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, int nrbins, int nzbins)
    : SequentialAnalyzer(info, filename), selectionScript_(sele), 
      evaluator_(info), seleMan_(info), solidZ_(solidZ),
      threshDens_(threshDens), nRBins_(nrbins), nZBins_(nzbins) {

    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 < nRBins_) && (whichZBin >= 0) && (whichZBin < 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 (unsigned int i = 0; i < nRBins_;  ++i) {
        RealType ther = dr * (i + 0.5);
        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;
        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]));
    RealType ev0 =  fabs(evals[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:	2038
Committed:	Tue Nov 4 22:02:45 2014 UTC (10 years, 5 months ago) by gezelter
File size:	9298 byte(s)
Log Message:	Fixed a arcsin sign bug
#	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
55			ContactAngle2::ContactAngle2(SimInfo* info, const std::string& filename,
56			const std::string& sele, RealType solidZ,
57			RealType threshDens, int nrbins, int nzbins)
58			: SequentialAnalyzer(info, filename), selectionScript_(sele),
59			evaluator_(info), seleMan_(info), solidZ_(solidZ),
60			threshDens_(threshDens), nRBins_(nrbins), nZBins_(nzbins) {
61	gezelter	2037
62	gezelter	2035	setOutputName(getPrefix(filename) + ".ca2");
63
64			evaluator_.loadScriptString(sele);
65
66			if (!evaluator_.isDynamic()) {
67			seleMan_.setSelectionSet(evaluator_.evaluate());
68			}
69			}
70
71			void ContactAngle2::doFrame() {
72			StuntDouble* sd;
73			int i;
74
75			// set up the bins for density analysis
76
77			Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
78			RealType len = std::min(hmat(0, 0), hmat(1, 1));
79			RealType zLen = hmat(2,2);
80	gezelter	2037
81	gezelter	2035	RealType dr = len / (RealType) nRBins_;
82			RealType dz = zLen / (RealType) nZBins_;
83
84			std::vector<std::vector<RealType> > histo;
85			histo.resize(nRBins_);
86	gezelter	2037	for (unsigned int i = 0; i < histo.size(); ++i){
87	gezelter	2035	histo[i].resize(nZBins_);
88			std::fill(histo[i].begin(), histo[i].end(), 0.0);
89			}
90
91			if (evaluator_.isDynamic()) {
92			seleMan_.setSelectionSet(evaluator_.evaluate());
93			}
94
95
96			RealType mtot = 0.0;
97			Vector3d com(V3Zero);
98			RealType mass;
99
100			for (sd = seleMan_.beginSelected(i); sd != NULL;
101			sd = seleMan_.nextSelected(i)) {
102			mass = sd->getMass();
103			mtot += mass;
104			com += sd->getPos() * mass;
105			}
106
107			com /= mtot;
108
109			// now that we have the centroid, we can make cylindrical density maps
110			Vector3d pos;
111			RealType r;
112			RealType z;
113
114			for (sd = seleMan_.beginSelected(i); sd != NULL;
115			sd = seleMan_.nextSelected(i)) {
116			pos = sd->getPos() - com;
117	gezelter	2037
118			// r goes from zero upwards
119	gezelter	2035	r = sqrt(pow(pos.x(), 2) + pow(pos.y(), 2));
120	gezelter	2037	// z is possibly symmetric around 0
121			z = pos.z();
122
123	gezelter	2035	int whichRBin = int(r / dr);
124	gezelter	2037	int whichZBin = int( (zLen/2.0 + z) / dz);
125	gezelter	2035
126	gezelter	2037	if ((whichRBin < nRBins_) && (whichZBin >= 0) && (whichZBin < nZBins_))
127	gezelter	2035	histo[whichRBin][whichZBin] += sd->getMass();
128
129			}
130
131			for(unsigned int i = 0 ; i < histo.size(); ++i){
132
133			RealType rL = i * dr;
134			RealType rU = rL + dr;
135			RealType volSlice = NumericConstant::PI * dz * (( rUrU ) - ( rLrL ));
136
137	gezelter	2037	for (unsigned int j = 0; j < histo[i].size(); ++j) {
138	gezelter	2035	histo[i][j] *= PhysicalConstants::densityConvert / volSlice;
139			}
140			}
141
142	gezelter	2037	std::vector<Vector<RealType, 2> > points;
143			points.clear();
144
145	gezelter	2036	for (unsigned int j = 0; j < nZBins_; ++j) {
146	gezelter	2037
147			// The z coordinates were measured relative to the selection
148			// center of mass. However, we're interested in the elevation
149			// above the solid surface. Also, the binning was done around
150			// zero with enough bins to cover the zLength of the box:
151
152			RealType thez = com.z() - solidZ_ - zLen/2.0 + dz * (j + 0.5);
153	gezelter	2036	bool aboveThresh = false;
154	gezelter	2037	bool foundThresh = false;
155			int rloc = 0;
156
157	gezelter	2036	for (unsigned int i = 0; i < nRBins_; ++i) {
158			RealType ther = dr * (i + 0.5);
159			if (histo[i][j] >= threshDens_) aboveThresh = true;
160
161			if (aboveThresh && (histo[i][j] <= threshDens_)) {
162	gezelter	2037	rloc = i;
163			foundThresh = true;
164			aboveThresh = false;
165	gezelter	2035	}
166	gezelter	2037
167	gezelter	2035	}
168	gezelter	2037	if (foundThresh) {
169			Vector<RealType,2> point;
170			point[0] = dr*(rloc+0.5);
171			point[1] = thez;
172			points.push_back( point );
173			}
174	gezelter	2035	}
175	gezelter	2037
176			int numPoints = points.size();
177
178			// Compute the average of the data points.
