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

Comparing trunk/src/applications/staticProps/DensityPlot.cpp (file contents):
Revision 558 by tim, Mon Jun 13 18:25:30 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 37 | Line 28
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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <algorithm>
44	+	#include <functional>
45		#include "applications/staticProps/DensityPlot.hpp"
46		#include "utils/simError.h"
47		#include "io/DumpReader.hpp"
48		#include "primitives/Molecule.hpp"
49		#include "utils/NumericConstant.hpp"
50	<	namespace oopse {
50	>	#include "types/LennardJonesAdapter.hpp"
51
52	+	namespace OpenMD {
53
51	–	DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, double len, int nrbins)
52	–	: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info),
53	–	cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info),
54	–	len_(len), nRBins_(nrbins), halfLen_(len/2)     {
54
55	+	DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, RealType len, int nrbins)
56	+	: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info),
57	+	cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info),
58	+	len_(len), nRBins_(nrbins), halfLen_(len/2)     {
59	+
60		setOutputName(getPrefix(filename) + ".density");
61
62		deltaR_ = len_ /nRBins_;
#	Line 75 | Line 79 | DensityPlot::DensityPlot(SimInfo* info, const std::str
79
80		}
81
82	<	void DensityPlot::process() {
83	<	Molecule* mol;
84	<	RigidBody* rb;
85	<	SimInfo::MoleculeIterator mi;
86	<	Molecule::RigidBodyIterator rbIter;
83	<
84	<	DumpReader reader(info_, dumpFilename_);
85	<	int nFrames = reader.getNFrames();
82	>	void DensityPlot::process() {
83	>	Molecule* mol;
84	>	RigidBody* rb;
85	>	SimInfo::MoleculeIterator mi;
86	>	Molecule::RigidBodyIterator rbIter;
87
88	<	for (int i = 0; i < nFrames; i += step_) {
89	<	reader.readFrame(i);
90	<	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
88	>	DumpReader reader(info_, dumpFilename_);
89	>	int nFrames = reader.getNFrames();
90	>	for (int i = 0; i < nFrames; i += step_) {
91	>	reader.readFrame(i);
92	>	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
93
94	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
94	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
95		//change the positions of atoms which belong to the rigidbodies
96		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
97	<	rb->updateAtoms();
97	>	rb->updateAtoms();
98		}
99
100	<	}
100	>	}
101
102	<	if (evaluator_.isDynamic()) {
102	>	if (evaluator_.isDynamic()) {
103		seleMan_.setSelectionSet(evaluator_.evaluate());
104	<	}
104	>	}
105
106	<	if (cmEvaluator_.isDynamic()) {
106	>	if (cmEvaluator_.isDynamic()) {
107		cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
108	<	}
108	>	}
109
110	<	Vector3d origin = calcNewOrigin();
110	>	Vector3d origin = calcNewOrigin();
111
112	<	Mat3x3d hmat = currentSnapshot_->getHmat();
113	<	double slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1);
114	<
115	<	int i;
113	<	for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
112	>	Mat3x3d hmat = currentSnapshot_->getHmat();
113	>	RealType slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1);
114	>	int k;
115	>	for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL; sd = seleMan_.nextSelected(k)) {
116
117
118	<	if (!sd->isAtom()) {
119	<	sprintf( painCave.errMsg, "Can not calculate electron density if it is not atom\n");
120	<	painCave.severity = OOPSE_ERROR;
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
118	>	if (!sd->isAtom()) {
119	>	sprintf( painCave.errMsg, "Can not calculate electron density if it is not atom\n");
120	>	painCave.severity = OPENMD_ERROR;
121	>	painCave.isFatal = 1;
122	>	simError();
123	>	}
124
125	<	Atom* atom = static_cast<Atom*>(sd);
126	<	GenericData* data = atom->getAtomType()->getPropertyByName("nelectron");
127	<	if (data == NULL) {
128	<	sprintf( painCave.errMsg, "Can not find Parameters for nelectron\n");
129	<	painCave.severity = OOPSE_ERROR;
130	<	painCave.isFatal = 1;
131	<	simError();
132	<	}
125	>	Atom* atom = static_cast<Atom*>(sd);
126	>	GenericData* data = atom->getAtomType()->getPropertyByName("nelectron");
127	>	if (data == NULL) {
128	>	sprintf( painCave.errMsg, "Can not find Parameters for nelectron\n");
129	>	painCave.severity = OPENMD_ERROR;
130	>	painCave.isFatal = 1;
131	>	simError();
132	>	}
133
134	<	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
135	<	if (doubleData == NULL) {
136	<	sprintf( painCave.errMsg,
137	<	"Can not cast GenericData to DoubleGenericData\n");
138	<	painCave.severity = OOPSE_ERROR;
