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root/OpenMD/trunk/src/applications/staticProps/RhoZ.cpp

Comparing trunk/src/applications/staticProps/RhoZ.cpp (file contents):
Revision 769 by chuckv, Wed Nov 30 21:00:39 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 38 | Line 29
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31		*
32	<	*
33	<	*  RhoZ.cpp
34	<	*  OOPSE-2.0
35	<	*
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, 234107 (2008).
39	>	* [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41		*  Created by Charles F. Vardeman II on 11/26/05.
42		*  @author  Charles F. Vardeman II
43	<	*  @version $Id: RhoZ.cpp,v 1.1 2005-11-30 21:00:39 chuckv Exp $
43	>	*  @version $Id$
44		*
45		*/
46
#	Line 54 | Line 50
50		#include <fstream>
51		#include "applications/staticProps/RhoZ.hpp"
52		#include "utils/simError.h"
53	<
54	<	namespace oopse {
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& sele1, const std::string& sele2, double len, int nrbins)
58	<	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
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	<	deltaR_ = len_ /nRBins_;
65	>	// fixed number of bins
66	>
67	>	sliceSDLists_.resize(nZBins_);
68	>	density_.resize(nZBins_);
69
65	–	histogram_.resize(nRBins_);
66	–	avgRhoZ_.resize(nRBins_);
67	–
70		setOutputName(getPrefix(filename) + ".RhoZ");
71		}
72	<
73	<
74	<	void RhoZ::preProcess() {
75	<	std::fill(avgRhoZ_.begin(), avgRhoZ_.end(), 0.0);
76	<	}
77	<
78	<	void RhoZ::initalizeHistogram() {
79	<	std::fill(histogram_.begin(), histogram_.end(), 0);
80	<	}
81	<
82	<
83	<	void RhoZ::processHistogram() {
84	<
85	<	int nPairs = getNPairs();
86	<	double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
87	<	double pairDensity = nPairs /volume * 2.0;
88	<	double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
89	<
90	<	for(int i = 0 ; i < histogram_.size(); ++i){
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	<	double rLower = i * deltaR_;
105	<	double rUpper = rLower + deltaR_;
106	<	double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
107	<	double nIdeal = volSlice * pairConstant;
104	>	RealType halfBoxZ_ = hmat(2,2) / 2.0;
105	>
106	>	if (evaluator_.isDynamic()) {
107	>	seleMan_.setSelectionSet(evaluator_.evaluate());
108	>	}
109
110	<	avgRhoZ_[i] += histogram_[i] / nIdeal;
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 (unsigned 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
100	–	void RhoZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
101	–
102	–	if (sd1 == sd2) {
103	–	return;
104	–	}
105	–
106	–	Vector3d pos1 = sd1->getPosZ();
107	–	Vector3d pos2 = sd2->getPosZ();
108	–	Vector3d r12 = pos2 - pos1;
109	–	currentSnapshot_->wrapVector(r12);
110	–
111	–	double distance = r12.length();
112	–
113	–	if (distance < len_) {
114	–	int whichBin = distance / deltaR_;
115	–	histogram_[whichBin] += 2;
116	–	}
117	–	}
140
141
142	<	void RhoZ::writeRdf() {
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 << "#radial distribution function\n";
155	<	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
156	<	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
157	<	rdfStream << "#r\tcorrValue\n";
158	<	for (int i = 0; i < avgRhoZ_.size(); ++i) {
159	<	double r = deltaR_ * (i + 0.5);
160	<	rdfStream << r << "\t" << avgRhoZ_[i]/nProcessed_ << "\n";
154	>	rdfStream << "#RhoZ\n";
155	>	rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
156	>	rdfStream << "#selection: (" << selectionScript_ << ")\n";
157	>	rdfStream << "#z\tdensity\n";
158	>	for (unsigned 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 {

Comparing trunk/src/applications/staticProps/RhoZ.cpp (property svn:keywords):
Revision 769 by chuckv, Wed Nov 30 21:00:39 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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