1 |
tim |
1703 |
/* |
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 SimCreator.cpp |
28 |
|
|
* @author tlin |
29 |
|
|
* @date 11/03/2004 |
30 |
|
|
* @time 13:51am |
31 |
|
|
* @version 1.0 |
32 |
|
|
*/ |
33 |
|
|
|
34 |
|
|
#include "brains/SimCreator.hpp" |
35 |
|
|
namespace oopse { |
36 |
|
|
|
37 |
tim |
1712 |
void SimSetup::parseFile(char* mdfile, MakeStamps* stamps, Globals* globals){ |
38 |
|
|
#ifdef IS_MPI |
39 |
|
|
if (worldRank == 0){ |
40 |
|
|
#endif // is_mpi |
41 |
|
|
|
42 |
|
|
|
43 |
|
|
globals->initalize(); |
44 |
|
|
set_interface_stamps(stamps, globals); |
45 |
|
|
|
46 |
|
|
#ifdef IS_MPI |
47 |
|
|
mpiEventInit(); |
48 |
|
|
#endif |
49 |
|
|
|
50 |
|
|
yacc_BASS(mdfile); |
51 |
|
|
|
52 |
|
|
#ifdef IS_MPI |
53 |
|
|
throwMPIEvent(NULL); |
54 |
|
|
} |
55 |
|
|
else{ |
56 |
|
|
set_interface_stamps(stamps, globals); |
57 |
|
|
mpiEventInit(); |
58 |
|
|
MPIcheckPoint(); |
59 |
|
|
mpiEventLoop(); |
60 |
|
|
} |
61 |
|
|
#endif |
62 |
|
|
|
63 |
tim |
1703 |
} |
64 |
|
|
|
65 |
tim |
1712 |
|
66 |
|
|
SimModel* SimCreator::createSim(const std::string& mdfile) { |
67 |
|
|
MakeStamps* stamps; |
68 |
|
|
|
69 |
|
|
Globals* globals = new Globals(); |
70 |
|
|
|
71 |
|
|
//parse meta-data file |
72 |
|
|
parseFile(mdfile, stamps, globals); |
73 |
|
|
|
74 |
|
|
//create the force field |
75 |
|
|
ForceFiled* ff = ForceFiledFactory::getInstance()->createForceField(globals->getForceField()); |
76 |
|
|
|
77 |
|
|
//create SimModel |
78 |
|
|
model = new SimInfo(); |
79 |
|
|
|
80 |
|
|
//gather parameters |
81 |
|
|
gatherParameters(model); |
82 |
|
|
|
83 |
|
|
|
84 |
|
|
|
85 |
|
|
//divide the molecules and determine the global index of molecules |
86 |
|
|
|
87 |
|
|
//create the molecules |
88 |
|
|
|
89 |
|
|
//create atoms, bonds, bend, torsions, rigidbodies |
90 |
|
|
|
91 |
|
|
//allocate memory for DataStorage(circular reference, need to break it) |
92 |
|
|
model->setSnapshotManager(new SimSnapshotManager(model); |
93 |
|
|
|
94 |
|
|
//load initial coordinates |
95 |
|
|
DumpReader reader(); |
96 |
|
|
reader.readFrame(model); |
97 |
|
|
|
98 |
|
|
//initialize fortran |
99 |
|
|
return model; |
100 |
|
|
} |
101 |
|
|
|
102 |
|
|
void SimCreator::gatherParameters(SimModel* model) { |
103 |
|
|
model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled())); |
104 |
|
|
model->addProperty(new DoubleGenericData("dt"), globals->getDt()); |
105 |
|
|
} |
106 |
|
|
|
107 |
|
|
#ifdef IS_MPI |
108 |
|
|
void SimCreator::mpiMolDivide() { |
109 |
|
|
|
110 |
|
|
|
111 |
|
|
} |
112 |
|
|
|
113 |
|
|
#endif |
114 |
tim |
1703 |
} //end namespace oopse |