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#include <algorithm> |
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#include <cstdlib> |
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#include <iostream> |
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#include <cmath> |
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#include <string> |
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|
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#include "SimSetup.hpp" |
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#include "parse_me.h" |
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#include "mpiSimulation.hpp" |
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#endif |
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|
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// some defines for ensemble and Forcefield cases |
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|
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#define NVE_ENS 0 |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTim_ENS 4 |
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#define NPTfm_ENS 5 |
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#define NVEZCONS_ENS 6 |
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#define NVTZCONS_ENS 7 |
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#define NPTiZCONS_ENS 8 |
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#define NPTfZCONS_ENS 9 |
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#define NPTimZCONS_ENS 10 |
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#define NPTfmZCONS_ENS 11 |
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|
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#define FF_DUFF 0 |
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#define FF_LJ 1 |
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#define FF_EAM 2 |
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|
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using namespace std; |
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|
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SimSetup::SimSetup(){ |
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|
40 |
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isInfoArray = 0; |
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nInfo = 1; |
42 |
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|
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stamps = new MakeStamps(); |
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globals = new Globals(); |
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|
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|
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "SimSetup creation successful" ); |
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MPIcheckPoint(); |
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delete globals; |
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} |
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|
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void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
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info = the_info; |
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nInfo = theNinfo; |
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isInfoArray = 1; |
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} |
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|
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|
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void SimSetup::parseFile( char* fileName ){ |
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|
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#ifdef IS_MPI |
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|
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#endif // is_mpi |
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|
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void SimSetup::createSim( void ){ |
100 |
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void SimSetup::createSim(void){ |
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|
102 |
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MakeStamps *the_stamps; |
103 |
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Globals* the_globals; |
104 |
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int i, j; |
102 |
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int i, j, k, globalAtomIndex; |
103 |
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|
104 |
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// gather all of the information from the Bass file |
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|
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gatherInfo(); |
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|
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// get the stamps and globals; |
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the_stamps = stamps; |
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the_globals = globals; |
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// creation of complex system objects |
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|
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// set the easy ones first |
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simnfo->target_temp = the_globals->getTargetTemp(); |
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simnfo->dt = the_globals->getDt(); |
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simnfo->run_time = the_globals->getRunTime(); |
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sysObjectsCreation(); |
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|
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// get the ones we know are there, yet still may need some work. |
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n_components = the_globals->getNComponents(); |
114 |
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strcpy( force_field, the_globals->getForceField() ); |
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strcpy( ensemble, the_globals->getEnsemble() ); |
84 |
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strcpy( simnfo->ensemble, ensemble ); |
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// check on the post processing info |
113 |
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|
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finalInfoCheck(); |
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|
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strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
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simnfo->usePBC = the_globals->getPBC(); |
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|
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// initialize the system coordinates |
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|
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if( !isInfoArray ) initSystemCoords(); |
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|
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if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
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else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
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else{ |
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sprintf( painCave.errMsg, |
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"SimSetup Error. Unrecognized force field -> %s\n", |
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force_field ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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// make the output filenames |
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|
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makeOutNames(); |
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|
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// make the integrator |
125 |
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|
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makeIntegrator(); |
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|
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "ForceField creation successful" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
129 |
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mpiSim->mpiRefresh(); |
130 |
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#endif |
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|
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|
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// initialize the Fortran |
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|
134 |
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// get the components and calculate the tot_nMol and indvidual n_mol |
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the_components = the_globals->getComponents(); |
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components_nmol = new int[n_components]; |
111 |
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comp_stamps = new MoleculeStamp*[n_components]; |
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initFortran(); |
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|
113 |
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if( !the_globals->haveNMol() ){ |
114 |
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// we don't have the total number of molecules, so we assume it is |
115 |
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// given in each component |
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|
117 |
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tot_nmol = 0; |
118 |
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for( i=0; i<n_components; i++ ){ |
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|
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if( !the_components[i]->haveNMol() ){ |
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// we have a problem |
122 |
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sprintf( painCave.errMsg, |
123 |
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"SimSetup Error. No global NMol or component NMol" |
124 |
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" given. Cannot calculate the number of atoms.\n" ); |
125 |
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painCave.isFatal = 1; |
126 |
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simError(); |
127 |
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} |
138 |
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} |
139 |
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|
140 |
< |
tot_nmol += the_components[i]->getNMol(); |
141 |
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components_nmol[i] = the_components[i]->getNMol(); |
142 |
< |
} |
143 |
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} |
144 |
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else{ |
145 |
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sprintf( painCave.errMsg, |
146 |
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"SimSetup error.\n" |
147 |
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"\tSorry, the ability to specify total" |
148 |
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" nMols and then give molfractions in the components\n" |
149 |
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"\tis not currently supported." |
150 |
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" Please give nMol in the components.\n" ); |
151 |
< |
painCave.isFatal = 1; |
152 |
< |
simError(); |
140 |
> |
|
141 |
> |
void SimSetup::makeMolecules( void ){ |
142 |
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|
143 |
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int k,l; |
144 |
> |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
145 |
> |
molInit molInfo; |
146 |
> |
DirectionalAtom* dAtom; |
147 |
> |
LinkedAssign* extras; |
148 |
> |
LinkedAssign* current_extra; |
149 |
> |
AtomStamp* currentAtom; |
150 |
> |
BondStamp* currentBond; |
151 |
> |
BendStamp* currentBend; |
152 |
> |
TorsionStamp* currentTorsion; |
