| 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 |
