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){

    usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions();

    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));
    }

  }

  RealType SCDElem::calcSCD(Snapshot* snapshot) {
    std::vector<SDTuple3>::iterator i;
    Vector3d normal(0.0, 0.0, 1.0);
    RealType 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();
      if (usePeriodicBoundaryConditions_)
        snapshot->wrapVector(zAxis);
      Vector3d v12 =  i->second->getPos() - i->first->getPos();
      if (usePeriodicBoundaryConditions_)
        snapshot->wrapVector(v12);
      Vector3d xAxis = cross(v12, zAxis);
      Vector3d yAxis = cross(zAxis, xAxis);

      xAxis.normalize();
      yAxis.normalize();
      zAxis.normalize();
      RealType cosThetaX = dot(xAxis, normal);
      RealType sxx = 0.5*(3*cosThetaX * cosThetaX - 1.0);
      RealType cosThetaY = dot(yAxis, normal);
      RealType 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:	3054
Committed:	Wed Oct 18 21:58:48 2006 UTC (17 years, 10 months ago) by gezelter
File size:	8608 byte(s)
Log Message:	fixing a wrapVector problem in staticProps, also making Shifted force and electrostatic damping the default behavior
#	User	Rev	Content
1	gezelter	3054	/*
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,
50			const std::string& sele2, const std::string& sele3) : sele1_(sele1), sele2_(sele2), sele3_(sele3){
51
52			usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions();
53
54			SelectionManager seleMan1_(info);
55			SelectionManager seleMan2_(info);
56			SelectionManager seleMan3_(info);
57			SelectionEvaluator evaluator1_(info);
58			SelectionEvaluator evaluator2_(info);
59			SelectionEvaluator evaluator3_(info);
60
61			evaluator1_.loadScriptString(sele1_);
62			evaluator2_.loadScriptString(sele2_);
63			evaluator3_.loadScriptString(sele3_);
64
65			if (!evaluator1_.isDynamic()) {
66			seleMan1_.setSelectionSet(evaluator1_.evaluate());
67			}else {
68			sprintf( painCave.errMsg,
69			"dynamic selection is not allowed\n");
70			painCave.severity = OOPSE_ERROR;
71			painCave.isFatal = 1;
72			simError();
73			}
74
75			if (!evaluator2_.isDynamic()) {
76			seleMan2_.setSelectionSet(evaluator2_.evaluate());
77			}else {
78			sprintf( painCave.errMsg,
79			"dynamic selection is not allowed\n");
80			painCave.severity = OOPSE_ERROR;
81			painCave.isFatal = 1;
82			simError();
83			}
84
85			if (!evaluator3_.isDynamic()) {
86			seleMan3_.setSelectionSet(evaluator3_.evaluate());
87			}else {
88			sprintf( painCave.errMsg,
89			"dynamic selection is not allowed\n");
90			painCave.severity = OOPSE_ERROR;
91			painCave.isFatal = 1;
92			simError();
93			}
94
95			int nselected1 = seleMan1_.getSelectionCount();
96			int nselected2 = seleMan2_.getSelectionCount();
97			int nselected3 = seleMan3_.getSelectionCount();
98
99			if ( nselected1 != nselected2 \|\| nselected1 != nselected3 ) {
100			sprintf( painCave.errMsg,
101			"The number of selected Stuntdoubles must be the same\n");
102			painCave.severity = OOPSE_ERROR;
103			painCave.isFatal = 1;
104			simError();
105			}
106
107			int i;
108			int j;
109			int k;
110			StuntDouble* sd1;
111			StuntDouble* sd2;
112			StuntDouble* sd3;
113			for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j), sd3 = seleMan3_.beginSelected(k);
114			sd1 != NULL && sd2 != NULL && sd3 != NULL;
115			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j), sd3 = seleMan3_.nextSelected(k)) {
116			tuples_.push_back(make_tuple3(sd1, sd2, sd3));
117			}
118
119			}
120
121			RealType SCDElem::calcSCD(Snapshot* snapshot) {
122			std::vector<SDTuple3>::iterator i;
123			Vector3d normal(0.0, 0.0, 1.0);
