63 |
|
} |
64 |
|
|
65 |
|
|
66 |
< |
SimModel* SimCreator::createSim(const std::string& mdfile) { |
67 |
< |
MakeStamps* stamps; |
66 |
> |
SimInfo* SimCreator::createSim(const std::string& mdfile) { |
67 |
> |
MakeStamps* stamps = new MakeStamps(); |
68 |
|
|
69 |
|
Globals* globals = new Globals(); |
70 |
|
|
74 |
|
//create the force field |
75 |
|
ForceFiled* ff = ForceFieldFactory::getInstance()->createForceField(globals->getForceField()); |
76 |
|
|
77 |
< |
//create SimModel |
78 |
< |
model = new SimInfo(); |
77 |
> |
//create SimInfo |
78 |
> |
SimInfo* info = new SimInfo(); |
79 |
> |
info->setGlobals(globals); |
80 |
> |
info->setForceField(ff); |
81 |
> |
|
82 |
> |
//extract the molecule stamps and add them into SimInfo |
83 |
> |
compList(stamps, info); |
84 |
|
|
85 |
< |
//gather parameters |
86 |
< |
gatherParameters(model); |
85 |
> |
//gather parameters (SimCreator only retrieves the parameters which will be used to create |
86 |
> |
// the simulation) |
87 |
> |
gatherParameters(info); |
88 |
|
|
89 |
|
//divide the molecules and determine the global index of molecules |
90 |
< |
|
90 |
> |
|
91 |
|
//create the molecules |
92 |
+ |
createMolecules(info); |
93 |
|
|
87 |
– |
//create atoms, bonds, bend, torsions, rigidbodies |
88 |
– |
|
94 |
|
//allocate memory for DataStorage(circular reference, need to break it) |
95 |
< |
model->setSnapshotManager(new SimSnapshotManager(model); |
95 |
> |
info->setSnapshotManager(new SimSnapshotManager(info); |
96 |
|
|
97 |
|
//load initial coordinates |
98 |
< |
DumpReader reader(); |
99 |
< |
reader.readFrame(model); |
98 |
> |
DumpReader reader(info->getInitFilename()); |
99 |
> |
int nframes = reader->getNframes(); |
100 |
> |
|
101 |
> |
if (nframes > 0) { |
102 |
> |
reader.readFrame(info, nframes - 1); |
103 |
> |
} else { |
104 |
> |
//invalid initial coordinate file |
105 |
> |
|
106 |
> |
} |
107 |
> |
|
108 |
|
|
109 |
|
//initialize fortran |
110 |
< |
return model; |
110 |
> |
|
111 |
> |
return info; |
112 |
|
} |
113 |
|
|
114 |
|
void SimCreator::gatherParameters(SimModel* model) { |
128 |
|
} |
129 |
|
#endif |
130 |
|
|
131 |
< |
Molecule* SimCreator::createMolecule() { |
118 |
< |
Molecule* mol = new Molecule(); |
131 |
> |
Molecule* SimCreator::createMolecules(SimInfo* info) { |
132 |
|
|
133 |
|
|
121 |
– |
//create atoms |
122 |
– |
mol->addAtom(); |
123 |
– |
|
124 |
– |
//create rigid bodies |
125 |
– |
createRigidBody(mol); |
134 |
|
|
135 |
< |
//create bonds |
135 |
> |
for (i = 0; i < mpiSim->getNMolGlobal(); i++){ |
136 |
> |
if (mol2proc[i] == worldRank){ |
137 |
|
|
138 |
< |
|
139 |
< |
|
138 |
> |
Molecule* mol = MoleculeCreator.createMolecule(molStamp, stampID, globalIndex); |
139 |
> |
|
140 |
> |
info->addMolecule(mol); |
141 |
> |
} |
142 |
> |
} |
143 |
> |
|
144 |
|
} |
145 |
|
|
146 |
+ |
|
147 |
+ |
void SimSetup::compList(MakeStamps* stamps,SimInfo* info) { |
148 |
+ |
int i; |
149 |
+ |
char* id; |
150 |
+ |
MoleculeStamp* currentStamp; |
151 |
+ |
Component* the_components = info->getGlobals()->getComponents(); |
152 |
+ |
int n_components = info->getGlobals()->getNComponents(); |
153 |
+ |
|
154 |
+ |
if (!globals->haveNMol()){ |
155 |
+ |
// we don't have the total number of molecules, so we assume it is |
156 |
+ |
// given in each component |
157 |
+ |
|
158 |
+ |
for (i = 0; i < n_components; i++){ |
159 |
+ |
if (!the_components[i]->haveNMol()){ |
160 |
+ |
// we have a problem |
161 |
+ |
sprintf(painCave.errMsg, |
162 |
+ |
"SimSetup Error. No global NMol or component NMol given.\n" |
163 |
+ |
"\tCannot calculate the number of atoms.\n"); |
164 |
+ |
painCave.isFatal = 1; |
165 |
+ |
simError(); |
166 |
+ |
} |
167 |
+ |
|
168 |
+ |
id = the_components[i]->getType(); |
169 |
+ |
currentStamp = stamps->extractMolStamp(id); |
170 |
+ |
if (currentStamp == NULL){ |
171 |
+ |
sprintf(painCave.errMsg, |
172 |
+ |
"SimSetup error: Component \"%s\" was not found in the " |
173 |
+ |
"list of declared molecules\n", |
174 |
+ |
id); |
175 |
+ |
painCave.isFatal = 1; |
176 |
+ |
simError(); |
177 |
+ |
} |
178 |
+ |
|
179 |
+ |
info.moleculeStamps.push_back(make_pair(currentStamp, the_components[i]->getNMol())); |
180 |
+ |
|
181 |
+ |
} //end for (i = 0; i < n_components; i++) |
182 |
+ |
|
183 |
+ |
} else{ |
184 |
+ |
sprintf(painCave.errMsg, |
185 |
+ |
"SimSetup error.\n" |
186 |
+ |
"\tSorry, the ability to specify total" |
187 |
+ |
" nMols and then give molfractions in the components\n" |
188 |
+ |
"\tis not currently supported." |
189 |
+ |
" Please give nMol in the components.\n"); |
190 |
+ |
painCave.isFatal = 1; |
191 |
+ |
simError(); |
192 |
+ |
} |
193 |
+ |
|
194 |
+ |
#ifdef IS_MPI |
195 |
+ |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
196 |
+ |
MPIcheckPoint(); |
197 |
+ |
#endif // is_mpi |
198 |
+ |
} |
199 |
+ |
|
200 |
+ |
|
201 |
|
} //end namespace oopse |