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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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#include <sys/time.h> |
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#include "SimSetup.hpp" |
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#include "ReadWrite.hpp" |
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#include "parse_me.h" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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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 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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|
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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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using namespace std; |
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SimSetup::SimSetup(){ |
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|
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isInfoArray = 0; |
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nInfo = 1; |
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|
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stamps = new MakeStamps(); |
40 |
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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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#ifdef IS_MPI |
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#endif // is_mpi |
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void SimSetup::createSim( void ){ |
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void SimSetup::createSim(void){ |
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int i, j, k, globalAtomIndex; |
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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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// creation of complex system objects |
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sysObjectsCreation(); |
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// check on the post processing info |
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|
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finalInfoCheck(); |
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// initialize the system coordinates |
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initSystemCoords(); |
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if( !isInfoArray ) initSystemCoords(); |
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// make the output filenames |
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void SimSetup::makeMolecules( void ){ |
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int k,l; |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
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molInit molInfo; |
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DirectionalAtom* dAtom; |
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|
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double ux, uy, uz, u, uSqr; |
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atomOffset = 0; |
148 |
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excludeOffset = 0; |
149 |
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for(i=0; i<info->n_mol; i++){ |
164 |
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for(k=0; k<nInfo; k++){ |
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|
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stampID = the_molecules[i].getStampID(); |
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the_ff->setSimInfo( &(info[k]) ); |
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|
168 |
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molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
169 |
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molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
170 |
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molInfo.nBends = comp_stamps[stampID]->getNBends(); |
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molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
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molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
168 |
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atomOffset = 0; |
169 |
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excludeOffset = 0; |
170 |
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for(i=0; i<info[k].n_mol; i++){ |
171 |
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|
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stampID = info[k].molecules[i].getStampID(); |
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|
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molInfo.myAtoms = &the_atoms[atomOffset]; |
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molInfo.myExcludes = &the_excludes[excludeOffset]; |
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molInfo.myBonds = new Bond*[molInfo.nBonds]; |
177 |
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molInfo.myBends = new Bend*[molInfo.nBends]; |
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molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
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molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
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molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
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molInfo.nBends = comp_stamps[stampID]->getNBends(); |
177 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
178 |
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molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
179 |
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|
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molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
181 |
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molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
182 |
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molInfo.myBonds = new Bond*[molInfo.nBonds]; |
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molInfo.myBends = new Bend*[molInfo.nBends]; |
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molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
