applications/sequentialProps/ContactAngle1.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/ContactAngle1.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
#include "math/Polynomial.hpp"

namespace OpenMD {

  ContactAngle1::ContactAngle1(SimInfo* info, const std::string& filename, 
                               const std::string& sele, RealType solidZ,
                               RealType dropletRadius)
    : SequentialAnalyzer(info, filename), selectionScript_(sele), 
      evaluator_(info), seleMan_(info), solidZ_(solidZ),
      dropletRadius_(dropletRadius)  {
    
    setOutputName(getPrefix(filename) + ".ca1");
    
    evaluator_.loadScriptString(sele);
    
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }            
  }

  void ContactAngle1::doFrame() {
    StuntDouble* sd;
    int i;
    
    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;

    RealType dz = com.z() - solidZ_;

    if (dz < 0.0) {
      sprintf(painCave.errMsg, 
              "ContactAngle1: Z-center of mass of selection, %lf, was\n"
              "\tlocated below the solid reference plane, %lf\n",
              com.z(), solidZ_);
      painCave.isFatal = 1;
      painCave.severity = OPENMD_ERROR;
      simError();
    }

    if (dz > dropletRadius_) {
      values_.push_back(180.0);
    } else {
    
      RealType k = pow(2.0, -4.0/3.0) * dropletRadius_;
      
      RealType z2 = dz*dz;
      RealType z3 = z2 * dz;
      RealType k2 = k*k;
      RealType k3 = k2*k;
      
      Polynomial<RealType> poly;
      poly.setCoefficient(4,      z3 +      k3);
      poly.setCoefficient(3,  8.0*z3 +  8.0*k3);
      poly.setCoefficient(2, 24.0*z3 + 18.0*k3);
      poly.setCoefficient(1, 32.0*z3          );
      poly.setCoefficient(0, 16.0*z3 - 27.0*k3);
      vector<RealType> realRoots = poly.FindRealRoots();

      RealType ct;
      
      vector<RealType>::iterator ri;


      RealType maxct = -1.0;
      for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
        ct = *ri;
        if (ct > 1.0)  ct = 1.0;
        if (ct < -1.0) ct = -1.0;

        // use the largest magnitude of ct that it finds:
        if (ct > maxct) {
          maxct = ct;
        }                  
      }
      
      values_.push_back( acos(maxct)*(180.0/M_PI) );
    }
  }    
}


Revision:	2030
Committed:	Thu Oct 30 20:50:53 2014 UTC (11 years ago) by gezelter
File size:	4908 byte(s)
Log Message:	Fixed the contact angle calculation.
#	User	Rev	Content
1	gezelter	2029	/*
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/ContactAngle1.hpp"
46			#include "utils/simError.h"
47			#include "io/DumpReader.hpp"
48			#include "primitives/Molecule.hpp"
49			#include "utils/NumericConstant.hpp"
50			#include "math/Polynomial.hpp"
51
52			namespace OpenMD {
53
54			ContactAngle1::ContactAngle1(SimInfo* info, const std::string& filename,
55			const std::string& sele, RealType solidZ,
56			RealType dropletRadius)
57			: SequentialAnalyzer(info, filename), selectionScript_(sele),
58			evaluator_(info), seleMan_(info), solidZ_(solidZ),
59			dropletRadius_(dropletRadius) {
60
61			setOutputName(getPrefix(filename) + ".ca1");
62
63			evaluator_.loadScriptString(sele);
64
65			if (!evaluator_.isDynamic()) {
66			seleMan_.setSelectionSet(evaluator_.evaluate());
67			}
68			}
69
70			void ContactAngle1::doFrame() {
71			StuntDouble* sd;
72			int i;
73
74			if (evaluator_.isDynamic()) {
75			seleMan_.setSelectionSet(evaluator_.evaluate());
76			}
77
78
79			RealType mtot = 0.0;
80			Vector3d com(V3Zero);
81			RealType mass;
82
83			for (sd = seleMan_.beginSelected(i); sd != NULL;
84			sd = seleMan_.nextSelected(i)) {
85			mass = sd->getMass();
86			mtot += mass;
87			com += sd->getPos() * mass;
88			}
89
90			com /= mtot;
91
92			RealType dz = com.z() - solidZ_;
93
94			if (dz < 0.0) {
95			sprintf(painCave.errMsg,
96			"ContactAngle1: Z-center of mass of selection, %lf, was\n"
97			"\tlocated below the solid reference plane, %lf\n",
98			com.z(), solidZ_);
99			painCave.isFatal = 1;
100			painCave.severity = OPENMD_ERROR;
101			simError();
102			}
103
104			if (dz > dropletRadius_) {
105			values_.push_back(180.0);
106			} else {
107
108			RealType k = pow(2.0, -4.0/3.0) * dropletRadius_;
109
110			RealType z2 = dz*dz;
111			RealType z3 = z2 * dz;
112			RealType k2 = k*k;
113			RealType k3 = k2*k;
114
115			Polynomial<RealType> poly;
116			poly.setCoefficient(4, z3 + k3);
117			poly.setCoefficient(3, 8.0z3 + 8.0k3);
118			poly.setCoefficient(2, 24.0z3 + 18.0k3);
119			poly.setCoefficient(1, 32.0*z3 );
120			poly.setCoefficient(0, 16.0z3 - 27.0k3);
121			vector<RealType> realRoots = poly.FindRealRoots();
122
123			RealType ct;
124
125			vector<RealType>::iterator ri;
126	gezelter	2030
127
128			RealType maxct = -1.0;
129	gezelter	2029	for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) {
130			ct = *ri;
131			if (ct > 1.0) ct = 1.0;
132			if (ct < -1.0) ct = -1.0;
133	gezelter	2030
134			// use the largest magnitude of ct that it finds:
135			if (ct > maxct) {
136			maxct = ct;
137			}
138	gezelter	2029	}
139
140	gezelter	2030	values_.push_back( acos(maxct)*(180.0/M_PI) );
141	gezelter	2029	}
142			}
143			}
144
145