153 |
> |
|
154 |
> |
bond_pair* theBonds; |
155 |
> |
bend_set* theBends; |
156 |
> |
torsion_set* theTorsions; |
157 |
> |
|
158 |
> |
|
159 |
> |
//init the forceField paramters |
160 |
> |
|
161 |
> |
the_ff->readParams(); |
162 |
> |
|
163 |
> |
|
164 |
> |
// init the atoms |
165 |
> |
|
166 |
> |
double ux, uy, uz, u, uSqr; |
167 |
> |
|
168 |
> |
for(k=0; k<nInfo; k++){ |
169 |
|
|
170 |
+ |
the_ff->setSimInfo( &(info[k]) ); |
171 |
+ |
|
172 |
+ |
atomOffset = 0; |
173 |
+ |
excludeOffset = 0; |
174 |
+ |
for(i=0; i<info[k].n_mol; i++){ |
175 |
|
|
176 |
< |
// tot_nmol = the_globals->getNMol(); |
176 |
> |
stampID = info[k].molecules[i].getStampID(); |
177 |
> |
|
178 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
179 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
180 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
181 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
182 |
> |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
183 |
> |
|
184 |
> |
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
185 |
> |
molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
186 |
> |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
187 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
188 |
> |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
189 |
> |
|
190 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
191 |
> |
theBends = new bend_set[molInfo.nBends]; |
192 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
193 |
|
|
194 |
< |
// //we have the total number of molecules, now we check for molfractions |
147 |
< |
// for( i=0; i<n_components; i++ ){ |
194 |
> |
// make the Atoms |
195 |
|
|
196 |
< |
// if( !the_components[i]->haveMolFraction() ){ |
196 |
> |
for(j=0; j<molInfo.nAtoms; j++){ |
197 |
> |
|
198 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
199 |
> |
if( currentAtom->haveOrientation() ){ |
200 |
> |
|
201 |
> |
dAtom = new DirectionalAtom( (j + atomOffset), |
202 |
> |
info[k].getConfiguration() ); |
203 |
> |
info[k].n_oriented++; |
204 |
> |
molInfo.myAtoms[j] = dAtom; |
205 |
> |
|
206 |
> |
ux = currentAtom->getOrntX(); |
207 |
> |
uy = currentAtom->getOrntY(); |
208 |
> |
uz = currentAtom->getOrntZ(); |
209 |
> |
|
210 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
211 |
> |
|
212 |
> |
u = sqrt( uSqr ); |
213 |
> |
ux = ux / u; |
214 |
> |
uy = uy / u; |
215 |
> |
uz = uz / u; |
216 |
> |
|
217 |
> |
dAtom->setSUx( ux ); |
218 |
> |
dAtom->setSUy( uy ); |
219 |
> |
dAtom->setSUz( uz ); |
220 |
> |
} |
221 |
> |
else{ |
222 |
> |
molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
223 |
> |
info[k].getConfiguration() ); |
224 |
> |
} |
225 |
> |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
226 |
|
|
151 |
– |
// if( !the_components[i]->haveNMol() ){ |
152 |
– |
// //we have a problem |
153 |
– |
// std::cerr << "SimSetup error. Neither molFraction nor " |
154 |
– |
// << " nMol was given in component |
155 |
– |
|
156 |
– |
} |
157 |
– |
|
227 |
|
#ifdef IS_MPI |
228 |
< |
strcpy( checkPointMsg, "Have the number of components" ); |
229 |
< |
MPIcheckPoint(); |
228 |
> |
|
229 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
230 |
> |
|
231 |
|
#endif // is_mpi |
232 |
< |
|
163 |
< |
// make an array of molecule stamps that match the components used. |
164 |
< |
// also extract the used stamps out into a separate linked list |
165 |
< |
|
166 |
< |
simnfo->nComponents = n_components; |
167 |
< |
simnfo->componentsNmol = components_nmol; |
168 |
< |
simnfo->compStamps = comp_stamps; |
169 |
< |
simnfo->headStamp = new LinkedMolStamp(); |
170 |
< |
|
171 |
< |
char* id; |
172 |
< |
LinkedMolStamp* headStamp = simnfo->headStamp; |
173 |
< |
LinkedMolStamp* currentStamp = NULL; |
174 |
< |
for( i=0; i<n_components; i++ ){ |
175 |
< |
|
176 |
< |
id = the_components[i]->getType(); |
177 |
< |
comp_stamps[i] = NULL; |
232 |
> |
} |
233 |
|
|
234 |
< |
// check to make sure the component isn't already in the list |
235 |
< |
|
181 |
< |
comp_stamps[i] = headStamp->match( id ); |
182 |
< |
if( comp_stamps[i] == NULL ){ |
234 |
> |
// make the bonds |
235 |
> |
for(j=0; j<molInfo.nBonds; j++){ |
236 |
|
|
237 |
< |
// extract the component from the list; |
237 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
238 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
239 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
240 |
> |
|
241 |
> |
exI = theBonds[j].a; |
242 |
> |
exJ = theBonds[j].b; |
243 |
> |
|
244 |
> |
// exclude_I must always be the smaller of the pair |
245 |
> |
if( exI > exJ ){ |
246 |
> |
tempEx = exI; |
247 |
> |
exI = exJ; |
248 |
> |
exJ = tempEx; |
249 |
> |
} |
250 |
> |
#ifdef IS_MPI |
251 |
> |
tempEx = exI; |
252 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
253 |
> |
tempEx = exJ; |
254 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
255 |
> |
|
256 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
257 |
> |
#else // isn't MPI |
258 |
> |
|
259 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
260 |
> |
#endif //is_mpi |
261 |
> |
} |
262 |
> |
excludeOffset += molInfo.nBonds; |
263 |
|
|
264 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
265 |
< |
if( currentStamp == NULL ){ |
266 |
< |
sprintf( painCave.errMsg, |
267 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
268 |
< |
"list of declared molecules\n", |
269 |
< |
id ); |
270 |
< |
painCave.isFatal = 1; |
271 |
< |
simError(); |
264 |
> |
//make the bends |
265 |
> |
for(j=0; j<molInfo.nBends; j++){ |
266 |
> |
|
267 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
268 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
269 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
270 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
271 |
> |
|
272 |
> |
if( currentBend->haveExtras() ){ |
273 |
> |
|
274 |
> |
extras = currentBend->getExtras(); |
275 |
> |
current_extra = extras; |
276 |
> |
|
277 |
> |
while( current_extra != NULL ){ |
278 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
279 |
> |
|
280 |
> |
switch( current_extra->getType() ){ |
281 |
> |
|
282 |
> |
case 0: |
283 |
> |
theBends[j].ghost = |
284 |
> |
current_extra->getInt() + atomOffset; |
285 |
> |
theBends[j].isGhost = 1; |
286 |
> |
break; |
287 |
> |
|
288 |
> |
case 1: |
289 |
> |
theBends[j].ghost = |
290 |
> |
(int)current_extra->getDouble() + atomOffset; |
291 |
> |
theBends[j].isGhost = 1; |
292 |
> |
break; |
293 |
> |
|
294 |
> |
default: |
295 |
> |
sprintf( painCave.errMsg, |
296 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
297 |
> |
"double nor an int.\n" |
298 |
> |
"-->Bend[%d] in %s\n", |
299 |
> |
j, comp_stamps[stampID]->getID() ); |
300 |
> |
painCave.isFatal = 1; |
301 |
> |
simError(); |
302 |
> |
} |
303 |
> |
} |
304 |
> |
|
305 |
> |
else{ |
306 |
> |
|
307 |
> |
sprintf( painCave.errMsg, |
308 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
309 |
> |
" -->%s in Bend[%d] in %s\n", |
310 |
> |
current_extra->getlhs(), |
311 |
> |
j, comp_stamps[stampID]->getID() ); |
312 |
> |
painCave.isFatal = 1; |
313 |
> |
simError(); |
314 |
> |
} |
315 |
> |
|
316 |
> |
current_extra = current_extra->getNext(); |
317 |
> |
} |
318 |
> |
} |
319 |
> |
|
320 |
> |
if( !theBends[j].isGhost ){ |
321 |
> |
|
322 |
> |
exI = theBends[j].a; |
323 |
> |
exJ = theBends[j].c; |
324 |
> |
} |
325 |
> |
else{ |
326 |
> |
|
327 |
> |
exI = theBends[j].a; |
328 |
> |
exJ = theBends[j].b; |
329 |
> |
} |
330 |
> |
|
331 |
> |
// exclude_I must always be the smaller of the pair |
332 |
> |
if( exI > exJ ){ |
333 |
> |
tempEx = exI; |
334 |
> |
exI = exJ; |
335 |
> |
exJ = tempEx; |
336 |
> |
} |
337 |
> |
#ifdef IS_MPI |
338 |
> |
tempEx = exI; |
339 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
340 |
> |
tempEx = exJ; |
341 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
342 |
> |
|
343 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
344 |
> |
#else // isn't MPI |
345 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
346 |
> |
#endif //is_mpi |
347 |
|
} |
348 |
+ |
excludeOffset += molInfo.nBends; |
349 |
|
|
350 |
< |
headStamp->add( currentStamp ); |
351 |
< |
comp_stamps[i] = headStamp->match( id ); |
350 |
> |
for(j=0; j<molInfo.nTorsions; j++){ |
351 |
> |
|
352 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
353 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
354 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
355 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
356 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
357 |
> |
|
358 |
> |
exI = theTorsions[j].a; |
359 |
> |
exJ = theTorsions[j].d; |
360 |
> |
|
361 |
> |
// exclude_I must always be the smaller of the pair |
362 |
> |
if( exI > exJ ){ |
363 |
> |
tempEx = exI; |
364 |
> |
exI = exJ; |
365 |
> |
exJ = tempEx; |
366 |
> |
} |
367 |
> |
#ifdef IS_MPI |
368 |
> |
tempEx = exI; |
369 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
370 |
> |
tempEx = exJ; |
371 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
372 |
> |
|
373 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
374 |
> |
#else // isn't MPI |
375 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
376 |
> |
#endif //is_mpi |
377 |
> |
} |
378 |
> |
excludeOffset += molInfo.nTorsions; |
379 |
> |
|
380 |
> |
|
381 |
> |
// send the arrays off to the forceField for init. |
382 |
> |
|
383 |
> |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
384 |
> |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
385 |
> |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
386 |
> |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
387 |
> |
|
388 |
> |
|
389 |
> |
info[k].molecules[i].initialize( molInfo ); |
390 |
> |
|
391 |
> |
|
392 |
> |
atomOffset += molInfo.nAtoms; |
393 |
> |
delete[] theBonds; |
394 |
> |
delete[] theBends; |
395 |
> |
delete[] theTorsions; |
396 |
|
} |
397 |
|
} |
398 |
< |
|
398 |
> |
|
399 |
|
#ifdef IS_MPI |
400 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
400 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
401 |
|
MPIcheckPoint(); |
402 |
|
#endif // is_mpi |
403 |
|
|
404 |
+ |
// clean up the forcefield |
405 |
|
|
406 |
+ |
the_ff->calcRcut(); |
407 |
+ |
the_ff->cleanMe(); |
408 |
+ |
|
409 |
+ |
} |
410 |
|
|
411 |
+ |
void SimSetup::initFromBass( void ){ |
412 |
|
|
413 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
413 |
> |
int i, j, k; |
414 |
> |
int n_cells; |
415 |
> |
double cellx, celly, cellz; |
416 |
> |
double temp1, temp2, temp3; |
417 |
> |
int n_per_extra; |
418 |
> |
int n_extra; |
419 |
> |
int have_extra, done; |
420 |
|
|
421 |
< |
tot_atoms = 0; |
422 |
< |
tot_bonds = 0; |
423 |
< |
tot_bends = 0; |
424 |
< |
tot_torsions = 0; |
215 |
< |
for( i=0; i<n_components; i++ ){ |
216 |
< |
|
217 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
218 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
219 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
220 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
221 |
< |
} |
421 |
> |
double vel[3]; |
422 |
> |
vel[0] = 0.0; |
423 |
> |
vel[1] = 0.0; |
424 |
> |
vel[2] = 0.0; |
425 |
|
|
426 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
426 |
> |
temp1 = (double)tot_nmol / 4.0; |
427 |
> |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
428 |
> |
temp3 = ceil( temp2 ); |
429 |
|
|
430 |
< |
simnfo->n_atoms = tot_atoms; |
431 |
< |
simnfo->n_bonds = tot_bonds; |
432 |
< |
simnfo->n_bends = tot_bends; |
228 |
< |
simnfo->n_torsions = tot_torsions; |
229 |
< |
simnfo->n_SRI = tot_SRI; |
230 |
< |
simnfo->n_mol = tot_nmol; |
430 |
> |
have_extra =0; |
431 |
> |
if( temp2 < temp3 ){ // we have a non-complete lattice |
432 |
> |
have_extra =1; |
433 |
|
|
434 |
< |
|
435 |
< |
#ifdef IS_MPI |
434 |
> |
n_cells = (int)temp3 - 1; |
435 |
> |
cellx = info[0].boxL[0] / temp3; |
436 |
> |
celly = info[0].boxL[1] / temp3; |
437 |
> |
cellz = info[0].boxL[2] / temp3; |
438 |
> |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
439 |
> |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
440 |
> |
n_per_extra = (int)ceil( temp1 ); |
441 |
|
|
442 |
< |
// divide the molecules among processors here. |
443 |
< |
|
444 |
< |
mpiSim = new mpiSimulation( simnfo ); |
445 |
< |
|
