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gezelter |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include <algorithm> |
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#include <functional> |
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#include "applications/sequentialProps/ContactAngle1.hpp" |
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#include "utils/simError.h" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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#include "math/Polynomial.hpp" |
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namespace OpenMD { |
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ContactAngle1::ContactAngle1(SimInfo* info, const std::string& filename, |
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const std::string& sele, RealType solidZ, |
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RealType dropletRadius) |
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: SequentialAnalyzer(info, filename), selectionScript_(sele), |
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evaluator_(info), seleMan_(info), solidZ_(solidZ), |
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dropletRadius_(dropletRadius) { |
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setOutputName(getPrefix(filename) + ".ca1"); |
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evaluator_.loadScriptString(sele); |
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if (!evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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} |
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void ContactAngle1::doFrame() { |
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StuntDouble* sd; |
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int i; |
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if (evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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RealType mtot = 0.0; |
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Vector3d com(V3Zero); |
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RealType mass; |
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for (sd = seleMan_.beginSelected(i); sd != NULL; |
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sd = seleMan_.nextSelected(i)) { |
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mass = sd->getMass(); |
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mtot += mass; |
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com += sd->getPos() * mass; |
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} |
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com /= mtot; |
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RealType dz = com.z() - solidZ_; |
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if (dz < 0.0) { |
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sprintf(painCave.errMsg, |
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"ContactAngle1: Z-center of mass of selection, %lf, was\n" |
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"\tlocated below the solid reference plane, %lf\n", |
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com.z(), solidZ_); |
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painCave.isFatal = 1; |
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painCave.severity = OPENMD_ERROR; |
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simError(); |
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} |
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if (dz > dropletRadius_) { |
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values_.push_back(180.0); |
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} else { |
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RealType k = pow(2.0, -4.0/3.0) * dropletRadius_; |
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RealType z2 = dz*dz; |
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RealType z3 = z2 * dz; |
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RealType k2 = k*k; |
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RealType k3 = k2*k; |
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Polynomial<RealType> poly; |
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poly.setCoefficient(4, z3 + k3); |
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poly.setCoefficient(3, 8.0*z3 + 8.0*k3); |
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poly.setCoefficient(2, 24.0*z3 + 18.0*k3); |
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poly.setCoefficient(1, 32.0*z3 ); |
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poly.setCoefficient(0, 16.0*z3 - 27.0*k3); |
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vector<RealType> realRoots = poly.FindRealRoots(); |
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RealType ct; |
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std::cerr << "nRealRoots = " << realRoots.size() << "\n"; |
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vector<RealType>::iterator ri; |
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vector<pair<RealType,RealType> > rps; |
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for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) { |
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ct = *ri; |
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if (ct > 1.0) ct = 1.0; |
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if (ct < -1.0) ct = -1.0; |
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} |
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values_.push_back( acos(ct)*(180.0/M_PI) ); |
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} |
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} |
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} |
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