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

Comparing trunk/src/applications/staticProps/GofXyz.cpp (file contents):
Revision 365 by tim, Thu Feb 17 20:15:29 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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>
#	Line 44 | Line 45
45		#include "applications/staticProps/GofXyz.hpp"
46		#include "utils/simError.h"
47		#include "primitives/Molecule.hpp"
48	<	namespace oopse {
48	>	#include "types/MultipoleAdapter.hpp"
49
50	<	GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins)
51	<	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), halfLen_(len/2), nRBins_(nrbins) {
50	>	namespace OpenMD {
51	>
52	>	GofXyz::GofXyz(SimInfo* info, const std::string& filename,
53	>	const std::string& sele1, const std::string& sele2,
54	>	const std::string& sele3, RealType len, int nrbins)
55	>	: RadialDistrFunc(info, filename, sele1, sele2), len_(len),
56	>	halfLen_(len/2), nRBins_(nrbins), evaluator3_(info), seleMan3_(info) {
57	>
58		setOutputName(getPrefix(filename) + ".gxyz");
59	<
59	>
60	>	evaluator3_.loadScriptString(sele3);
61	>	if (!evaluator3_.isDynamic()) {
62	>	seleMan3_.setSelectionSet(evaluator3_.evaluate());
63	>	}
64	>
65		deltaR_ =  len_ / nRBins_;
66
67		histogram_.resize(nRBins_);
68		for (int i = 0 ; i < nRBins_; ++i) {
69	<	histogram_[i].resize(nRBins_);
70	<	for(int j = 0; j < nRBins_; ++j) {
71	<	histogram_[i][j].resize(nRBins_);
72	<	}
69	>	histogram_[i].resize(nRBins_);
70	>	for(int j = 0; j < nRBins_; ++j) {
71	>	histogram_[i][j].resize(nRBins_);
72	>	}
73	>	}
74	>	}
75	>
76	>	void GofXyz::preProcess() {
77	>	for (int i = 0 ; i < nRBins_; ++i) {
78	>	histogram_[i].resize(nRBins_);
79	>	for(int j = 0; j < nRBins_; ++j) {
80	>	std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
81	>	}
82		}
83	+	}
84	+
85	+
86	+	void GofXyz::initializeHistogram() {
87	+	// Calculate the center of mass of the molecule of selected
88	+	// StuntDouble in selection1
89	+
90	+	if (!evaluator3_.isDynamic()) {
91	+	seleMan3_.setSelectionSet(evaluator3_.evaluate());
92	+	}
93
94	<	//create atom2Mol mapping (should be other class' responsibility)
64	<	atom2Mol_.insert(atom2Mol_.begin(), info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(), static_cast<Molecule*>(NULL));
94	>	assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
95
96	<	SimInfo::MoleculeIterator mi;
97	<	Molecule* mol;
98	<	Molecule::AtomIterator ai;
99	<	Atom* atom;
100	<	Molecule::RigidBodyIterator rbIter;
101	<	RigidBody* rb;
96	>	// The Dipole direction of selection3 and position of selection3 will
97	>	// be used to determine the y-z plane
98	>	// v1 = s3 -s1,
99	>	// z = origin.dipole
100	>	// x = v1 X z
101	>	// y = z X x
102	>	rotMats_.clear();
103	>
104	>	int i;
105	>	int j;
106	>	StuntDouble* sd1;
107	>	StuntDouble* sd3;
108
109	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
110	<
111	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
76	<	atom2Mol_[atom->getGlobalIndex()] = mol;
77	<	}
109	>	for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
110	>	sd1 != NULL || sd3 != NULL;
111	>	sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
112
113	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
114	<	atom2Mol_[rb->getGlobalIndex()] = mol;
115	<	}
116	<
117	<	}
84	<	}
113	>	Vector3d r3 = sd3->getPos();
114	>	Vector3d r1 = sd1->getPos();
115	>	Vector3d v1 =  r3 - r1;
116	>	if (usePeriodicBoundaryConditions_)
117	>	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
118
119	+	AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
120	+	MultipoleAdapter ma1 = MultipoleAdapter(atype1);
121
122	<	void GofXyz::preProcess() {
123	<	for (int i = 0 ; i < nRBins_; ++i) {
124	<	histogram_[i].resize(nRBins_);
125	<	for(int j = 0; j < nRBins_; ++j) {
126	<	std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
92	<	}
93	<	}
94	<	}
122	>	Vector3d zaxis;
123	>	if (ma1.isDipole())
124	>	zaxis = sd1->getDipole();
125	>	else
126	>	zaxis = sd1->getA().transpose() * V3Z;
127
128	+	Vector3d xaxis = cross(v1, zaxis);
129	+	Vector3d yaxis = cross(zaxis, xaxis);
130
131	<	void GofXyz::initalizeHistogram() {
132	<	//calculate the center of mass of the molecule of selected stuntdouble in selection1
131	>	xaxis.normalize();
132	>	yaxis.normalize();
133	>	zaxis.normalize();
134