446 |
< |
|
442 |
> |
if( n_per_extra > 4){ |
443 |
> |
sprintf( painCave.errMsg, |
444 |
> |
"SimSetup error. There has been an error in constructing" |
445 |
> |
" the non-complete lattice.\n" ); |
446 |
> |
painCave.isFatal = 1; |
447 |
> |
simError(); |
448 |
> |
} |
449 |
> |
} |
450 |
> |
else{ |
451 |
> |
n_cells = (int)temp3; |
452 |
> |
cellx = info[0].boxL[0] / temp3; |
453 |
> |
celly = info[0].boxL[1] / temp3; |
454 |
> |
cellz = info[0].boxL[2] / temp3; |
455 |
> |
} |
456 |
|
|
457 |
< |
globalIndex = mpiSim->divideLabor(); |
457 |
> |
current_mol = 0; |
458 |
> |
current_comp_mol = 0; |
459 |
> |
current_comp = 0; |
460 |
> |
current_atom_ndx = 0; |
461 |
|
|
462 |
< |
// set up the local variables |
463 |
< |
|
464 |
< |
int localMol, allMol; |
246 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
462 |
> |
for( i=0; i < n_cells ; i++ ){ |
463 |
> |
for( j=0; j < n_cells; j++ ){ |
464 |
> |
for( k=0; k < n_cells; k++ ){ |
465 |
|
|
466 |
< |
int* mol2proc = mpiSim->getMolToProcMap(); |
467 |
< |
int* molCompType = mpiSim->getMolComponentType(); |
468 |
< |
|
251 |
< |
allMol = 0; |
252 |
< |
localMol = 0; |
253 |
< |
local_atoms = 0; |
254 |
< |
local_bonds = 0; |
255 |
< |
local_bends = 0; |
256 |
< |
local_torsions = 0; |
257 |
< |
for( i=0; i<n_components; i++ ){ |
466 |
> |
makeElement( i * cellx, |
467 |
> |
j * celly, |
468 |
> |
k * cellz ); |
469 |
|
|
470 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
471 |
< |
|
472 |
< |
if( mol2proc[j] == worldRank ){ |
473 |
< |
|
474 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
475 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
476 |
< |
local_bends += comp_stamps[i]->getNBends(); |
477 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
478 |
< |
localMol++; |
479 |
< |
} |
480 |
< |
allMol++; |
470 |
> |
makeElement( i * cellx + 0.5 * cellx, |
471 |
> |
j * celly + 0.5 * celly, |
472 |
> |
k * cellz ); |
473 |
> |
|
474 |
> |
makeElement( i * cellx, |
475 |
> |
j * celly + 0.5 * celly, |
476 |
> |
k * cellz + 0.5 * cellz ); |
477 |
> |
|
478 |
> |
makeElement( i * cellx + 0.5 * cellx, |
479 |
> |
j * celly, |
480 |
> |
k * cellz + 0.5 * cellz ); |
481 |
> |
} |
482 |
|
} |
483 |
|
} |
272 |
– |
local_SRI = local_bonds + local_bends + local_torsions; |
273 |
– |
|
484 |
|
|
485 |
< |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
486 |
< |
|
277 |
< |
if( local_atoms != simnfo->n_atoms ){ |
278 |
< |
sprintf( painCave.errMsg, |
279 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
280 |
< |
" localAtom (%d) are not equal.\n", |
281 |
< |
simnfo->n_atoms, |
282 |
< |
local_atoms ); |
283 |
< |
painCave.isFatal = 1; |
284 |
< |
simError(); |
285 |
< |
} |
485 |
> |
if( have_extra ){ |
486 |
> |
done = 0; |
487 |
|
|
488 |
< |
simnfo->n_bonds = local_bonds; |
489 |
< |
simnfo->n_bends = local_bends; |
490 |
< |
simnfo->n_torsions = local_torsions; |
290 |
< |
simnfo->n_SRI = local_SRI; |
291 |
< |
simnfo->n_mol = localMol; |
488 |
> |
int start_ndx; |
489 |
> |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
490 |
> |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
491 |
|
|
492 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
294 |
< |
MPIcheckPoint(); |
295 |
< |
|
296 |
< |
|
297 |
< |
#endif // is_mpi |
298 |
< |
|
492 |
> |
if( i < n_cells ){ |
493 |
|
|
494 |
< |
// create the atom and short range interaction arrays |
494 |
> |
if( j < n_cells ){ |
495 |
> |
start_ndx = n_cells; |
496 |
> |
} |
497 |
> |
else start_ndx = 0; |
498 |
> |
} |
499 |
> |
else start_ndx = 0; |
500 |
|
|
501 |
< |
Atom::createArrays(simnfo->n_atoms); |
303 |
< |
the_atoms = new Atom*[simnfo->n_atoms]; |
304 |
< |
the_molecules = new Molecule[simnfo->n_mol]; |
305 |
< |
int molIndex; |
501 |
> |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
502 |
|
|
503 |
< |
// initialize the molecule's stampID's |
503 |
> |
makeElement( i * cellx, |
504 |
> |
j * celly, |
505 |
> |
k * cellz ); |
506 |
> |
done = ( current_mol >= tot_nmol ); |
507 |
|
|
508 |
< |
#ifdef IS_MPI |
509 |
< |
|
508 |
> |
if( !done && n_per_extra > 1 ){ |
509 |
> |
makeElement( i * cellx + 0.5 * cellx, |
510 |
> |
j * celly + 0.5 * celly, |
511 |
> |
k * cellz ); |
512 |
> |
done = ( current_mol >= tot_nmol ); |
513 |
> |
} |
514 |
|
|
515 |
< |
molIndex = 0; |
516 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
517 |
< |
|
518 |
< |
if(mol2proc[i] == worldRank ){ |
519 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
520 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
521 |
< |
molIndex++; |
515 |
> |
if( !done && n_per_extra > 2){ |
516 |
> |
makeElement( i * cellx, |
517 |
> |
j * celly + 0.5 * celly, |
518 |
> |
k * cellz + 0.5 * cellz ); |
519 |
> |
done = ( current_mol >= tot_nmol ); |
520 |
> |
} |
521 |
> |
|
522 |
> |
if( !done && n_per_extra > 3){ |
523 |
> |
makeElement( i * cellx + 0.5 * cellx, |
524 |
> |
j * celly, |
525 |
> |
k * cellz + 0.5 * cellz ); |
526 |
> |
done = ( current_mol >= tot_nmol ); |
527 |
> |
} |
528 |
> |
} |
529 |
> |
} |
530 |
|
} |
531 |
|
} |
532 |
|
|
533 |
< |
#else // is_mpi |
534 |
< |
|
324 |
< |
molIndex = 0; |
325 |
< |
for(i=0; i<n_components; i++){ |
326 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
327 |
< |
the_molecules[molIndex].setStampID( i ); |
328 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
329 |
< |
molIndex++; |
330 |
< |
} |
533 |
> |
for( i=0; i<info[0].n_atoms; i++ ){ |
534 |
> |
info[0].atoms[i]->setVel( vel ); |
535 |
|
} |
536 |
< |
|
536 |
> |
} |
537 |
|
|
538 |
< |
#endif // is_mpi |
538 |
> |
void SimSetup::makeElement( double x, double y, double z ){ |
539 |
|
|
540 |
+ |
int k; |
541 |
+ |
AtomStamp* current_atom; |
542 |
+ |
DirectionalAtom* dAtom; |
543 |
+ |
double rotMat[3][3]; |
544 |
+ |
double pos[3]; |
545 |
|
|
546 |
< |
if( simnfo->n_SRI ){ |
546 |
> |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
547 |
> |
|
548 |
> |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
549 |
> |
if( !current_atom->havePosition() ){ |
550 |
> |
sprintf( painCave.errMsg, |
551 |
> |
"SimSetup:initFromBass error.\n" |
552 |
> |
"\tComponent %s, atom %s does not have a position specified.\n" |
553 |
> |
"\tThe initialization routine is unable to give a start" |
554 |
> |
" position.\n", |
555 |
> |
comp_stamps[current_comp]->getID(), |
556 |
> |
current_atom->getType() ); |
557 |
> |
painCave.isFatal = 1; |
558 |
> |
simError(); |
559 |
> |
} |
560 |
|
|
561 |
< |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
561 |
> |
pos[0] = x + current_atom->getPosX(); |
562 |
> |
pos[1] = y + current_atom->getPosY(); |
563 |
> |
pos[2] = z + current_atom->getPosZ(); |
564 |
|
|
565 |
< |
Exclude::createArray(simnfo->n_SRI); |
566 |
< |
the_excludes = new Exclude*[simnfo->n_SRI]; |
567 |
< |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
568 |
< |
simnfo->globalExcludes = new int; |
569 |
< |
simnfo->n_exclude = simnfo->n_SRI; |
565 |
> |
info[0].atoms[current_atom_ndx]->setPos( pos ); |
566 |
> |
|
567 |
> |
if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
568 |
> |
|
569 |
> |
dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
570 |
> |
|
571 |
> |
rotMat[0][0] = 1.0; |
572 |
> |
rotMat[0][1] = 0.0; |
573 |
> |
rotMat[0][2] = 0.0; |
574 |
> |
|
575 |
> |
rotMat[1][0] = 0.0; |
576 |
> |
rotMat[1][1] = 1.0; |
577 |
> |
rotMat[1][2] = 0.0; |
578 |
> |
|
579 |
> |
rotMat[2][0] = 0.0; |
580 |
> |
rotMat[2][1] = 0.0; |
581 |
> |
rotMat[2][2] = 1.0; |
582 |
> |
|
583 |
> |
dAtom->setA( rotMat ); |
584 |
> |
} |
585 |
> |
|
586 |
> |
current_atom_ndx++; |
587 |
|
} |
588 |
< |
else{ |
589 |
< |
|
590 |
< |
Exclude::createArray( 1 ); |
591 |
< |
the_excludes = new Exclude*; |
592 |
< |
the_excludes[0] = new Exclude(0); |
593 |
< |
the_excludes[0]->setPair( 0,0 ); |
594 |
< |
simnfo->globalExcludes = new int; |
595 |
< |
simnfo->globalExcludes[0] = 0; |
355 |
< |
simnfo->n_exclude = 0; |
588 |
> |
|
589 |
> |
current_mol++; |
590 |
> |
current_comp_mol++; |
591 |
> |
|
592 |
> |
if( current_comp_mol >= components_nmol[current_comp] ){ |
593 |
> |
|
594 |
> |
current_comp_mol = 0; |
595 |
> |
current_comp++; |
596 |
|
} |
597 |
+ |
} |
598 |
|
|
358 |
– |
// set the arrays into the SimInfo object |
599 |
|
|
600 |
< |
simnfo->atoms = the_atoms; |
601 |
< |
simnfo->molecules = the_molecules; |
362 |
< |
simnfo->nGlobalExcludes = 0; |
363 |
< |
simnfo->excludes = the_excludes; |
600 |
> |
void SimSetup::gatherInfo( void ){ |
601 |
> |
int i,j,k; |
602 |
|
|
603 |
+ |
ensembleCase = -1; |
604 |
+ |
ffCase = -1; |
605 |
|
|
606 |
< |
// get some of the tricky things that may still be in the globals |
606 |
> |
// set the easy ones first |
607 |
|
|
608 |
< |
|
609 |
< |
if( the_globals->haveBox() ){ |
610 |
< |
simnfo->box_x = the_globals->getBox(); |
611 |
< |
simnfo->box_y = the_globals->getBox(); |
372 |
< |
simnfo->box_z = the_globals->getBox(); |
608 |
> |
for( i=0; i<nInfo; i++){ |
609 |
> |
info[i].target_temp = globals->getTargetTemp(); |
610 |
> |
info[i].dt = globals->getDt(); |
611 |
> |
info[i].run_time = globals->getRunTime(); |
612 |
|
} |
613 |
< |
else if( the_globals->haveDensity() ){ |
613 |
> |
n_components = globals->getNComponents(); |
614 |
|
|
376 |
– |
double vol; |
377 |
– |
vol = (double)tot_nmol / the_globals->getDensity(); |
378 |
– |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
379 |
– |
simnfo->box_y = simnfo->box_x; |
380 |
– |
simnfo->box_z = simnfo->box_x; |
381 |
– |
} |
382 |
– |
else{ |
383 |
– |
if( !the_globals->haveBoxX() ){ |
384 |
– |
sprintf( painCave.errMsg, |
385 |
– |
"SimSetup error, no periodic BoxX size given.\n" ); |
386 |
– |
painCave.isFatal = 1; |
387 |
– |
simError(); |
388 |
– |
} |
389 |
– |
simnfo->box_x = the_globals->getBoxX(); |
615 |
|
|
616 |
< |
if( !the_globals->haveBoxY() ){ |
392 |
< |
sprintf( painCave.errMsg, |
393 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
394 |
< |
painCave.isFatal = 1; |
395 |
< |
simError(); |
396 |
< |
} |
397 |
< |
simnfo->box_y = the_globals->getBoxY(); |
616 |
> |
// get the forceField |
617 |
|
|
618 |
< |
if( !the_globals->haveBoxZ() ){ |
619 |
< |
sprintf( painCave.errMsg, |
620 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
621 |
< |
painCave.isFatal = 1; |
622 |
< |
simError(); |
623 |
< |
} |
624 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
618 |
> |
strcpy( force_field, globals->getForceField() ); |
619 |
> |
|
620 |
> |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
621 |
> |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
622 |
> |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
623 |
> |
else{ |
624 |
> |
sprintf( painCave.errMsg, |
625 |
> |
"SimSetup Error. Unrecognized force field -> %s\n", |
626 |
> |
force_field ); |
627 |
> |
painCave.isFatal = 1; |
628 |
> |
simError(); |
629 |
|
} |
630 |
|
|
631 |
< |
#ifdef IS_MPI |
409 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
410 |
< |
MPIcheckPoint(); |
411 |
< |
#endif // is_mpi |
631 |
> |
// get the ensemble |
632 |
|
|
633 |
+ |
strcpy( ensemble, globals->getEnsemble() ); |
634 |
|
|
635 |
< |
// initialize the arrays |
635 |
> |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
636 |
> |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
637 |
> |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
638 |
> |
ensembleCase = NPTi_ENS; |
639 |
> |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
640 |
> |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
641 |
> |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
642 |
|
|
643 |
< |
the_ff->setSimInfo( simnfo ); |
643 |
> |
else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
644 |
> |
else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; |
645 |
> |
else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS")) |
646 |
> |
ensembleCase = NPTiZCONS_ENS; |
647 |
> |
else if( !strcasecmp( ensemble, "NPTfZCONS")) ensembleCase = NPTfZCONS_ENS; |
648 |
> |
else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; |
649 |
> |
else if( !strcasecmp( ensemble, "NPTfmZCONS")) ensembleCase = NPTfmZCONS_ENS; |
650 |
> |
|
651 |
> |
else{ |
652 |
> |
sprintf( painCave.errMsg, |
653 |
> |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
654 |
> |
"reverting to NVE for this simulation.\n", |
