applications/staticProps/DensityPlot.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 <algorithm>
#include <functional>
#include "applications/staticProps/DensityPlot.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
namespace oopse {


DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, RealType len, int nrbins)
  : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), 
    cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info),     
    len_(len), nRBins_(nrbins), halfLen_(len/2)     {

    setOutputName(getPrefix(filename) + ".density");

    deltaR_ = len_ /nRBins_;  
    histogram_.resize(nRBins_);
    density_.resize(nRBins_);
    
    std::fill(histogram_.begin(), histogram_.end(), 0);  
    
    evaluator_.loadScriptString(sele);

    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }

    cmEvaluator_.loadScriptString(cmSele);
    if (!cmEvaluator_.isDynamic()) {
      cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
    }
    
    
  }

void DensityPlot::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();
        }
        
    }
    
    if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
    }

    if (cmEvaluator_.isDynamic()) {
        cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
    }

    Vector3d origin = calcNewOrigin();

    Mat3x3d hmat = currentSnapshot_->getHmat();
    RealType slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1);
    int k; 
    for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL; sd = seleMan_.nextSelected(k)) {


            if (!sd->isAtom()) {
                sprintf( painCave.errMsg, "Can not calculate electron density if it is not atom\n");
                painCave.severity = OOPSE_ERROR;
                painCave.isFatal = 1;
                simError(); 
            }
            
            Atom* atom = static_cast<Atom*>(sd);
            GenericData* data = atom->getAtomType()->getPropertyByName("nelectron");
            if (data == NULL) {
                sprintf( painCave.errMsg, "Can not find Parameters for nelectron\n");
                painCave.severity = OOPSE_ERROR;
                painCave.isFatal = 1;
                simError(); 
            }
            
            DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
            if (doubleData == NULL) {
                sprintf( painCave.errMsg,
                     "Can not cast GenericData to DoubleGenericData\n");
                painCave.severity = OOPSE_ERROR;
                painCave.isFatal = 1;
                simError();   
            }
            
            RealType nelectron = doubleData->getData();

            data = atom->getAtomType()->getPropertyByName("LennardJones");
            if (data == NULL) {
                sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
                painCave.severity = OOPSE_ERROR;
                painCave.isFatal = 1;
                simError(); 
            }

            LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
            if (ljData == NULL) {
                sprintf( painCave.errMsg,
                     "Can not cast GenericData to LJParam\n");
                painCave.severity = OOPSE_ERROR;
                painCave.isFatal = 1;
                simError();          
            }

            LJParam ljParam = ljData->getData();
            RealType sigma = ljParam.sigma * 0.5;
            RealType sigma2 = sigma * sigma;

            Vector3d pos = sd->getPos() - origin;
            for (int j =0; j < nRBins_; ++j) {
                Vector3d tmp(pos);
                RealType zdist =j * deltaR_ - halfLen_;
                tmp[2] += zdist;
                if (usePeriodicBoundaryConditions_) 
                  currentSnapshot_->wrapVector(tmp);

                RealType wrappedZdist = tmp.z() + halfLen_;
                if (wrappedZdist < 0.0 || wrappedZdist > len_) {
                    continue;
                }
                
                int which =wrappedZdist / deltaR_;        
                density_[which] += nelectron * exp(-zdist*zdist/(sigma2*2.0)) /(slabVolume* sqrt(2*NumericConstant::PI*sigma*sigma));
                    
            }
            
            
        }        
    }

  int nProcessed = nFrames /step_;
  std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<RealType>(), nProcessed));  
  writeDensity();
        

}

Vector3d DensityPlot::calcNewOrigin() {

    int i;
    Vector3d newOrigin(0.0);
    RealType totalMass = 0.0;
    for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
        RealType mass = sd->getMass();
        totalMass += mass;
        newOrigin += sd->getPos() * mass;        
    }
    newOrigin /= totalMass;
    return newOrigin;
}

void DensityPlot::writeDensity() {
    std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
    if (ofs.is_open()) {
      ofs << "#g(x, y, z)\n";
      ofs << "#selection: (" << selectionScript_ << ")\n";
      ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n";
      ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "\tdeltaR = " << deltaR_ <<"\n";
      for (int i = 0; i < histogram_.size(); ++i) {
          ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl;
      }        
    } else {

      sprintf(painCave.errMsg, "DensityPlot: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }

    ofs.close();


