applications/sequentialProps/ContactAngle2.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).
 */

#include <algorithm>
#include <functional>
#include "applications/sequentialProps/ContactAngle2.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
#include "utils/PhysicalConstants.hpp"
#include "math/Eigenvalue.hpp"

namespace OpenMD {
  
  ContactAngle2::ContactAngle2(SimInfo* info, const std::string& filename, 
                               const std::string& sele, RealType solidZ,
                               RealType threshDens, RealType bufferLength,
                               int nrbins, int nzbins)
  : SequentialAnalyzer(info, filename), solidZ_(solidZ), 
    threshDens_(threshDens), bufferLength_(bufferLength), nRBins_(nrbins), 
    nZBins_(nzbins), selectionScript_(sele), seleMan_(info), 
    evaluator_(info) {
    
    setOutputName(getPrefix(filename) + ".ca2");
    
    evaluator_.loadScriptString(sele);
    
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }            
  }

  void ContactAngle2::doFrame() {
    StuntDouble* sd;
    int i;

    // set up the bins for density analysis

    Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
    RealType len = std::min(hmat(0, 0), hmat(1, 1));
    RealType zLen = hmat(2,2);

    RealType dr = len / (RealType) nRBins_;
    RealType dz = zLen / (RealType) nZBins_;

    std::vector<std::vector<RealType> > histo;
    histo.resize(nRBins_);
    for (unsigned int i = 0; i < histo.size(); ++i){
      histo[i].resize(nZBins_);
      std::fill(histo[i].begin(), histo[i].end(), 0.0);
    }      
        
    if (evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
    

    RealType mtot = 0.0;
    Vector3d com(V3Zero);
    RealType mass;
    
    for (sd = seleMan_.beginSelected(i); sd != NULL;
         sd = seleMan_.nextSelected(i)) {      
      mass = sd->getMass();
      mtot += mass;
      com += sd->getPos() * mass;
    }

    com /= mtot;

    // now that we have the centroid, we can make cylindrical density maps
    Vector3d pos;
    RealType r;
    RealType z;
    
    for (sd = seleMan_.beginSelected(i); sd != NULL;
         sd = seleMan_.nextSelected(i)) {      
      pos = sd->getPos() - com;

      // r goes from zero upwards
      r = sqrt(pow(pos.x(), 2) + pow(pos.y(), 2));
      // z is possibly symmetric around 0
      z = pos.z();
          
      int whichRBin = int(r / dr);
      int whichZBin = int( (zLen/2.0 + z) / dz);
      
      if ((whichRBin < int(nRBins_)) && (whichZBin >= 0) && (whichZBin < int(nZBins_))) {
        histo[whichRBin][whichZBin] += sd->getMass();
      }
      
    }
    
    for(unsigned int i = 0 ; i < histo.size(); ++i){

      RealType rL = i * dr;
      RealType rU = rL + dr;
      RealType volSlice = NumericConstant::PI * dz * (( rU*rU ) - ( rL*rL ));

      for (unsigned int j = 0; j < histo[i].size(); ++j) {
        histo[i][j] *= PhysicalConstants::densityConvert / volSlice;
      }
    }

    std::vector<Vector<RealType, 2> > points;
    points.clear();
    
    for (unsigned int j = 0; j < nZBins_;  ++j) {

      // The z coordinates were measured relative to the selection
      // center of mass.  However, we're interested in the elevation
      // above the solid surface.  Also, the binning was done around
      // zero with enough bins to cover the zLength of the box:
      
      RealType thez =  com.z() - solidZ_  - zLen/2.0 + dz * (j + 0.5);
      bool aboveThresh = false;
      bool foundThresh = false;
      int rloc = 0;
      
      for (std::size_t i = 0; i < nRBins_;  ++i) {

        if (histo[i][j] >= threshDens_) aboveThresh = true;

        if (aboveThresh && (histo[i][j] <= threshDens_)) {
          rloc = i;
          foundThresh = true;
          aboveThresh = false;
        }

      }
      if (foundThresh) {
        Vector<RealType,2> point;
        point[0] = dr*(rloc+0.5);
        point[1] = thez;

        if (thez > bufferLength_) {
          points.push_back( point );
        }
      }      
    }

    int numPoints = points.size();

    // Compute the average of the data points.
    Vector<RealType, 2> average = points[0];
    int i0;
    for (i0 = 1; i0 < numPoints; ++i0) {
      average += points[i0];
    }
    RealType invNumPoints = ((RealType)1)/(RealType)numPoints;
    average *= invNumPoints;
    