139	<	painCave.isFatal = 1;
140	<	simError();
141	<	}
134	>	DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data);
135	>	if (doubleData == NULL) {
136	>	sprintf( painCave.errMsg,
137	>	"Can not cast GenericData to DoubleGenericData\n");
138	>	painCave.severity = OPENMD_ERROR;
139	>	painCave.isFatal = 1;
140	>	simError();
141	>	}
142
143	<	double nelectron = doubleData->getData();
144	<
145	<	data = atom->getAtomType()->getPropertyByName("LennardJones");
146	<	if (data == NULL) {
145	<	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
146	<	painCave.severity = OOPSE_ERROR;
147	<	painCave.isFatal = 1;
148	<	simError();
149	<	}
150	<
151	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
152	<	if (ljData == NULL) {
153	<	sprintf( painCave.errMsg,
154	<	"Can not cast GenericData to LJParam\n");
155	<	painCave.severity = OOPSE_ERROR;
156	<	painCave.isFatal = 1;
157	<	simError();
158	<	}
159	<
160	<	LJParam ljParam = ljData->getData();
161	<	double sigma = ljParam.sigma * 0.5;
162	<	double sigma2 = sigma * sigma;
163	<
164	<	Vector3d pos = sd->getPos() - origin;
165	<	/*
166	<	currentSnapshot_->wrapVector(pos);
167	<	double wrappedZdist = pos.z() + halfLen_;
168	<	if (wrappedZdist < 0.0 || wrappedZdist > len_) {
169	<	continue;
170	<	}
143	>	RealType nelectron = doubleData->getData();
144	>	LennardJonesAdapter lja = LennardJonesAdapter(atom->getAtomType());
145	>	RealType sigma = lja.getSigma() * 0.5;
146	>	RealType sigma2 = sigma * sigma;
147
148	<	int which =wrappedZdist / deltaR_;
149	<	density_[which] += nelectron;
150	<	*/
151	<	for (int j =0; j < nRBins_; ++j) {
152	<	Vector3d tmp(pos);
153	<	double zdist =j * deltaR_ - halfLen_;
154	<	tmp[2] += zdist;
155	<	currentSnapshot_->wrapVector(tmp);
156	<
157	<	double wrappedZdist = tmp.z() + halfLen_;
158	<	if (wrappedZdist < 0.0 || wrappedZdist > len_) {
159	<	continue;
160	<	}
161	<
162	<	int which =wrappedZdist / deltaR_;
163	<	density_[which] += nelectron * exp(-zdist*zdist/(sigma2*2.0)) /(slabVolume* sqrt(2*NumericConstant::PI*sigma*sigma));
164	<
165	<	}
190	<
191	<
192	<
193	<	}
148	>	Vector3d pos = sd->getPos() - origin;
149	>	for (int j =0; j < nRBins_; ++j) {
150	>	Vector3d tmp(pos);
151	>	RealType zdist =j * deltaR_ - halfLen_;
152	>	tmp[2] += zdist;
153	>	if (usePeriodicBoundaryConditions_)
154	>	currentSnapshot_->wrapVector(tmp);
155	>
156	>	RealType wrappedZdist = tmp.z() + halfLen_;
157	>	if (wrappedZdist < 0.0 || wrappedZdist > len_) {
158	>	continue;
159	>	}
160	>
161	>	int which = int(wrappedZdist / deltaR_);
162	>	density_[which] += nelectron * exp(-zdist*zdist/(sigma2*2.0)) /(slabVolume* sqrt(2*NumericConstant::PI*sigma*sigma));
163	>
164	>	}
165	>	}
166		}
167	<
168	<	int nProcessed = nFrames /step_;
169	<	std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<double>(), nProcessed));
170	<	writeDensity();
167	>
168	>	int nProcessed = nFrames /step_;
169	>	std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<RealType>(), nProcessed));
170	>	writeDensity();
171
172
173
174	<	}
174	>	}
175
176	<	Vector3d DensityPlot::calcNewOrigin() {
176	>	Vector3d DensityPlot::calcNewOrigin() {
177
178		int i;
179		Vector3d newOrigin(0.0);
180	<	double totalMass = 0.0;
180	>	RealType totalMass = 0.0;
181		for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
182	<	double mass = sd->getMass();
183	<	totalMass += mass;
184	<	newOrigin += sd->getPos() * mass;
182	>	RealType mass = sd->getMass();
183	>	totalMass += mass;
184	>	newOrigin += sd->getPos() * mass;
185		}
186		newOrigin /= totalMass;
187		return newOrigin;
188	<	}
188	>	}
189
190	<	void DensityPlot::writeDensity() {
190	>	void DensityPlot::writeDensity() {
191		std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
192		if (ofs.is_open()) {
193		ofs << "#g(x, y, z)\n";
194		ofs << "#selection: (" << selectionScript_ << ")\n";
195		ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n";
196		ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "\tdeltaR = " << deltaR_ <<"\n";
197	<	for (int i = 0; i < histogram_.size(); ++i) {
198	<	ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl;
197	>	for (unsigned int i = 0; i < histogram_.size(); ++i) {
198	>	ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl;
199		}
200		} else {
201
#	Line 235 | Line 207 | void DensityPlot::writeDensity() {
207		ofs.close();
208
209
210	<	}
210	>	}
211
212		}
213

Comparing trunk/src/applications/staticProps/DensityPlot.cpp (property svn:keywords):
Revision 558 by tim, Mon Jun 13 18:25:30 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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