}

}


Revision:	1078
Committed:	Wed Oct 18 21:58:48 2006 UTC (18 years, 6 months ago) by gezelter
File size:	8370 byte(s)
Log Message:	fixing a wrapVector problem in staticProps, also making Shifted force and electrostatic damping the default behavior
#	User	Rev	Content
1	tim	545	/*
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 <algorithm>
43	tim	565	#include <functional>
44	tim	545	#include "applications/staticProps/DensityPlot.hpp"
45			#include "utils/simError.h"
46			#include "io/DumpReader.hpp"
47			#include "primitives/Molecule.hpp"
48			#include "utils/NumericConstant.hpp"
49			namespace oopse {
50
51
52	tim	963	DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, RealType len, int nrbins)
53	tim	545	: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info),
54	tim	558	cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info),
55	tim	545	len_(len), nRBins_(nrbins), halfLen_(len/2) {
56
57			setOutputName(getPrefix(filename) + ".density");
58
59			deltaR_ = len_ /nRBins_;
60			histogram_.resize(nRBins_);
61			density_.resize(nRBins_);
62
63			std::fill(histogram_.begin(), histogram_.end(), 0);
64
65			evaluator_.loadScriptString(sele);
66
67			if (!evaluator_.isDynamic()) {
68			seleMan_.setSelectionSet(evaluator_.evaluate());
69			}
70	tim	558
71			cmEvaluator_.loadScriptString(cmSele);
72			if (!cmEvaluator_.isDynamic()) {
73			cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
74			}
75	tim	545
76	tim	558
77	tim	545	}
78
79			void DensityPlot::process() {
80			Molecule* mol;
81			RigidBody* rb;
82			SimInfo::MoleculeIterator mi;
83			Molecule::RigidBodyIterator rbIter;
84
85			DumpReader reader(info_, dumpFilename_);
86			int nFrames = reader.getNFrames();
87	tim	565	for (int i = 0; i < nFrames; i += step_) {
88	tim	545	reader.readFrame(i);
89			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
90
91			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
92			//change the positions of atoms which belong to the rigidbodies
93			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
94			rb->updateAtoms();
95			}
96
97			}
98
99			if (evaluator_.isDynamic()) {
100			seleMan_.setSelectionSet(evaluator_.evaluate());
101			}
102
103	tim	558	if (cmEvaluator_.isDynamic()) {
104			cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
105			}
106
107			Vector3d origin = calcNewOrigin();
108
109			Mat3x3d hmat = currentSnapshot_->getHmat();
110	tim	963	RealType slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1);
111	tim	565	int k;
112			for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL; sd = seleMan_.nextSelected(k)) {
113	tim	545
114	tim	558
115			if (!sd->isAtom()) {
116			sprintf( painCave.errMsg, "Can not calculate electron density if it is not atom\n");
117			painCave.severity = OOPSE_ERROR;
118			painCave.isFatal = 1;
119			simError();
120			}
121
122			Atom* atom = static_cast<Atom*>(sd);
123			GenericData* data = atom->getAtomType()->getPropertyByName("nelectron");
124			if (data == NULL) {
125			sprintf( painCave.errMsg, "Can not find Parameters for nelectron\n");
126			painCave.severity = OOPSE_ERROR;
127			painCave.isFatal = 1;
128			simError();
129			}
130
131			DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
132			if (doubleData == NULL) {
133			sprintf( painCave.errMsg,
134			"Can not cast GenericData to DoubleGenericData\n");
135			painCave.severity = OOPSE_ERROR;
136			painCave.isFatal = 1;
137			simError();
138			}
139
140	tim	963	RealType nelectron = doubleData->getData();
141	tim	558
142			data = atom->getAtomType()->getPropertyByName("LennardJones");
143			if (data == NULL) {
144			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
145			painCave.severity = OOPSE_ERROR;
146			painCave.isFatal = 1;
147			simError();
148			}
149
150			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
151			if (ljData == NULL) {
152			sprintf( painCave.errMsg,
153			"Can not cast GenericData to LJParam\n");
154			painCave.severity = OOPSE_ERROR;
155			painCave.isFatal = 1;
156			simError();
157			}
158
159			LJParam ljParam = ljData->getData();
160	tim	963	RealType sigma = ljParam.sigma * 0.5;
161			RealType sigma2 = sigma * sigma;
162	tim	558
163			Vector3d pos = sd->getPos() - origin;
164			for (int j =0; j < nRBins_; ++j) {
165			Vector3d tmp(pos);
166	tim	963	RealType zdist =j * deltaR_ - halfLen_;
167	tim	558	tmp[2] += zdist;
168	gezelter	1078	if (usePeriodicBoundaryConditions_)
169			currentSnapshot_->wrapVector(tmp);
170	tim	558
171	tim	963	RealType wrappedZdist = tmp.z() + halfLen_;
172	tim	558	if (wrappedZdist < 0.0 \|\| wrappedZdist > len_) {
173			continue;
174			}
175
176			int which =wrappedZdist / deltaR_;
177			density_[which] += nelectron * exp(-zdistzdist/(sigma22.0)) /(slabVolume* sqrt(2NumericConstant::PIsigma*sigma));
178
179			}
180
181
182
183	tim	545	}
184			}
185	tim	558
186			int nProcessed = nFrames /step_;
187	tim	963	std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<RealType>(), nProcessed));
188	tim	558	writeDensity();
189	tim	545
190
191
192			}
193
194	tim	558	Vector3d DensityPlot::calcNewOrigin() {
195
196			int i;
197			Vector3d newOrigin(0.0);
198	tim	963	RealType totalMass = 0.0;
199	tim	558	for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
200	tim	963	RealType mass = sd->getMass();
201	tim	558	totalMass += mass;
202			newOrigin += sd->getPos() * mass;
203			}
204			newOrigin /= totalMass;
205			return newOrigin;
206			}
207
208	tim	545	void DensityPlot::writeDensity() {
209			std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
210			if (ofs.is_open()) {
211			ofs << "#g(x, y, z)\n";
212	tim	558	ofs << "#selection: (" << selectionScript_ << ")\n";
213			ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n";
214			ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "\tdeltaR = " << deltaR_ <<"\n";
215	tim	545	for (int i = 0; i < histogram_.size(); ++i) {
216			ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl;
217			}
218			} else {
219
220			sprintf(painCave.errMsg, "DensityPlot: unable to open %s\n", outputFilename_.c_str());
221			painCave.isFatal = 1;
222			simError();
223			}
224
225			ofs.close();
226
227
228			}
229
230			}
231
232