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|
186 |
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theBonds = new bond_pair[molInfo.nBonds]; |
187 |
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theBends = new bend_set[molInfo.nBends]; |
188 |
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theTorsions = new torsion_set[molInfo.nTorsions]; |
186 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
187 |
> |
theBends = new bend_set[molInfo.nBends]; |
188 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
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|
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// make the Atoms |
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// make the Atoms |
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|
192 |
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for(j=0; j<molInfo.nAtoms; j++){ |
193 |
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|
194 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
195 |
< |
if( currentAtom->haveOrientation() ){ |
175 |
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|
176 |
< |
dAtom = new DirectionalAtom(j + atomOffset); |
177 |
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info->n_oriented++; |
178 |
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molInfo.myAtoms[j] = dAtom; |
179 |
< |
|
180 |
< |
ux = currentAtom->getOrntX(); |
181 |
< |
uy = currentAtom->getOrntY(); |
182 |
< |
uz = currentAtom->getOrntZ(); |
183 |
< |
|
184 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
185 |
< |
|
186 |
< |
u = sqrt( uSqr ); |
187 |
< |
ux = ux / u; |
188 |
< |
uy = uy / u; |
189 |
< |
uz = uz / u; |
190 |
< |
|
191 |
< |
dAtom->setSUx( ux ); |
192 |
< |
dAtom->setSUy( uy ); |
193 |
< |
dAtom->setSUz( uz ); |
194 |
< |
} |
195 |
< |
else{ |
196 |
< |
molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
197 |
< |
} |
198 |
< |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
192 |
> |
for(j=0; j<molInfo.nAtoms; j++){ |
193 |
> |
|
194 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
195 |
> |
if( currentAtom->haveOrientation() ){ |
196 |
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|
197 |
+ |
dAtom = new DirectionalAtom( (j + atomOffset), |
198 |
+ |
info[k].getConfiguration() ); |
199 |
+ |
info[k].n_oriented++; |
200 |
+ |
molInfo.myAtoms[j] = dAtom; |
201 |
+ |
|
202 |
+ |
ux = currentAtom->getOrntX(); |
203 |
+ |
uy = currentAtom->getOrntY(); |
204 |
+ |
uz = currentAtom->getOrntZ(); |
205 |
+ |
|
206 |
+ |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
207 |
+ |
|
208 |
+ |
u = sqrt( uSqr ); |
209 |
+ |
ux = ux / u; |
210 |
+ |
uy = uy / u; |
211 |
+ |
uz = uz / u; |
212 |
+ |
|
213 |
+ |
dAtom->setSUx( ux ); |
214 |
+ |
dAtom->setSUy( uy ); |
215 |
+ |
dAtom->setSUz( uz ); |
216 |
+ |
} |
217 |
+ |
else{ |
218 |
+ |
molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
219 |
+ |
info[k].getConfiguration() ); |
220 |
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} |
221 |
+ |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
222 |
+ |
|
223 |
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#ifdef IS_MPI |
224 |
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|
225 |
< |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
225 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
226 |
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|
227 |
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#endif // is_mpi |
228 |
< |
} |
228 |
> |
} |
229 |
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|
230 |
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// make the bonds |
231 |
< |
for(j=0; j<molInfo.nBonds; j++){ |
231 |
> |
for(j=0; j<molInfo.nBonds; j++){ |
232 |
|
|
233 |
< |
currentBond = comp_stamps[stampID]->getBond( j ); |
234 |
< |
theBonds[j].a = currentBond->getA() + atomOffset; |
235 |
< |
theBonds[j].b = currentBond->getB() + atomOffset; |
236 |
< |
|
237 |
< |
exI = theBonds[j].a; |
238 |
< |
exJ = theBonds[j].b; |
239 |
< |
|
240 |
< |
// exclude_I must always be the smaller of the pair |
241 |
< |
if( exI > exJ ){ |
242 |
< |
tempEx = exI; |
243 |
< |
exI = exJ; |
244 |
< |
exJ = tempEx; |
245 |
< |
} |
233 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
234 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
235 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
236 |
> |
|
237 |
> |
exI = theBonds[j].a; |
238 |
> |
exJ = theBonds[j].b; |
239 |
> |
|
240 |
> |
// exclude_I must always be the smaller of the pair |
241 |
> |
if( exI > exJ ){ |
242 |
> |
tempEx = exI; |
243 |
> |
exI = exJ; |
244 |
> |
exJ = tempEx; |
245 |
> |
} |
246 |
|
#ifdef IS_MPI |
247 |
< |
tempEx = exI; |
248 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
249 |
< |
tempEx = exJ; |
250 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
251 |
< |
|
252 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
247 |
> |
tempEx = exI; |
248 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
249 |
> |
tempEx = exJ; |
250 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
251 |
> |
|
252 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
253 |
|
#else // isn't MPI |
254 |
< |
|
255 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
254 |
> |
|
255 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
256 |
|
#endif //is_mpi |
234 |
– |
} |
235 |
– |
excludeOffset += molInfo.nBonds; |
236 |
– |
|
237 |
– |
//make the bends |
238 |
– |
for(j=0; j<molInfo.nBends; j++){ |
239 |
– |
|
240 |
– |
currentBend = comp_stamps[stampID]->getBend( j ); |
241 |
– |
theBends[j].a = currentBend->getA() + atomOffset; |
242 |
– |
theBends[j].b = currentBend->getB() + atomOffset; |
243 |
– |
theBends[j].c = currentBend->getC() + atomOffset; |
244 |
– |
|
245 |
– |
if( currentBend->haveExtras() ){ |
246 |
– |
|
247 |
– |
extras = currentBend->getExtras(); |
248 |
– |
current_extra = extras; |
249 |
– |
|
250 |
– |
while( current_extra != NULL ){ |
251 |
– |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
252 |
– |
|
253 |
– |
switch( current_extra->getType() ){ |
254 |
– |
|
255 |
– |
case 0: |
256 |
– |
theBends[j].ghost = |
257 |
– |
current_extra->getInt() + atomOffset; |
258 |
– |
theBends[j].isGhost = 1; |
259 |
– |
break; |
260 |
– |
|
261 |
– |
case 1: |
262 |
– |
theBends[j].ghost = |
263 |
– |
(int)current_extra->getDouble() + atomOffset; |
264 |
– |
theBends[j].isGhost = 1; |
265 |
– |
break; |
266 |
– |
|
267 |
– |
default: |
