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 ago) by tim
File size:	8640 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 <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	DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, double len, int nrbins)
52	: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info),
53	cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info),
54	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
70	cmEvaluator_.loadScriptString(cmSele);
71	if (!cmEvaluator_.isDynamic()) {
72	cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
73	}
74
75
76	}
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	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	int i;
113	for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
114
115
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	}
194	}
195
196	int nProcessed = nFrames /step_;
197	std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<double>(), nProcessed));
198	writeDensity();
199
200
201
202	}
203
204	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	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	ofs << "#selection: (" << selectionScript_ << ")\n";
223	ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n";
224	ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "\tdeltaR = " << deltaR_ <<"\n";
225	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