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, 234107 (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"
#include "types/LennardJonesAdapter.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();
        LennardJonesAdapter lja = LennardJonesAdapter(atom->getAtomType());
        RealType sigma = lja.getSigma() * 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 = int(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 (unsigned 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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	7713 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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	1782	#include "types/LennardJonesAdapter.hpp"
51
52	gezelter	1390	namespace OpenMD {
53	tim	545
54
55	gezelter	1782	DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, RealType len, int nrbins)
56			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info),
57			cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info),
58			len_(len), nRBins_(nrbins), halfLen_(len/2) {
59	tim	545
60			setOutputName(getPrefix(filename) + ".density");
61
62			deltaR_ = len_ /nRBins_;
63			histogram_.resize(nRBins_);
64			density_.resize(nRBins_);
65
66			std::fill(histogram_.begin(), histogram_.end(), 0);
67
68			evaluator_.loadScriptString(sele);
69
70			if (!evaluator_.isDynamic()) {
71			seleMan_.setSelectionSet(evaluator_.evaluate());
72			}
73	tim	558
74			cmEvaluator_.loadScriptString(cmSele);
75			if (!cmEvaluator_.isDynamic()) {
76			cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
77			}
78	tim	545
79	tim	558
80	tim	545	}
81
82	gezelter	1782	void DensityPlot::process() {
83			Molecule* mol;
84			RigidBody* rb;
85			SimInfo::MoleculeIterator mi;
86			Molecule::RigidBodyIterator rbIter;
87	tim	545
88	gezelter	1782	DumpReader reader(info_, dumpFilename_);
89			int nFrames = reader.getNFrames();
90			for (int i = 0; i < nFrames; i += step_) {
91			reader.readFrame(i);
92			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
93
94			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
95	tim	545	//change the positions of atoms which belong to the rigidbodies
96			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
97	gezelter	1782	rb->updateAtoms();
98	tim	545	}
99
100	gezelter	1782	}
101	tim	545
102	gezelter	1782	if (evaluator_.isDynamic()) {
103	tim	545	seleMan_.setSelectionSet(evaluator_.evaluate());
104	gezelter	1782	}
105	tim	545
106	gezelter	1782	if (cmEvaluator_.isDynamic()) {
107	tim	558	cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
108	gezelter	1782	}
109	tim	558
110	gezelter	1782	Vector3d origin = calcNewOrigin();
111	tim	558
112	gezelter	1782	Mat3x3d hmat = currentSnapshot_->getHmat();
113			RealType slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1);
114			int k;
115			for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL; sd = seleMan_.nextSelected(k)) {
116	tim	545
117	tim	558
118	gezelter	1782	if (!sd->isAtom()) {
119			sprintf( painCave.errMsg, "Can not calculate electron density if it is not atom\n");
120			painCave.severity = OPENMD_ERROR;
121			painCave.isFatal = 1;
122			simError();
123			}
124	tim	558
125	gezelter	1782	Atom* atom = static_cast<Atom*>(sd);
126			GenericData* data = atom->getAtomType()->getPropertyByName("nelectron");
127			if (data == NULL) {
128			sprintf( painCave.errMsg, "Can not find Parameters for nelectron\n");
129			painCave.severity = OPENMD_ERROR;
130			painCave.isFatal = 1;
131			simError();
132			}
133	tim	558
134	gezelter	1782	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
135			if (doubleData == NULL) {
136			sprintf( painCave.errMsg,
137			"Can not cast GenericData to DoubleGenericData\n");
138			painCave.severity = OPENMD_ERROR;
139			painCave.isFatal = 1;
140			simError();
141			}
142	tim	558
143	gezelter	1782	RealType nelectron = doubleData->getData();
144			LennardJonesAdapter lja = LennardJonesAdapter(atom->getAtomType());
145			RealType sigma = lja.getSigma() * 0.5;
146			RealType sigma2 = sigma * sigma;
147	tim	558
148	gezelter	1782	Vector3d pos = sd->getPos() - origin;
149			for (int j =0; j < nRBins_; ++j) {
150			Vector3d tmp(pos);
151			RealType zdist =j * deltaR_ - halfLen_;
152			tmp[2] += zdist;
153			if (usePeriodicBoundaryConditions_)
154			currentSnapshot_->wrapVector(tmp);
155
156			RealType wrappedZdist = tmp.z() + halfLen_;
157			if (wrappedZdist < 0.0 \|\| wrappedZdist > len_) {
158			continue;
159			}
160
161	gezelter	1790	int which = int(wrappedZdist / deltaR_);
162	gezelter	1782	density_[which] += nelectron * exp(-zdistzdist/(sigma22.0)) /(slabVolume* sqrt(2NumericConstant::PIsigma*sigma));
163
164			}
165			}
166	tim	545	}
167	gezelter	1782
168			int nProcessed = nFrames /step_;
169			std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<RealType>(), nProcessed));
170			writeDensity();
171	tim	545
172
173
174	gezelter	1782	}
175	tim	545
176	gezelter	1782	Vector3d DensityPlot::calcNewOrigin() {
177	tim	558
178			int i;
179			Vector3d newOrigin(0.0);
180	tim	963	RealType totalMass = 0.0;
181	tim	558	for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
182	gezelter	1782	RealType mass = sd->getMass();
183			totalMass += mass;
184			newOrigin += sd->getPos() * mass;
185	tim	558	}
186			newOrigin /= totalMass;
187			return newOrigin;
188	gezelter	1782	}
189	tim	558
190	gezelter	1782	void DensityPlot::writeDensity() {
191	tim	545	std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
192			if (ofs.is_open()) {
193			ofs << "#g(x, y, z)\n";
194	tim	558	ofs << "#selection: (" << selectionScript_ << ")\n";
195			ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n";
196			ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "\tdeltaR = " << deltaR_ <<"\n";
197	gezelter	1782	for (unsigned int i = 0; i < histogram_.size(); ++i) {
198			ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl;
199	tim	545	}
200			} else {
201
202			sprintf(painCave.errMsg, "DensityPlot: unable to open %s\n", outputFilename_.c_str());
203			painCave.isFatal = 1;
204			simError();
205			}
206
207			ofs.close();
208
209
210	gezelter	1782	}
211	tim	545
212			}
213
214