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 < nRBins_) && (whichZBin >= 0) && (whichZBin < nZBins_)) {
        std::size_t i = static_cast<std::size_t>(whichRBin);
        std::size_t j = static_cast<std::size_t>(whichZBin);
        histo[i][j] += 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:	2072
Committed:	Sat Mar 7 22:54:56 2015 UTC (10 years, 1 month ago) by gezelter
File size:	9468 byte(s)
Log Message:	One bug fix
#	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	*/
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	#include "math/Eigenvalue.hpp"
52
53	namespace OpenMD {
54
55	ContactAngle2::ContactAngle2(SimInfo* info, const std::string& filename,
56	const std::string& sele, RealType solidZ,
57	RealType threshDens, RealType bufferLength,
58	int nrbins, int nzbins)
59	: SequentialAnalyzer(info, filename), solidZ_(solidZ),
60	threshDens_(threshDens), bufferLength_(bufferLength), nRBins_(nrbins),
61	nZBins_(nzbins), selectionScript_(sele), seleMan_(info),
62	evaluator_(info) {
63
64	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
83	RealType dr = len / (RealType) nRBins_;
84	RealType dz = zLen / (RealType) nZBins_;
85
86	std::vector<std::vector<RealType> > histo;
87	histo.resize(nRBins_);
88	for (unsigned int i = 0; i < histo.size(); ++i){
89	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
120	// r goes from zero upwards
121	r = sqrt(pow(pos.x(), 2) + pow(pos.y(), 2));
122	// z is possibly symmetric around 0
123	z = pos.z();
124
125	int whichRBin = int(r / dr);
126	int whichZBin = int( (zLen/2.0 + z) / dz);
127
128	if ((whichRBin < nRBins_) && (whichZBin >= 0) && (whichZBin < nZBins_)) {
129	std::size_t i = static_cast<std::size_t>(whichRBin);
130	std::size_t j = static_cast<std::size_t>(whichZBin);
131	histo[i][j] += sd->getMass();
132	}
133
134	}
135
136	for(unsigned int i = 0 ; i < histo.size(); ++i){
137
138	RealType rL = i * dr;
139	RealType rU = rL + dr;
140	RealType volSlice = NumericConstant::PI * dz * (( rUrU ) - ( rLrL ));
141
142	for (unsigned int j = 0; j < histo[i].size(); ++j) {
143	histo[i][j] *= PhysicalConstants::densityConvert / volSlice;
144	}
145	}
146
147	std::vector<Vector<RealType, 2> > points;
148	points.clear();
149
150	for (unsigned int j = 0; j < nZBins_; ++j) {
151
152	// The z coordinates were measured relative to the selection
153	// center of mass. However, we're interested in the elevation
154	// above the solid surface. Also, the binning was done around
155	// zero with enough bins to cover the zLength of the box:
156
157	RealType thez = com.z() - solidZ_ - zLen/2.0 + dz * (j + 0.5);
158	bool aboveThresh = false;
159	bool foundThresh = false;
160	int rloc = 0;
161
162	for (std::size_t i = 0; i < nRBins_; ++i) {
163
164	if (histo[i][j] >= threshDens_) aboveThresh = true;
165
166	if (aboveThresh && (histo[i][j] <= threshDens_)) {
167	rloc = i;
168	foundThresh = true;
169	aboveThresh = false;
170	}
171
172	}
173	if (foundThresh) {
174	Vector<RealType,2> point;
175	point[0] = dr*(rloc+0.5);
176	point[1] = thez;
177
178	if (thez > bufferLength_) {
179	points.push_back( point );
180	}
181	}
182	}
183
184	int numPoints = points.size();
185
186	// Compute the average of the data points.
187	Vector<RealType, 2> average = points[0];
188	int i0;
189	for (i0 = 1; i0 < numPoints; ++i0) {
190	average += points[i0];
191	}
192	RealType invNumPoints = ((RealType)1)/(RealType)numPoints;
193	average *= invNumPoints;
194
195	DynamicRectMatrix<RealType> mat(4, 4);
196	int row, col;
197	for (row = 0; row < 4; ++row) {
198	for (col = 0; col < 4; ++col){
199	mat(row,col) = 0.0;
200	}
201	}
202	for (int i = 0; i < numPoints; ++i) {
203	RealType x = points[i][0];
204	RealType y = points[i][1];
205	RealType x2 = x*x;
206	RealType y2 = y*y;
207	RealType xy = x*y;
208	RealType r2 = x2+y2;
209	RealType xr2 = x*r2;
210	RealType yr2 = y*r2;
211	RealType r4 = r2*r2;
212
213	mat(0,1) += x;
214	mat(0,2) += y;
215	mat(0,3) += r2;
216	mat(1,1) += x2;
217	mat(1,2) += xy;
218	mat(1,3) += xr2;
219	mat(2,2) += y2;
220	mat(2,3) += yr2;
221	mat(3,3) += r4;
222	}
223	mat(0,0) = (RealType)numPoints;
224
225	for (row = 0; row < 4; ++row) {
226	for (col = 0; col < row; ++col) {
227	mat(row,col) = mat(col,row);
228	}
229	}
230
231	for (row = 0; row < 4; ++row) {
232	for (col = 0; col < 4; ++col) {
233	mat(row,col) *= invNumPoints;
234	}
235	}
236
237	JAMA::Eigenvalue<RealType> eigensystem(mat);
238	DynamicRectMatrix<RealType> evects(4, 4);
239	DynamicVector<RealType> evals(4);
240
241	eigensystem.getRealEigenvalues(evals);
242	eigensystem.getV(evects);
243
244	DynamicVector<RealType> evector = evects.getColumn(0);
245	RealType inv = ((RealType)1)/evector[3]; // beware zero divide
246	RealType coeff[3];
247	for (row = 0; row < 3; ++row) {
248	coeff[row] = inv*evector[row];
249	}
250
251	Vector<RealType, 2> center;
252
253	center[0] = -((RealType)0.5)*coeff[1];
254	center[1] = -((RealType)0.5)*coeff[2];
255	RealType radius = sqrt(fabs(center[0]center[0] + center[1]center[1]
256	- coeff[0]));
257
258	int i1;
259	for (i1 = 0; i1 < 100; ++i1) {
260	// Update the iterates.
261	Vector<RealType, 2> current = center;
262
263	// Compute average L, dL/da, dL/db.
264	RealType lenAverage = (RealType)0;
265	Vector<RealType, 2> derLenAverage = Vector<RealType, 2>(0.0);
266	for (i0 = 0; i0 < numPoints; ++i0) {
267	Vector<RealType, 2> diff = points[i0] - center;
268	RealType length = diff.length();
269	if (length > 1e-6) {
270	lenAverage += length;
271	RealType invLength = ((RealType)1)/length;
272	derLenAverage -= invLength*diff;
273	}
274	}
275	lenAverage *= invNumPoints;
276	derLenAverage *= invNumPoints;
277
278	center = average + lenAverage*derLenAverage;
279	radius = lenAverage;
280
281	Vector<RealType, 2> diff = center - current;
282	if (fabs(diff[0]) <= 1e-6 && fabs(diff[1]) <= 1e-6) {
283	break;
284	}
285	}
286
287	RealType zCen = center[1];
288	RealType rDrop = radius;
289	RealType ca;
290
291	if (fabs(zCen) > rDrop) {
292	ca = 180.0;
293	} else {
294	ca = 90.0 + asin(zCen/rDrop)*(180.0/M_PI);
295	}
296
297	values_.push_back( ca );
298
299	}
300	}
301
302