applications/staticProps/RhoZ.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.
 *
 *
 *  RhoZ.cpp
 *  OOPSE-2.0
 *
 *  Created by Charles F. Vardeman II on 11/26/05.
 *  @author  Charles F. Vardeman II 
 *  @version $Id: RhoZ.cpp,v 1.7 2008-06-30 17:53:42 gpuliti Exp $
 *
 */

/* Calculates Rho(Z) for density profile of liquid slab. */

#include <algorithm>
#include <fstream>
#include "applications/staticProps/RhoZ.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
namespace oopse {
  
  RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int nzbins)
    : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info), seleMan_(info), nZBins_(nzbins){

    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }       
    
    // fixed number of bins

    sliceSDLists_.resize(nZBins_);
    density_.resize(nZBins_);
    
    setOutputName(getPrefix(filename) + ".RhoZ");
  }

  void RhoZ::process() {
    Molecule* mol;
    RigidBody* rb;
    StuntDouble* sd;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;

    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    nProcessed_ = nFrames/step_;

    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      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();
        }
      }

      int i;    
      for (i=0; i < nZBins_; i++) {
        sliceSDLists_[i].clear();
      }

      RealType sliceVolume = currentSnapshot_->getVolume() /nZBins_;
      Mat3x3d hmat = currentSnapshot_->getHmat();
      zBox_.push_back(hmat(2,2));
      
      RealType halfBoxZ_ = hmat(2,2) / 2.0;      

      if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }
      
      //wrap the stuntdoubles into a cell      
      for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
        Vector3d pos = sd->getPos();
        if (usePeriodicBoundaryConditions_)
          currentSnapshot_->wrapVector(pos);
        sd->setPos(pos);
      }
      
      //determine which atom belongs to which slice
      for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
        Vector3d pos = sd->getPos();
        // shift molecules by half a box to have bins start at 0
        int binNo = int(nZBins_ * (halfBoxZ_ + pos.z()) / hmat(2,2));
        sliceSDLists_[binNo].push_back(sd);
      }

      //loop over the slices to calculate the densities
      for (i = 0; i < nZBins_; i++) {
        RealType totalMass = 0;
        for (int k = 0; k < sliceSDLists_[i].size(); ++k) {
          totalMass += sliceSDLists_[i][k]->getMass();
        }
        density_[i] += totalMass/sliceVolume;
      }
    }
    
    writeDensity();

  }
  
  
  
  void RhoZ::writeDensity() {

    // compute average box length:
    std::vector<RealType>::iterator j;
    RealType zSum = 0.0;
    for (j = zBox_.begin(); j != zBox_.end(); ++j) {
      zSum += *j;       
    }
    RealType zAve = zSum / zBox_.size();

    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#RhoZ\n";
      rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
      rdfStream << "#selection: (" << selectionScript_ << ")\n";
      rdfStream << "#z\tdensity\n";
      for (int i = 0; i < density_.size(); ++i) {
        RealType z = zAve * (i+0.5)/density_.size();
        rdfStream << z << "\t" << 1.660535*density_[i]/nProcessed_ << "\n";
      }
      
    } else {
      
      sprintf(painCave.errMsg, "RhoZ: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }
    
