applications/staticProps/SCDOrderParameter.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */

#include "applications/staticProps/SCDOrderParameter.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
namespace oopse {

SCDElem::SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2, 
    const std::string& sele3) : sele1_(sele1), sele2_(sele2), sele3_(sele3){
    SelectionManager seleMan1_(info);
    SelectionManager seleMan2_(info);       
    SelectionManager seleMan3_(info);       
    SelectionEvaluator evaluator1_(info);
    SelectionEvaluator evaluator2_(info);    
    SelectionEvaluator evaluator3_(info);    
    
    evaluator1_.loadScriptString(sele1_);
    evaluator2_.loadScriptString(sele2_);
    evaluator3_.loadScriptString(sele3_);

    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }else {
        sprintf( painCave.errMsg,
                 "dynamic selection is not allowed\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();  
    }

    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }else {
        sprintf( painCave.errMsg,
            "dynamic selection is not allowed\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();  
    }

    if (!evaluator3_.isDynamic()) {
      seleMan3_.setSelectionSet(evaluator3_.evaluate());
    }else {
        sprintf( painCave.errMsg,
            "dynamic selection is not allowed\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();  
    }

    int nselected1 = seleMan1_.getSelectionCount();
    int nselected2 = seleMan2_.getSelectionCount();
    int nselected3 = seleMan3_.getSelectionCount();
    
    if ( nselected1 != nselected2 || nselected1 != nselected3 ) {
        sprintf( painCave.errMsg,
                 "The number of selected Stuntdoubles must be the same\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();  
    }

    int i;
    int j;
    int k;
    StuntDouble* sd1;
    StuntDouble* sd2;
    StuntDouble* sd3;    
    for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j), sd3 = seleMan3_.beginSelected(k);
       sd1 != NULL && sd2 != NULL && sd3 != NULL;
       sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j), sd3 = seleMan3_.nextSelected(k)) {
       tuples_.push_back(make_tuple3(sd1, sd2, sd3));
    }

}

double SCDElem::calcSCD(Snapshot* snapshot) {
    std::vector<SDTuple3>::iterator i;
    Vector3d normal(0.0, 0.0, 1.0);
    double scd = 0.0;
    for (i = tuples_.begin(); i != tuples_.end(); ++i) {        
        //Egberts B. and Berendsen H.J.C, J.Chem.Phys. 89(6), 3718-3732, 1988
        
        Vector3d zAxis =   i->third->getPos() - i->first->getPos();
        snapshot->wrapVector(zAxis);
        Vector3d v12 =  i->second->getPos() - i->first->getPos();
        snapshot->wrapVector(v12);
        Vector3d xAxis = cross(v12, zAxis);
        Vector3d yAxis = cross(zAxis, xAxis);

        xAxis.normalize();
        yAxis.normalize();
        zAxis.normalize();
        double cosThetaX = dot(xAxis, normal);
        double sxx = 0.5*(3*cosThetaX * cosThetaX - 1.0);
        double cosThetaY = dot(yAxis, normal);
        double syy = 0.5*(3*cosThetaY * cosThetaY - 1.0);
        scd += 2.0/3.0*sxx + 1.0/3.0*syy;
    }
    scd /= tuples_.size();
    return scd;

}

SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename,
    const std::string& sele1, const std::string& sele2, const std::string& sele3)
  : StaticAnalyser(info, filename) {

    setOutputName(getPrefix(filename) + ".scd");

    scdElems_.push_back(SCDElem(info, sele1, sele2, sele3));
    scdParam_.resize(scdElems_.size());
    std::fill(scdParam_.begin(), scdParam_.end(), 0.0);
    
}

SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename,
    const std::string& molname, int beginIndex, int endIndex)
  : StaticAnalyser(info, filename) {

    setOutputName(getPrefix(filename) + ".scd");

    assert(beginIndex >=0 && endIndex >=0 && beginIndex <= endIndex - 2);
    for (int i = beginIndex; i <= endIndex -2 ; ++i) {
        std::string selectionTemplate = "select " + molname + ".";
        std::string sele1 = selectionTemplate + OOPSE_itoa(i);
        std::string sele2 = selectionTemplate + OOPSE_itoa(i+1); 
        std::string sele3 = selectionTemplate + OOPSE_itoa(i+2);
        
        scdElems_.push_back(SCDElem(info, sele1, sele2, sele3));
    }
    
    scdParam_.resize(scdElems_.size());    
    std::fill(scdParam_.begin(), scdParam_.end(), 0.0);
}


void SCDOrderParameter::process() {
  Molecule* mol;
  RigidBody* rb;
  SimInfo::MoleculeIterator mi;
  Molecule::RigidBodyIterator rbIter;
  
