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 (17 years, 4 months ago) by gpuliti
File size:	6142 byte(s)
Log Message:	Fixed a number of bugs in slab_density calculation
#	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. 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	* @version $Id: RhoZ.cpp,v 1.7 2008-06-30 17:53:42 gpuliti Exp $
48	*
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	#include "io/DumpReader.hpp"
58	#include "primitives/Molecule.hpp"
59	namespace oopse {
60
61	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
64	evaluator_.loadScriptString(sele);
65	if (!evaluator_.isDynamic()) {
66	seleMan_.setSelectionSet(evaluator_.evaluate());
67	}
68
69	// fixed number of bins
70
71	sliceSDLists_.resize(nZBins_);
72	density_.resize(nZBins_);
73
74	setOutputName(getPrefix(filename) + ".RhoZ");
75	}
76
77	void RhoZ::process() {
78	Molecule* mol;
79	RigidBody* rb;
80	StuntDouble* sd;
81	SimInfo::MoleculeIterator mi;
82	Molecule::RigidBodyIterator rbIter;
83
84	DumpReader reader(info_, dumpFilename_);
85	int nFrames = reader.getNFrames();
86	nProcessed_ = nFrames/step_;
87
88	for (int istep = 0; istep < nFrames; istep += step_) {
89	reader.readFrame(istep);
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	int i;
100	for (i=0; i < nZBins_; i++) {
101	sliceSDLists_[i].clear();
102	}
103
104	RealType sliceVolume = currentSnapshot_->getVolume() /nZBins_;
105	Mat3x3d hmat = currentSnapshot_->getHmat();
106	zBox_.push_back(hmat(2,2));
107
108	RealType halfBoxZ_ = hmat(2,2) / 2.0;
109
110	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
130	//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	}
136	density_[i] += totalMass/sliceVolume;
137	}
138	}
139
140	writeDensity();
141
142	}
143
144
145
146	void RhoZ::writeDensity() {
147
148	// 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	std::ofstream rdfStream(outputFilename_.c_str());
157	if (rdfStream.is_open()) {
158	rdfStream << "#RhoZ\n";
159	rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
160	rdfStream << "#selection: (" << selectionScript_ << ")\n";
161	rdfStream << "#z\tdensity\n";
162	for (int i = 0; i < density_.size(); ++i) {
163	RealType z = zAve * (i+0.5)/density_.size();
164	rdfStream << z << "\t" << 1.660535*density_[i]/nProcessed_ << "\n";
165	}
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