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] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *  Created by Charles F. Vardeman II on 11/26/05.
 *  @author  Charles F. Vardeman II 
 *  @version $Id$
 *
 */

/* 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 (unsigned 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 (unsigned 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:	1782
Committed:	Wed Aug 22 02:28:28 2012 UTC (13 years, 2 months ago) by gezelter
File size:	6175 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	769	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	769	* 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	gezelter	1390	* 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	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	chuckv	769	* Created by Charles F. Vardeman II on 11/26/05.
42			* @author Charles F. Vardeman II
43	gezelter	1442	* @version $Id$
44	chuckv	769	*
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	tim	840	#include "io/DumpReader.hpp"
54			#include "primitives/Molecule.hpp"
55	gezelter	1390	namespace OpenMD {
56	chuckv	769
57	gpuliti	1267	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	tim	840
60			evaluator_.loadScriptString(sele);
61			if (!evaluator_.isDynamic()) {
62			seleMan_.setSelectionSet(evaluator_.evaluate());
63	gpuliti	1267	}
64	chuckv	769
65	gpuliti	1267	// fixed number of bins
66
67			sliceSDLists_.resize(nZBins_);
68			density_.resize(nZBins_);
69	chuckv	769
70			setOutputName(getPrefix(filename) + ".RhoZ");
71			}
72	tim	840
73			void RhoZ::process() {
74	gpuliti	1267	Molecule* mol;
75			RigidBody* rb;
76			StuntDouble* sd;
77			SimInfo::MoleculeIterator mi;
78			Molecule::RigidBodyIterator rbIter;
79
80	tim	840	DumpReader reader(info_, dumpFilename_);
81			int nFrames = reader.getNFrames();
82	gezelter	894	nProcessed_ = nFrames/step_;
83	tim	840
84			for (int istep = 0; istep < nFrames; istep += step_) {
85	gpuliti	1267	reader.readFrame(istep);
86			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
87	tim	840
88	gpuliti	1267	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	gezelter	894	int i;
96	gpuliti	1267	for (i=0; i < nZBins_; i++) {
97	gezelter	894	sliceSDLists_[i].clear();
98			}
99	tim	840
100	gpuliti	1267	RealType sliceVolume = currentSnapshot_->getVolume() /nZBins_;
101			Mat3x3d hmat = currentSnapshot_->getHmat();
102			zBox_.push_back(hmat(2,2));
103	gezelter	894
104	gpuliti	1267	RealType halfBoxZ_ = hmat(2,2) / 2.0;
105	tim	840
106	gpuliti	1267	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	tim	840
126	gpuliti	1267	//loop over the slices to calculate the densities
127			for (i = 0; i < nZBins_; i++) {
128			RealType totalMass = 0;
129	gezelter	1782	for (unsigned int k = 0; k < sliceSDLists_[i].size(); ++k) {
130	gpuliti	1267	totalMass += sliceSDLists_[i][k]->getMass();
131	tim	840	}
132	gpuliti	1267	density_[i] += totalMass/sliceVolume;
133			}
134	chuckv	769	}
135	gpuliti	1267
136	tim	840	writeDensity();
137
138	chuckv	769	}
139	gpuliti	1267
140
141
142			void RhoZ::writeDensity() {
143	tim	840
144	gpuliti	1267	// 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	chuckv	769	std::ofstream rdfStream(outputFilename_.c_str());
153			if (rdfStream.is_open()) {
154	tim	840	rdfStream << "#RhoZ\n";
155	gezelter	894	rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
156			rdfStream << "#selection: (" << selectionScript_ << ")\n";
157	tim	840	rdfStream << "#z\tdensity\n";
158	gezelter	1782	for (unsigned int i = 0; i < density_.size(); ++i) {
159	gpuliti	1267	RealType z = zAve * (i+0.5)/density_.size();
160			rdfStream << z << "\t" << 1.660535*density_[i]/nProcessed_ << "\n";
161	chuckv	769	}
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