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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	8724 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include "applications/staticProps/SCDOrderParameter.hpp"
44	#include "utils/simError.h"
45	#include "io/DumpReader.hpp"
46	#include "primitives/Molecule.hpp"
47	#include "utils/NumericConstant.hpp"
48	namespace OpenMD {
49
50	SCDElem::SCDElem(SimInfo* info, const std::string& sele1,
51	const std::string& sele2, const std::string& sele3) : sele1_(sele1), sele2_(sele2), sele3_(sele3){
52
53	usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions();
54
55	SelectionManager seleMan1_(info);
56	SelectionManager seleMan2_(info);
57	SelectionManager seleMan3_(info);
58	SelectionEvaluator evaluator1_(info);
59	SelectionEvaluator evaluator2_(info);
60	SelectionEvaluator evaluator3_(info);
61
62	evaluator1_.loadScriptString(sele1_);
63	evaluator2_.loadScriptString(sele2_);
64	evaluator3_.loadScriptString(sele3_);
65
66	if (!evaluator1_.isDynamic()) {
67	seleMan1_.setSelectionSet(evaluator1_.evaluate());
68	}else {
69	sprintf( painCave.errMsg,
70	"dynamic selection is not allowed\n");
71	painCave.severity = OPENMD_ERROR;
72	painCave.isFatal = 1;
73	simError();
74	}
75
76	if (!evaluator2_.isDynamic()) {
77	seleMan2_.setSelectionSet(evaluator2_.evaluate());
78	}else {
79	sprintf( painCave.errMsg,
80	"dynamic selection is not allowed\n");
81	painCave.severity = OPENMD_ERROR;
82	painCave.isFatal = 1;
83	simError();
84	}
85
86	if (!evaluator3_.isDynamic()) {
87	seleMan3_.setSelectionSet(evaluator3_.evaluate());
88	}else {
89	sprintf( painCave.errMsg,
90	"dynamic selection is not allowed\n");
91	painCave.severity = OPENMD_ERROR;
92	painCave.isFatal = 1;
93	simError();
94	}
95
96	int nselected1 = seleMan1_.getSelectionCount();
97	int nselected2 = seleMan2_.getSelectionCount();
98	int nselected3 = seleMan3_.getSelectionCount();
99
100	if ( nselected1 != nselected2 \|\| nselected1 != nselected3 ) {
101	sprintf( painCave.errMsg,
102	"The number of selected Stuntdoubles must be the same\n");
103	painCave.severity = OPENMD_ERROR;
104	painCave.isFatal = 1;
105	simError();
106	}
107
108	int i;
109	int j;
110	int k;
111	StuntDouble* sd1;
112	StuntDouble* sd2;
113	StuntDouble* sd3;
114	for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j), sd3 = seleMan3_.beginSelected(k);
115	sd1 != NULL && sd2 != NULL && sd3 != NULL;
116	sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j), sd3 = seleMan3_.nextSelected(k)) {
117	tuples_.push_back(make_tuple3(sd1, sd2, sd3));
118	}
119
120	}
121
122	RealType SCDElem::calcSCD(Snapshot* snapshot) {
123	std::vector<SDTuple3>::iterator i;
124	Vector3d normal(0.0, 0.0, 1.0);
125	RealType scd = 0.0;
126	for (i = tuples_.begin(); i != tuples_.end(); ++i) {
127	//Egberts B. and Berendsen H.J.C, J.Chem.Phys. 89(6), 3718-3732, 1988
128
129	Vector3d zAxis = i->third->getPos() - i->first->getPos();
130	if (usePeriodicBoundaryConditions_)
131	snapshot->wrapVector(zAxis);
132	Vector3d v12 = i->second->getPos() - i->first->getPos();
133	if (usePeriodicBoundaryConditions_)
134	snapshot->wrapVector(v12);
135	Vector3d xAxis = cross(v12, zAxis);
136	Vector3d yAxis = cross(zAxis, xAxis);
137
138	xAxis.normalize();
139	yAxis.normalize();
140	zAxis.normalize();
141	RealType cosThetaX = dot(xAxis, normal);
142	RealType sxx = 0.5(3cosThetaX * cosThetaX - 1.0);
143	RealType cosThetaY = dot(yAxis, normal);
144	RealType syy = 0.5(3cosThetaY * cosThetaY - 1.0);
145	scd += 2.0/3.0sxx + 1.0/3.0syy;
146	}
147	scd /= tuples_.size();
148	return scd;
149
150	}
151
152	SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename,
153	const std::string& sele1, const std::string& sele2, const std::string& sele3)
154	: StaticAnalyser(info, filename) {
155
156	setOutputName(getPrefix(filename) + ".scd");
157
158	scdElems_.push_back(SCDElem(info, sele1, sele2, sele3));
159	scdParam_.resize(scdElems_.size());
160	std::fill(scdParam_.begin(), scdParam_.end(), 0.0);
161
162	}
163
164	SCDOrderParameter::SCDOrderParameter(SimInfo* info, const std::string& filename,
165	const std::string& molname, int beginIndex, int endIndex)
166	: StaticAnalyser(info, filename) {
167
168	setOutputName(getPrefix(filename) + ".scd");
169
170	assert(beginIndex >=0 && endIndex >=0 && beginIndex <= endIndex - 2);
171	for (int i = beginIndex; i <= endIndex -2 ; ++i) {
172	std::string selectionTemplate = "select " + molname + ".";
173	std::string sele1 = selectionTemplate + OpenMD_itoa(i);
174	std::string sele2 = selectionTemplate + OpenMD_itoa(i+1);
175	std::string sele3 = selectionTemplate + OpenMD_itoa(i+2);
176
177	scdElems_.push_back(SCDElem(info, sele1, sele2, sele3));
178	}
179
180	scdParam_.resize(scdElems_.size());
181	std::fill(scdParam_.begin(), scdParam_.end(), 0.0);
182	}
183
184
185	void SCDOrderParameter::process() {
186	Molecule* mol;
187	RigidBody* rb;
188	SimInfo::MoleculeIterator mi;
189	Molecule::RigidBodyIterator rbIter;
190
191	DumpReader reader(info_, dumpFilename_);
192	int nFrames = reader.getNFrames();
193
194	for (int i = 0; i < nFrames; i += step_) {
195	reader.readFrame(i);
196	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
197
198
199	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
200	//change the positions of atoms which belong to the rigidbodies
201	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
202	rb->updateAtoms();
203	}
204
205	}
206
207	for (std::size_t j = 0; j < scdElems_.size(); ++j) {
208	scdParam_[j] += scdElems_[j].calcSCD(currentSnapshot_);
209	}
210
211	}
212
213	int nProcessed = nFrames /step_;
214	for (std::size_t j = 0; j < scdElems_.size(); ++j) {
215	scdParam_[j] /= nProcessed;
216	}
217
218	writeSCD();
219
220	}
221
222	void SCDOrderParameter::writeSCD() {
223
224	std::ofstream os(getOutputFileName().c_str());
225	os << "#scd parameter\n";
226	for (std::size_t i = 0; i < scdElems_.size(); ++i) {
227	os << "#[column " << i+1 << "]\t"
228	<< "sele1: \"" << scdElems_[i].getSelection1() << "\",\t"
229	<< "sele2: \"" << scdElems_[i].getSelection2() << "\",\t"
230	<< "sele3: \"" << scdElems_[i].getSelection3() << "\"\n";
231	}
232
233	for (std::size_t i = 0; i < scdElems_.size(); ++i) {
234	os << scdParam_[i]<< "\t";
235	}
236	os << std::endl;
237	}
238
239
240	}
241
242