  DumpReader reader(info_, dumpFilename_);    
  int nFrames = reader.getNFrames();

  for (int i = 0; i < nFrames; i += step_) {
    reader.readFrame(i);
    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();

    
    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
        //change the positions of atoms which belong to the rigidbodies
        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
            rb->updateAtoms();
        }
        
    }      

    for (std::size_t j = 0; j < scdElems_.size(); ++j) {
        scdParam_[j] += scdElems_[j].calcSCD(currentSnapshot_);
    }
        
  }

  int nProcessed = nFrames /step_;
  for (std::size_t j = 0; j < scdElems_.size(); ++j) {
      scdParam_[j] /= nProcessed;
  }

  writeSCD();
  
}

void SCDOrderParameter::writeSCD() {

    std::ofstream os(getOutputFileName().c_str());
    os << "#scd parameter\n";
    for (std::size_t i = 0; i < scdElems_.size(); ++i) {
        os <<  "#[column " << i+1 << "]\t"
            <<  "sele1: \"" << scdElems_[i].getSelection1() << "\",\t"
            <<  "sele2: \"" << scdElems_[i].getSelection2() << "\",\t"
            <<  "sele3: \"" << scdElems_[i].getSelection3() << "\"\n";
    }
    
    for (std::size_t i = 0; i < scdElems_.size(); ++i) {
        os <<  scdParam_[i]<< "\t";
    }
    os << std::endl;
}


