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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

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

  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 = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();  
    }

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

    if (!evaluator3_.isDynamic()) {
      seleMan3_.setSelectionSet(evaluator3_.evaluate());
    }else {
      sprintf( painCave.errMsg,
               "dynamic selection is not allowed\n");
      painCave.severity = OPENMD_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 = OPENMD_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 + OpenMD_itoa(i);
      std::string sele2 = selectionTemplate + OpenMD_itoa(i+1); 
      std::string sele3 = selectionTemplate + OpenMD_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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size:	8657 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
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 OpenMD {
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 = OPENMD_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 = OPENMD_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 = OPENMD_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 = OPENMD_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 + OpenMD_itoa(i);
173	std::string sele2 = selectionTemplate + OpenMD_itoa(i+1);
174	std::string sele3 = selectionTemplate + OpenMD_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