655 |
> |
ensemble ); |
656 |
> |
painCave.isFatal = 0; |
657 |
> |
simError(); |
658 |
> |
strcpy( ensemble, "NVE" ); |
659 |
> |
ensembleCase = NVE_ENS; |
660 |
> |
} |
661 |
> |
|
662 |
> |
for(i=0; i<nInfo; i++){ |
663 |
> |
|
664 |
> |
strcpy( info[i].ensemble, ensemble ); |
665 |
|
|
666 |
< |
makeMolecules(); |
667 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
668 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
669 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
666 |
> |
// get the mixing rule |
667 |
> |
|
668 |
> |
strcpy( info[i].mixingRule, globals->getMixingRule() ); |
669 |
> |
info[i].usePBC = globals->getPBC(); |
670 |
|
} |
671 |
|
|
672 |
< |
if (the_globals->getUseRF() ) { |
425 |
< |
simnfo->useReactionField = 1; |
426 |
< |
|
427 |
< |
if( !the_globals->haveECR() ){ |
428 |
< |
sprintf( painCave.errMsg, |
429 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
430 |
< |
"box length for the electrostaticCutoffRadius.\n" |
431 |
< |
"I hope you have a very fast processor!\n"); |
432 |
< |
painCave.isFatal = 0; |
433 |
< |
simError(); |
434 |
< |
double smallest; |
435 |
< |
smallest = simnfo->box_x; |
436 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
437 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
438 |
< |
simnfo->ecr = 0.5 * smallest; |
439 |
< |
} else { |
440 |
< |
simnfo->ecr = the_globals->getECR(); |
441 |
< |
} |
442 |
< |
|
443 |
< |
if( !the_globals->haveEST() ){ |
444 |
< |
sprintf( painCave.errMsg, |
445 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
446 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
447 |
< |
); |
448 |
< |
painCave.isFatal = 0; |
449 |
< |
simError(); |
450 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
451 |
< |
} else { |
452 |
< |
simnfo->est = the_globals->getEST(); |
453 |
< |
} |
454 |
< |
|
455 |
< |
if(!the_globals->haveDielectric() ){ |
456 |
< |
sprintf( painCave.errMsg, |
457 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
458 |
< |
"setting a dielectric constant!\n" |
459 |
< |
); |
460 |
< |
painCave.isFatal = 1; |
461 |
< |
simError(); |
462 |
< |
} |
463 |
< |
simnfo->dielectric = the_globals->getDielectric(); |
464 |
< |
} else { |
465 |
< |
if (simnfo->n_dipoles) { |
466 |
< |
|
467 |
< |
if( !the_globals->haveECR() ){ |
468 |
< |
sprintf( painCave.errMsg, |
469 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
470 |
< |
"box length for the electrostaticCutoffRadius.\n" |
471 |
< |
"I hope you have a very fast processor!\n"); |
472 |
< |
painCave.isFatal = 0; |
473 |
< |
simError(); |
474 |
< |
double smallest; |
475 |
< |
smallest = simnfo->box_x; |
476 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
477 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
478 |
< |
simnfo->ecr = 0.5 * smallest; |
479 |
< |
} else { |
480 |
< |
simnfo->ecr = the_globals->getECR(); |
481 |
< |
} |
482 |
< |
|
483 |
< |
if( !the_globals->haveEST() ){ |
484 |
< |
sprintf( painCave.errMsg, |
485 |
< |
"SimSetup Warning: using default value of 5% of the" |
486 |
< |
"electrostaticCutoffRadius for the " |
487 |
< |
"electrostaticSkinThickness\n" |
488 |
< |
); |
489 |
< |
painCave.isFatal = 0; |
490 |
< |
simError(); |
491 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
492 |
< |
} else { |
493 |
< |
simnfo->est = the_globals->getEST(); |
494 |
< |
} |
495 |
< |
} |
496 |
< |
} |
497 |
< |
|
498 |
< |
#ifdef IS_MPI |
499 |
< |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
500 |
< |
MPIcheckPoint(); |
501 |
< |
#endif // is_mpi |
502 |
< |
|
503 |
< |
if( the_globals->haveInitialConfig() ){ |
672 |
> |
// get the components and calculate the tot_nMol and indvidual n_mol |
673 |
|
|
674 |
< |
InitializeFromFile* fileInit; |
675 |
< |
#ifdef IS_MPI // is_mpi |
507 |
< |
if( worldRank == 0 ){ |
508 |
< |
#endif //is_mpi |
509 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
510 |
< |
#ifdef IS_MPI |
511 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
512 |
< |
#endif |
513 |
< |
fileInit->read_xyz( simnfo ); // default velocities on |
674 |
> |
the_components = globals->getComponents(); |
675 |
> |
components_nmol = new int[n_components]; |
676 |
|
|
515 |
– |
delete fileInit; |
516 |
– |
} |
517 |
– |
else{ |
677 |
|
|
678 |
< |
#ifdef IS_MPI |
678 |
> |
if( !globals->haveNMol() ){ |
679 |
> |
// we don't have the total number of molecules, so we assume it is |
680 |
> |
// given in each component |
681 |
|
|
682 |
< |
// no init from bass |
683 |
< |
|
523 |
< |
sprintf( painCave.errMsg, |
524 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
525 |
< |
painCave.isFatal; |
526 |
< |
simError(); |
527 |
< |
|
528 |
< |
#else |
682 |
> |
tot_nmol = 0; |
683 |
> |
for( i=0; i<n_components; i++ ){ |
684 |
|
|
685 |
< |
initFromBass(); |
685 |
> |
if( !the_components[i]->haveNMol() ){ |
686 |
> |
// we have a problem |
687 |
> |
sprintf( painCave.errMsg, |
688 |
> |
"SimSetup Error. No global NMol or component NMol" |
689 |
> |
" given. Cannot calculate the number of atoms.\n" ); |
690 |
> |
painCave.isFatal = 1; |
691 |
> |
simError(); |
692 |
> |
} |
693 |
|
|
694 |
+ |
tot_nmol += the_components[i]->getNMol(); |
695 |
+ |
components_nmol[i] = the_components[i]->getNMol(); |
696 |
+ |
} |
697 |
+ |
} |
698 |
+ |
else{ |
699 |
+ |
sprintf( painCave.errMsg, |
700 |
+ |
"SimSetup error.\n" |
701 |
+ |
"\tSorry, the ability to specify total" |
702 |
+ |
" nMols and then give molfractions in the components\n" |
703 |
+ |
"\tis not currently supported." |
704 |
+ |
" Please give nMol in the components.\n" ); |
705 |
+ |
painCave.isFatal = 1; |
706 |
+ |
simError(); |
707 |
+ |
} |
708 |
|
|
709 |
< |
#endif |
534 |
< |
} |
535 |
< |
|
536 |
< |
#ifdef IS_MPI |
537 |
< |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
538 |
< |
MPIcheckPoint(); |
539 |
< |
#endif // is_mpi |
540 |
< |
|
541 |
< |
|
542 |
< |
|
543 |
< |
|
709 |
> |
// set the status, sample, and thermal kick times |
710 |
|
|
711 |
+ |
for(i=0; i<nInfo; i++){ |
712 |
|
|
713 |
< |
|
714 |
< |
#ifdef IS_MPI |
715 |
< |
if( worldRank == 0 ){ |
716 |
< |
#endif // is_mpi |
550 |
< |
|
551 |
< |
if( the_globals->haveFinalConfig() ){ |
552 |
< |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
713 |
> |
if( globals->haveSampleTime() ){ |
714 |
> |
info[i].sampleTime = globals->getSampleTime(); |
715 |
> |
info[i].statusTime = info[i].sampleTime; |
716 |
> |
info[i].thermalTime = info[i].sampleTime; |
717 |
|
} |
718 |
|
else{ |
719 |
< |
strcpy( simnfo->finalName, inFileName ); |
720 |
< |
char* endTest; |
721 |
< |
int nameLength = strlen( simnfo->finalName ); |
558 |
< |
endTest = &(simnfo->finalName[nameLength - 5]); |
559 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
560 |
< |
strcpy( endTest, ".eor" ); |
561 |
< |
} |
562 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
563 |
< |
strcpy( endTest, ".eor" ); |
564 |
< |
} |
565 |
< |
else{ |
566 |
< |
endTest = &(simnfo->finalName[nameLength - 4]); |
567 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
568 |
< |
strcpy( endTest, ".eor" ); |
569 |
< |
} |
570 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
571 |
< |
strcpy( endTest, ".eor" ); |
572 |
< |
} |
573 |
< |
else{ |
574 |
< |
strcat( simnfo->finalName, ".eor" ); |
575 |
< |
} |
576 |
< |
} |
719 |
> |
info[i].sampleTime = globals->getRunTime(); |
720 |
> |
info[i].statusTime = info[i].sampleTime; |
721 |
> |
info[i].thermalTime = info[i].sampleTime; |
722 |
|
} |
723 |
|
|
724 |
< |
// make the sample and status out names |
724 |
> |
if( globals->haveStatusTime() ){ |
725 |
> |
info[i].statusTime = globals->getStatusTime(); |
726 |
> |
} |
727 |
|
|
728 |
< |
strcpy( simnfo->sampleName, inFileName ); |
729 |
< |
char* endTest; |
583 |
< |
int nameLength = strlen( simnfo->sampleName ); |
584 |
< |
endTest = &(simnfo->sampleName[nameLength - 5]); |
585 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
586 |
< |
strcpy( endTest, ".dump" ); |
728 |
> |
if( globals->haveThermalTime() ){ |
729 |
> |
info[i].thermalTime = globals->getThermalTime(); |
730 |
|
} |
731 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
732 |
< |
strcpy( endTest, ".dump" ); |
731 |
> |
|
732 |
> |
// check for the temperature set flag |
733 |
> |
|
734 |
> |
if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
735 |
> |
|
736 |
> |
// get some of the tricky things that may still be in the globals |
737 |
> |
|
738 |
> |
double boxVector[3]; |
739 |
> |
if( globals->haveBox() ){ |
740 |
> |
boxVector[0] = globals->getBox(); |
741 |
> |
boxVector[1] = globals->getBox(); |
742 |
> |
boxVector[2] = globals->getBox(); |
743 |
> |
|
744 |
> |
info[i].setBox( boxVector ); |
745 |
|
} |
746 |
+ |
else if( globals->haveDensity() ){ |
747 |
+ |
|
748 |
+ |
double vol; |
749 |
+ |
vol = (double)tot_nmol / globals->getDensity(); |
750 |
+ |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
751 |
+ |
boxVector[1] = boxVector[0]; |
752 |
+ |
boxVector[2] = boxVector[0]; |
753 |
+ |
|
754 |
+ |
info[i].setBox( boxVector ); |
755 |
+ |
} |
756 |
|
else{ |
757 |
< |
endTest = &(simnfo->sampleName[nameLength - 4]); |
758 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
759 |
< |
strcpy( endTest, ".dump" ); |
757 |
> |
if( !globals->haveBoxX() ){ |
758 |
> |
sprintf( painCave.errMsg, |
759 |
> |
"SimSetup error, no periodic BoxX size given.\n" ); |
760 |
> |
painCave.isFatal = 1; |
761 |
> |
simError(); |
762 |
|
} |
763 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
764 |
< |
strcpy( endTest, ".dump" ); |
765 |
< |
} |
766 |
< |
else{ |
767 |
< |
strcat( simnfo->sampleName, ".dump" ); |
768 |
< |
} |
769 |
< |
} |
603 |
< |
|
604 |
< |
strcpy( simnfo->statusName, inFileName ); |
605 |
< |
nameLength = strlen( simnfo->statusName ); |
606 |
< |
endTest = &(simnfo->statusName[nameLength - 5]); |
607 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
608 |
< |
strcpy( endTest, ".stat" ); |
609 |
< |
} |
610 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
611 |
< |
strcpy( endTest, ".stat" ); |
612 |
< |
} |
613 |
< |
else{ |
614 |
< |
endTest = &(simnfo->statusName[nameLength - 4]); |
615 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
616 |
< |
strcpy( endTest, ".stat" ); |
763 |
> |
boxVector[0] = globals->getBoxX(); |
764 |
> |
|
765 |
> |
if( !globals->haveBoxY() ){ |
766 |
> |
sprintf( painCave.errMsg, |
767 |
> |
"SimSetup error, no periodic BoxY size given.\n" ); |
768 |
> |
painCave.isFatal = 1; |
769 |
> |
simError(); |
770 |
|
} |
771 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
772 |
< |
strcpy( endTest, ".stat" ); |
771 |
> |
boxVector[1] = globals->getBoxY(); |
772 |
> |
|
773 |
> |
if( !globals->haveBoxZ() ){ |
774 |
> |
sprintf( painCave.errMsg, |
775 |
> |
"SimSetup error, no periodic BoxZ size given.\n" ); |
776 |
> |
painCave.isFatal = 1; |
777 |
> |
simError(); |
778 |
|
} |
779 |
< |
else{ |
780 |
< |
strcat( simnfo->statusName, ".stat" ); |
781 |
< |
} |
779 |
> |
boxVector[2] = globals->getBoxZ(); |
780 |
> |
|
781 |
> |
info[i].setBox( boxVector ); |
782 |
|
} |
783 |
+ |
|
784 |
+ |
} |
785 |
|
|
786 |
|
#ifdef IS_MPI |
787 |
< |
} |
787 |
> |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
788 |
> |
MPIcheckPoint(); |
789 |
|
#endif // is_mpi |
629 |
– |
|
630 |
– |
// set the status, sample, and themal kick times |
631 |
– |
|
632 |
– |
if( the_globals->haveSampleTime() ){ |
633 |
– |
simnfo->sampleTime = the_globals->getSampleTime(); |
634 |
– |
simnfo->statusTime = simnfo->sampleTime; |
635 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
636 |
– |
} |
637 |
– |
else{ |
638 |
– |
simnfo->sampleTime = the_globals->getRunTime(); |
639 |
– |
simnfo->statusTime = simnfo->sampleTime; |
640 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
641 |
– |
} |
790 |
|
|
791 |
< |
if( the_globals->haveStatusTime() ){ |
644 |
< |
simnfo->statusTime = the_globals->getStatusTime(); |
645 |
< |
} |
791 |
> |
} |
792 |
|
|
647 |
– |
if( the_globals->haveThermalTime() ){ |
648 |
– |
simnfo->thermalTime = the_globals->getThermalTime(); |
649 |
– |
} |
793 |
|
|
794 |
< |
// check for the temperature set flag |
794 |
> |
void SimSetup::finalInfoCheck( void ){ |
795 |
> |
int index; |
796 |
> |
int usesDipoles; |
797 |
> |
int i; |
798 |
|
|
799 |