179			Vector<RealType, 2> average = points[0];
180			int i0;
181			for (i0 = 1; i0 < numPoints; ++i0) {
182			average += points[i0];
183			}
184			RealType invNumPoints = ((RealType)1)/(RealType)numPoints;
185			average *= invNumPoints;
186	gezelter	2036
187	gezelter	2037	DynamicRectMatrix<RealType> mat(4, 4);
188			int row, col;
189			for (row = 0; row < 4; ++row) {
190			for (col = 0; col < 4; ++col){
191			mat(row,col) = 0.0;
192			}
193			}
194			for (int i = 0; i < numPoints; ++i) {
195			RealType x = points[i][0];
196			RealType y = points[i][1];
197			RealType x2 = x*x;
198			RealType y2 = y*y;
199			RealType xy = x*y;
200			RealType r2 = x2+y2;
201			RealType xr2 = x*r2;
202			RealType yr2 = y*r2;
203			RealType r4 = r2*r2;
204
205			mat(0,1) += x;
206			mat(0,2) += y;
207			mat(0,3) += r2;
208			mat(1,1) += x2;
209			mat(1,2) += xy;
210			mat(1,3) += xr2;
211			mat(2,2) += y2;
212			mat(2,3) += yr2;
213			mat(3,3) += r4;
214			}
215			mat(0,0) = (RealType)numPoints;
216
217			for (row = 0; row < 4; ++row) {
218			for (col = 0; col < row; ++col) {
219			mat(row,col) = mat(col,row);
220			}
221			}
222
223			for (row = 0; row < 4; ++row) {
224			for (col = 0; col < 4; ++col) {
225			mat(row,col) *= invNumPoints;
226			}
227			}
228
229			JAMA::Eigenvalue<RealType> eigensystem(mat);
230			DynamicRectMatrix<RealType> evects(4, 4);
231			DynamicVector<RealType> evals(4);
232
233			eigensystem.getRealEigenvalues(evals);
234			eigensystem.getV(evects);
235
236			DynamicVector<RealType> evector = evects.getColumn(0);
237			RealType inv = ((RealType)1)/evector[3]; // beware zero divide
238			RealType coeff[3];
239			for (row = 0; row < 3; ++row) {
240			coeff[row] = inv*evector[row];
241			}
242
243			Vector<RealType, 2> center;
244	gezelter	2035
245	gezelter	2037	center[0] = -((RealType)0.5)*coeff[1];
246			center[1] = -((RealType)0.5)*coeff[2];
247			RealType radius = sqrt(fabs(center[0]center[0] + center[1]center[1]
248			- coeff[0]));
249			RealType ev0 = fabs(evals[0]);
250
251			int i1;
252			for (i1 = 0; i1 < 100; ++i1) {
253			// Update the iterates.
254			Vector<RealType, 2> current = center;
255
256			// Compute average L, dL/da, dL/db.
257			RealType lenAverage = (RealType)0;
258			Vector<RealType, 2> derLenAverage = Vector<RealType, 2>(0.0);
259			for (i0 = 0; i0 < numPoints; ++i0) {
260			Vector<RealType, 2> diff = points[i0] - center;
261			RealType length = diff.length();
262			if (length > 1e-6) {
263			lenAverage += length;
264			RealType invLength = ((RealType)1)/length;
265			derLenAverage -= invLength*diff;
266			}
267			}
268			lenAverage *= invNumPoints;
269			derLenAverage *= invNumPoints;
270
271			center = average + lenAverage*derLenAverage;
272			radius = lenAverage;
273
274			Vector<RealType, 2> diff = center - current;
275			if (fabs(diff[0]) <= 1e-6 && fabs(diff[1]) <= 1e-6) {
276			break;
277			}
278			}
279
280			RealType zCen = center[1];
281			RealType rDrop = radius;
282			RealType ca;
283
284			if (fabs(zCen) > rDrop) {
285			ca = 180.0;
286			} else {
287	gezelter	2038	ca = 90.0 + asin(zCen/rDrop)*(180.0/M_PI);
288	gezelter	2037	}
289
290			values_.push_back( ca );
291
292	gezelter	2035	}
293			}
294
295