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, 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 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();   
            }
            
            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;
            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:	2264
Committed:	Wed Jul 13 16:48:49 2005 UTC (18 years, 11 months ago) by tim
File size:	8295 byte(s)
Log Message:	std::bind2nd is in <functional>
#	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 <functional>
44	#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	DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, double len, int nrbins)
53	: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info),
54	cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info),
55	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
71	cmEvaluator_.loadScriptString(cmSele);
72	if (!cmEvaluator_.isDynamic()) {
73	cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
74	}
75
76
77	}
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	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	int k;
112	for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL; sd = seleMan_.nextSelected(k)) {
113
114
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	double nelectron = doubleData->getData();
141
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	double sigma = ljParam.sigma * 0.5;
161	double sigma2 = sigma * sigma;
162
163	Vector3d pos = sd->getPos() - origin;
164	for (int j =0; j < nRBins_; ++j) {
165	Vector3d tmp(pos);
166	double zdist =j * deltaR_ - halfLen_;
167	tmp[2] += zdist;
168	currentSnapshot_->wrapVector(tmp);
169
170	double wrappedZdist = tmp.z() + halfLen_;
171	if (wrappedZdist < 0.0 \|\| wrappedZdist > len_) {
172	continue;
173	}
174
175	int which =wrappedZdist / deltaR_;
176	density_[which] += nelectron * exp(-zdistzdist/(sigma22.0)) /(slabVolume* sqrt(2NumericConstant::PIsigma*sigma));
177
178	}
179
180
181
182	}
183	}
184
185	int nProcessed = nFrames /step_;
186	std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<double>(), nProcessed));
187	writeDensity();
188
189
190
191	}
192
193	Vector3d DensityPlot::calcNewOrigin() {
194
195	int i;
196	Vector3d newOrigin(0.0);
197	double totalMass = 0.0;
198	for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
199	double mass = sd->getMass();
200	totalMass += mass;
201	newOrigin += sd->getPos() * mass;
202	}
203	newOrigin /= totalMass;
204	return newOrigin;
205	}
206
207	void DensityPlot::writeDensity() {
208	std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
209	if (ofs.is_open()) {
210	ofs << "#g(x, y, z)\n";
211	ofs << "#selection: (" << selectionScript_ << ")\n";
212	ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n";
213	ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "\tdeltaR = " << deltaR_ <<"\n";
214	for (int i = 0; i < histogram_.size(); ++i) {
215	ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl;
216	}
217	} else {
218
219	sprintf(painCave.errMsg, "DensityPlot: unable to open %s\n", outputFilename_.c_str());
220	painCave.isFatal = 1;
221	simError();
222	}
223
224	ofs.close();
225
226
227	}
228
229	}
230
231