1 |
/* |
2 |
* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
3 |
* |
4 |
* Contact: oopse@oopse.org |
5 |
* |
6 |
* This program is free software; you can redistribute it and/or |
7 |
* modify it under the terms of the GNU Lesser General Public License |
8 |
* as published by the Free Software Foundation; either version 2.1 |
9 |
* of the License, or (at your option) any later version. |
10 |
* All we ask is that proper credit is given for our work, which includes |
11 |
* - but is not limited to - adding the above copyright notice to the beginning |
12 |
* of your source code files, and to any copyright notice that you may distribute |
13 |
* with programs based on this work. |
14 |
* |
15 |
* This program is distributed in the hope that it will be useful, |
16 |
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
17 |
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
18 |
* GNU Lesser General Public License for more details. |
19 |
* |
20 |
* You should have received a copy of the GNU Lesser General Public License |
21 |
* along with this program; if not, write to the Free Software |
22 |
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
23 |
* |
24 |
*/ |
25 |
|
26 |
/** |
27 |
* @file SimInfo.cpp |
28 |
* @author tlin |
29 |
* @date 11/02/2004 |
30 |
* @version 1.0 |
31 |
*/ |
32 |
|
33 |
#include <algorithm> |
34 |
|
35 |
#include "brains/SimInfo.hpp" |
36 |
#include "utils/MemoryUtils.hpp" |
37 |
|
38 |
namespace oopse { |
39 |
|
40 |
SimInfo::SimInfo() : nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
41 |
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), sman_(NULL){ |
42 |
|
43 |
} |
44 |
|
45 |
SimInfo::~SimInfo() { |
46 |
MemoryUtils::deleteVectorOfPointer(molecules_); |
47 |
delete sman_; |
48 |
|
49 |
} |
50 |
|
51 |
|
52 |
bool SimInfo::addMolecule(Molecule* mol) { |
53 |
std::vector<Molecule*>::iterator i; |
54 |
i = std::find(molecules_.begin(), molecules_.end(), mol); |
55 |
if (i != molecules_.end() ) { |
56 |
molecules_.push_back(mol); |
57 |
|
58 |
nAtoms_ += mol->getNAtoms(); |
59 |
nBonds_ += mol->getNBonds(); |
60 |
nBends_ += mol->getNBends(); |
61 |
nTorsions_ += mol->getNTorsions(); |
62 |
nRigidBodies_ += mol->getNRigidBodies(); |
63 |
nIntegrableObjects_ += mol->getNIntegrableObjects(); |
64 |
nCutoffGroups_ += mol->getNCutoffGroups(); |
65 |
nConstraints_ += mol->getNConstraints(); |
66 |
|
67 |
return true; |
68 |
} else { |
69 |
return false; |
70 |
} |
71 |
} |
72 |
|
73 |
bool SimInfo::removeMolecule(Molecule* mol) { |
74 |
std::vector<Molecule*>::iterator i; |
75 |
i = std::find(molecules_.begin(), molecules_.end(), mol); |
76 |
|
77 |
if (i != molecules_.end() ) { |
78 |
molecules_.push_back(mol); |
79 |
nAtoms_ -= mol->getNAtoms(); |
80 |
nBonds_ -= mol->getNBonds(); |
81 |
nBends_ -= mol->getNBends(); |
82 |
nTorsions_ -= mol->getNTorsions(); |
83 |
nRigidBodies_ -= mol->getNRigidBodies(); |
84 |
nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
85 |
nCutoffGroups_ -= mol->getNCutoffGroups(); |
86 |
nConstraints_ -= mol->getNConstraints(); |
87 |
|
88 |
return true; |
89 |
} else { |
90 |
return false; |
91 |
} |
92 |
|
93 |
|
94 |
} |
95 |
|
96 |
|
97 |
Molecule* SimInfo::beginMolecule(std::vector<Molecule*>::iterator& i) { |
98 |
i = molecules_.begin(); |
99 |
return i == molecules_.end() ? NULL : *i; |
100 |
} |
101 |
|
102 |
Molecule* SimInfo::nextMolecule(std::vector<Molecule*>::iterator& i) { |
103 |
++i; |
104 |
return i == molecules_.end() ? NULL : *i; |
105 |
} |
106 |
|
107 |
|
108 |
void SimInfo::calcNDF() { |
109 |
int ndf_local; |
110 |
std::vector<Molecule*>::iterator i; |
111 |
std::vector<StuntDouble*>::iterator j; |
112 |
Molecule* mol; |
113 |
StuntDouble* integrableObject; |
114 |
|
115 |
ndf_local = 0; |
116 |
|
117 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
118 |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
119 |
integrableObject = mol->nextIntegrableObject(j)) { |
120 |
|
121 |
ndf_local += 3; |
122 |
|
123 |
if (integrableObject->isDirectional()) { |
124 |
if (integrableObject->isLinear()) { |
125 |
ndf_local += 2; |
126 |
} else { |
127 |
ndf_local += 3; |
128 |
} |
129 |
} |
130 |
|
131 |
}//end for (integrableObject) |
132 |
}// end for (mol) |
133 |
|
134 |
// n_constraints is local, so subtract them on each processor |
135 |
ndf_local -= nConstraints_; |
136 |
|
137 |
#ifdef IS_MPI |
138 |
MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
139 |
#else |
140 |
ndf_ = ndf_local; |
141 |
#endif |
142 |
|
143 |
// nZconstraints is global, as are the 3 COM translations for the |
144 |
// entire system: |
145 |
ndf_ = ndf_ - 3 - nZconstraints; |
146 |
|
147 |
} |
148 |
|
149 |
void SimInfo::calcNDFRaw() { |
150 |
int ndfRaw_local; |
151 |
|
152 |
std::vector<Molecule*>::iterator i; |
153 |
std::vector<StuntDouble*>::iterator j; |
154 |
Molecule* mol; |
155 |
StuntDouble* integrableObject; |
156 |
|
157 |
// Raw degrees of freedom that we have to set |
158 |
ndfRaw_local = 0; |
159 |
|
160 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
161 |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
162 |
integrableObject = mol->nextIntegrableObject(j)) { |
163 |
|
164 |
ndfRaw_local += 3; |
165 |
|
166 |
if (integrableObject->isDirectional()) { |
167 |
if (integrableObject->isLinear()) { |
168 |
ndfRaw_local += 2; |
169 |
} else { |
170 |
ndfRaw_local += 3; |
171 |
} |
172 |
} |
173 |
|
174 |
} |
175 |
} |
176 |
|
177 |
#ifdef IS_MPI |
178 |
MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
179 |
#else |
180 |
ndfRaw_ = ndfRaw_local; |
181 |
#endif |
182 |
} |
183 |
|
184 |
void SimInfo::calcNDFTrans() { |
185 |
int ndfTrans_local; |
186 |
|
187 |
ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
188 |
|
189 |
|
190 |
#ifdef IS_MPI |
191 |
MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
192 |
#else |
193 |
ndfTrans_ = ndfTrans_local; |
194 |
#endif |
195 |
|
196 |
ndfTrans_ = ndfTrans_ - 3 - nZconstraints; |
197 |
|
198 |
} |
199 |
|
200 |
|
201 |
}//end namespace oopse |