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. 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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 *
 *  Created by Charles F. Vardeman II on 11/26/05.
 *  @author  Charles F. Vardeman II 
 *  @version $Id: RhoZ.cpp,v 1.8 2009-11-25 20:01:59 gezelter 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 OpenMD {
  
  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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 11 months ago) by gezelter
File size:	6152 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
40	*
41	* Created by Charles F. Vardeman II on 11/26/05.
42	* @author Charles F. Vardeman II
43	* @version $Id: RhoZ.cpp,v 1.8 2009-11-25 20:01:59 gezelter Exp $
44	*
45	*/
46
47	/* Calculates Rho(Z) for density profile of liquid slab. */
48
49	#include <algorithm>
50	#include <fstream>
51	#include "applications/staticProps/RhoZ.hpp"
52	#include "utils/simError.h"
53	#include "io/DumpReader.hpp"
54	#include "primitives/Molecule.hpp"
55	namespace OpenMD {
56
57	RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int nzbins)
58	: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), nZBins_(nzbins){
59
60	evaluator_.loadScriptString(sele);
61	if (!evaluator_.isDynamic()) {
62	seleMan_.setSelectionSet(evaluator_.evaluate());
63	}
64
65	// fixed number of bins
66
67	sliceSDLists_.resize(nZBins_);
68	density_.resize(nZBins_);
69
70	setOutputName(getPrefix(filename) + ".RhoZ");
71	}
72
73	void RhoZ::process() {
74	Molecule* mol;
75	RigidBody* rb;
76	StuntDouble* sd;
77	SimInfo::MoleculeIterator mi;
78	Molecule::RigidBodyIterator rbIter;
79
80	DumpReader reader(info_, dumpFilename_);
81	int nFrames = reader.getNFrames();
82	nProcessed_ = nFrames/step_;
83
84	for (int istep = 0; istep < nFrames; istep += step_) {
85	reader.readFrame(istep);
86	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
87
88	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
89	//change the positions of atoms which belong to the rigidbodies
90	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
91	rb->updateAtoms();
92	}
93	}
94
95	int i;
96	for (i=0; i < nZBins_; i++) {
97	sliceSDLists_[i].clear();
98	}
99
100	RealType sliceVolume = currentSnapshot_->getVolume() /nZBins_;
101	Mat3x3d hmat = currentSnapshot_->getHmat();
102	zBox_.push_back(hmat(2,2));
103
104	RealType halfBoxZ_ = hmat(2,2) / 2.0;
105
106	if (evaluator_.isDynamic()) {
107	seleMan_.setSelectionSet(evaluator_.evaluate());
108	}
109
110	//wrap the stuntdoubles into a cell
111	for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
112	Vector3d pos = sd->getPos();
113	if (usePeriodicBoundaryConditions_)
114	currentSnapshot_->wrapVector(pos);
115	sd->setPos(pos);
116	}
117
118	//determine which atom belongs to which slice
119	for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
120	Vector3d pos = sd->getPos();
121	// shift molecules by half a box to have bins start at 0
122	int binNo = int(nZBins_ * (halfBoxZ_ + pos.z()) / hmat(2,2));
123	sliceSDLists_[binNo].push_back(sd);
124	}
125
126	//loop over the slices to calculate the densities
127	for (i = 0; i < nZBins_; i++) {
128	RealType totalMass = 0;
129	for (int k = 0; k < sliceSDLists_[i].size(); ++k) {
130	totalMass += sliceSDLists_[i][k]->getMass();
131	}
132	density_[i] += totalMass/sliceVolume;
133	}
134	}
135
136	writeDensity();
137
138	}
139
140
141
142	void RhoZ::writeDensity() {
143
144	// compute average box length:
145	std::vector<RealType>::iterator j;
146	RealType zSum = 0.0;
147	for (j = zBox_.begin(); j != zBox_.end(); ++j) {
148	zSum += *j;
149	}
150	RealType zAve = zSum / zBox_.size();
151
152	std::ofstream rdfStream(outputFilename_.c_str());
153	if (rdfStream.is_open()) {
154	rdfStream << "#RhoZ\n";
155	rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
156	rdfStream << "#selection: (" << selectionScript_ << ")\n";
157	rdfStream << "#z\tdensity\n";
158	for (int i = 0; i < density_.size(); ++i) {
159	RealType z = zAve * (i+0.5)/density_.size();
160	rdfStream << z << "\t" << 1.660535*density_[i]/nProcessed_ << "\n";
161	}
162
163	} else {
164
165	sprintf(painCave.errMsg, "RhoZ: unable to open %s\n", outputFilename_.c_str());
166	painCave.isFatal = 1;
167	simError();
168	}
169
170	rdfStream.close();
171	}
172
173	}
174