    rdfStream.close();
  }
  
}

Revision:	1267
Committed:	Mon Jun 30 17:53:42 2008 UTC (16 years, 10 months ago) by gpuliti
Original Path:	*trunk/src/applications/staticProps/RhoZ.cpp*
File size:	6142 byte(s)
Log Message:	Fixed a number of bugs in slab_density calculation
#	User	Rev	Content
1	chuckv	769	/*
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			* RhoZ.cpp
43			* OOPSE-2.0
44			*
45			* Created by Charles F. Vardeman II on 11/26/05.
46			* @author Charles F. Vardeman II
47	gpuliti	1267	* @version $Id: RhoZ.cpp,v 1.7 2008-06-30 17:53:42 gpuliti Exp $
48	chuckv	769	*
49			*/
50
51			/* Calculates Rho(Z) for density profile of liquid slab. */
52
53			#include <algorithm>
54			#include <fstream>
55			#include "applications/staticProps/RhoZ.hpp"
56			#include "utils/simError.h"
57	tim	840	#include "io/DumpReader.hpp"
58			#include "primitives/Molecule.hpp"
59	chuckv	769	namespace oopse {
60
61	gpuliti	1267	RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int nzbins)
62			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), nZBins_(nzbins){
63	tim	840
64			evaluator_.loadScriptString(sele);
65			if (!evaluator_.isDynamic()) {
66			seleMan_.setSelectionSet(evaluator_.evaluate());
67	gpuliti	1267	}
68	chuckv	769
69	gpuliti	1267	// fixed number of bins
70
71			sliceSDLists_.resize(nZBins_);
72			density_.resize(nZBins_);
73	chuckv	769
74			setOutputName(getPrefix(filename) + ".RhoZ");
75			}
76	tim	840
77			void RhoZ::process() {
78	gpuliti	1267	Molecule* mol;
79			RigidBody* rb;
80			StuntDouble* sd;
81			SimInfo::MoleculeIterator mi;
82			Molecule::RigidBodyIterator rbIter;
83
84	tim	840	DumpReader reader(info_, dumpFilename_);
85			int nFrames = reader.getNFrames();
86	gezelter	894	nProcessed_ = nFrames/step_;
87	tim	840
88			for (int istep = 0; istep < nFrames; istep += step_) {
89	gpuliti	1267	reader.readFrame(istep);
90			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
91	tim	840
92	gpuliti	1267	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	gezelter	894	int i;
100	gpuliti	1267	for (i=0; i < nZBins_; i++) {
101	gezelter	894	sliceSDLists_[i].clear();
102			}
103	tim	840
104	gpuliti	1267	RealType sliceVolume = currentSnapshot_->getVolume() /nZBins_;
105			Mat3x3d hmat = currentSnapshot_->getHmat();
106			zBox_.push_back(hmat(2,2));
107	gezelter	894
108	gpuliti	1267	RealType halfBoxZ_ = hmat(2,2) / 2.0;
109	tim	840
110	gpuliti	1267	if (evaluator_.isDynamic()) {
111			seleMan_.setSelectionSet(evaluator_.evaluate());
112			}
113
114			//wrap the stuntdoubles into a cell
115			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
116			Vector3d pos = sd->getPos();
117			if (usePeriodicBoundaryConditions_)
118			currentSnapshot_->wrapVector(pos);
119			sd->setPos(pos);
120			}
121
122			//determine which atom belongs to which slice
123			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
124			Vector3d pos = sd->getPos();
125			// shift molecules by half a box to have bins start at 0
126			int binNo = int(nZBins_ * (halfBoxZ_ + pos.z()) / hmat(2,2));
127			sliceSDLists_[binNo].push_back(sd);
128			}
129	tim	840
130	gpuliti	1267	//loop over the slices to calculate the densities
131			for (i = 0; i < nZBins_; i++) {
132			RealType totalMass = 0;
133			for (int k = 0; k < sliceSDLists_[i].size(); ++k) {
134			totalMass += sliceSDLists_[i][k]->getMass();
135	tim	840	}
136	gpuliti	1267	density_[i] += totalMass/sliceVolume;
137			}
138	chuckv	769	}
139	gpuliti	1267
140	tim	840	writeDensity();
141
142	chuckv	769	}
143	gpuliti	1267
144
145
146			void RhoZ::writeDensity() {
147	tim	840
148	gpuliti	1267	// compute average box length:
149			std::vector<RealType>::iterator j;
150			RealType zSum = 0.0;
151			for (j = zBox_.begin(); j != zBox_.end(); ++j) {
152			zSum += *j;
153			}
154			RealType zAve = zSum / zBox_.size();
155
156	chuckv	769	std::ofstream rdfStream(outputFilename_.c_str());
157			if (rdfStream.is_open()) {
158	tim	840	rdfStream << "#RhoZ\n";
159	gezelter	894	rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
160			rdfStream << "#selection: (" << selectionScript_ << ")\n";
161	tim	840	rdfStream << "#z\tdensity\n";
162			for (int i = 0; i < density_.size(); ++i) {
163	gpuliti	1267	RealType z = zAve * (i+0.5)/density_.size();
164			rdfStream << z << "\t" << 1.660535*density_[i]/nProcessed_ << "\n";
165	chuckv	769	}
166
167			} else {
168
169			sprintf(painCave.errMsg, "RhoZ: unable to open %s\n", outputFilename_.c_str());
170			painCave.isFatal = 1;
171			simError();
172			}
173
174			rdfStream.close();
175			}
176
177			}
178