< |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
799 |
> |
for(i=0; i<nInfo; i++){ |
800 |
> |
// check electrostatic parameters |
801 |
> |
|
802 |
> |
index = 0; |
803 |
> |
usesDipoles = 0; |
804 |
> |
while( (index < info[i].n_atoms) && !usesDipoles ){ |
805 |
> |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
806 |
> |
index++; |
807 |
> |
} |
808 |
> |
|
809 |
> |
#ifdef IS_MPI |
810 |
> |
int myUse = usesDipoles; |
811 |
> |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
812 |
> |
#endif //is_mpi |
813 |
> |
|
814 |
> |
double theEcr, theEst; |
815 |
> |
|
816 |
> |
if (globals->getUseRF() ) { |
817 |
> |
info[i].useReactionField = 1; |
818 |
> |
|
819 |
> |
if( !globals->haveECR() ){ |
820 |
> |
sprintf( painCave.errMsg, |
821 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
822 |
> |
"box length for the electrostaticCutoffRadius.\n" |
823 |
> |
"I hope you have a very fast processor!\n"); |
824 |
> |
painCave.isFatal = 0; |
825 |
> |
simError(); |
826 |
> |
double smallest; |
827 |
> |
smallest = info[i].boxL[0]; |
828 |
> |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
829 |
> |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
830 |
> |
theEcr = 0.5 * smallest; |
831 |
> |
} else { |
832 |
> |
theEcr = globals->getECR(); |
833 |
> |
} |
834 |
> |
|
835 |
> |
if( !globals->haveEST() ){ |
836 |
> |
sprintf( painCave.errMsg, |
837 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
838 |
> |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
839 |
> |
); |
840 |
> |
painCave.isFatal = 0; |
841 |
> |
simError(); |
842 |
> |
theEst = 0.05 * theEcr; |
843 |
> |
} else { |
844 |
> |
theEst= globals->getEST(); |
845 |
> |
} |
846 |
> |
|
847 |
> |
info[i].setEcr( theEcr, theEst ); |
848 |
> |
|
849 |
> |
if(!globals->haveDielectric() ){ |
850 |
> |
sprintf( painCave.errMsg, |
851 |
> |
"SimSetup Error: You are trying to use Reaction Field without" |
852 |
> |
"setting a dielectric constant!\n" |
853 |
> |
); |
854 |
> |
painCave.isFatal = 1; |
855 |
> |
simError(); |
856 |
> |
} |
857 |
> |
info[i].dielectric = globals->getDielectric(); |
858 |
> |
} |
859 |
> |
else { |
860 |
> |
if (usesDipoles) { |
861 |
> |
|
862 |
> |
if( !globals->haveECR() ){ |
863 |
> |
sprintf( painCave.errMsg, |
864 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
865 |
> |
"box length for the electrostaticCutoffRadius.\n" |
866 |
> |
"I hope you have a very fast processor!\n"); |
867 |
> |
painCave.isFatal = 0; |
868 |
> |
simError(); |
869 |
> |
double smallest; |
870 |
> |
smallest = info[i].boxL[0]; |
871 |
> |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
872 |
> |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
873 |
> |
theEcr = 0.5 * smallest; |
874 |
> |
} else { |
875 |
> |
theEcr = globals->getECR(); |
876 |
> |
} |
877 |
> |
|
878 |
> |
if( !globals->haveEST() ){ |
879 |
> |
sprintf( painCave.errMsg, |
880 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
881 |
> |
"electrostaticCutoffRadius for the " |
882 |
> |
"electrostaticSkinThickness\n" |
883 |
> |
); |
884 |
> |
painCave.isFatal = 0; |
885 |
> |
simError(); |
886 |
> |
theEst = 0.05 * theEcr; |
887 |
> |
} else { |
888 |
> |
theEst= globals->getEST(); |
889 |
> |
} |
890 |
> |
|
891 |
> |
info[i].setEcr( theEcr, theEst ); |
892 |
> |
} |
893 |
> |
} |
894 |
> |
} |
895 |
|
|
655 |
– |
|
656 |
– |
// // make the longe range forces and the integrator |
657 |
– |
|
658 |
– |
// new AllLong( simnfo ); |
659 |
– |
|
660 |
– |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
661 |
– |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
662 |
– |
|
896 |
|
#ifdef IS_MPI |
897 |
< |
mpiSim->mpiRefresh(); |
898 |
< |
#endif |
897 |
> |
strcpy( checkPointMsg, "post processing checks out" ); |
898 |
> |
MPIcheckPoint(); |
899 |
> |
#endif // is_mpi |
900 |
|
|
901 |
< |
// initialize the Fortran |
901 |
> |
} |
902 |
|
|
903 |
+ |
void SimSetup::initSystemCoords( void ){ |
904 |
+ |
int i; |
905 |
+ |
|
906 |
+ |
std::cerr << "Setting atom Coords\n"; |
907 |
|
|
908 |
< |
simnfo->refreshSim(); |
908 |
> |
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
909 |
|
|
910 |
< |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
911 |
< |
the_ff->initForceField( LB_MIXING_RULE ); |
910 |
> |
for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
911 |
> |
|
912 |
> |
if( globals->haveInitialConfig() ){ |
913 |
> |
|
914 |
> |
InitializeFromFile* fileInit; |
915 |
> |
#ifdef IS_MPI // is_mpi |
916 |
> |
if( worldRank == 0 ){ |
917 |
> |
#endif //is_mpi |
918 |
> |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
919 |
> |
#ifdef IS_MPI |
920 |
> |
}else fileInit = new InitializeFromFile( NULL ); |
921 |
> |
#endif |
922 |
> |
fileInit->readInit( info ); // default velocities on |
923 |
> |
|
924 |
> |
delete fileInit; |
925 |
|
} |
675 |
– |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
676 |
– |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
677 |
– |
} |
926 |
|
else{ |
927 |
+ |
|
928 |
+ |
#ifdef IS_MPI |
929 |
+ |
|
930 |
+ |
// no init from bass |
931 |
+ |
|
932 |
|
sprintf( painCave.errMsg, |
933 |
< |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
934 |
< |
simnfo->mixingRule ); |
682 |
< |
painCave.isFatal = 1; |
933 |
> |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
934 |
> |
painCave.isFatal; |
935 |
|
simError(); |
936 |
+ |
|
937 |
+ |
#else |
938 |
+ |
|
939 |
+ |
initFromBass(); |
940 |
+ |
|
941 |
+ |
|
942 |
+ |
#endif |
943 |
|
} |
944 |
< |
|
686 |
< |
|
944 |
> |
|
945 |
|
#ifdef IS_MPI |
946 |
< |
strcpy( checkPointMsg, |
689 |
< |
"Successfully intialized the mixingRule for Fortran." ); |
946 |
> |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
947 |
|
MPIcheckPoint(); |
948 |
|
#endif // is_mpi |
949 |
+ |
|
950 |
|
} |
951 |
|
|
952 |
|
|
953 |
< |
void SimSetup::makeMolecules( void ){ |
696 |
< |
|
697 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
698 |
< |
molInit info; |
699 |
< |
DirectionalAtom* dAtom; |
700 |
< |
LinkedAssign* extras; |
701 |
< |
LinkedAssign* current_extra; |
702 |
< |
AtomStamp* currentAtom; |
703 |
< |
BondStamp* currentBond; |
704 |
< |
BendStamp* currentBend; |
705 |
< |
TorsionStamp* currentTorsion; |
706 |
< |
|
707 |
< |
bond_pair* theBonds; |
708 |
< |
bend_set* theBends; |
709 |
< |
torsion_set* theTorsions; |
710 |
< |
|
953 |
> |
void SimSetup::makeOutNames( void ){ |
954 |
|
|
955 |
< |
//init the forceField paramters |
955 |
> |
int k; |
956 |
|
|
714 |
– |
the_ff->readParams(); |
715 |
– |
|
957 |
|
|
958 |
< |
// init the atoms |
958 |
> |
for(k=0; k<nInfo; k++){ |
959 |
|
|
960 |
< |
double ux, uy, uz, u, uSqr; |
961 |
< |
|
962 |
< |
atomOffset = 0; |
722 |
< |
excludeOffset = 0; |
723 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
724 |
< |
|
725 |
< |
stampID = the_molecules[i].getStampID(); |
726 |
< |
|
727 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
728 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
729 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
730 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
731 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
732 |
< |
|
733 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
734 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
735 |
< |
info.myBonds = new Bond*[info.nBonds]; |
736 |
< |
info.myBends = new Bend*[info.nBends]; |
737 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
738 |
< |
|
739 |
< |
theBonds = new bond_pair[info.nBonds]; |
740 |
< |
theBends = new bend_set[info.nBends]; |
741 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
742 |
< |
|
743 |
< |
// make the Atoms |
744 |
< |
|
745 |
< |
for(j=0; j<info.nAtoms; j++){ |
960 |
> |
#ifdef IS_MPI |
961 |
> |
if( worldRank == 0 ){ |
962 |
> |
#endif // is_mpi |
963 |
|
|
964 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
965 |
< |
if( currentAtom->haveOrientation() ){ |
749 |
< |
|
750 |
< |
dAtom = new DirectionalAtom(j + atomOffset); |
751 |
< |
simnfo->n_oriented++; |
752 |
< |
info.myAtoms[j] = dAtom; |
753 |
< |
|
754 |
< |
ux = currentAtom->getOrntX(); |
755 |
< |
uy = currentAtom->getOrntY(); |
756 |
< |
uz = currentAtom->getOrntZ(); |
757 |
< |
|
758 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
759 |
< |
|
760 |
< |
u = sqrt( uSqr ); |
761 |
< |
ux = ux / u; |
762 |
< |
uy = uy / u; |
763 |
< |
uz = uz / u; |
764 |
< |
|
765 |
< |
dAtom->setSUx( ux ); |
766 |
< |
dAtom->setSUy( uy ); |
767 |
< |
dAtom->setSUz( uz ); |
964 |
> |
if( globals->haveFinalConfig() ){ |
965 |
> |
strcpy( info[k].finalName, globals->getFinalConfig() ); |
966 |
|
} |
967 |
|
else{ |
968 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
968 |
> |
strcpy( info[k].finalName, inFileName ); |
969 |
> |
char* endTest; |
970 |
> |
int nameLength = strlen( info[k].finalName ); |
971 |
> |
endTest = &(info[k].finalName[nameLength - 5]); |
972 |
> |
if( !strcmp( endTest, ".bass" ) ){ |
973 |
> |
strcpy( endTest, ".eor" ); |
974 |
> |
} |
975 |
> |
else if( !strcmp( endTest, ".BASS" ) ){ |
976 |
> |
strcpy( endTest, ".eor" ); |
977 |
> |
} |
978 |
> |
else{ |
979 |
> |
endTest = &(info[k].finalName[nameLength - 4]); |
980 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
981 |
> |
strcpy( endTest, ".eor" ); |
982 |
> |
} |
983 |
> |
else if( !strcmp( endTest, ".mdl" ) ){ |
984 |
> |
strcpy( endTest, ".eor" ); |
985 |
> |
} |
986 |
> |
else{ |
987 |
> |
strcat( info[k].finalName, ".eor" ); |
988 |
> |
} |
989 |
> |
} |
990 |
|
} |
772 |
– |
info.myAtoms[j]->setType( currentAtom->getType() ); |
773 |
– |
|
774 |
– |
#ifdef IS_MPI |
991 |
|
|
992 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
992 |
> |
// make the sample and status out names |
993 |
|
|
994 |
< |
#endif // is_mpi |
995 |
< |
} |
996 |
< |
|
997 |
< |
// make the bonds |
998 |
< |
for(j=0; j<info.nBonds; j++){ |
999 |
< |
|
784 |
< |
currentBond = comp_stamps[stampID]->getBond( j ); |
785 |
< |
theBonds[j].a = currentBond->getA() + atomOffset; |
786 |
< |
theBonds[j].b = currentBond->getB() + atomOffset; |
787 |
< |
|
788 |
< |
exI = theBonds[j].a; |
789 |
< |
exJ = theBonds[j].b; |
790 |
< |
|
791 |
< |
// exclude_I must always be the smaller of the pair |
792 |
< |
if( exI > exJ ){ |
793 |
< |
tempEx = exI; |
794 |
< |
exI = exJ; |
795 |
< |
exJ = tempEx; |
994 |
> |
strcpy( info[k].sampleName, inFileName ); |
995 |
> |
char* endTest; |
996 |
> |
int nameLength = strlen( info[k].sampleName ); |
997 |
> |
endTest = &(info[k].sampleName[nameLength - 5]); |
998 |
> |
if( !strcmp( endTest, ".bass" ) ){ |
999 |
> |
strcpy( endTest, ".dump" ); |
1000 |
|
} |
1001 |
< |
#ifdef IS_MPI |
1002 |
< |
tempEx = exI; |
1003 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1004 |
< |
tempEx = exJ; |
1005 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1006 |
< |
|
1007 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
804 |
< |
#else // isn't MPI |
805 |
< |
|
806 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
807 |
< |
#endif //is_mpi |
808 |
< |
} |
809 |
< |
excludeOffset += info.nBonds; |
810 |
< |
|
811 |
< |
//make the bends |
812 |
< |
for(j=0; j<info.nBends; j++){ |
813 |
< |
|
814 |
< |
currentBend = comp_stamps[stampID]->getBend( j ); |
815 |
< |
theBends[j].a = currentBend->getA() + atomOffset; |
816 |
< |
theBends[j].b = currentBend->getB() + atomOffset; |
817 |
< |
theBends[j].c = currentBend->getC() + atomOffset; |
818 |
< |
|
819 |
< |
if( currentBend->haveExtras() ){ |
820 |
< |
|
821 |
< |
extras = currentBend->getExtras(); |
822 |
< |
current_extra = extras; |
823 |
< |
|
824 |
< |
while( current_extra != NULL ){ |
825 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
826 |
< |
|
827 |
< |
switch( current_extra->getType() ){ |
828 |
< |
|
829 |
< |
case 0: |
830 |
< |
theBends[j].ghost = |
831 |
< |
current_extra->getInt() + atomOffset; |
832 |
< |
theBends[j].isGhost = 1; |
833 |
< |
break; |
834 |
< |
|
835 |
< |
case 1: |
836 |
< |
theBends[j].ghost = |
837 |
< |
(int)current_extra->getDouble() + atomOffset; |
838 |
< |
theBends[j].isGhost = 1; |
839 |
< |
break; |
840 |
< |
|
841 |
< |
default: |
842 |
< |
sprintf( painCave.errMsg, |
843 |
< |
"SimSetup Error: ghostVectorSource was neither a " |
844 |
< |
"double nor an int.\n" |
845 |
< |