268 |
– |
sprintf( painCave.errMsg, |
269 |
– |
"SimSetup Error: ghostVectorSource was neither a " |
270 |
– |
"double nor an int.\n" |
271 |
– |
"-->Bend[%d] in %s\n", |
272 |
– |
j, comp_stamps[stampID]->getID() ); |
273 |
– |
painCave.isFatal = 1; |
274 |
– |
simError(); |
275 |
– |
} |
276 |
– |
} |
277 |
– |
|
278 |
– |
else{ |
279 |
– |
|
280 |
– |
sprintf( painCave.errMsg, |
281 |
– |
"SimSetup Error: unhandled bend assignment:\n" |
282 |
– |
" -->%s in Bend[%d] in %s\n", |
283 |
– |
current_extra->getlhs(), |
284 |
– |
j, comp_stamps[stampID]->getID() ); |
285 |
– |
painCave.isFatal = 1; |
286 |
– |
simError(); |
287 |
– |
} |
288 |
– |
|
289 |
– |
current_extra = current_extra->getNext(); |
290 |
– |
} |
257 |
|
} |
258 |
< |
|
293 |
< |
if( !theBends[j].isGhost ){ |
294 |
< |
|
295 |
< |
exI = theBends[j].a; |
296 |
< |
exJ = theBends[j].c; |
297 |
< |
} |
298 |
< |
else{ |
299 |
< |
|
300 |
< |
exI = theBends[j].a; |
301 |
< |
exJ = theBends[j].b; |
302 |
< |
} |
258 |
> |
excludeOffset += molInfo.nBonds; |
259 |
|
|
260 |
< |
// exclude_I must always be the smaller of the pair |
261 |
< |
if( exI > exJ ){ |
262 |
< |
tempEx = exI; |
263 |
< |
exI = exJ; |
264 |
< |
exJ = tempEx; |
265 |
< |
} |
266 |
< |
#ifdef IS_MPI |
267 |
< |
tempEx = exI; |
268 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
269 |
< |
tempEx = exJ; |
270 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
271 |
< |
|
272 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
273 |
< |
#else // isn't MPI |
274 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
275 |
< |
#endif //is_mpi |
276 |
< |
} |
277 |
< |
excludeOffset += molInfo.nBends; |
278 |
< |
|
279 |
< |
for(j=0; j<molInfo.nTorsions; j++){ |
260 |
> |
//make the bends |
261 |
> |
for(j=0; j<molInfo.nBends; j++){ |
262 |
> |
|
263 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
264 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
265 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
266 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
267 |
> |
|
268 |
> |
if( currentBend->haveExtras() ){ |
269 |
> |
|
270 |
> |
extras = currentBend->getExtras(); |
271 |
> |
current_extra = extras; |
272 |
> |
|
273 |
> |
while( current_extra != NULL ){ |
274 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
275 |
> |
|
276 |
> |
switch( current_extra->getType() ){ |
277 |
> |
|
278 |
> |
case 0: |
279 |
> |
theBends[j].ghost = |
280 |
> |
current_extra->getInt() + atomOffset; |
281 |
> |
theBends[j].isGhost = 1; |
282 |
> |
break; |
283 |
> |
|
284 |
> |
case 1: |
285 |
> |
theBends[j].ghost = |
286 |
> |
(int)current_extra->getDouble() + atomOffset; |
287 |
> |
theBends[j].isGhost = 1; |
288 |
> |
break; |
289 |
> |
|
290 |
> |
default: |
291 |
> |
sprintf( painCave.errMsg, |
292 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
293 |
> |
"double nor an int.\n" |
294 |
> |
"-->Bend[%d] in %s\n", |
295 |
> |
j, comp_stamps[stampID]->getID() ); |
296 |
> |
painCave.isFatal = 1; |
297 |
> |
simError(); |
298 |
> |
} |
299 |
> |
} |
300 |
|
|
301 |
< |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
302 |
< |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
303 |
< |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
304 |
< |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
305 |
< |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
306 |
< |
|
307 |
< |
exI = theTorsions[j].a; |
308 |
< |
exJ = theTorsions[j].d; |
309 |
< |
|
334 |
< |
// exclude_I must always be the smaller of the pair |
335 |
< |
if( exI > exJ ){ |
336 |
< |
tempEx = exI; |
337 |
< |
exI = exJ; |
338 |
< |
exJ = tempEx; |
301 |
> |
else{ |
302 |
> |
|
303 |
> |
sprintf( painCave.errMsg, |
304 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
305 |
> |
" -->%s in Bend[%d] in %s\n", |
306 |
> |
current_extra->getlhs(), |
307 |
> |
j, comp_stamps[stampID]->getID() ); |
308 |
> |
painCave.isFatal = 1; |
309 |
> |
simError(); |
310 |
|
} |
311 |
+ |
|
312 |
+ |
current_extra = current_extra->getNext(); |
313 |
+ |
} |
314 |
+ |
} |
315 |
+ |
|
316 |
+ |
if( !theBends[j].isGhost ){ |
317 |
+ |
|
318 |
+ |
exI = theBends[j].a; |
319 |
+ |
exJ = theBends[j].c; |
320 |
+ |
} |
321 |
+ |
else{ |
322 |
+ |
|
323 |
+ |
exI = theBends[j].a; |
324 |
+ |
exJ = theBends[j].b; |
325 |
+ |
} |
326 |
+ |
|
327 |
+ |
// exclude_I must always be the smaller of the pair |
328 |
+ |
if( exI > exJ ){ |
329 |
+ |
tempEx = exI; |
330 |
+ |
exI = exJ; |
331 |
+ |
exJ = tempEx; |
332 |
+ |
} |
333 |
|
#ifdef IS_MPI |
334 |
< |
tempEx = exI; |
335 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
336 |
< |
tempEx = exJ; |
337 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
334 |
> |
tempEx = exI; |
335 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
336 |
> |
tempEx = exJ; |
337 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
338 |
|
|
339 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
339 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
340 |
|
#else // isn't MPI |
341 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
341 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
342 |
|
#endif //is_mpi |
343 |
< |
} |
344 |
< |
excludeOffset += molInfo.nTorsions; |
345 |
< |
|
346 |
< |
|
347 |
< |
// send the arrays off to the forceField for init. |
348 |
< |
|
349 |
< |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
350 |
< |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
351 |
< |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
352 |
< |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
353 |
< |
|
354 |
< |
|
355 |
< |
the_molecules[i].initialize( molInfo ); |
356 |
< |
|
357 |
< |
|
358 |
< |
atomOffset += molInfo.nAtoms; |
359 |
< |
delete[] theBonds; |
360 |
< |
delete[] theBends; |
361 |
< |
delete[] theTorsions; |
343 |
> |
} |
344 |
> |
excludeOffset += molInfo.nBends; |
345 |
> |
|
346 |
> |
for(j=0; j<molInfo.nTorsions; j++){ |
347 |
> |
|
348 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
349 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
350 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
351 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
352 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
353 |
> |
|
354 |
> |
exI = theTorsions[j].a; |
355 |
> |
exJ = theTorsions[j].d; |
356 |
> |
|
357 |
> |
// exclude_I must always be the smaller of the pair |
358 |
> |
if( exI > exJ ){ |
