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), 
      len_(len), halfLen_(len/2), nRBins_(nrbins),
      selectionScript_(sele), seleMan_(info), evaluator_(info), 
      cmSelectionScript_(cmSele), cmSeleMan_(info), cmEvaluator_(info) {

    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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 1 month ago) by gezelter
File size:	7769 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include <algorithm>
44	#include <functional>
45	#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	#include "types/LennardJonesAdapter.hpp"
51
52	namespace OpenMD {
53
54
55	DensityPlot::DensityPlot(SimInfo* info, const std::string& filename,
56	const std::string& sele, const std::string& cmSele,
57	RealType len, int nrbins)
58	: StaticAnalyser(info, filename),
59	len_(len), halfLen_(len/2), nRBins_(nrbins),
60	selectionScript_(sele), seleMan_(info), evaluator_(info),
61	cmSelectionScript_(cmSele), cmSeleMan_(info), cmEvaluator_(info) {
62
63	setOutputName(getPrefix(filename) + ".density");
64
65	deltaR_ = len_ /nRBins_;
66	histogram_.resize(nRBins_);
67	density_.resize(nRBins_);
68
69	std::fill(histogram_.begin(), histogram_.end(), 0);
70
71	evaluator_.loadScriptString(sele);
72
73	if (!evaluator_.isDynamic()) {
74	seleMan_.setSelectionSet(evaluator_.evaluate());
75	}
76
77	cmEvaluator_.loadScriptString(cmSele);
78	if (!cmEvaluator_.isDynamic()) {
79	cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
80	}
81	}
82
83	void DensityPlot::process() {
84	Molecule* mol;
85	RigidBody* rb;
86	SimInfo::MoleculeIterator mi;
87	Molecule::RigidBodyIterator rbIter;
88
89	DumpReader reader(info_, dumpFilename_);
90	int nFrames = reader.getNFrames();
91	for (int i = 0; i < nFrames; i += step_) {
92	reader.readFrame(i);
93	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
94
95	for (mol = info_->beginMolecule(mi); mol != NULL;
96	mol = info_->nextMolecule(mi)) {
97	//change the positions of atoms which belong to the rigidbodies
98	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
99	rb = mol->nextRigidBody(rbIter)) {
100	rb->updateAtoms();
101	}
102
103	}
104
105	if (evaluator_.isDynamic()) {
106	seleMan_.setSelectionSet(evaluator_.evaluate());
107	}
108
109	if (cmEvaluator_.isDynamic()) {
110	cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
111	}
112
113	Vector3d origin = calcNewOrigin();
114
115	Mat3x3d hmat = currentSnapshot_->getHmat();
116	RealType slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1);
117	int k;
118	for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL;
119	sd = seleMan_.nextSelected(k)) {
120
121
122	if (!sd->isAtom()) {
123	sprintf( painCave.errMsg,
124	"Can not calculate electron density if it is not atom\n");
125	painCave.severity = OPENMD_ERROR;
126	painCave.isFatal = 1;
127	simError();
128	}
129
130	Atom* atom = static_cast<Atom*>(sd);
131	GenericData* data = atom->getAtomType()->getPropertyByName("nelectron");
132	if (data == NULL) {
133	sprintf( painCave.errMsg, "Can not find Parameters for nelectron\n");
134	painCave.severity = OPENMD_ERROR;
135	painCave.isFatal = 1;
136	simError();
137	}
138
139	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
140	if (doubleData == NULL) {
141	sprintf( painCave.errMsg,
142	"Can not cast GenericData to DoubleGenericData\n");
143	painCave.severity = OPENMD_ERROR;
144	painCave.isFatal = 1;
145	simError();
146	}
147
148	RealType nelectron = doubleData->getData();
149	LennardJonesAdapter lja = LennardJonesAdapter(atom->getAtomType());
150	RealType sigma = lja.getSigma() * 0.5;
151	RealType sigma2 = sigma * sigma;
152
153	Vector3d pos = sd->getPos() - origin;
154	for (int j =0; j < nRBins_; ++j) {
155	Vector3d tmp(pos);
156	RealType zdist =j * deltaR_ - halfLen_;
157	tmp[2] += zdist;
158	if (usePeriodicBoundaryConditions_)
159	currentSnapshot_->wrapVector(tmp);
160
161	RealType wrappedZdist = tmp.z() + halfLen_;
162	if (wrappedZdist < 0.0 \|\| wrappedZdist > len_) {
163	continue;
164	}
165
166	int which = int(wrappedZdist / deltaR_);
167	density_[which] += nelectron * exp(-zdistzdist/(sigma22.0)) /(slabVolume* sqrt(2NumericConstant::PIsigma*sigma));
168
169	}
170	}
171	}
172
173	int nProcessed = nFrames /step_;
174	std::transform(density_.begin(), density_.end(), density_.begin(),
175	std::bind2nd(std::divides<RealType>(), nProcessed));
176	writeDensity();
177
178
179
180	}
181
182	Vector3d DensityPlot::calcNewOrigin() {
183
184	int i;
185	Vector3d newOrigin(0.0);
186	RealType totalMass = 0.0;
187	for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL;
188	sd = seleMan_.nextSelected(i)) {
189	RealType mass = sd->getMass();
190	totalMass += mass;
191	newOrigin += sd->getPos() * mass;
192	}
193	newOrigin /= totalMass;
194	return newOrigin;
195	}
196
197	void DensityPlot::writeDensity() {
198	std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
199	if (ofs.is_open()) {
200	ofs << "#g(x, y, z)\n";
201	ofs << "#selection: (" << selectionScript_ << ")\n";
202	ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n";
203	ofs << "#nRBins = " << nRBins_ << "\t maxLen = "
204	<< len_ << "\tdeltaR = " << deltaR_ <<"\n";
205	for (unsigned int i = 0; i < histogram_.size(); ++i) {
206	ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl;
207	}
208	} else {
209
210	sprintf(painCave.errMsg, "DensityPlot: unable to open %s\n",
211	outputFilename_.c_str());
212	painCave.isFatal = 1;
213	simError();
214	}
215
216	ofs.close();
217
218
219	}
220
221	}
222
223