"-->Bend[%d] in %s\n", |
846 |
< |
j, comp_stamps[stampID]->getID() ); |
847 |
< |
painCave.isFatal = 1; |
848 |
< |
simError(); |
849 |
< |
} |
850 |
< |
} |
851 |
< |
|
852 |
< |
else{ |
853 |
< |
|
854 |
< |
sprintf( painCave.errMsg, |
855 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
856 |
< |
" -->%s in Bend[%d] in %s\n", |
857 |
< |
current_extra->getlhs(), |
858 |
< |
j, comp_stamps[stampID]->getID() ); |
859 |
< |
painCave.isFatal = 1; |
860 |
< |
simError(); |
861 |
< |
} |
862 |
< |
|
863 |
< |
current_extra = current_extra->getNext(); |
1001 |
> |
else if( !strcmp( endTest, ".BASS" ) ){ |
1002 |
> |
strcpy( endTest, ".dump" ); |
1003 |
> |
} |
1004 |
> |
else{ |
1005 |
> |
endTest = &(info[k].sampleName[nameLength - 4]); |
1006 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
1007 |
> |
strcpy( endTest, ".dump" ); |
1008 |
|
} |
1009 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
1010 |
+ |
strcpy( endTest, ".dump" ); |
1011 |
+ |
} |
1012 |
+ |
else{ |
1013 |
+ |
strcat( info[k].sampleName, ".dump" ); |
1014 |
+ |
} |
1015 |
|
} |
1016 |
< |
|
1017 |
< |
if( !theBends[j].isGhost ){ |
1018 |
< |
|
1019 |
< |
exI = theBends[j].a; |
1020 |
< |
exJ = theBends[j].c; |
1016 |
> |
|
1017 |
> |
strcpy( info[k].statusName, inFileName ); |
1018 |
> |
nameLength = strlen( info[k].statusName ); |
1019 |
> |
endTest = &(info[k].statusName[nameLength - 5]); |
1020 |
> |
if( !strcmp( endTest, ".bass" ) ){ |
1021 |
> |
strcpy( endTest, ".stat" ); |
1022 |
|
} |
1023 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
1024 |
+ |
strcpy( endTest, ".stat" ); |
1025 |
+ |
} |
1026 |
|
else{ |
1027 |
< |
|
1028 |
< |
exI = theBends[j].a; |
1029 |
< |
exJ = theBends[j].b; |
1027 |
> |
endTest = &(info[k].statusName[nameLength - 4]); |
1028 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
1029 |
> |
strcpy( endTest, ".stat" ); |
1030 |
> |
} |
1031 |
> |
else if( !strcmp( endTest, ".mdl" ) ){ |
1032 |
> |
strcpy( endTest, ".stat" ); |
1033 |
> |
} |
1034 |
> |
else{ |
1035 |
> |
strcat( info[k].statusName, ".stat" ); |
1036 |
> |
} |
1037 |
|
} |
1038 |
|
|
878 |
– |
// exclude_I must always be the smaller of the pair |
879 |
– |
if( exI > exJ ){ |
880 |
– |
tempEx = exI; |
881 |
– |
exI = exJ; |
882 |
– |
exJ = tempEx; |
883 |
– |
} |
1039 |
|
#ifdef IS_MPI |
885 |
– |
tempEx = exI; |
886 |
– |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
887 |
– |
tempEx = exJ; |
888 |
– |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
889 |
– |
|
890 |
– |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
891 |
– |
#else // isn't MPI |
892 |
– |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
893 |
– |
#endif //is_mpi |
1040 |
|
} |
1041 |
< |
excludeOffset += info.nBends; |
1041 |
> |
#endif // is_mpi |
1042 |
> |
} |
1043 |
> |
} |
1044 |
|
|
897 |
– |
for(j=0; j<info.nTorsions; j++){ |
898 |
– |
|
899 |
– |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
900 |
– |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
901 |
– |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
902 |
– |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
903 |
– |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
904 |
– |
|
905 |
– |
exI = theTorsions[j].a; |
906 |
– |
exJ = theTorsions[j].d; |
1045 |
|
|
1046 |
< |
// exclude_I must always be the smaller of the pair |
1047 |
< |
if( exI > exJ ){ |
1048 |
< |
tempEx = exI; |
1049 |
< |
exI = exJ; |
1050 |
< |
exJ = tempEx; |
1051 |
< |
} |
1046 |
> |
void SimSetup::sysObjectsCreation( void ){ |
1047 |
> |
|
1048 |
> |
int i,k; |
1049 |
> |
|
1050 |
> |
// create the forceField |
1051 |
> |
|
1052 |
> |
createFF(); |
1053 |
> |
|
1054 |
> |
// extract componentList |
1055 |
> |
|
1056 |
> |
compList(); |
1057 |
> |
|
1058 |
> |
// calc the number of atoms, bond, bends, and torsions |
1059 |
> |
|
1060 |
> |
calcSysValues(); |
1061 |
> |
|
1062 |
|
#ifdef IS_MPI |
1063 |
< |
tempEx = exI; |
1064 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1065 |
< |
tempEx = exJ; |
1066 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1067 |
< |
|
1068 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1069 |
< |
#else // isn't MPI |
1070 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1071 |
< |
#endif //is_mpi |
1063 |
> |
// divide the molecules among the processors |
1064 |
> |
|
1065 |
> |
mpiMolDivide(); |
1066 |
> |
#endif //is_mpi |
1067 |
> |
|
1068 |
> |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1069 |
> |
|
1070 |
> |
makeSysArrays(); |
1071 |
> |
|
1072 |
> |
// make and initialize the molecules (all but atomic coordinates) |
1073 |
> |
|
1074 |
> |
makeMolecules(); |
1075 |
> |
|
1076 |
> |
for(k=0; k<nInfo; k++){ |
1077 |
> |
info[k].identArray = new int[info[k].n_atoms]; |
1078 |
> |
for(i=0; i<info[k].n_atoms; i++){ |
1079 |
> |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1080 |
|
} |
1081 |
< |
excludeOffset += info.nTorsions; |
1081 |
> |
} |
1082 |
> |
} |
1083 |
|
|
927 |
– |
|
928 |
– |
// send the arrays off to the forceField for init. |
1084 |
|
|
1085 |
< |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
931 |
< |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
932 |
< |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
933 |
< |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1085 |
> |
void SimSetup::createFF( void ){ |
1086 |
|
|
1087 |
+ |
switch( ffCase ){ |
1088 |
|
|
1089 |
< |
the_molecules[i].initialize( info ); |
1089 |
> |
case FF_DUFF: |
1090 |
> |
the_ff = new DUFF(); |
1091 |
> |
break; |
1092 |
|
|
1093 |
+ |
case FF_LJ: |
1094 |
+ |
the_ff = new LJFF(); |
1095 |
+ |
break; |
1096 |
|
|
1097 |
< |
atomOffset += info.nAtoms; |
1098 |
< |
delete[] theBonds; |
1099 |
< |
delete[] theBends; |
1100 |
< |
delete[] theTorsions; |
1097 |
> |
case FF_EAM: |
1098 |
> |
the_ff = new EAM_FF(); |
1099 |
> |
break; |
1100 |
> |
|
1101 |
> |
default: |
1102 |
> |
sprintf( painCave.errMsg, |
1103 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1104 |
> |
painCave.isFatal = 1; |
1105 |
> |
simError(); |
1106 |
|
} |
1107 |
|
|
1108 |
|
#ifdef IS_MPI |
1109 |
< |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1109 |
> |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1110 |
|
MPIcheckPoint(); |
1111 |
|
#endif // is_mpi |
1112 |
|
|
950 |
– |
// clean up the forcefield |
951 |
– |
the_ff->calcRcut(); |
952 |
– |
the_ff->cleanMe(); |
953 |
– |
|
1113 |
|
} |
1114 |
|
|
956 |
– |
void SimSetup::initFromBass( void ){ |
1115 |
|
|
1116 |
< |
int i, j, k; |
959 |
< |
int n_cells; |
960 |
< |
double cellx, celly, cellz; |
961 |
< |
double temp1, temp2, temp3; |
962 |
< |
int n_per_extra; |
963 |
< |
int n_extra; |
964 |
< |
int have_extra, done; |
1116 |
> |
void SimSetup::compList( void ){ |
1117 |
|
|
1118 |
< |
temp1 = (double)tot_nmol / 4.0; |
1119 |
< |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1120 |
< |
temp3 = ceil( temp2 ); |
1121 |
< |
|
1122 |
< |
have_extra =0; |
1123 |
< |
if( temp2 < temp3 ){ // we have a non-complete lattice |
1124 |
< |
have_extra =1; |
1125 |
< |
|
1126 |
< |
n_cells = (int)temp3 - 1; |
1127 |
< |
cellx = simnfo->box_x / temp3; |
1128 |
< |
celly = simnfo->box_y / temp3; |
1129 |
< |
cellz = simnfo->box_z / temp3; |
1130 |
< |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1131 |
< |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
980 |
< |
n_per_extra = (int)ceil( temp1 ); |
981 |
< |
|
982 |
< |
if( n_per_extra > 4){ |
983 |
< |
sprintf( painCave.errMsg, |
984 |
< |
"SimSetup error. There has been an error in constructing" |
985 |
< |
" the non-complete lattice.\n" ); |
986 |
< |
painCave.isFatal = 1; |
987 |
< |
simError(); |
988 |
< |
} |
1118 |
> |
int i; |
1119 |
> |
char* id; |
1120 |
> |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1121 |
> |
LinkedMolStamp* currentStamp = NULL; |
1122 |
> |
comp_stamps = new MoleculeStamp*[n_components]; |
1123 |
> |
|
1124 |
> |
// make an array of molecule stamps that match the components used. |
1125 |
> |
// also extract the used stamps out into a separate linked list |
1126 |
> |
|
1127 |
> |
for(i=0; i<nInfo; i++){ |
1128 |
> |
info[i].nComponents = n_components; |
1129 |
> |
info[i].componentsNmol = components_nmol; |
1130 |
> |
info[i].compStamps = comp_stamps; |
1131 |
> |
info[i].headStamp = headStamp; |
1132 |
|
} |
1133 |
< |
else{ |
991 |
< |
n_cells = (int)temp3; |
992 |
< |
cellx = simnfo->box_x / temp3; |
993 |
< |
celly = simnfo->box_y / temp3; |
994 |
< |
cellz = simnfo->box_z / temp3; |
995 |
< |
} |
1133 |
> |
|
1134 |
|
|
1135 |
< |
current_mol = 0; |
998 |
< |
current_comp_mol = 0; |
999 |
< |
current_comp = 0; |
1000 |
< |
current_atom_ndx = 0; |
1135 |
> |
for( i=0; i<n_components; i++ ){ |
1136 |
|
|
1137 |
< |
for( i=0; i < n_cells ; i++ ){ |
1138 |
< |
for( j=0; j < n_cells; j++ ){ |
1139 |
< |
for( k=0; k < n_cells; k++ ){ |
1137 |
> |
id = the_components[i]->getType(); |
1138 |
> |
comp_stamps[i] = NULL; |
1139 |
> |
|
1140 |
> |
// check to make sure the component isn't already in the list |
1141 |
|
|
1142 |
< |
makeElement( i * cellx, |
1143 |
< |
j * celly, |
1144 |
< |
k * cellz ); |
1145 |
< |
|
1146 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1147 |
< |
j * celly + 0.5 * celly, |
1148 |
< |
k * cellz ); |
1149 |
< |
|
1150 |
< |
makeElement( i * cellx, |
1151 |
< |
j * celly + 0.5 * celly, |
1152 |
< |
k * cellz + 0.5 * cellz ); |
1153 |
< |
|
1154 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1019 |
< |
j * celly, |
1020 |
< |
k * cellz + 0.5 * cellz ); |
1142 |
> |
comp_stamps[i] = headStamp->match( id ); |
1143 |
> |
if( comp_stamps[i] == NULL ){ |
1144 |
> |
|
1145 |
> |
// extract the component from the list; |
1146 |
> |
|
1147 |
> |
currentStamp = stamps->extractMolStamp( id ); |
1148 |
> |
if( currentStamp == NULL ){ |
1149 |
> |
sprintf( painCave.errMsg, |
1150 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
1151 |
> |
"list of declared molecules\n", |
1152 |
> |
id ); |
1153 |
> |
painCave.isFatal = 1; |
1154 |
> |
simError(); |
1155 |
|
} |
1156 |
+ |
|
1157 |
+ |
headStamp->add( currentStamp ); |
1158 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1159 |
|
} |
1160 |
|
} |
1161 |
|
|
1162 |
< |
if( have_extra ){ |
1163 |
< |
done = 0; |
1162 |
> |
#ifdef IS_MPI |
1163 |
> |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1164 |
> |
MPIcheckPoint(); |
1165 |
> |
#endif // is_mpi |
1166 |
|
|
1028 |
– |
int start_ndx; |
1029 |
– |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
1030 |
– |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
1167 |
|
|
1168 |
< |
if( i < n_cells ){ |
1168 |
> |
} |
1169 |
|
|
1170 |
< |
if( j < n_cells ){ |
1171 |
< |
start_ndx = n_cells; |
1172 |
< |
} |
1173 |
< |
else start_ndx = 0; |
1174 |
< |
} |
1175 |
< |
else start_ndx = 0; |
1176 |
< |
|
1177 |
< |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1178 |
< |
|
1179 |
< |
makeElement( i * cellx, |
1180 |
< |
j * celly, |
1181 |
< |
k * cellz ); |
1182 |
< |
done = ( current_mol >= tot_nmol ); |
1183 |
< |
|
1184 |
< |
if( !done && n_per_extra > 1 ){ |
1185 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1186 |
< |
j * celly + 0.5 * celly, |
1187 |
< |
k * cellz ); |
1188 |
< |
done = ( current_mol >= tot_nmol ); |
1189 |
< |
} |
1170 |
> |
void SimSetup::calcSysValues( void ){ |
1171 |
> |
int i, j, k; |
1172 |
> |
|
1173 |
> |
int *molMembershipArray; |
1174 |
> |
|
1175 |
> |
tot_atoms = 0; |
1176 |
> |
tot_bonds = 0; |
1177 |
> |
tot_bends = 0; |
1178 |
> |
tot_torsions = 0; |
1179 |
> |
for( i=0; i<n_components; i++ ){ |
1180 |
> |
|
1181 |
> |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1182 |
> |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1183 |
> |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1184 |
> |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1185 |
> |
} |
1186 |
> |
|
1187 |
> |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1188 |
> |
molMembershipArray = new int[tot_atoms]; |
1189 |
> |
|
1190 |
> |
for(i=0; i<nInfo; i++){ |
1191 |
> |
info[i].n_atoms = tot_atoms; |
1192 |
> |
info[i].n_bonds = tot_bonds; |
1193 |
> |
info[i].n_bends = tot_bends; |
1194 |
> |
info[i].n_torsions = tot_torsions; |
1195 |
> |
info[i].n_SRI = tot_SRI; |
1196 |
> |
