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 1.4 2006-03-03 21:05:34 khaygart 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 len, int nrbins)
    : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){

    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
      
    
    deltaR_ = len_ /nRBins_;
    
    sliceSDLists_.resize(nRBins_);
    density_.resize(nRBins_);
    
    setOutputName(getPrefix(filename) + ".RhoZ");
  }

  void RhoZ::process() {
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    nProcessed_ = nFrames/step_;

    for (int istep = 0; istep < nFrames; istep += step_) {

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

      StuntDouble* sd;
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      
      double sliceVolume = currentSnapshot_->getVolume() /nRBins_;
      //assume simulation box will never change
      //Mat3x3d hmat = currentSnapshot_->getHmat();
      double halfBoxZ_ = len_ /2;      
        
        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();
            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();
           int binNo = (pos.z() + halfBoxZ_) /deltaR_;
           sliceSDLists_[binNo].push_back(sd);
        }

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

    writeDensity();

  }

 
    
  void RhoZ::writeDensity() {
    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) {
        double r = deltaR_ * (i + 0.5)-82;
        rdfStream << r << "\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:	2600
Committed:	Fri Mar 3 21:05:34 2006 UTC (18 years, 6 months ago) by khaygart
File size:	5449 byte(s)
Log Message:	Bug fix - KSH
#	User	Rev	Content
1	chuckv	2468	/*
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	khaygart	2600	* @version $Id: RhoZ.cpp,v 1.4 2006-03-03 21:05:34 khaygart Exp $
48	chuckv	2468	*
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	2539	#include "io/DumpReader.hpp"
58			#include "primitives/Molecule.hpp"
59	chuckv	2468	namespace oopse {
60
61	tim	2539	RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int len, int nrbins)
62	khaygart	2600	: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){
63	tim	2539
64			evaluator_.loadScriptString(sele);
65			if (!evaluator_.isDynamic()) {
66			seleMan_.setSelectionSet(evaluator_.evaluate());
67			}
68
69	chuckv	2468
70			deltaR_ = len_ /nRBins_;
71
72	tim	2539	sliceSDLists_.resize(nRBins_);
73			density_.resize(nRBins_);
74	chuckv	2468
75			setOutputName(getPrefix(filename) + ".RhoZ");
76			}
77	tim	2539
78			void RhoZ::process() {
79			DumpReader reader(info_, dumpFilename_);
80			int nFrames = reader.getNFrames();
81	khaygart	2600	nProcessed_ = nFrames/step_;
82	tim	2539
83			for (int istep = 0; istep < nFrames; istep += step_) {
84
85	khaygart	2600	int i;
86			for (i=0; i < nRBins_; i++) {
87			sliceSDLists_[i].clear();
88			}
89	tim	2539
90	khaygart	2600	StuntDouble* sd;
91			reader.readFrame(istep);
92			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
93
94			double sliceVolume = currentSnapshot_->getVolume() /nRBins_;
95			//assume simulation box will never change
96			//Mat3x3d hmat = currentSnapshot_->getHmat();
97			double halfBoxZ_ = len_ /2;
98	tim	2539
99			if (evaluator_.isDynamic()) {
100			seleMan_.setSelectionSet(evaluator_.evaluate());
101			}
102
103			//wrap the stuntdoubles into a cell
104			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
105			Vector3d pos = sd->getPos();
106			currentSnapshot_->wrapVector(pos);
107			sd->setPos(pos);
108			}
109
110	tim	2544	//determine which atom belongs to which slice
111	tim	2539	for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
112			Vector3d pos = sd->getPos();
113	khaygart	2600	int binNo = (pos.z() + halfBoxZ_) /deltaR_;
114	tim	2539	sliceSDLists_[binNo].push_back(sd);
115			}
116
117			//loop over the slices to calculate the densities
118	khaygart	2600	for (i = 0; i < nRBins_; i++) {
119	tim	2539	double totalMass = 0;
120	khaygart	2600	for (int k = 0; k < sliceSDLists_[i].size(); ++k) {
121			totalMass += sliceSDLists_[i][k]->getMass();
122	tim	2539	}
123	khaygart	2600	density_[i] += totalMass/sliceVolume;
124	tim	2539	}
125	chuckv	2468	}
126	tim	2539
127			writeDensity();
128
129	chuckv	2468	}
130	tim	2539
131
132	chuckv	2468
133	tim	2539	void RhoZ::writeDensity() {
134	chuckv	2468	std::ofstream rdfStream(outputFilename_.c_str());
135			if (rdfStream.is_open()) {
136	tim	2539	rdfStream << "#RhoZ\n";
137	khaygart	2600	rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
138			rdfStream << "#selection: (" << selectionScript_ << ")\n";
139	tim	2539	rdfStream << "#z\tdensity\n";
140			for (int i = 0; i < density_.size(); ++i) {
141	khaygart	2600	double r = deltaR_ * (i + 0.5)-82;
142			rdfStream << r << "\t" << 1.660535*density_[i]/nProcessed_ << "\n";
143	chuckv	2468	}
144
145			} else {
146
147			sprintf(painCave.errMsg, "RhoZ: unable to open %s\n", outputFilename_.c_str());
148			painCave.isFatal = 1;
149			simError();
150			}
151
152			rdfStream.close();
153			}
154
155			}
156