359 |
> |
tempEx = exI; |
360 |
> |
exI = exJ; |
361 |
> |
exJ = tempEx; |
362 |
|
} |
363 |
+ |
#ifdef IS_MPI |
364 |
+ |
tempEx = exI; |
365 |
+ |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
366 |
+ |
tempEx = exJ; |
367 |
+ |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
368 |
+ |
|
369 |
+ |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
370 |
+ |
#else // isn't MPI |
371 |
+ |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
372 |
+ |
#endif //is_mpi |
373 |
+ |
} |
374 |
+ |
excludeOffset += molInfo.nTorsions; |
375 |
+ |
|
376 |
+ |
|
377 |
+ |
// send the arrays off to the forceField for init. |
378 |
+ |
|
379 |
+ |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
380 |
+ |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
381 |
+ |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
382 |
+ |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
383 |
+ |
|
384 |
+ |
|
385 |
+ |
info[k].molecules[i].initialize( molInfo ); |
386 |
|
|
387 |
+ |
|
388 |
+ |
atomOffset += molInfo.nAtoms; |
389 |
+ |
delete[] theBonds; |
390 |
+ |
delete[] theBends; |
391 |
+ |
delete[] theTorsions; |
392 |
+ |
} |
393 |
+ |
} |
394 |
+ |
|
395 |
|
#ifdef IS_MPI |
396 |
|
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
397 |
|
MPIcheckPoint(); |
398 |
|
#endif // is_mpi |
399 |
< |
|
399 |
> |
|
400 |
|
// clean up the forcefield |
401 |
+ |
|
402 |
|
the_ff->calcRcut(); |
403 |
|
the_ff->cleanMe(); |
404 |
< |
|
404 |
> |
|
405 |
|
} |
406 |
|
|
407 |
|
void SimSetup::initFromBass( void ){ |
414 |
|
int n_extra; |
415 |
|
int have_extra, done; |
416 |
|
|
417 |
+ |
double vel[3]; |
418 |
+ |
vel[0] = 0.0; |
419 |
+ |
vel[1] = 0.0; |
420 |
+ |
vel[2] = 0.0; |
421 |
+ |
|
422 |
|
temp1 = (double)tot_nmol / 4.0; |
423 |
|
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
424 |
|
temp3 = ceil( temp2 ); |
428 |
|
have_extra =1; |
429 |
|
|
430 |
|
n_cells = (int)temp3 - 1; |
431 |
< |
cellx = info->boxL[0] / temp3; |
432 |
< |
celly = info->boxL[1] / temp3; |
433 |
< |
cellz = info->boxL[2] / temp3; |
431 |
> |
cellx = info[0].boxL[0] / temp3; |
432 |
> |
celly = info[0].boxL[1] / temp3; |
433 |
> |
cellz = info[0].boxL[2] / temp3; |
434 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
435 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
436 |
|
n_per_extra = (int)ceil( temp1 ); |
437 |
|
|
438 |
|
if( n_per_extra > 4){ |
439 |
|
sprintf( painCave.errMsg, |
440 |
< |
"SimSetup error. There has been an error in constructing" |
441 |
< |
" the non-complete lattice.\n" ); |
440 |
> |
"SimSetup error. There has been an error in constructing" |
441 |
> |
" the non-complete lattice.\n" ); |
442 |
|
painCave.isFatal = 1; |
443 |
|
simError(); |
444 |
|
} |
445 |
|
} |
446 |
|
else{ |
447 |
|
n_cells = (int)temp3; |
448 |
< |
cellx = info->boxL[0] / temp3; |
449 |
< |
celly = info->boxL[1] / temp3; |
450 |
< |
cellz = info->boxL[2] / temp3; |
448 |
> |
cellx = info[0].boxL[0] / temp3; |
449 |
> |
celly = info[0].boxL[1] / temp3; |
450 |
> |
cellz = info[0].boxL[2] / temp3; |
451 |
|
} |
452 |
|
|
453 |
|
current_mol = 0; |
459 |
|
for( j=0; j < n_cells; j++ ){ |
460 |
|
for( k=0; k < n_cells; k++ ){ |
461 |
|
|
462 |
< |
makeElement( i * cellx, |
463 |
< |
j * celly, |
464 |
< |
k * cellz ); |
462 |
> |
makeElement( i * cellx, |
463 |
> |
j * celly, |
464 |
> |
k * cellz ); |
465 |
|
|
466 |
< |
makeElement( i * cellx + 0.5 * cellx, |
467 |
< |
j * celly + 0.5 * celly, |
468 |
< |
k * cellz ); |
466 |
> |
makeElement( i * cellx + 0.5 * cellx, |
467 |
> |
j * celly + 0.5 * celly, |
468 |
> |
k * cellz ); |
469 |
|
|
470 |
< |
makeElement( i * cellx, |
471 |
< |
j * celly + 0.5 * celly, |
472 |
< |
k * cellz + 0.5 * cellz ); |
470 |
> |
makeElement( i * cellx, |
471 |
> |
j * celly + 0.5 * celly, |
472 |
> |
k * cellz + 0.5 * cellz ); |
473 |
|
|
474 |
< |
makeElement( i * cellx + 0.5 * cellx, |
475 |
< |
j * celly, |
476 |
< |
k * cellz + 0.5 * cellz ); |
474 |
> |
makeElement( i * cellx + 0.5 * cellx, |
475 |
> |
j * celly, |
476 |
> |
k * cellz + 0.5 * cellz ); |
477 |
|
} |
478 |
|
} |
479 |
|
} |
485 |
|
for( i=0; i < (n_cells+1) && !done; i++ ){ |
486 |
|
for( j=0; j < (n_cells+1) && !done; j++ ){ |
487 |
|
|
488 |
< |
if( i < n_cells ){ |
488 |
> |
if( i < n_cells ){ |
489 |
|
|
490 |
< |
if( j < n_cells ){ |
491 |
< |
start_ndx = n_cells; |
492 |
< |
} |
493 |
< |
else start_ndx = 0; |
494 |
< |
} |
495 |
< |
else start_ndx = 0; |
490 |
> |
if( j < n_cells ){ |
491 |
> |
start_ndx = n_cells; |
492 |
> |
} |
493 |
> |
else start_ndx = 0; |
494 |
> |
} |
495 |
> |
else start_ndx = 0; |
496 |
|
|
497 |
< |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
497 |
> |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
498 |
|
|
499 |
< |
makeElement( i * cellx, |
500 |
< |
j * celly, |
501 |
< |
k * cellz ); |
502 |
< |
done = ( current_mol >= tot_nmol ); |
499 |
> |
makeElement( i * cellx, |
500 |
> |
j * celly, |
501 |
> |
k * cellz ); |
502 |
> |
done = ( current_mol >= tot_nmol ); |
503 |
|
|
504 |
< |
if( !done && n_per_extra > 1 ){ |
505 |
< |
makeElement( i * cellx + 0.5 * cellx, |
506 |
< |
j * celly + 0.5 * celly, |
507 |
< |
k * cellz ); |
508 |
< |
done = ( current_mol >= tot_nmol ); |
509 |
< |
} |
504 |
> |
if( !done && n_per_extra > 1 ){ |
505 |
> |
makeElement( i * cellx + 0.5 * cellx, |
506 |
> |
j * celly + 0.5 * celly, |
507 |
> |
k * cellz ); |
508 |
> |
done = ( current_mol >= tot_nmol ); |
509 |
> |
} |
510 |
|
|
511 |
< |
if( !done && n_per_extra > 2){ |
512 |
< |
makeElement( i * cellx, |
513 |
< |
j * celly + 0.5 * celly, |
514 |
< |
k * cellz + 0.5 * cellz ); |
515 |
< |
done = ( current_mol >= tot_nmol ); |
516 |
< |
} |
511 |
> |
if( !done && n_per_extra > 2){ |
512 |
> |
makeElement( i * cellx, |
513 |
> |
j * celly + 0.5 * celly, |
514 |
> |
k * cellz + 0.5 * cellz ); |
515 |
> |
done = ( current_mol >= tot_nmol ); |
516 |
> |
} |
517 |
|
|
518 |
< |
if( !done && n_per_extra > 3){ |
519 |
< |
makeElement( i * cellx + 0.5 * cellx, |
520 |
< |
j * celly, |
521 |
< |
k * cellz + 0.5 * cellz ); |
522 |
< |
done = ( current_mol >= tot_nmol ); |
523 |
< |
} |
524 |
< |
} |
518 |
> |
if( !done && n_per_extra > 3){ |
519 |
> |
makeElement( i * cellx + 0.5 * cellx, |
520 |
> |
j * celly, |
521 |
> |
k * cellz + 0.5 * cellz ); |
522 |
> |
done = ( current_mol >= tot_nmol ); |
523 |
> |
} |
524 |
> |
} |
525 |
|
} |
526 |
|
} |
527 |
|
} |
528 |
|
|
529 |