info[i].n_mol = tot_nmol; |
1197 |
> |
|
1198 |
> |
info[i].molMembershipArray = molMembershipArray; |
1199 |
> |
} |
1200 |
> |
} |
1201 |
|
|
1202 |
< |
if( !done && n_per_extra > 2){ |
1056 |
< |
makeElement( i * cellx, |
1057 |
< |
j * celly + 0.5 * celly, |
1058 |
< |
k * cellz + 0.5 * cellz ); |
1059 |
< |
done = ( current_mol >= tot_nmol ); |
1060 |
< |
} |
1202 |
> |
#ifdef IS_MPI |
1203 |
|
|
1204 |
< |
if( !done && n_per_extra > 3){ |
1205 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1206 |
< |
j * celly, |
1207 |
< |
k * cellz + 0.5 * cellz ); |
1208 |
< |
done = ( current_mol >= tot_nmol ); |
1209 |
< |
} |
1210 |
< |
} |
1204 |
> |
void SimSetup::mpiMolDivide( void ){ |
1205 |
> |
|
1206 |
> |
int i, j, k; |
1207 |
> |
int localMol, allMol; |
1208 |
> |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1209 |
> |
|
1210 |
> |
mpiSim = new mpiSimulation( info ); |
1211 |
> |
|
1212 |
> |
globalIndex = mpiSim->divideLabor(); |
1213 |
> |
|
1214 |
> |
// set up the local variables |
1215 |
> |
|
1216 |
> |
mol2proc = mpiSim->getMolToProcMap(); |
1217 |
> |
molCompType = mpiSim->getMolComponentType(); |
1218 |
> |
|
1219 |
> |
allMol = 0; |
1220 |
> |
localMol = 0; |
1221 |
> |
local_atoms = 0; |
1222 |
> |
local_bonds = 0; |
1223 |
> |
local_bends = 0; |
1224 |
> |
local_torsions = 0; |
1225 |
> |
globalAtomIndex = 0; |
1226 |
> |
|
1227 |
> |
|
1228 |
> |
for( i=0; i<n_components; i++ ){ |
1229 |
> |
|
1230 |
> |
for( j=0; j<components_nmol[i]; j++ ){ |
1231 |
> |
|
1232 |
> |
if( mol2proc[allMol] == worldRank ){ |
1233 |
> |
|
1234 |
> |
local_atoms += comp_stamps[i]->getNAtoms(); |
1235 |
> |
local_bonds += comp_stamps[i]->getNBonds(); |
1236 |
> |
local_bends += comp_stamps[i]->getNBends(); |
1237 |
> |
local_torsions += comp_stamps[i]->getNTorsions(); |
1238 |
> |
localMol++; |
1239 |
> |
} |
1240 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1241 |
> |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1242 |
> |
globalAtomIndex++; |
1243 |
|
} |
1244 |
+ |
|
1245 |
+ |
allMol++; |
1246 |
|
} |
1247 |
|
} |
1248 |
+ |
local_SRI = local_bonds + local_bends + local_torsions; |
1249 |
+ |
|
1250 |
+ |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1251 |
+ |
|
1252 |
+ |
if( local_atoms != info[0].n_atoms ){ |
1253 |
+ |
sprintf( painCave.errMsg, |
1254 |
+ |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1255 |
+ |
" localAtom (%d) are not equal.\n", |
1256 |
+ |
info[0].n_atoms, |
1257 |
+ |
local_atoms ); |
1258 |
+ |
painCave.isFatal = 1; |
1259 |
+ |
simError(); |
1260 |
+ |
} |
1261 |
|
|
1262 |
+ |
info[0].n_bonds = local_bonds; |
1263 |
+ |
info[0].n_bends = local_bends; |
1264 |
+ |
info[0].n_torsions = local_torsions; |
1265 |
+ |
info[0].n_SRI = local_SRI; |
1266 |
+ |
info[0].n_mol = localMol; |
1267 |
|
|
1268 |
< |
for( i=0; i<simnfo->n_atoms; i++ ){ |
1269 |
< |
simnfo->atoms[i]->set_vx( 0.0 ); |
1076 |
< |
simnfo->atoms[i]->set_vy( 0.0 ); |
1077 |
< |
simnfo->atoms[i]->set_vz( 0.0 ); |
1078 |
< |
} |
1268 |
> |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1269 |
> |
MPIcheckPoint(); |
1270 |
|
} |
1271 |
+ |
|
1272 |
+ |
#endif // is_mpi |
1273 |
|
|
1081 |
– |
void SimSetup::makeElement( double x, double y, double z ){ |
1274 |
|
|
1275 |
< |
int k; |
1276 |
< |
AtomStamp* current_atom; |
1085 |
< |
DirectionalAtom* dAtom; |
1086 |
< |
double rotMat[3][3]; |
1275 |
> |
void SimSetup::makeSysArrays( void ){ |
1276 |
> |
int i, j, k, l; |
1277 |
|
|
1278 |
< |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1278 |
> |
Atom** the_atoms; |
1279 |
> |
Molecule* the_molecules; |
1280 |
> |
Exclude** the_excludes; |
1281 |
|
|
1282 |
< |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
1283 |
< |
if( !current_atom->havePosition() ){ |
1284 |
< |
sprintf( painCave.errMsg, |
1285 |
< |
"SimSetup:initFromBass error.\n" |
1286 |
< |
"\tComponent %s, atom %s does not have a position specified.\n" |
1287 |
< |
"\tThe initialization routine is unable to give a start" |
1288 |
< |
" position.\n", |
1289 |
< |
comp_stamps[current_comp]->getID(), |
1290 |
< |
current_atom->getType() ); |
1291 |
< |
painCave.isFatal = 1; |
1292 |
< |
simError(); |
1282 |
> |
|
1283 |
> |
for(l=0; l<nInfo; l++){ |
1284 |
> |
|
1285 |
> |
// create the atom and short range interaction arrays |
1286 |
> |
|
1287 |
> |
the_atoms = new Atom*[info[l].n_atoms]; |
1288 |
> |
the_molecules = new Molecule[info[l].n_mol]; |
1289 |
> |
int molIndex; |
1290 |
> |
|
1291 |
> |
// initialize the molecule's stampID's |
1292 |
> |
|
1293 |
> |
#ifdef IS_MPI |
1294 |
> |
|
1295 |
> |
|
1296 |
> |
molIndex = 0; |
1297 |
> |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1298 |
> |
|
1299 |
> |
if(mol2proc[i] == worldRank ){ |
1300 |
> |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1301 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
1302 |
> |
the_molecules[molIndex].setGlobalIndex( i ); |
1303 |
> |
molIndex++; |
1304 |
> |
} |
1305 |
|
} |
1306 |
+ |
|
1307 |
+ |
#else // is_mpi |
1308 |
+ |
|
1309 |
+ |
molIndex = 0; |
1310 |
+ |
globalAtomIndex = 0; |
1311 |
+ |
for(i=0; i<n_components; i++){ |
1312 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
1313 |
+ |
the_molecules[molIndex].setStampID( i ); |
1314 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1315 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1316 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1317 |
+ |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1318 |
+ |
globalAtomIndex++; |
1319 |
+ |
} |
1320 |
+ |
molIndex++; |
1321 |
+ |
} |
1322 |
+ |
} |
1323 |
+ |
|
1324 |
+ |
|
1325 |
+ |
#endif // is_mpi |
1326 |
|
|
1103 |
– |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1104 |
– |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1105 |
– |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1327 |
|
|
1328 |
< |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1328 |
> |
if( info[l].n_SRI ){ |
1329 |
> |
|
1330 |
> |
Exclude::createArray(info[l].n_SRI); |
1331 |
> |
the_excludes = new Exclude*[info[l].n_SRI]; |
1332 |
> |
for( int ex=0; ex<info[l].n_SRI; ex++){ |
1333 |
> |
the_excludes[ex] = new Exclude(ex); |
1334 |
> |
} |
1335 |
> |
info[l].globalExcludes = new int; |
1336 |
> |
info[l].n_exclude = info[l].n_SRI; |
1337 |
> |
} |
1338 |
> |
else{ |
1339 |
> |
|
1340 |
> |
Exclude::createArray( 1 ); |
1341 |
> |
the_excludes = new Exclude*; |
1342 |
> |
the_excludes[0] = new Exclude(0); |
1343 |
> |
the_excludes[0]->setPair( 0,0 ); |
1344 |
> |
info[l].globalExcludes = new int; |
1345 |
> |
info[l].globalExcludes[0] = 0; |
1346 |
> |
info[l].n_exclude = 0; |
1347 |
> |
} |
1348 |
|
|
1349 |
< |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1349 |
> |
// set the arrays into the SimInfo object |
1350 |
|
|
1351 |
< |
rotMat[0][0] = 1.0; |
1352 |
< |
rotMat[0][1] = 0.0; |
1353 |
< |
rotMat[0][2] = 0.0; |
1351 |
> |
info[l].atoms = the_atoms; |
1352 |
> |
info[l].molecules = the_molecules; |
1353 |
> |
info[l].nGlobalExcludes = 0; |
1354 |
> |
info[l].excludes = the_excludes; |
1355 |
|
|
1356 |
< |
rotMat[1][0] = 0.0; |
1357 |
< |
rotMat[1][1] = 1.0; |
1358 |
< |
rotMat[1][2] = 0.0; |
1356 |
> |
the_ff->setSimInfo( info ); |
1357 |
> |
|
1358 |
> |
} |
1359 |
> |
} |
1360 |
|
|
1361 |
< |
rotMat[2][0] = 0.0; |
1120 |
< |
rotMat[2][1] = 0.0; |
1121 |
< |
rotMat[2][2] = 1.0; |
1361 |
> |
void SimSetup::makeIntegrator( void ){ |
1362 |
|
|
1363 |
< |
dAtom->setA( rotMat ); |
1363 |
> |
int k; |
1364 |
> |
|
1365 |
> |
NVT<RealIntegrator>* myNVT = NULL; |
1366 |
> |
NPTi<RealIntegrator>* myNPTi = NULL; |
1367 |
> |
NPTf<RealIntegrator>* myNPTf = NULL; |
1368 |
> |
NPTim<RealIntegrator>* myNPTim = NULL; |
1369 |
> |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1370 |
> |
ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1371 |
> |
ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL; |
1372 |
> |
ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL; |
1373 |
> |
ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL; |
1374 |
> |
ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL; |
1375 |
> |
ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL; |
1376 |
> |
|
1377 |
> |
for(k=0; k<nInfo; k++){ |
1378 |
> |
|
1379 |
> |
switch( ensembleCase ){ |
1380 |
> |
|
1381 |
> |
case NVE_ENS: |
1382 |
> |
new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1383 |
> |
break; |
1384 |
> |
|
1385 |
> |
case NVT_ENS: |
1386 |
> |
myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1387 |
> |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1388 |
> |
|
1389 |
> |
if (globals->haveTauThermostat()) |
1390 |
> |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1391 |
> |
|
1392 |
> |
else { |
1393 |
> |
sprintf( painCave.errMsg, |
1394 |
> |
"SimSetup error: If you use the NVT\n" |
1395 |
> |
" ensemble, you must set tauThermostat.\n"); |
1396 |
> |
painCave.isFatal = 1; |
1397 |
> |
simError(); |
1398 |
> |
} |
1399 |
> |
break; |
1400 |
> |
|
1401 |
> |
case NPTi_ENS: |
1402 |
> |
myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1403 |
> |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1404 |
> |
|
1405 |
> |
if (globals->haveTargetPressure()) |
1406 |
> |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1407 |
> |
else { |
1408 |
> |
sprintf( painCave.errMsg, |
1409 |
> |
"SimSetup error: If you use a constant pressure\n" |
1410 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1411 |
> |
painCave.isFatal = 1; |
1412 |
> |
simError(); |
1413 |
> |
} |
1414 |
> |
|
1415 |
> |
if( globals->haveTauThermostat() ) |
1416 |
> |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1417 |
> |
else{ |
1418 |
> |
sprintf( painCave.errMsg, |
1419 |
> |
"SimSetup error: If you use an NPT\n" |
1420 |
> |
" ensemble, you must set tauThermostat.\n"); |
1421 |
> |
painCave.isFatal = 1; |
1422 |
> |
simError(); |
1423 |
> |
} |
1424 |
> |
|
1425 |
> |
if( globals->haveTauBarostat() ) |
1426 |
> |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1427 |
> |
else{ |
1428 |
> |
sprintf( painCave.errMsg, |
1429 |
> |
"SimSetup error: If you use an NPT\n" |
1430 |
> |
" ensemble, you must set tauBarostat.\n"); |
1431 |
> |
painCave.isFatal = 1; |
1432 |
> |
simError(); |
1433 |
> |
} |
1434 |
> |
break; |
1435 |
> |
|
1436 |
> |
case NPTf_ENS: |
1437 |
> |
myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1438 |
> |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1439 |
> |
|
1440 |
> |
if (globals->haveTargetPressure()) |
1441 |
> |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1442 |
> |
else { |
1443 |
> |
sprintf( painCave.errMsg, |
1444 |
> |
"SimSetup error: If you use a constant pressure\n" |
1445 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1446 |
> |
painCave.isFatal = 1; |
1447 |
> |
simError(); |
1448 |
> |
} |
1449 |
> |
|
1450 |
> |
if( globals->haveTauThermostat() ) |
1451 |
> |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1452 |
> |
else{ |
1453 |
> |
sprintf( painCave.errMsg, |
1454 |
> |
"SimSetup error: If you use an NPT\n" |
1455 |
> |
" ensemble, you must set tauThermostat.\n"); |
1456 |
> |
painCave.isFatal = 1; |
1457 |
> |
simError(); |
1458 |
> |
} |
1459 |
> |
|
1460 |
> |
if( globals->haveTauBarostat() ) |
1461 |
> |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1462 |
> |
else{ |
1463 |
> |
sprintf( painCave.errMsg, |
1464 |
> |
"SimSetup error: If you use an NPT\n" |
1465 |
> |
" ensemble, you must set tauBarostat.\n"); |
1466 |
> |
painCave.isFatal = 1; |
1467 |
> |
simError(); |
1468 |
> |
} |
1469 |
> |
break; |
1470 |
> |
|
1471 |
> |
case NPTim_ENS: |
1472 |
> |
myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1473 |
> |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1474 |
> |
|
1475 |
> |
if (globals->haveTargetPressure()) |
1476 |
> |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1477 |
> |
else { |
1478 |
> |
sprintf( painCave.errMsg, |
1479 |
> |
"SimSetup error: If you use a constant pressure\n" |
1480 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1481 |
> |
painCave.isFatal = 1; |
1482 |
> |
simError(); |
1483 |
> |
} |
1484 |
> |
|
1485 |
> |
if( globals->haveTauThermostat() ) |
1486 |
> |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1487 |
> |
else{ |
1488 |
> |
