
252	plouden	2016	hist_[i][j][k] = hist_[i][j][k] / count_[i][j][k];
253	gezelter	2015	}
254			}
255			}
256
257			std::ofstream qXYZstream(outputFilename_.c_str());
258			if (qXYZstream.is_open()) {
259	plouden	2016	qXYZstream << "# AmiraMesh ASCII 1.0\n\n";
260			qXYZstream << "# Dimensions in x-, y-, and z-direction\n";
261			qXYZstream << " define Lattice " << hist_.size() << " " << hist_[0].size() << " " << hist_[0][0].size() << "\n";
262
263			qXYZstream << "Parameters {\n";
264			qXYZstream << " CoordType \"uniform\",\n";
265			qXYZstream << " # BoundingBox is xmin xmax ymin ymax zmin zmax\n";
266			qXYZstream << " BoundingBox 0.0 " << hmat(0,0) <<
267			" 0.0 " << hmat(1,1) <<
268			" 0.0 " << hmat(2,2) << "\n";
269			qXYZstream << "}\n";
270
271			qXYZstream << "Lattice { double ScalarField } = @1\n";
272
273			qXYZstream << "@1\n";
274	gezelter	2015
275	plouden	2016	int xsize = hist_.size();
276			int ysize = hist_[0].size();
277			int zsize = hist_[0][0].size();
278
279			for (unsigned int k = 0; k < zsize; ++k) {
280			for(unsigned int j = 0; j < ysize; ++j) {
281			for(unsigned int i = 0; i < xsize; ++i) {
282			qXYZstream << hist_[i][j][k] << " ";
283
284			//qXYZstream.write(reinterpret_cast<char *>( &hist_[i][j][k] ),
285			// sizeof( hist_[i][j][k] ));
286	gezelter	2015	}
287			}
288			}
289
290			} else {
291			sprintf(painCave.errMsg, "TetrahedralityParamXYZ: unable to open %s\n",
292			outputFilename_.c_str());
293			painCave.isFatal = 1;
294			simError();
295			}
296			qXYZstream.close();
297			}
298			}
299
300
301