< |
|
530 |
< |
for( i=0; i<info->n_atoms; i++ ){ |
501 |
< |
info->atoms[i]->set_vx( 0.0 ); |
502 |
< |
info->atoms[i]->set_vy( 0.0 ); |
503 |
< |
info->atoms[i]->set_vz( 0.0 ); |
529 |
> |
for( i=0; i<info[0].n_atoms; i++ ){ |
530 |
> |
info[0].atoms[i]->setVel( vel ); |
531 |
|
} |
532 |
|
} |
533 |
|
|
537 |
|
AtomStamp* current_atom; |
538 |
|
DirectionalAtom* dAtom; |
539 |
|
double rotMat[3][3]; |
540 |
+ |
double pos[3]; |
541 |
|
|
542 |
|
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
543 |
|
|
544 |
|
current_atom = comp_stamps[current_comp]->getAtom( k ); |
545 |
|
if( !current_atom->havePosition() ){ |
546 |
|
sprintf( painCave.errMsg, |
547 |
< |
"SimSetup:initFromBass error.\n" |
548 |
< |
"\tComponent %s, atom %s does not have a position specified.\n" |
549 |
< |
"\tThe initialization routine is unable to give a start" |
550 |
< |
" position.\n", |
551 |
< |
comp_stamps[current_comp]->getID(), |
552 |
< |
current_atom->getType() ); |
547 |
> |
"SimSetup:initFromBass error.\n" |
548 |
> |
"\tComponent %s, atom %s does not have a position specified.\n" |
549 |
> |
"\tThe initialization routine is unable to give a start" |
550 |
> |
" position.\n", |
551 |
> |
comp_stamps[current_comp]->getID(), |
552 |
> |
current_atom->getType() ); |
553 |
|
painCave.isFatal = 1; |
554 |
|
simError(); |
555 |
|
} |
556 |
+ |
|
557 |
+ |
pos[0] = x + current_atom->getPosX(); |
558 |
+ |
pos[1] = y + current_atom->getPosY(); |
559 |
+ |
pos[2] = z + current_atom->getPosZ(); |
560 |
+ |
|
561 |
+ |
info[0].atoms[current_atom_ndx]->setPos( pos ); |
562 |
|
|
563 |
< |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
530 |
< |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
531 |
< |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
563 |
> |
if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
564 |
|
|
565 |
< |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
565 |
> |
dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
566 |
|
|
535 |
– |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
536 |
– |
|
567 |
|
rotMat[0][0] = 1.0; |
568 |
|
rotMat[0][1] = 0.0; |
569 |
|
rotMat[0][2] = 0.0; |
599 |
|
ensembleCase = -1; |
600 |
|
ffCase = -1; |
601 |
|
|
572 |
– |
// get the stamps and globals; |
573 |
– |
stamps = stamps; |
574 |
– |
globals = globals; |
575 |
– |
|
602 |
|
// set the easy ones first |
603 |
< |
info->target_temp = globals->getTargetTemp(); |
604 |
< |
info->dt = globals->getDt(); |
605 |
< |
info->run_time = globals->getRunTime(); |
603 |
> |
|
604 |
> |
for( i=0; i<nInfo; i++){ |
605 |
> |
info[i].target_temp = globals->getTargetTemp(); |
606 |
> |
info[i].dt = globals->getDt(); |
607 |
> |
info[i].run_time = globals->getRunTime(); |
608 |
> |
} |
609 |
|
n_components = globals->getNComponents(); |
610 |
|
|
611 |
|
|
615 |
|
|
616 |
|
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
617 |
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
618 |
+ |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
619 |
|
else{ |
620 |
|
sprintf( painCave.errMsg, |
621 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
622 |
< |
force_field ); |
621 |
> |
"SimSetup Error. Unrecognized force field -> %s\n", |
622 |
> |
force_field ); |
623 |
|
painCave.isFatal = 1; |
624 |
|
simError(); |
625 |
|
} |
637 |
|
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
638 |
|
else{ |
639 |
|
sprintf( painCave.errMsg, |
640 |
< |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
640 |
> |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
641 |
|
"reverting to NVE for this simulation.\n", |
642 |
< |
ensemble ); |
642 |
> |
ensemble ); |
643 |
|
painCave.isFatal = 0; |
644 |
|
simError(); |
645 |
|
strcpy( ensemble, "NVE" ); |
646 |
|
ensembleCase = NVE_ENS; |
647 |
|
} |
648 |
< |
strcpy( info->ensemble, ensemble ); |
648 |
> |
|
649 |
> |
for(i=0; i<nInfo; i++){ |
650 |
> |
|
651 |
> |
strcpy( info[i].ensemble, ensemble ); |
652 |
|
|
653 |
< |
// get the mixing rule |
653 |
> |
// get the mixing rule |
654 |
|
|
655 |
< |
strcpy( info->mixingRule, globals->getMixingRule() ); |
656 |
< |
info->usePBC = globals->getPBC(); |
657 |
< |
|
655 |
> |
strcpy( info[i].mixingRule, globals->getMixingRule() ); |
656 |
> |
info[i].usePBC = globals->getPBC(); |
657 |
> |
} |
658 |
|
|
659 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
660 |
|
|
670 |
|
for( i=0; i<n_components; i++ ){ |
671 |
|
|
672 |
|
if( !the_components[i]->haveNMol() ){ |
673 |
< |
// we have a problem |
674 |
< |
sprintf( painCave.errMsg, |
675 |
< |
"SimSetup Error. No global NMol or component NMol" |
676 |
< |
" given. Cannot calculate the number of atoms.\n" ); |
677 |
< |
painCave.isFatal = 1; |
678 |
< |
simError(); |
673 |
> |
// we have a problem |
674 |
> |
sprintf( painCave.errMsg, |
675 |
> |
"SimSetup Error. No global NMol or component NMol" |
676 |
> |
" given. Cannot calculate the number of atoms.\n" ); |
677 |
> |
painCave.isFatal = 1; |
678 |
> |
simError(); |
679 |
|
} |
680 |
|
|
681 |
|
tot_nmol += the_components[i]->getNMol(); |
684 |
|
} |
685 |
|
else{ |
686 |
|
sprintf( painCave.errMsg, |
687 |
< |
"SimSetup error.\n" |
688 |
< |
"\tSorry, the ability to specify total" |
689 |
< |
" nMols and then give molfractions in the components\n" |
690 |
< |
"\tis not currently supported." |
691 |
< |
" Please give nMol in the components.\n" ); |
687 |
> |
"SimSetup error.\n" |
688 |
> |
"\tSorry, the ability to specify total" |
689 |
> |
" nMols and then give molfractions in the components\n" |
690 |
> |
"\tis not currently supported." |
691 |
> |
" Please give nMol in the components.\n" ); |
692 |
|
painCave.isFatal = 1; |
693 |
|
simError(); |
694 |
|
} |
695 |
|
|
696 |
|
// set the status, sample, and thermal kick times |
697 |
|
|
698 |
< |
if( globals->haveSampleTime() ){ |
699 |
< |
info->sampleTime = globals->getSampleTime(); |
700 |
< |
info->statusTime = info->sampleTime; |
701 |
< |
info->thermalTime = info->sampleTime; |
702 |
< |
} |
703 |
< |
else{ |
704 |
< |
info->sampleTime = globals->getRunTime(); |
705 |
< |
info->statusTime = info->sampleTime; |
706 |
< |
info->thermalTime = info->sampleTime; |
707 |
< |
} |
698 |
> |
for(i=0; i<nInfo; i++){ |
699 |
> |
|
700 |
> |
if( globals->haveSampleTime() ){ |
701 |
> |
info[i].sampleTime = globals->getSampleTime(); |
702 |
> |
info[i].statusTime = info[i].sampleTime; |
703 |
> |
info[i].thermalTime = info[i].sampleTime; |
704 |
> |