135	<	//determine the new coordinate set of selection1
136	<	//v1 = Rs1 -Rcom,
137	<	//z = Rs1.dipole
138	<	//x = v1 X z
139	<	//y = z X x
140	<	coorSets_.clear();
106	<
107	<	int i;
108	<	StuntDouble* sd;
109	<	for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) {
110	<	Vector3d rcom = getMolCom(sd);
111	<	Vector3d rs1 = sd->getPos();
112	<	Vector3d v1 =  rcom - rs1;
113	<	CoorSet currCoorSet;
114	<	currCoorSet.zaxis = sd->getElectroFrame().getColumn(2);
115	<	v1.normalize();
116	<	currCoorSet.zaxis.normalize();
117	<	currCoorSet.xaxis = cross(v1, currCoorSet.zaxis);
118	<	currCoorSet.yaxis = cross(currCoorSet.zaxis, currCoorSet.xaxis);
119	<	coorSets_.insert(std::map<int, CoorSet>::value_type(sd->getGlobalIndex(), currCoorSet));
135	>	RotMat3x3d rotMat;
136	>	rotMat.setRow(0, xaxis);
137	>	rotMat.setRow(1, yaxis);
138	>	rotMat.setRow(2, zaxis);
139	>
140	>	rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
141		}
142
143	<	}
143	>	}
144
145	<	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
145	>	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
146
147		Vector3d pos1 = sd1->getPos();
148		Vector3d pos2 = sd2->getPos();
149		Vector3d r12 = pos2 - pos1;
150	<	currentSnapshot_->wrapVector(r12);
150	>	if (usePeriodicBoundaryConditions_)
151	>	currentSnapshot_->wrapVector(r12);
152
153	<	std::map<int, CoorSet>::iterator i = coorSets_.find(sd1->getGlobalIndex());
154	<	assert(i != coorSets_.end());
153	>	std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
154	>	assert(i != rotMats_.end());
155
156	<	double x = dot(r12, i->second.xaxis);
135	<	double y = dot(r12, i->second.yaxis);
136	<	double z = dot(r12, i->second.zaxis);
137	<
156	>	Vector3d newR12 = i->second * r12;
157		// x, y and z's possible values range -halfLen_ to halfLen_
158	<	int xbin = (x+ halfLen_) / deltaR_;
159	<	int ybin = (y + halfLen_) / deltaR_;
160	<	int zbin = (z + halfLen_) / deltaR_;
158	>	int xbin = int( (newR12.x() + halfLen_) / deltaR_);
159	>	int ybin = int( (newR12.y() + halfLen_) / deltaR_);
160	>	int zbin = int( (newR12.z() + halfLen_) / deltaR_);
161
162		if (xbin < nRBins_ && xbin >=0 &&
163		ybin < nRBins_ && ybin >= 0 &&
164		zbin < nRBins_ && zbin >=0 ) {
165	<	++histogram_[xbin][ybin][zbin];
165	>	++histogram_[xbin][ybin][zbin];
166		}
167
168	<	}
168	>	}
169
170	<	void GofXyz::writeRdf() {
170	>	void GofXyz::writeRdf() {
171		std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
172		if (rdfStream.is_open()) {
173	<	//rdfStream << "#g(x, y, z)\n";
174	<	//rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
175	<	//rdfStream << "selection2: (" << selectionScript2_ << ")\n";
176	<	//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
177	<	for (int i = 0; i < histogram_.size(); ++i) {
178	<
179	<	for(int j = 0; j < histogram_[i].size(); ++j) {
180	<
181	<	for(int k = 0;k < histogram_[i].size(); ++k) {
182	<	rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
183	<	}
184	<	}
185	<	}
173	>	//rdfStream << "#g(x, y, z)\n";
174	>	//rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
175	>	//rdfStream << "selection2: (" << selectionScript2_ << ")\n";
176	>	//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = "
177	>	//          << len_ << "deltaR = " << deltaR_ <<"\n";
178	>	for (unsigned int i = 0; i < histogram_.size(); ++i) {
179	>	for(unsigned int j = 0; j < histogram_[i].size(); ++j) {
180	>	for(unsigned int k = 0;k < histogram_[i][j].size(); ++k) {
181	>	rdfStream.write(reinterpret_cast<char *>( &histogram_[i][j][k] ),
182	>	sizeof( histogram_[i][j][k] ));
183	>	}
184	>	}
185	>	}
186
187		} else {
188
189	<	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
190	<	painCave.isFatal = 1;
191	<	simError();
189	>	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n",
190	>	outputFilename_.c_str());
191	>	painCave.isFatal = 1;
192	>	simError();
193		}
194
195		rdfStream.close();
196	<	}
196	>	}
197
178	–	Vector3d GofXyz::getMolCom(StuntDouble* sd){
179	–	Molecule* mol = atom2Mol_[sd->getGlobalIndex()];
180	–	assert(mol);
181	–	return mol->getCom();
198		}
183	–
184	–	}

Comparing trunk/src/applications/staticProps/GofXyz.cpp (property svn:keywords):
Revision 365 by tim, Thu Feb 17 20:15:29 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 0 | Line 1
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