}


Revision:	2257
Committed:	Mon Jun 13 18:25:30 2005 UTC (19 years, 1 month ago) by tim
File size:	8580 byte(s)
Log Message:	working version of DensityPlot
#	User	Rev	Content
1	tim	2242	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "applications/staticProps/SCDOrderParameter.hpp"
43			#include "utils/simError.h"
44			#include "io/DumpReader.hpp"
45			#include "primitives/Molecule.hpp"
46			#include "utils/NumericConstant.hpp"
47			namespace oopse {
48
49			SCDElem::SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2,
50			const std::string& sele3) : sele1_(sele1), sele2_(sele2), sele3_(sele3){
51			SelectionManager seleMan1_(info);
52			SelectionManager seleMan2_(info);
53			SelectionManager seleMan3_(info);
54			SelectionEvaluator evaluator1_(info);
55			SelectionEvaluator evaluator2_(info);
56			SelectionEvaluator evaluator3_(info);
57
58			evaluator1_.loadScriptString(sele1_);
59			evaluator2_.loadScriptString(sele2_);
60			evaluator3_.loadScriptString(sele3_);
61
62			if (!evaluator1_.isDynamic()) {
63			seleMan1_.setSelectionSet(evaluator1_.evaluate());
64			}else {
65			sprintf( painCave.errMsg,
66			"dynamic selection is not allowed\n");
67			painCave.severity = OOPSE_ERROR;
68			painCave.isFatal = 1;
69			simError();
70			}
71
72			if (!evaluator2_.isDynamic()) {
73			seleMan2_.setSelectionSet(evaluator2_.evaluate());
74			}else {
75			sprintf( painCave.errMsg,
76			"dynamic selection is not allowed\n");
77			painCave.severity = OOPSE_ERROR;
78			painCave.isFatal = 1;
79			simError();
80			}
81
82			if (!evaluator3_.isDynamic()) {
83			seleMan3_.setSelectionSet(evaluator3_.evaluate());
84			}else {
85			sprintf( painCave.errMsg,
86			"dynamic selection is not allowed\n");
87			painCave.severity = OOPSE_ERROR;
88			painCave.isFatal = 1;
89			simError();
90			}
91
92			int nselected1 = seleMan1_.getSelectionCount();
93			int nselected2 = seleMan2_.getSelectionCount();
94			int nselected3 = seleMan3_.getSelectionCount();
95
96			if ( nselected1 != nselected2 \|\| nselected1 != nselected3 ) {
97			sprintf( painCave.errMsg,
98			"The number of selected Stuntdoubles must be the same\n");
99			painCave.severity = OOPSE_ERROR;
100			painCave.isFatal = 1;
101			simError();
102			}
103
104			int i;
105			int j;
106			int k;
107			StuntDouble* sd1;
108			StuntDouble* sd2;
109			StuntDouble* sd3;
110			for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j), sd3 = seleMan3_.beginSelected(k);
111			sd1 != NULL && sd2 != NULL && sd3 != NULL;
112			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j), sd3 = seleMan3_.nextSelected(k)) {
113			tuples_.push_back(make_tuple3(sd1, sd2, sd3));
114			}
115
116			}
117
118			double SCDElem::calcSCD(Snapshot* snapshot) {
119			std::vector<SDTuple3>::iterator i;
120			Vector3d normal(0.0, 0.0, 1.0);
121			double scd = 0.0;
122	tim	2257	for (i = tuples_.begin(); i != tuples_.end(); ++i) {
123			//Egberts B. and Berendsen H.J.C, J.Chem.Phys. 89(6), 3718-3732, 1988
124
125			Vector3d zAxis = i->third->getPos() - i->first->getPos();
126	tim	2242	snapshot->wrapVector(zAxis);
127			Vector3d v12 = i->second->getPos() - i->first->getPos();
128			snapshot->wrapVector(v12);
129			Vector3d xAxis = cross(v12, zAxis);
130			Vector3d yAxis = cross(zAxis, xAxis);
131
132			xAxis.normalize();
133			yAxis.normalize();
134			zAxis.normalize();
135			double cosThetaX = dot(xAxis, normal);
136			double sxx = 0.5(3cosThetaX * cosThetaX - 1.0);
137			double cosThetaY = dot(yAxis, normal);
138			double syy = 0.5(3cosThetaY * cosThetaY - 1.0);
139			scd += 2.0/3.0sxx + 1.0/3.0syy;
140			}
141			scd /= tuples_.size();
142			return scd;
143
144			}
145
146			SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename,
147			const std::string& sele1, const std::string& sele2, const std::string& sele3)
148			: StaticAnalyser(info, filename) {
149
150			setOutputName(getPrefix(filename) + ".scd");
151
152			scdElems_.push_back(SCDElem(info, sele1, sele2, sele3));
153			scdParam_.resize(scdElems_.size());
154			std::fill(scdParam_.begin(), scdParam_.end(), 0.0);
155
156			}
157
158			SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename,
159			const std::string& molname, int beginIndex, int endIndex)
160			: StaticAnalyser(info, filename) {
161
162			setOutputName(getPrefix(filename) + ".scd");
163
164			assert(beginIndex >=0 && endIndex >=0 && beginIndex <= endIndex - 2);
165			for (int i = beginIndex; i <= endIndex -2 ; ++i) {
166			std::string selectionTemplate = "select " + molname + ".";
167			std::string sele1 = selectionTemplate + OOPSE_itoa(i);
168			std::string sele2 = selectionTemplate + OOPSE_itoa(i+1);
169			std::string sele3 = selectionTemplate + OOPSE_itoa(i+2);
170
171			scdElems_.push_back(SCDElem(info, sele1, sele2, sele3));
172			}
173
174			scdParam_.resize(scdElems_.size());
175			std::fill(scdParam_.begin(), scdParam_.end(), 0.0);
176			}
177
178
179			void SCDOrderParameter::process() {
180			Molecule* mol;
181			RigidBody* rb;
182			SimInfo::MoleculeIterator mi;
183			Molecule::RigidBodyIterator rbIter;
184
185			DumpReader reader(info_, dumpFilename_);
186			int nFrames = reader.getNFrames();
187
188			for (int i = 0; i < nFrames; i += step_) {
189			reader.readFrame(i);
190			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
191
192
193			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
194			//change the positions of atoms which belong to the rigidbodies
195			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
196			rb->updateAtoms();
197			}
198
199			}
200
201			for (std::size_t j = 0; j < scdElems_.size(); ++j) {
202			scdParam_[j] += scdElems_[j].calcSCD(currentSnapshot_);
203			}
204
205			}
206
207			int nProcessed = nFrames /step_;
208			for (std::size_t j = 0; j < scdElems_.size(); ++j) {
209			scdParam_[j] /= nProcessed;
210			}
211
212			writeSCD();
213
214			}
215
216			void SCDOrderParameter::writeSCD() {
217
218			std::ofstream os(getOutputFileName().c_str());
219			os << "#scd parameter\n";
220			for (std::size_t i = 0; i < scdElems_.size(); ++i) {
221			os << "#[column " << i+1 << "]\t"
222			<< "sele1: \"" << scdElems_[i].getSelection1() << "\",\t"
223			<< "sele2: \"" << scdElems_[i].getSelection2() << "\",\t"
224			<< "sele3: \"" << scdElems_[i].getSelection3() << "\"\n";
225			}
226
227			for (std::size_t i = 0; i < scdElems_.size(); ++i) {
228			os << scdParam_[i]<< "\t";
229			}
230			os << std::endl;
231			}
232
233
234			}
235
236