} |
705 |
> |
else{ |
706 |
> |
info[i].sampleTime = globals->getRunTime(); |
707 |
> |
info[i].statusTime = info[i].sampleTime; |
708 |
> |
info[i].thermalTime = info[i].sampleTime; |
709 |
> |
} |
710 |
> |
|
711 |
> |
if( globals->haveStatusTime() ){ |
712 |
> |
info[i].statusTime = globals->getStatusTime(); |
713 |
> |
} |
714 |
> |
|
715 |
> |
if( globals->haveThermalTime() ){ |
716 |
> |
info[i].thermalTime = globals->getThermalTime(); |
717 |
> |
} |
718 |
|
|
719 |
< |
if( globals->haveStatusTime() ){ |
677 |
< |
info->statusTime = globals->getStatusTime(); |
678 |
< |
} |
719 |
> |
// check for the temperature set flag |
720 |
|
|
721 |
< |
if( globals->haveThermalTime() ){ |
681 |
< |
info->thermalTime = globals->getThermalTime(); |
682 |
< |
} |
683 |
< |
|
684 |
< |
// check for the temperature set flag |
685 |
< |
|
686 |
< |
if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
687 |
< |
|
688 |
< |
// get some of the tricky things that may still be in the globals |
689 |
< |
|
690 |
< |
double boxVector[3]; |
691 |
< |
if( globals->haveBox() ){ |
692 |
< |
boxVector[0] = globals->getBox(); |
693 |
< |
boxVector[1] = globals->getBox(); |
694 |
< |
boxVector[2] = globals->getBox(); |
721 |
> |
if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
722 |
|
|
723 |
< |
info->setBox( boxVector ); |
723 |
> |
// get some of the tricky things that may still be in the globals |
724 |
> |
|
725 |
> |
double boxVector[3]; |
726 |
> |
if( globals->haveBox() ){ |
727 |
> |
boxVector[0] = globals->getBox(); |
728 |
> |
boxVector[1] = globals->getBox(); |
729 |
> |
boxVector[2] = globals->getBox(); |
730 |
> |
|
731 |
> |
info[i].setBox( boxVector ); |
732 |
> |
} |
733 |
> |
else if( globals->haveDensity() ){ |
734 |
> |
|
735 |
> |
double vol; |
736 |
> |
vol = (double)tot_nmol / globals->getDensity(); |
737 |
> |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
738 |
> |
boxVector[1] = boxVector[0]; |
739 |
> |
boxVector[2] = boxVector[0]; |
740 |
> |
|
741 |
> |
info[i].setBox( boxVector ); |
742 |
|
} |
743 |
< |
else if( globals->haveDensity() ){ |
743 |
> |
else{ |
744 |
> |
if( !globals->haveBoxX() ){ |
745 |
> |
sprintf( painCave.errMsg, |
746 |
> |
"SimSetup error, no periodic BoxX size given.\n" ); |
747 |
> |
painCave.isFatal = 1; |
748 |
> |
simError(); |
749 |
> |
} |
750 |
> |
boxVector[0] = globals->getBoxX(); |
751 |
> |
|
752 |
> |
if( !globals->haveBoxY() ){ |
753 |
> |
sprintf( painCave.errMsg, |
754 |
> |
"SimSetup error, no periodic BoxY size given.\n" ); |
755 |
> |
painCave.isFatal = 1; |
756 |
> |
simError(); |
757 |
> |
} |
758 |
> |
boxVector[1] = globals->getBoxY(); |
759 |
> |
|
760 |
> |
if( !globals->haveBoxZ() ){ |
761 |
> |
sprintf( painCave.errMsg, |
762 |
> |
"SimSetup error, no periodic BoxZ size given.\n" ); |
763 |
> |
painCave.isFatal = 1; |
764 |
> |
simError(); |
765 |
> |
} |
766 |
> |
boxVector[2] = globals->getBoxZ(); |
767 |
> |
|
768 |
> |
info[i].setBox( boxVector ); |
769 |
> |
} |
770 |
> |
} |
771 |
|
|
772 |
< |
double vol; |
773 |
< |
vol = (double)tot_nmol / globals->getDensity(); |
774 |
< |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
703 |
< |
boxVector[1] = boxVector[0]; |
704 |
< |
boxVector[2] = boxVector[0]; |
772 |
> |
int seedValue; |
773 |
> |
struct timeval now_time_val; |
774 |
> |
struct timezone time_zone; |
775 |
|
|
776 |
< |
info->setBox( boxVector ); |
776 |
> |
if(globals->haveSeed()){ |
777 |
> |
seedValue = globals->getSeed(); |
778 |
|
} |
779 |
|
else{ |
780 |
< |
if( !globals->haveBoxX() ){ |
781 |
< |
sprintf( painCave.errMsg, |
782 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
783 |
< |
painCave.isFatal = 1; |
784 |
< |
simError(); |
780 |
> |
#ifndef IS_MPI |
781 |
> |
gettimeofday(&now_time_val, &time_zone); // get the time now |
782 |
> |
seedValue = (int) now_time_val.tv_sec; // convert to epoch time |
783 |
> |
#else |
784 |
> |
if(worldRank == 0){ |
785 |
> |
gettimeofday(&now_time_val, &time_zone); // get the time now |
786 |
> |
seedValue = (int) now_time_val.tv_sec; // convert to epoch time |
787 |
|
} |
788 |
< |
boxVector[0] = globals->getBoxX(); |
788 |
> |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
789 |
> |
#endif |
790 |
> |
} |
791 |
|
|
792 |
< |
if( !globals->haveBoxY() ){ |
793 |
< |
sprintf( painCave.errMsg, |
719 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
720 |
< |
painCave.isFatal = 1; |
721 |
< |
simError(); |
722 |
< |
} |
723 |
< |
boxVector[1] = globals->getBoxY(); |
724 |
< |
|
725 |
< |
if( !globals->haveBoxZ() ){ |
726 |
< |
sprintf( painCave.errMsg, |
727 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
728 |
< |
painCave.isFatal = 1; |
729 |
< |
simError(); |
730 |
< |
} |
731 |
< |
boxVector[2] = globals->getBoxZ(); |
732 |
< |
|
733 |
< |
info->setBox( boxVector ); |
792 |
> |
for(int i = 0; i < nInfo; i++){ |
793 |
> |
info[i].setSeed(seedValue); |
794 |
|
} |
795 |
|
|
736 |
– |
|
737 |
– |
|
796 |
|
#ifdef IS_MPI |
797 |
|
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
798 |
|
MPIcheckPoint(); |
804 |
|
void SimSetup::finalInfoCheck( void ){ |
805 |
|
int index; |
806 |
|
int usesDipoles; |
807 |
< |
|
807 |
> |
int i; |
808 |
|
|
809 |
< |
// check electrostatic parameters |
810 |
< |
|
753 |
< |
index = 0; |
754 |
< |
usesDipoles = 0; |
755 |
< |
while( (index < info->n_atoms) && !usesDipoles ){ |
756 |
< |
usesDipoles = ((info->atoms)[index])->hasDipole(); |
757 |
< |
index++; |
758 |
< |
} |
759 |
< |
|
760 |
< |
#ifdef IS_MPI |
761 |
< |
int myUse = usesDipoles; |
762 |
< |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
763 |
< |
#endif //is_mpi |
764 |
< |
|
765 |
< |
double theEcr, theEst; |
766 |
< |
|
767 |
< |
if (globals->getUseRF() ) { |
768 |
< |
info->useReactionField = 1; |
809 |
> |
for(i=0; i<nInfo; i++){ |
810 |
> |
// check electrostatic parameters |
811 |
|
|
812 |
< |
if( !globals->haveECR() ){ |
813 |
< |
sprintf( painCave.errMsg, |
814 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
815 |
< |
"box length for the electrostaticCutoffRadius.\n" |
816 |
< |
"I hope you have a very fast processor!\n"); |
775 |
< |
painCave.isFatal = 0; |
776 |
< |
simError(); |
777 |
< |
double smallest; |
778 |
< |
smallest = info->boxL[0]; |
779 |
< |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
780 |
< |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
781 |
< |
theEcr = 0.5 * smallest; |
782 |
< |
} else { |
