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 "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, double 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();
    double slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1);
    
    int i;        
    for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {


            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();   
            }
            
            double 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();
            double sigma = ljParam.sigma * 0.5;
            double sigma2 = sigma * sigma;

            Vector3d pos = sd->getPos() - origin;
            /*
            currentSnapshot_->wrapVector(pos);            
            double wrappedZdist = pos.z() + halfLen_;
            if (wrappedZdist < 0.0 || wrappedZdist > len_) {
                continue;
            }
            
            int which =wrappedZdist / deltaR_;        
            density_[which] += nelectron;
            */
            for (int j =0; j < nRBins_; ++j) {
                Vector3d tmp(pos);
                double zdist =j * deltaR_ - halfLen_;
                tmp[2] += zdist;
                currentSnapshot_->wrapVector(tmp);

                double 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<double>(), nProcessed));  
  writeDensity();
        

}

Vector3d DensityPlot::calcNewOrigin() {

    int i;
    Vector3d newOrigin(0.0);
    double totalMass = 0.0;
    for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
        double 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:	2257
Committed:	Mon Jun 13 18:25:30 2005 UTC (19 years, 1 month ago) by tim
File size:	8640 byte(s)
Log Message:	working version of DensityPlot
#	User	Rev	Content
1	tim	2242	/*
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			#include "applications/staticProps/DensityPlot.hpp"
44			#include "utils/simError.h"
45			#include "io/DumpReader.hpp"
46			#include "primitives/Molecule.hpp"
47			#include "utils/NumericConstant.hpp"
48			namespace oopse {
49
50
51	tim	2257	DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, double len, int nrbins)
52	tim	2242	: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info),
53	tim	2257	cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info),
54	tim	2242	len_(len), nRBins_(nrbins), halfLen_(len/2) {
55
56			setOutputName(getPrefix(filename) + ".density");
57
58			deltaR_ = len_ /nRBins_;
59			histogram_.resize(nRBins_);
60			density_.resize(nRBins_);
61
62			std::fill(histogram_.begin(), histogram_.end(), 0);
63
64			evaluator_.loadScriptString(sele);
65
66			if (!evaluator_.isDynamic()) {
67			seleMan_.setSelectionSet(evaluator_.evaluate());
68			}
69	tim	2257
70			cmEvaluator_.loadScriptString(cmSele);
71			if (!cmEvaluator_.isDynamic()) {
72			cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
73			}
74	tim	2242
75	tim	2257
76	tim	2242	}
77
78			void DensityPlot::process() {
79			Molecule* mol;
80			RigidBody* rb;
81			SimInfo::MoleculeIterator mi;
82			Molecule::RigidBodyIterator rbIter;
83
84			DumpReader reader(info_, dumpFilename_);
85			int nFrames = reader.getNFrames();
86
87			for (int i = 0; i < nFrames; i += step_) {
88			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	2257	if (cmEvaluator_.isDynamic()) {
104			cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
105			}
106
107			Vector3d origin = calcNewOrigin();
108
109			Mat3x3d hmat = currentSnapshot_->getHmat();
110			double slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1);
111
112	tim	2242	int i;
113			for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
114
115	tim	2257
116			if (!sd->isAtom()) {
117			sprintf( painCave.errMsg, "Can not calculate electron density if it is not atom\n");
118			painCave.severity = OOPSE_ERROR;
119			painCave.isFatal = 1;
120			simError();
121			}
122
123			Atom* atom = static_cast<Atom*>(sd);
124			GenericData* data = atom->getAtomType()->getPropertyByName("nelectron");
125			if (data == NULL) {
126			sprintf( painCave.errMsg, "Can not find Parameters for nelectron\n");
127			painCave.severity = OOPSE_ERROR;
128			painCave.isFatal = 1;
129			simError();
130			}
131
132			DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
133			if (doubleData == NULL) {
134			sprintf( painCave.errMsg,
135			"Can not cast GenericData to DoubleGenericData\n");
136			painCave.severity = OOPSE_ERROR;
137			painCave.isFatal = 1;
138			simError();
139			}
140
141			double nelectron = doubleData->getData();
142
143			data = atom->getAtomType()->getPropertyByName("LennardJones");
144			if (data == NULL) {
145			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
146			painCave.severity = OOPSE_ERROR;
147			painCave.isFatal = 1;
148			simError();
149			}
150
151			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
152			if (ljData == NULL) {
153			sprintf( painCave.errMsg,
154			"Can not cast GenericData to LJParam\n");
155			painCave.severity = OOPSE_ERROR;
156			painCave.isFatal = 1;
157			simError();
158			}
159
160			LJParam ljParam = ljData->getData();
161			double sigma = ljParam.sigma * 0.5;
162			double sigma2 = sigma * sigma;
163
164			Vector3d pos = sd->getPos() - origin;
165			/*
166			currentSnapshot_->wrapVector(pos);
167			double wrappedZdist = pos.z() + halfLen_;
168			if (wrappedZdist < 0.0 \|\| wrappedZdist > len_) {
169			continue;
170			}
171
172			int which =wrappedZdist / deltaR_;
173			density_[which] += nelectron;
174			*/
175			for (int j =0; j < nRBins_; ++j) {
176			Vector3d tmp(pos);
177			double zdist =j * deltaR_ - halfLen_;
178			tmp[2] += zdist;
179			currentSnapshot_->wrapVector(tmp);
180
181			double wrappedZdist = tmp.z() + halfLen_;
182			if (wrappedZdist < 0.0 \|\| wrappedZdist > len_) {
183			continue;
184			}
185
186			int which =wrappedZdist / deltaR_;
187			density_[which] += nelectron * exp(-zdistzdist/(sigma22.0)) /(slabVolume* sqrt(2NumericConstant::PIsigma*sigma));
188
189			}
190
191
192
193	tim	2242	}
194			}
195	tim	2257
196			int nProcessed = nFrames /step_;
197			std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<double>(), nProcessed));
198			writeDensity();
199	tim	2242
200
201
202			}
203
204	tim	2257	Vector3d DensityPlot::calcNewOrigin() {
205
206			int i;
207			Vector3d newOrigin(0.0);
208			double totalMass = 0.0;
209			for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
210			double mass = sd->getMass();
211			totalMass += mass;
212			newOrigin += sd->getPos() * mass;
213			}
214			newOrigin /= totalMass;
215			return newOrigin;
216			}
217
218	tim	2242	void DensityPlot::writeDensity() {
219			std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
220			if (ofs.is_open()) {
221			ofs << "#g(x, y, z)\n";
222	tim	2257	ofs << "#selection: (" << selectionScript_ << ")\n";
223			ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n";
224			ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "\tdeltaR = " << deltaR_ <<"\n";
225	tim	2242	for (int i = 0; i < histogram_.size(); ++i) {
226			ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl;
227			}
228			} else {
229
230			sprintf(painCave.errMsg, "DensityPlot: unable to open %s\n", outputFilename_.c_str());
231			painCave.isFatal = 1;
232			simError();
233			}
234
235			ofs.close();
236
237
238			}
239
240			}
241
242