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root/OpenMD/trunk/src/applications/hydrodynamics/BeadModel.cpp

Comparing trunk/src/applications/hydrodynamics/BeadModel.cpp (file contents):
Revision 898 by tim, Wed Mar 15 15:51:44 2006 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 "applications/hydrodynamics/BeadModel.hpp"
44	+	#include "types/LennardJonesAdapter.hpp"
45
46	<	namespace oopse {
47	<	bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
48	<
46	>	namespace OpenMD {
47	>	bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
48	>
49		if (sd_->isAtom()) {
50	<	createSingleBead(static_cast<Atom*>(sd_), beads);
50	>	if (!createSingleBead(static_cast<Atom*>(sd_), beads)) {
51	>	sprintf( painCave.errMsg,
52	>	"BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
53	>	painCave.severity = OPENMD_ERROR;
54	>	painCave.isFatal = 1;
55	>	simError();
56	>	return false;
57	>	}
58		}
59		else if (sd_->isRigidBody()) {
60	<	RigidBody* rb = static_cast<RigidBody*>(sd_);
61	<	std::vector<Atom*>::iterator ai;
62	<	Atom* atom;
63	<	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
64	<	if (!createSingleBead(atom, beads))
65	<	return false;
60	>	RigidBody* rb = static_cast<RigidBody*>(sd_);
61	>	std::vector<Atom*>::iterator ai;
62	>	Atom* atom;
63	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
64	>	if (!createSingleBead(atom, beads)) {
65	>	sprintf( painCave.errMsg,
66	>	"BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
67	>	painCave.severity = OPENMD_ERROR;
68	>	painCave.isFatal = 1;
69	>	simError();
70	>	return false;
71		}
72	<	}
73	<
72	>	}
73	>	}
74		return true;
75	<	}
76	<
77	<	bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
75	>	}
76	>
77	>	bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
78		AtomType* atomType = atom->getAtomType();
79	<
79	>	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
80		if (atomType->isGayBerne()) {
81	<	return false;
82	<	} else if (atomType->isLennardJones()){
83	<	GenericData* data = atomType->getPropertyByName("LennardJones");
84	<	if (data != NULL) {
85	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
86	<
87	<	if (ljData != NULL) {
88	<	LJParam ljParam = ljData->getData();
89	<	BeadParam currBead;
90	<	currBead.atomName = atom->getType();
91	<	currBead.pos = atom->getPos();
92	<	currBead.radius = ljParam.sigma/2.0;
93	<	beads.push_back(currBead);
94	<	} else {
95	<	sprintf( painCave.errMsg,
96	<	"Can not cast GenericData to LJParam\n");
97	<	painCave.severity = OOPSE_ERROR;
98	<	painCave.isFatal = 1;
99	<	simError();
100	<	}
101	<	}
81	>	return false;
82	>	} else if (lja.isLennardJones()){
83	>	BeadParam currBead;
84	>	currBead.atomName = atom->getType();
85	>	currBead.pos = atom->getPos();
86	>	currBead.radius = lja.getSigma()/2.0;
87	>	beads.push_back(currBead);
88	>	} else {
89	>	int obanum = etab.GetAtomicNum((atom->getType()).c_str());
90	>	if (obanum != 0) {
91	>	BeadParam currBead;
92	>	currBead.atomName = atom->getType();
93	>	currBead.pos = atom->getPos();
94	>	currBead.radius = etab.GetVdwRad(obanum);
95	>	std::cout << "using rvdw = " << currBead.radius << " for atomic number " << obanum << "\n";
96	>	beads.push_back(currBead);
97	>	} else {
98	>	sprintf( painCave.errMsg,
99	>	"Could not find atom type in default element.txt\n");
100	>	painCave.severity = OPENMD_ERROR;
101	>	painCave.isFatal = 1;
102	>	simError();
103	>	}
104		}
105	<
106	<	return true;
105	>	return true;
106	>	}
107		}
92	–
93	–	}

Comparing trunk/src/applications/hydrodynamics/BeadModel.cpp (property svn:keywords):
Revision 898 by tim, Wed Mar 15 15:51:44 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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