783 |
< |
theEcr = globals->getECR(); |
812 |
> |
index = 0; |
813 |
> |
usesDipoles = 0; |
814 |
> |
while( (index < info[i].n_atoms) && !usesDipoles ){ |
815 |
> |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
816 |
> |
index++; |
817 |
|
} |
785 |
– |
|
786 |
– |
if( !globals->haveEST() ){ |
787 |
– |
sprintf( painCave.errMsg, |
788 |
– |
"SimSetup Warning: using default value of 0.05 * the " |
789 |
– |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
790 |
– |
); |
791 |
– |
painCave.isFatal = 0; |
792 |
– |
simError(); |
793 |
– |
theEst = 0.05 * theEcr; |
794 |
– |
} else { |
795 |
– |
theEst= globals->getEST(); |
796 |
– |
} |
797 |
– |
|
798 |
– |
info->setEcr( theEcr, theEst ); |
818 |
|
|
819 |
< |
if(!globals->haveDielectric() ){ |
820 |
< |
sprintf( painCave.errMsg, |
821 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
822 |
< |
"setting a dielectric constant!\n" |
823 |
< |
); |
824 |
< |
painCave.isFatal = 1; |
825 |
< |
simError(); |
826 |
< |
} |
827 |
< |
info->dielectric = globals->getDielectric(); |
809 |
< |
} |
810 |
< |
else { |
811 |
< |
if (usesDipoles) { |
819 |
> |
#ifdef IS_MPI |
820 |
> |
int myUse = usesDipoles; |
821 |
> |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
822 |
> |
#endif //is_mpi |
823 |
> |
|
824 |
> |
double theEcr, theEst; |
825 |
> |
|
826 |
> |
if (globals->getUseRF() ) { |
827 |
> |
info[i].useReactionField = 1; |
828 |
|
|
829 |
|
if( !globals->haveECR() ){ |
830 |
< |
sprintf( painCave.errMsg, |
831 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
832 |
< |
"box length for the electrostaticCutoffRadius.\n" |
833 |
< |
"I hope you have a very fast processor!\n"); |
834 |
< |
painCave.isFatal = 0; |
835 |
< |
simError(); |
836 |
< |
double smallest; |
837 |
< |
smallest = info->boxL[0]; |
838 |
< |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
839 |
< |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
840 |
< |
theEcr = 0.5 * smallest; |
830 |
> |
sprintf( painCave.errMsg, |
831 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
832 |
> |
"box length for the electrostaticCutoffRadius.\n" |
833 |
> |
"I hope you have a very fast processor!\n"); |
834 |
> |
painCave.isFatal = 0; |
835 |
> |
simError(); |
836 |
> |
double smallest; |
837 |
> |
smallest = info[i].boxL[0]; |
838 |
> |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
839 |
> |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
840 |
> |
theEcr = 0.5 * smallest; |
841 |
|
} else { |
842 |
< |
theEcr = globals->getECR(); |
842 |
> |
theEcr = globals->getECR(); |
843 |
|
} |
844 |
|
|
845 |
|
if( !globals->haveEST() ){ |
846 |
< |
sprintf( painCave.errMsg, |
847 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
848 |
< |
"electrostaticCutoffRadius for the " |
849 |
< |
"electrostaticSkinThickness\n" |
850 |
< |
); |
851 |
< |
painCave.isFatal = 0; |
852 |
< |
simError(); |
837 |
< |
theEst = 0.05 * theEcr; |
846 |
> |
sprintf( painCave.errMsg, |
847 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
848 |
> |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
849 |
> |
); |
850 |
> |
painCave.isFatal = 0; |
851 |
> |
simError(); |
852 |
> |
theEst = 0.05 * theEcr; |
853 |
|
} else { |
854 |
< |
theEst= globals->getEST(); |
854 |
> |
theEst= globals->getEST(); |
855 |
|
} |
856 |
+ |
|
857 |
+ |
info[i].setEcr( theEcr, theEst ); |
858 |
+ |
|
859 |
+ |
if(!globals->haveDielectric() ){ |
860 |
+ |
sprintf( painCave.errMsg, |
861 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
862 |
+ |
"setting a dielectric constant!\n" |
863 |
+ |
); |
864 |
+ |
painCave.isFatal = 1; |
865 |
+ |
simError(); |
866 |
+ |
} |
867 |
+ |
info[i].dielectric = globals->getDielectric(); |
868 |
+ |
} |
869 |
+ |
else { |
870 |
+ |
if (usesDipoles) { |
871 |
+ |
|
872 |
+ |
if( !globals->haveECR() ){ |
873 |
+ |
sprintf( painCave.errMsg, |
874 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
875 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
876 |
+ |
"I hope you have a very fast processor!\n"); |
877 |
+ |
painCave.isFatal = 0; |
878 |
+ |
simError(); |
879 |
+ |
double smallest; |
880 |
+ |
smallest = info[i].boxL[0]; |
881 |
+ |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
882 |
+ |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
883 |
+ |
theEcr = 0.5 * smallest; |
884 |
+ |
} else { |
885 |
+ |
theEcr = globals->getECR(); |
886 |
+ |
} |
887 |
+ |
|
888 |
+ |
if( !globals->haveEST() ){ |
889 |
+ |
sprintf( painCave.errMsg, |
890 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
891 |
+ |
"electrostaticCutoffRadius for the " |
892 |
+ |
"electrostaticSkinThickness\n" |
893 |
+ |
); |
894 |
+ |
painCave.isFatal = 0; |
895 |
+ |
simError(); |
896 |
+ |
theEst = 0.05 * theEcr; |
897 |
+ |
} else { |
898 |
+ |
theEst= globals->getEST(); |
899 |
+ |
} |
900 |
+ |
|
901 |
+ |
info[i].setEcr( theEcr, theEst ); |
902 |
+ |
} |
903 |
+ |
} |
904 |
+ |
} |
905 |
|
|
842 |
– |
info->setEcr( theEcr, theEst ); |
843 |
– |
} |
844 |
– |
} |
845 |
– |
|
906 |
|
#ifdef IS_MPI |
907 |
|
strcpy( checkPointMsg, "post processing checks out" ); |
908 |
|
MPIcheckPoint(); |
911 |
|
} |
912 |
|
|
913 |
|
void SimSetup::initSystemCoords( void ){ |
914 |
+ |
int i; |
915 |
+ |
|
916 |
+ |
char* inName; |
917 |
|
|
918 |
< |
if( globals->haveInitialConfig() ){ |
919 |
< |
|
920 |
< |
InitializeFromFile* fileInit; |
918 |
> |
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
919 |
> |
|
920 |
> |
for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
921 |
> |
|
922 |
> |
if( globals->haveInitialConfig() ){ |
923 |
> |
|
924 |
> |
InitializeFromFile* fileInit; |
925 |
|
#ifdef IS_MPI // is_mpi |
926 |
< |
if( worldRank == 0 ){ |
926 |
> |
if( worldRank == 0 ){ |
927 |
|
#endif //is_mpi |
928 |
< |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
928 |
> |
inName = globals->getInitialConfig(); |
929 |
> |
double* tempDouble = new double[1000000]; |
930 |
> |
fileInit = new InitializeFromFile( inName ); |
931 |
|
#ifdef IS_MPI |
932 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
932 |
> |
}else fileInit = new InitializeFromFile( NULL ); |
933 |
|
#endif |
934 |
< |
fileInit->readInit( info ); // default velocities on |
935 |
< |
|
936 |
< |
delete fileInit; |
937 |
< |
} |
938 |
< |
else{ |
939 |
< |
|
934 |
> |
fileInit->readInit( info ); // default velocities on |
935 |
> |
|
936 |
> |
delete fileInit; |
937 |
> |
} |
938 |
> |
else{ |
939 |
