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. 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, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#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 OpenMD {


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 = OPENMD_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 = OPENMD_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 = OPENMD_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 = OPENMD_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 = OPENMD_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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 6 months ago) by gezelter
File size:	8483 byte(s)
Log Message:	updated copyright notices
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	545	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	545	* 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	gezelter	1390	*
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, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	545	*/
42
43			#include <algorithm>
44	tim	565	#include <functional>
45	tim	545	#include "applications/staticProps/DensityPlot.hpp"
46			#include "utils/simError.h"
47			#include "io/DumpReader.hpp"
48			#include "primitives/Molecule.hpp"
49			#include "utils/NumericConstant.hpp"
50	gezelter	1390	namespace OpenMD {
51	tim	545
52
53	tim	963	DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, RealType len, int nrbins)
54	tim	545	: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info),
55	tim	558	cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info),
56	tim	545	len_(len), nRBins_(nrbins), halfLen_(len/2) {
57
58			setOutputName(getPrefix(filename) + ".density");
59
60			deltaR_ = len_ /nRBins_;
61			histogram_.resize(nRBins_);
62			density_.resize(nRBins_);
63
64			std::fill(histogram_.begin(), histogram_.end(), 0);
65
66			evaluator_.loadScriptString(sele);
67
68			if (!evaluator_.isDynamic()) {
69			seleMan_.setSelectionSet(evaluator_.evaluate());
70			}
71	tim	558
72			cmEvaluator_.loadScriptString(cmSele);
73			if (!cmEvaluator_.isDynamic()) {
74			cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
75			}
76	tim	545
77	tim	558
78	tim	545	}
79
80			void DensityPlot::process() {
81			Molecule* mol;
82			RigidBody* rb;
83			SimInfo::MoleculeIterator mi;
84			Molecule::RigidBodyIterator rbIter;
85
86			DumpReader reader(info_, dumpFilename_);
87			int nFrames = reader.getNFrames();
88	tim	565	for (int i = 0; i < nFrames; i += step_) {
89	tim	545	reader.readFrame(i);
90			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
91
92			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
93			//change the positions of atoms which belong to the rigidbodies
94			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
95			rb->updateAtoms();
96			}
97
98			}
99
100			if (evaluator_.isDynamic()) {
101			seleMan_.setSelectionSet(evaluator_.evaluate());
102			}
103
104	tim	558	if (cmEvaluator_.isDynamic()) {
105			cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
106			}
107
108			Vector3d origin = calcNewOrigin();
109
110			Mat3x3d hmat = currentSnapshot_->getHmat();
111	tim	963	RealType slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1);
112	tim	565	int k;
113			for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL; sd = seleMan_.nextSelected(k)) {
114	tim	545
115	tim	558
116			if (!sd->isAtom()) {
117			sprintf( painCave.errMsg, "Can not calculate electron density if it is not atom\n");
118	gezelter	1390	painCave.severity = OPENMD_ERROR;
119	tim	558	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	gezelter	1390	painCave.severity = OPENMD_ERROR;
128	tim	558	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	gezelter	1390	painCave.severity = OPENMD_ERROR;
137	tim	558	painCave.isFatal = 1;
138			simError();
139			}
140
141	tim	963	RealType nelectron = doubleData->getData();
142	tim	558
143			data = atom->getAtomType()->getPropertyByName("LennardJones");
144			if (data == NULL) {
145			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
146	gezelter	1390	painCave.severity = OPENMD_ERROR;
147	tim	558	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	gezelter	1390	painCave.severity = OPENMD_ERROR;
156	tim	558	painCave.isFatal = 1;
157			simError();
158			}
159
160			LJParam ljParam = ljData->getData();
161	tim	963	RealType sigma = ljParam.sigma * 0.5;
162			RealType sigma2 = sigma * sigma;
163	tim	558
164			Vector3d pos = sd->getPos() - origin;
165			for (int j =0; j < nRBins_; ++j) {
166			Vector3d tmp(pos);
167	tim	963	RealType zdist =j * deltaR_ - halfLen_;
168	tim	558	tmp[2] += zdist;
169	gezelter	1078	if (usePeriodicBoundaryConditions_)
170			currentSnapshot_->wrapVector(tmp);
171	tim	558
172	tim	963	RealType wrappedZdist = tmp.z() + halfLen_;
173	tim	558	if (wrappedZdist < 0.0 \|\| wrappedZdist > len_) {
174			continue;
175			}
176
177			int which =wrappedZdist / deltaR_;
178			density_[which] += nelectron * exp(-zdistzdist/(sigma22.0)) /(slabVolume* sqrt(2NumericConstant::PIsigma*sigma));
179
180			}
181
182
183
184	tim	545	}
185			}
186	tim	558
187			int nProcessed = nFrames /step_;
188	tim	963	std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<RealType>(), nProcessed));
189	tim	558	writeDensity();
190	tim	545
191
192
193			}
194
195	tim	558	Vector3d DensityPlot::calcNewOrigin() {
196
197			int i;
198			Vector3d newOrigin(0.0);
199	tim	963	RealType totalMass = 0.0;
200	tim	558	for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
201	tim	963	RealType mass = sd->getMass();
202	tim	558	totalMass += mass;
203			newOrigin += sd->getPos() * mass;
204			}
205			newOrigin /= totalMass;
206			return newOrigin;
207			}
208
209	tim	545	void DensityPlot::writeDensity() {
210			std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
211			if (ofs.is_open()) {
212			ofs << "#g(x, y, z)\n";
213	tim	558	ofs << "#selection: (" << selectionScript_ << ")\n";
214			ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n";
215			ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "\tdeltaR = " << deltaR_ <<"\n";
216	tim	545	for (int i = 0; i < histogram_.size(); ++i) {
217			ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl;
218			}
219			} else {
220
221			sprintf(painCave.errMsg, "DensityPlot: unable to open %s\n", outputFilename_.c_str());
222			painCave.isFatal = 1;
223			simError();
224			}
225
226			ofs.close();
227
228
229			}
230
231			}
232
233