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:	558
Committed:	Mon Jun 13 18:25:30 2005 UTC (20 years, 4 months ago) by tim
File size:	8580 byte(s)
Log Message:	working version of DensityPlot
#	Content
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	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	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	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