    DynamicRectMatrix<RealType> mat(4, 4);
    int row, col;
    for (row = 0; row < 4; ++row) {
      for (col = 0; col < 4; ++col){
        mat(row,col) = 0.0;        
      }
    }
    for (int i = 0; i < numPoints; ++i) {
      RealType x = points[i][0];
      RealType y = points[i][1];
      RealType x2 = x*x;
      RealType y2 = y*y;
      RealType xy = x*y;
      RealType r2 = x2+y2;
      RealType xr2 = x*r2;
      RealType yr2 = y*r2;
      RealType r4 = r2*r2;

      mat(0,1) += x;
      mat(0,2) += y;
      mat(0,3) += r2;
      mat(1,1) += x2;
      mat(1,2) += xy;
      mat(1,3) += xr2;
      mat(2,2) += y2;
      mat(2,3) += yr2;
      mat(3,3) += r4;
    }
    mat(0,0) = (RealType)numPoints;

    for (row = 0; row < 4; ++row) {
      for (col = 0; col < row; ++col) {
        mat(row,col) = mat(col,row);
      }
    }

    for (row = 0; row < 4; ++row) {
      for (col = 0; col < 4; ++col) {
        mat(row,col) *= invNumPoints;
      }
    }

    JAMA::Eigenvalue<RealType> eigensystem(mat);
    DynamicRectMatrix<RealType> evects(4, 4);
    DynamicVector<RealType> evals(4);

    eigensystem.getRealEigenvalues(evals);
    eigensystem.getV(evects);

    DynamicVector<RealType> evector = evects.getColumn(0);
    RealType inv = ((RealType)1)/evector[3];  // beware zero divide
    RealType coeff[3];
    for (row = 0; row < 3; ++row) {
      coeff[row] = inv*evector[row];
    }

    Vector<RealType, 2> center;
    
    center[0] = -((RealType)0.5)*coeff[1];
    center[1] = -((RealType)0.5)*coeff[2];
    RealType radius = sqrt(fabs(center[0]*center[0] + center[1]*center[1]
                                - coeff[0]));

    int i1;
    for (i1 = 0; i1 < 100; ++i1) {
      // Update the iterates.
      Vector<RealType, 2> current = center;
      
      // Compute average L, dL/da, dL/db.
      RealType lenAverage = (RealType)0;
      Vector<RealType, 2> derLenAverage = Vector<RealType, 2>(0.0);
      for (i0 = 0; i0 < numPoints; ++i0) {
        Vector<RealType, 2> diff = points[i0] - center;
        RealType length = diff.length();
        if (length > 1e-6) {
          lenAverage += length;
          RealType invLength = ((RealType)1)/length;
          derLenAverage -= invLength*diff;
        }
      }
      lenAverage *= invNumPoints;
      derLenAverage *= invNumPoints;

      center = average + lenAverage*derLenAverage;
      radius = lenAverage;

      Vector<RealType, 2> diff = center - current;
      if (fabs(diff[0]) <= 1e-6 &&  fabs(diff[1]) <= 1e-6) {
        break;
      }
    }

    RealType zCen = center[1];
    RealType rDrop = radius;
    RealType ca;

    if (fabs(zCen) > rDrop) {
      ca = 180.0;
    } else {
      ca = 90.0 + asin(zCen/rDrop)*(180.0/M_PI);
    }

    values_.push_back( ca );
    