sprintf( painCave.errMsg, |
1489 |
> |
"SimSetup error: If you use an NPT\n" |
1490 |
> |
" ensemble, you must set tauThermostat.\n"); |
1491 |
> |
painCave.isFatal = 1; |
1492 |
> |
simError(); |
1493 |
> |
} |
1494 |
> |
|
1495 |
> |
if( globals->haveTauBarostat() ) |
1496 |
> |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1497 |
> |
else{ |
1498 |
> |
sprintf( painCave.errMsg, |
1499 |
> |
"SimSetup error: If you use an NPT\n" |
1500 |
> |
" ensemble, you must set tauBarostat.\n"); |
1501 |
> |
painCave.isFatal = 1; |
1502 |
> |
simError(); |
1503 |
> |
} |
1504 |
> |
break; |
1505 |
> |
|
1506 |
> |
case NPTfm_ENS: |
1507 |
> |
myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1508 |
> |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1509 |
> |
|
1510 |
> |
if (globals->haveTargetPressure()) |
1511 |
> |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1512 |
> |
else { |
1513 |
> |
sprintf( painCave.errMsg, |
1514 |
> |
"SimSetup error: If you use a constant pressure\n" |
1515 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1516 |
> |
painCave.isFatal = 1; |
1517 |
> |
simError(); |
1518 |
> |
} |
1519 |
> |
|
1520 |
> |
if( globals->haveTauThermostat() ) |
1521 |
> |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1522 |
> |
else{ |
1523 |
> |
sprintf( painCave.errMsg, |
1524 |
> |
"SimSetup error: If you use an NPT\n" |
1525 |
> |
" ensemble, you must set tauThermostat.\n"); |
1526 |
> |
painCave.isFatal = 1; |
1527 |
> |
simError(); |
1528 |
> |
} |
1529 |
> |
|
1530 |
> |
if( globals->haveTauBarostat() ) |
1531 |
> |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1532 |
> |
else{ |
1533 |
> |
sprintf( painCave.errMsg, |
1534 |
> |
"SimSetup error: If you use an NPT\n" |
1535 |
> |
" ensemble, you must set tauBarostat.\n"); |
1536 |
> |
painCave.isFatal = 1; |
1537 |
> |
simError(); |
1538 |
> |
} |
1539 |
> |
break; |
1540 |
> |
|
1541 |
> |
case NVEZCONS_ENS: |
1542 |
> |
|
1543 |
> |
|
1544 |
> |
//setup index of z-constraint molecules, z-constraint sampel time |
1545 |
> |
//and z-constraint force output name. These parameter should be known |
1546 |
> |
//before constructing the z-constraint integrator |
1547 |
> |
setupZConstraint(); |
1548 |
> |
|
1549 |
> |
myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1550 |
> |
|
1551 |
> |
break; |
1552 |
> |
|
1553 |
> |
|
1554 |
> |
case NVTZCONS_ENS: |
1555 |
> |
|
1556 |
> |
setupZConstraint(); |
1557 |
> |
|
1558 |
> |
myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1559 |
> |
myNVTZCons->setTargetTemp(globals->getTargetTemp()); |
1560 |
> |
|
1561 |
> |
if (globals->haveTauThermostat()) |
1562 |
> |
myNVTZCons->setTauThermostat(globals->getTauThermostat()); |
1563 |
> |
|
1564 |
> |
else { |
1565 |
> |
sprintf( painCave.errMsg, |
1566 |
> |
"SimSetup error: If you use the NVT\n" |
1567 |
> |
" ensemble, you must set tauThermostat.\n"); |
1568 |
> |
painCave.isFatal = 1; |
1569 |
> |
simError(); |
1570 |
> |
} |
1571 |
> |
break; |
1572 |
> |
|
1573 |
> |
case NPTiZCONS_ENS: |
1574 |
> |
|
1575 |
> |
setupZConstraint(); |
1576 |
> |
|
1577 |
> |
myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1578 |
> |
myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); |
1579 |
> |
|
1580 |
> |
if (globals->haveTargetPressure()) |
1581 |
> |
myNPTiZCons->setTargetPressure(globals->getTargetPressure()); |
1582 |
> |
else { |
1583 |
> |
sprintf( painCave.errMsg, |
1584 |
> |
"SimSetup error: If you use a constant pressure\n" |
1585 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1586 |
> |
painCave.isFatal = 1; |
1587 |
> |
simError(); |
1588 |
> |
} |
1589 |
> |
|
1590 |
> |
if( globals->haveTauThermostat() ) |
1591 |
> |
myNPTiZCons->setTauThermostat( globals->getTauThermostat() ); |
1592 |
> |
else{ |
1593 |
> |
sprintf( painCave.errMsg, |
1594 |
> |
"SimSetup error: If you use an NPT\n" |
1595 |
> |
" ensemble, you must set tauThermostat.\n"); |
1596 |
> |
painCave.isFatal = 1; |
1597 |
> |
simError(); |
1598 |
> |
} |
1599 |
> |
|
1600 |
> |
if( globals->haveTauBarostat() ) |
1601 |
> |
myNPTiZCons->setTauBarostat( globals->getTauBarostat() ); |
1602 |
> |
else{ |
1603 |
> |
sprintf( painCave.errMsg, |
1604 |
> |
"SimSetup error: If you use an NPT\n" |
1605 |
> |
" ensemble, you must set tauBarostat.\n"); |
1606 |
> |
painCave.isFatal = 1; |
1607 |
> |
simError(); |
1608 |
> |
} |
1609 |
> |
|
1610 |
> |
break; |
1611 |
> |
|
1612 |
> |
case NPTfZCONS_ENS: |
1613 |
> |
|
1614 |
> |
setupZConstraint(); |
1615 |
> |
|
1616 |
> |
myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1617 |
> |
myNPTfZCons->setTargetTemp( globals->getTargetTemp()); |
1618 |
> |
|
1619 |
> |
if (globals->haveTargetPressure()) |
1620 |
> |
myNPTfZCons->setTargetPressure(globals->getTargetPressure()); |
1621 |
> |
else { |
1622 |
> |
sprintf( painCave.errMsg, |
1623 |
> |
"SimSetup error: If you use a constant pressure\n" |
1624 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1625 |
> |
painCave.isFatal = 1; |
1626 |
> |
simError(); |
1627 |
> |
} |
1628 |
> |
|
1629 |
> |
if( globals->haveTauThermostat() ) |
1630 |
> |
myNPTfZCons->setTauThermostat( globals->getTauThermostat() ); |
1631 |
> |
else{ |
1632 |
> |
sprintf( painCave.errMsg, |
1633 |
> |
"SimSetup error: If you use an NPT\n" |
1634 |
> |
" ensemble, you must set tauThermostat.\n"); |
1635 |
> |
painCave.isFatal = 1; |
1636 |
> |
simError(); |
1637 |
> |
} |
1638 |
> |
|
1639 |
> |
if( globals->haveTauBarostat() ) |
1640 |
> |
myNPTfZCons->setTauBarostat( globals->getTauBarostat() ); |
1641 |
> |
else{ |
1642 |
> |
sprintf( painCave.errMsg, |
1643 |
> |
"SimSetup error: If you use an NPT\n" |
1644 |
> |
" ensemble, you must set tauBarostat.\n"); |
1645 |
> |
painCave.isFatal = 1; |
1646 |
> |
simError(); |
1647 |
> |
} |
1648 |
> |
|
1649 |
> |
break; |
1650 |
> |
|
1651 |
> |
case NPTimZCONS_ENS: |
1652 |
> |
|
1653 |
> |
setupZConstraint(); |
1654 |
> |
|
1655 |
> |
myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1656 |
> |
myNPTimZCons->setTargetTemp( globals->getTargetTemp()); |
1657 |
> |
|
1658 |
> |
if (globals->haveTargetPressure()) |
1659 |
> |
myNPTimZCons->setTargetPressure(globals->getTargetPressure()); |
1660 |
> |
else { |
1661 |
> |
sprintf( painCave.errMsg, |
1662 |
> |
"SimSetup error: If you use a constant pressure\n" |
1663 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1664 |
> |
painCave.isFatal = 1; |
1665 |
> |
simError(); |
1666 |
> |
} |
1667 |
> |
|
1668 |
> |
if( globals->haveTauThermostat() ) |
1669 |
> |
myNPTimZCons->setTauThermostat( globals->getTauThermostat() ); |
1670 |
> |
else{ |
1671 |
> |
sprintf( painCave.errMsg, |
1672 |
> |
"SimSetup error: If you use an NPT\n" |
1673 |
> |
" ensemble, you must set tauThermostat.\n"); |
1674 |
> |
painCave.isFatal = 1; |
1675 |
> |
simError(); |
1676 |
> |
} |
1677 |
> |
|
1678 |
> |
if( globals->haveTauBarostat() ) |
1679 |
> |
myNPTimZCons->setTauBarostat( globals->getTauBarostat() ); |
1680 |
> |
else{ |
1681 |
> |
sprintf( painCave.errMsg, |
1682 |
> |
"SimSetup error: If you use an NPT\n" |
1683 |
> |
" ensemble, you must set tauBarostat.\n"); |
1684 |
> |
painCave.isFatal = 1; |
1685 |
> |
simError(); |
1686 |
> |
} |
1687 |
> |
|
1688 |
> |
break; |
1689 |
> |
|
1690 |
> |
case NPTfmZCONS_ENS: |
1691 |
> |
|
1692 |
> |
setupZConstraint(); |
1693 |
> |
|
1694 |
> |
myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1695 |
> |
myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); |
1696 |
> |
|
1697 |
> |
if (globals->haveTargetPressure()) |
1698 |
> |
myNPTfmZCons->setTargetPressure(globals->getTargetPressure()); |
1699 |
> |
else { |
1700 |
> |
sprintf( painCave.errMsg, |
1701 |
> |
"SimSetup error: If you use a constant pressure\n" |
1702 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1703 |
> |
painCave.isFatal = 1; |
1704 |
> |
simError(); |
1705 |
> |
} |
1706 |
> |
|
1707 |
> |
if( globals->haveTauThermostat() ) |
1708 |
> |
myNPTfmZCons->setTauThermostat( globals->getTauThermostat() ); |
1709 |
> |
else{ |
1710 |
> |
sprintf( painCave.errMsg, |
1711 |
> |
"SimSetup error: If you use an NPT\n" |
1712 |
> |
" ensemble, you must set tauThermostat.\n"); |
1713 |
> |
painCave.isFatal = 1; |
1714 |
> |
simError(); |
1715 |
> |
} |
1716 |
> |
|
1717 |
> |
if( globals->haveTauBarostat() ) |
1718 |
> |
myNPTfmZCons->setTauBarostat( globals->getTauBarostat() ); |
1719 |
> |
else{ |
1720 |
> |
sprintf( painCave.errMsg, |
1721 |
> |
"SimSetup error: If you use an NPT\n" |
1722 |
> |
" ensemble, you must set tauBarostat.\n"); |
1723 |
> |
painCave.isFatal = 1; |
1724 |
> |
simError(); |
1725 |
> |
} |
1726 |
> |
break; |
1727 |
> |
|
1728 |
> |
|
1729 |
> |
|
1730 |
> |
default: |
1731 |
> |
sprintf( painCave.errMsg, |
1732 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1733 |
> |
painCave.isFatal = 1; |
1734 |
> |
simError(); |
1735 |
|
} |
1736 |
+ |
} |
1737 |
+ |
} |
1738 |
|
|
1739 |
< |
current_atom_ndx++; |
1739 |
> |
void SimSetup::initFortran( void ){ |
1740 |
> |
|
1741 |
> |
info[0].refreshSim(); |
1742 |
> |
|
1743 |
> |
if( !strcmp( info[0].mixingRule, "standard") ){ |
1744 |
> |
the_ff->initForceField( LB_MIXING_RULE ); |
1745 |
|
} |
1746 |
+ |
else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1747 |
+ |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1748 |
+ |
} |
1749 |
+ |
else{ |
1750 |
+ |
sprintf( painCave.errMsg, |
1751 |
+ |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1752 |
+ |
info[0].mixingRule ); |
1753 |
+ |
painCave.isFatal = 1; |
1754 |
+ |
simError(); |
1755 |
+ |
} |
1756 |
|
|
1129 |
– |
current_mol++; |
1130 |
– |
current_comp_mol++; |
1757 |
|
|
1758 |
< |
if( current_comp_mol >= components_nmol[current_comp] ){ |
1758 |
> |
#ifdef IS_MPI |
1759 |
> |
strcpy( checkPointMsg, |
1760 |
> |
"Successfully intialized the mixingRule for Fortran." ); |
1761 |
> |
MPIcheckPoint(); |
1762 |
> |
#endif // is_mpi |
1763 |
|
|
1764 |
< |
current_comp_mol = 0; |
1765 |
< |
current_comp++; |
1764 |
> |
} |
1765 |
> |
|
1766 |
> |
void SimSetup::setupZConstraint() |
1767 |
> |
{ |
1768 |
> |
int k; |
1769 |
> |
|
1770 |
> |
for(k=0; k<nInfo; k++){ |
1771 |
> |
|
1772 |
> |
if(globals->haveZConsTime()){ |
1773 |
> |
|
1774 |
> |
//add sample time of z-constraint into SimInfo's property list |
1775 |
> |
DoubleData* zconsTimeProp = new DoubleData(); |
1776 |
> |
zconsTimeProp->setID("zconstime"); |
1777 |
> |
zconsTimeProp->setData(globals->getZConsTime()); |
1778 |
> |
info[k].addProperty(zconsTimeProp); |
1779 |
> |
} |
1780 |
> |
else{ |
1781 |
> |
sprintf( painCave.errMsg, |
1782 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
1783 |
> |
" , you must set sample time.\n"); |
1784 |
> |
painCave.isFatal = 1; |
1785 |
> |
simError(); |
1786 |
> |
} |
1787 |
> |
|
1788 |
> |
if(globals->haveIndexOfAllZConsMols()){ |
1789 |
> |
|
1790 |
> |
//add index of z-constraint molecules into SimInfo's property list |
1791 |
> |
vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1792 |
> |
|
1793 |
> |
//sort the index |
1794 |
> |
sort(tempIndex.begin(), tempIndex.end()); |
1795 |
> |
|
1796 |
> |
IndexData* zconsIndex = new IndexData(); |
1797 |
> |
zconsIndex->setID("zconsindex"); |
1798 |
> |
zconsIndex->setIndexData(tempIndex); |
1799 |
> |
info[k].addProperty(zconsIndex); |
1800 |
> |
} |
1801 |
> |
else{ |
1802 |
> |
sprintf( painCave.errMsg, |
1803 |
> |
"SimSetup error: If you use an ZConstraint\n" |
1804 |
> |
" , you must set index of z-constraint molecules.\n"); |
1805 |
> |
painCave.isFatal = 1; |
1806 |
> |
simError(); |
1807 |
> |
|
1808 |
> |
} |
1809 |
> |
|
1810 |
> |
//Determine the name of ouput file and add it into SimInfo's property list |
1811 |
> |
//Be careful, do not use inFileName, since it is a pointer which |
1812 |
> |
//point to a string at master node, and slave nodes do not contain that string |
1813 |
> |
|
1814 |
> |
string zconsOutput(info[k].finalName); |
1815 |
> |
|
1816 |
> |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1817 |
> |
|
1818 |
> |
StringData* zconsFilename = new StringData(); |
1819 |
> |
zconsFilename->setID("zconsfilename"); |
1820 |
> |
zconsFilename->setData(zconsOutput); |
1821 |
> |
|
1822 |
> |
info[k].addProperty(zconsFilename); |
1823 |
|
} |
1824 |
|
} |