124			RealType scd = 0.0;
125			for (i = tuples_.begin(); i != tuples_.end(); ++i) {
126			//Egberts B. and Berendsen H.J.C, J.Chem.Phys. 89(6), 3718-3732, 1988
127
128			Vector3d zAxis = i->third->getPos() - i->first->getPos();
129			if (usePeriodicBoundaryConditions_)
130			snapshot->wrapVector(zAxis);
131			Vector3d v12 = i->second->getPos() - i->first->getPos();
132			if (usePeriodicBoundaryConditions_)
133			snapshot->wrapVector(v12);
134			Vector3d xAxis = cross(v12, zAxis);
135			Vector3d yAxis = cross(zAxis, xAxis);
136
137			xAxis.normalize();
138			yAxis.normalize();
139			zAxis.normalize();
140			RealType cosThetaX = dot(xAxis, normal);
141			RealType sxx = 0.5(3cosThetaX * cosThetaX - 1.0);
142			RealType cosThetaY = dot(yAxis, normal);
143			RealType syy = 0.5(3cosThetaY * cosThetaY - 1.0);
144			scd += 2.0/3.0sxx + 1.0/3.0syy;
145			}
146			scd /= tuples_.size();
147			return scd;
148
149			}
150
151			SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename,
152			const std::string& sele1, const std::string& sele2, const std::string& sele3)
153			: StaticAnalyser(info, filename) {
154
155			setOutputName(getPrefix(filename) + ".scd");
156
157			scdElems_.push_back(SCDElem(info, sele1, sele2, sele3));
158			scdParam_.resize(scdElems_.size());
159			std::fill(scdParam_.begin(), scdParam_.end(), 0.0);
160
161			}
162
163			SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename,
164			const std::string& molname, int beginIndex, int endIndex)
165			: StaticAnalyser(info, filename) {
166
167			setOutputName(getPrefix(filename) + ".scd");
168
169			assert(beginIndex >=0 && endIndex >=0 && beginIndex <= endIndex - 2);
170			for (int i = beginIndex; i <= endIndex -2 ; ++i) {
171			std::string selectionTemplate = "select " + molname + ".";
172			std::string sele1 = selectionTemplate + OOPSE_itoa(i);
173			std::string sele2 = selectionTemplate + OOPSE_itoa(i+1);
174			std::string sele3 = selectionTemplate + OOPSE_itoa(i+2);
175
176			scdElems_.push_back(SCDElem(info, sele1, sele2, sele3));
177			}
178
179			scdParam_.resize(scdElems_.size());
180			std::fill(scdParam_.begin(), scdParam_.end(), 0.0);
181			}
182
183
184			void SCDOrderParameter::process() {
185			Molecule* mol;
186			RigidBody* rb;
187			SimInfo::MoleculeIterator mi;
188			Molecule::RigidBodyIterator rbIter;
189
190			DumpReader reader(info_, dumpFilename_);
191			int nFrames = reader.getNFrames();
192
193			for (int i = 0; i < nFrames; i += step_) {
194			reader.readFrame(i);
195			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
196
197
198			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
199			//change the positions of atoms which belong to the rigidbodies
200			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
201			rb->updateAtoms();
202			}
203
204			}
205
206			for (std::size_t j = 0; j < scdElems_.size(); ++j) {
207			scdParam_[j] += scdElems_[j].calcSCD(currentSnapshot_);
208			}
209
210			}
211
212			int nProcessed = nFrames /step_;
213			for (std::size_t j = 0; j < scdElems_.size(); ++j) {
214			scdParam_[j] /= nProcessed;
215			}
216
217			writeSCD();
218
219			}
220
221			void SCDOrderParameter::writeSCD() {
222
223			std::ofstream os(getOutputFileName().c_str());
224			os << "#scd parameter\n";
225			for (std::size_t i = 0; i < scdElems_.size(); ++i) {
226			os << "#[column " << i+1 << "]\t"
227			<< "sele1: \"" << scdElems_[i].getSelection1() << "\",\t"
228			<< "sele2: \"" << scdElems_[i].getSelection2() << "\",\t"
229			<< "sele3: \"" << scdElems_[i].getSelection3() << "\"\n";
230			}
231
232			for (std::size_t i = 0; i < scdElems_.size(); ++i) {
233			os << scdParam_[i]<< "\t";
234			}
235			os << std::endl;
236			}
237
238
239			}
240
241