ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-4/src/applications/staticProps/SCDOrderParameter.cpp
(Generate patch)

Comparing trunk/OOPSE-4/src/applications/staticProps/SCDOrderParameter.cpp (file contents):
Revision 2759 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 3054 by gezelter, Wed Oct 18 21:58:48 2006 UTC

# Line 1 | Line 1
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. 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 < RealType SCDElem::calcSCD(Snapshot* snapshot) {
119 <    std::vector<SDTuple3>::iterator i;
120 <    Vector3d normal(0.0, 0.0, 1.0);
121 <    RealType scd = 0.0;
122 <    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 <        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 <        RealType cosThetaX = dot(xAxis, normal);
136 <        RealType sxx = 0.5*(3*cosThetaX * cosThetaX - 1.0);
137 <        RealType cosThetaY = dot(yAxis, normal);
138 <        RealType syy = 0.5*(3*cosThetaY * cosThetaY - 1.0);
139 <        scd += 2.0/3.0*sxx + 1.0/3.0*syy;
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 <
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. 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*(3*cosThetaX * cosThetaX - 1.0);
142 >      RealType cosThetaY = dot(yAxis, normal);
143 >      RealType syy = 0.5*(3*cosThetaY * cosThetaY - 1.0);
144 >      scd += 2.0/3.0*sxx + 1.0/3.0*syy;
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 >

Diff Legend

Removed lines
+ Added lines
< Changed lines
> Changed lines