  }   
}


Revision:	2073
Committed:	Sat Mar 7 23:52:07 2015 UTC (10 years, 1 month ago) by gezelter
File size:	9372 byte(s)
Log Message:	added a skipToken function to StringTokenizer, and used this to remove some silly warnings on compilation.
#	User	Rev	Content
1	gezelter	2035	/*
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			*/
42
43			#include <algorithm>
44			#include <functional>
45			#include "applications/sequentialProps/ContactAngle2.hpp"
46			#include "utils/simError.h"
47			#include "io/DumpReader.hpp"
48			#include "primitives/Molecule.hpp"
49			#include "utils/NumericConstant.hpp"
50			#include "utils/PhysicalConstants.hpp"
51	gezelter	2037	#include "math/Eigenvalue.hpp"
52	gezelter	2035
53			namespace OpenMD {
54	gezelter	2071
55	gezelter	2035	ContactAngle2::ContactAngle2(SimInfo* info, const std::string& filename,
56			const std::string& sele, RealType solidZ,
57	gezelter	2039	RealType threshDens, RealType bufferLength,
58			int nrbins, int nzbins)
59	gezelter	2071	: SequentialAnalyzer(info, filename), solidZ_(solidZ),
60			threshDens_(threshDens), bufferLength_(bufferLength), nRBins_(nrbins),
61			nZBins_(nzbins), selectionScript_(sele), seleMan_(info),
62			evaluator_(info) {
63
64	gezelter	2035	setOutputName(getPrefix(filename) + ".ca2");
65
66			evaluator_.loadScriptString(sele);
67
68			if (!evaluator_.isDynamic()) {
69			seleMan_.setSelectionSet(evaluator_.evaluate());
70			}
71			}
72
73			void ContactAngle2::doFrame() {
74			StuntDouble* sd;
75			int i;
76
77			// set up the bins for density analysis
78
79			Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
80			RealType len = std::min(hmat(0, 0), hmat(1, 1));
81			RealType zLen = hmat(2,2);
82	gezelter	2037
83	gezelter	2035	RealType dr = len / (RealType) nRBins_;
84			RealType dz = zLen / (RealType) nZBins_;
85
86			std::vector<std::vector<RealType> > histo;
87			histo.resize(nRBins_);
88	gezelter	2037	for (unsigned int i = 0; i < histo.size(); ++i){
89	gezelter	2035	histo[i].resize(nZBins_);
90			std::fill(histo[i].begin(), histo[i].end(), 0.0);
91			}
92
93			if (evaluator_.isDynamic()) {
94			seleMan_.setSelectionSet(evaluator_.evaluate());
95			}
96
97
98			RealType mtot = 0.0;
99			Vector3d com(V3Zero);
100			RealType mass;
101
102			for (sd = seleMan_.beginSelected(i); sd != NULL;
103			sd = seleMan_.nextSelected(i)) {
104			mass = sd->getMass();
105			mtot += mass;
106			com += sd->getPos() * mass;
107			}
108
109			com /= mtot;
110
111			// now that we have the centroid, we can make cylindrical density maps
112			Vector3d pos;
113			RealType r;
114			RealType z;
115
116			for (sd = seleMan_.beginSelected(i); sd != NULL;
117			sd = seleMan_.nextSelected(i)) {
118			pos = sd->getPos() - com;
119	gezelter	2037
120			// r goes from zero upwards
121	gezelter	2035	r = sqrt(pow(pos.x(), 2) + pow(pos.y(), 2));
122	gezelter	2037	// z is possibly symmetric around 0
123			z = pos.z();
124
125	gezelter	2072	int whichRBin = int(r / dr);
126			int whichZBin = int( (zLen/2.0 + z) / dz);
127	gezelter	2035
128	gezelter	2073	if ((whichRBin < int(nRBins_)) && (whichZBin >= 0) && (whichZBin < int(nZBins_))) {
129			histo[whichRBin][whichZBin] += sd->getMass();
130	gezelter	2072	}
131	gezelter	2035
132			}
133
134			for(unsigned int i = 0 ; i < histo.size(); ++i){
135
136			RealType rL = i * dr;
137			RealType rU = rL + dr;
138			RealType volSlice = NumericConstant::PI * dz * (( rUrU ) - ( rLrL ));
139
140	gezelter	2037	for (unsigned int j = 0; j < histo[i].size(); ++j) {
141	gezelter	2035	histo[i][j] *= PhysicalConstants::densityConvert / volSlice;
142			}
143			}
144
145	gezelter	2037	std::vector<Vector<RealType, 2> > points;
146			points.clear();
147
148	gezelter	2036	for (unsigned int j = 0; j < nZBins_; ++j) {
149	gezelter	2037
150			// The z coordinates were measured relative to the selection
151			// center of mass. However, we're interested in the elevation
152			// above the solid surface. Also, the binning was done around
153			// zero with enough bins to cover the zLength of the box:
154
155			RealType thez = com.z() - solidZ_ - zLen/2.0 + dz * (j + 0.5);
156	gezelter	2036	bool aboveThresh = false;
157	gezelter	2037	bool foundThresh = false;
158			int rloc = 0;
159
160	gezelter	2071	for (std::size_t i = 0; i < nRBins_; ++i) {
161
162	gezelter	2036	if (histo[i][j] >= threshDens_) aboveThresh = true;
163
164			if (aboveThresh && (histo[i][j] <= threshDens_)) {
165	gezelter	2037	rloc = i;
166			foundThresh = true;
167			aboveThresh = false;
168	gezelter	2035	}
169	gezelter	2037
170	gezelter	2035	}
171	gezelter	2037	if (foundThresh) {
172			Vector<RealType,2> point;
173			point[0] = dr*(rloc+0.5);
174			point[1] = thez;
175	gezelter	2039
176			if (thez > bufferLength_) {
177			points.push_back( point );
178			}
179	gezelter	2037	}
180	gezelter	2035	}
181	gezelter	2037
182			int numPoints = points.size();
183
184			// Compute the average of the data points.
185			Vector<RealType, 2> average = points[0];
186			int i0;
187			for (i0 = 1; i0 < numPoints; ++i0) {
188			average += points[i0];
189			}
190			RealType invNumPoints = ((RealType)1)/(RealType)numPoints;
191			average *= invNumPoints;
192	gezelter	2036
193	gezelter	2037	DynamicRectMatrix<RealType> mat(4, 4);
194			int row, col;
195			for (row = 0; row < 4; ++row) {
196			for (col = 0; col < 4; ++col){
197			mat(row,col) = 0.0;
198			}
199			}
200			for (int i = 0; i < numPoints; ++i) {
201			RealType x = points[i][0];
202			RealType y = points[i][1];
203			RealType x2 = x*x;
204			RealType y2 = y*y;
205			RealType xy = x*y;
206			RealType r2 = x2+y2;
207			RealType xr2 = x*r2;
208			RealType yr2 = y*r2;
209			RealType r4 = r2*r2;
210
211			mat(0,1) += x;
212			mat(0,2) += y;
213			mat(0,3) += r2;
214			mat(1,1) += x2;
215			mat(1,2) += xy;
216			mat(1,3) += xr2;
217			mat(2,2) += y2;
218			mat(2,3) += yr2;
219			mat(3,3) += r4;
220			}
221			mat(0,0) = (RealType)numPoints;
222
223			for (row = 0; row < 4; ++row) {
224			for (col = 0; col < row; ++col) {
225			mat(row,col) = mat(col,row);
226			}
227			}
228
229			for (row = 0; row < 4; ++row) {
230			for (col = 0; col < 4; ++col) {
231			mat(row,col) *= invNumPoints;
232			}
233			}
234
235			JAMA::Eigenvalue<RealType> eigensystem(mat);
236			DynamicRectMatrix<RealType> evects(4, 4);
237			DynamicVector<RealType> evals(4);
238
239			eigensystem.getRealEigenvalues(evals);
240			eigensystem.getV(evects);
241
242			DynamicVector<RealType> evector = evects.getColumn(0);
243			RealType inv = ((RealType)1)/evector[3]; // beware zero divide
244			RealType coeff[3];
245			for (row = 0; row < 3; ++row) {
246			coeff[row] = inv*evector[row];
247			}
248
249			Vector<RealType, 2> center;
250	gezelter	2035
251	gezelter	2037	center[0] = -((RealType)0.5)*coeff[1];
252			center[1] = -((RealType)0.5)*coeff[2];
253			RealType radius = sqrt(fabs(center[0]center[0] + center[1]center[1]
254			- coeff[0]));
255
256			int i1;
257			for (i1 = 0; i1 < 100; ++i1) {
258			// Update the iterates.
259			Vector<RealType, 2> current = center;
260
261			// Compute average L, dL/da, dL/db.
262			RealType lenAverage = (RealType)0;
263			Vector<RealType, 2> derLenAverage = Vector<RealType, 2>(0.0);
264			for (i0 = 0; i0 < numPoints; ++i0) {
265			Vector<RealType, 2> diff = points[i0] - center;
266			RealType length = diff.length();
267			if (length > 1e-6) {
268			lenAverage += length;
269			RealType invLength = ((RealType)1)/length;
270			derLenAverage -= invLength*diff;
271			}
272			}
273			lenAverage *= invNumPoints;
274			derLenAverage *= invNumPoints;
275
276			center = average + lenAverage*derLenAverage;
277			radius = lenAverage;
278
279			Vector<RealType, 2> diff = center - current;
280			if (fabs(diff[0]) <= 1e-6 && fabs(diff[1]) <= 1e-6) {
281			break;
282			}
283			}
284
285			RealType zCen = center[1];
286			RealType rDrop = radius;
287			RealType ca;
288
289			if (fabs(zCen) > rDrop) {
290			ca = 180.0;
291			} else {
292	gezelter	2038	ca = 90.0 + asin(zCen/rDrop)*(180.0/M_PI);
293	gezelter	2037	}
294
295			values_.push_back( ca );
296
297	gezelter	2035	}
298			}
299
300