> |
|
940 |
|
#ifdef IS_MPI |
941 |
< |
|
942 |
< |
// no init from bass |
943 |
< |
|
944 |
< |
sprintf( painCave.errMsg, |
945 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
946 |
< |
painCave.isFatal; |
947 |
< |
simError(); |
948 |
< |
|
941 |
> |
|
942 |
> |
// no init from bass |
943 |
> |
|
944 |
> |
sprintf( painCave.errMsg, |
945 |
> |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
946 |
> |
painCave.isFatal; |
947 |
> |
simError(); |
948 |
> |
|
949 |
|
#else |
950 |
< |
|
951 |
< |
initFromBass(); |
952 |
< |
|
953 |
< |
|
950 |
> |
|
951 |
> |
initFromBass(); |
952 |
> |
|
953 |
> |
|
954 |
|
#endif |
955 |
< |
} |
956 |
< |
|
955 |
> |
} |
956 |
> |
|
957 |
|
#ifdef IS_MPI |
958 |
|
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
959 |
|
MPIcheckPoint(); |
960 |
|
#endif // is_mpi |
961 |
< |
|
961 |
> |
|
962 |
|
} |
963 |
|
|
964 |
|
|
965 |
|
void SimSetup::makeOutNames( void ){ |
966 |
+ |
|
967 |
+ |
int k; |
968 |
|
|
969 |
+ |
|
970 |
+ |
for(k=0; k<nInfo; k++){ |
971 |
+ |
|
972 |
|
#ifdef IS_MPI |
973 |
< |
if( worldRank == 0 ){ |
973 |
> |
if( worldRank == 0 ){ |
974 |
|
#endif // is_mpi |
975 |
< |
|
976 |
< |
if( globals->haveFinalConfig() ){ |
977 |
< |
strcpy( info->finalName, globals->getFinalConfig() ); |
975 |
> |
|
976 |
> |
if( globals->haveFinalConfig() ){ |
977 |
> |
strcpy( info[k].finalName, globals->getFinalConfig() ); |
978 |
> |
} |
979 |
> |
else{ |
980 |
> |
strcpy( info[k].finalName, inFileName ); |
981 |
> |
char* endTest; |
982 |
> |
int nameLength = strlen( info[k].finalName ); |
983 |
> |
endTest = &(info[k].finalName[nameLength - 5]); |
984 |
> |
if( !strcmp( endTest, ".bass" ) ){ |
985 |
> |
strcpy( endTest, ".eor" ); |
986 |
> |
} |
987 |
> |
else if( !strcmp( endTest, ".BASS" ) ){ |
988 |
> |
strcpy( endTest, ".eor" ); |
989 |
> |
} |
990 |
> |
else{ |
991 |
> |
endTest = &(info[k].finalName[nameLength - 4]); |
992 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
993 |
> |
strcpy( endTest, ".eor" ); |
994 |
|
} |
995 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
996 |
+ |
strcpy( endTest, ".eor" ); |
997 |
+ |
} |
998 |
|
else{ |
999 |
< |
strcpy( info->finalName, inFileName ); |
999 |
> |
strcat( info[k].finalName, ".eor" ); |
1000 |
> |
} |
1001 |
> |
} |
1002 |
> |
} |
1003 |
> |
|
1004 |
> |
// make the sample and status out names |
1005 |
> |
|
1006 |
> |
strcpy( info[k].sampleName, inFileName ); |
1007 |
|
char* endTest; |
1008 |
< |
int nameLength = strlen( info->finalName ); |
1009 |
< |
endTest = &(info->finalName[nameLength - 5]); |
1008 |
> |
int nameLength = strlen( info[k].sampleName ); |
1009 |
> |
endTest = &(info[k].sampleName[nameLength - 5]); |
1010 |
|
if( !strcmp( endTest, ".bass" ) ){ |
1011 |
< |
strcpy( endTest, ".eor" ); |
1011 |
> |
strcpy( endTest, ".dump" ); |
1012 |
|
} |
1013 |
|
else if( !strcmp( endTest, ".BASS" ) ){ |
1014 |
< |
strcpy( endTest, ".eor" ); |
1014 |
> |
strcpy( endTest, ".dump" ); |
1015 |
|
} |
1016 |
|
else{ |
1017 |
< |
endTest = &(info->finalName[nameLength - 4]); |
1018 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
1019 |
< |
strcpy( endTest, ".eor" ); |
1020 |
< |
} |
1021 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
1022 |
< |
strcpy( endTest, ".eor" ); |
1023 |
< |
} |
1024 |
< |
else{ |
1025 |
< |
strcat( info->finalName, ".eor" ); |
1026 |
< |
} |
1017 |
> |
endTest = &(info[k].sampleName[nameLength - 4]); |
1018 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
1019 |
> |
strcpy( endTest, ".dump" ); |
1020 |
> |
} |
1021 |
> |
else if( !strcmp( endTest, ".mdl" ) ){ |
1022 |
> |
strcpy( endTest, ".dump" ); |
1023 |
> |
} |
1024 |
> |
else{ |
1025 |
> |
strcat( info[k].sampleName, ".dump" ); |
1026 |
> |
} |
1027 |
|
} |
1028 |
< |
} |
1029 |
< |
|
1030 |
< |
// make the sample and status out names |
1031 |
< |
|
1032 |
< |
strcpy( info->sampleName, inFileName ); |
1033 |
< |
char* endTest; |
934 |
< |
int nameLength = strlen( info->sampleName ); |
935 |
< |
endTest = &(info->sampleName[nameLength - 5]); |
936 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
937 |
< |
strcpy( endTest, ".dump" ); |
938 |
< |
} |
939 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
940 |
< |
strcpy( endTest, ".dump" ); |
941 |
< |
} |
942 |
< |
else{ |
943 |
< |
endTest = &(info->sampleName[nameLength - 4]); |
944 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
945 |
< |
strcpy( endTest, ".dump" ); |
946 |
< |
} |
947 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
948 |
< |
strcpy( endTest, ".dump" ); |
1028 |
> |
|
1029 |
> |
strcpy( info[k].statusName, inFileName ); |
1030 |
> |
nameLength = strlen( info[k].statusName ); |
1031 |
> |
endTest = &(info[k].statusName[nameLength - 5]); |
1032 |
> |
if( !strcmp( endTest, ".bass" ) ){ |
1033 |
> |
strcpy( endTest, ".stat" ); |
1034 |
|
} |
1035 |
< |
else{ |
1036 |
< |
strcat( info->sampleName, ".dump" ); |
1035 |
> |
else if( !strcmp( endTest, ".BASS" ) ){ |
1036 |
> |
strcpy( endTest, ".stat" ); |
1037 |
|
} |
953 |
– |
} |
954 |
– |
|
955 |
– |
strcpy( info->statusName, inFileName ); |
956 |
– |
nameLength = strlen( info->statusName ); |
957 |
– |
endTest = &(info->statusName[nameLength - 5]); |
958 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
959 |
– |
strcpy( endTest, ".stat" ); |
960 |
– |
} |
961 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
962 |
– |
strcpy( endTest, ".stat" ); |
963 |
– |
} |
964 |
– |
else{ |
965 |
– |
endTest = &(info->statusName[nameLength - 4]); |
966 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
967 |
– |
strcpy( endTest, ".stat" ); |
968 |
– |
} |
969 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
970 |
– |
strcpy( endTest, ".stat" ); |
971 |
– |
} |
1038 |
|
else{ |
1039 |
< |
strcat( info->statusName, ".stat" ); |
1039 |
> |
endTest = &(info[k].statusName[nameLength - 4]); |
1040 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
1041 |
> |
strcpy( endTest, ".stat" ); |
1042 |
> |
} |
1043 |
> |
else if( !strcmp( endTest, ".mdl" ) ){ |
1044 |
> |
strcpy( endTest, ".stat" ); |
1045 |
> |
} |
1046 |
> |
else{ |
1047 |
> |
strcat( info[k].statusName, ".stat" ); |
1048 |
> |
} |
1049 |
|
} |
1050 |
< |
} |
976 |
< |
|
1050 |
> |
|
1051 |
|
#ifdef IS_MPI |
1052 |
< |
} |
1052 |
> |
} |
1053 |
|
#endif // is_mpi |
1054 |
< |
|
1054 |
> |
} |
1055 |
|
} |
1056 |
|
|
1057 |
|
|
1058 |
|
void SimSetup::sysObjectsCreation( void ){ |
1059 |
< |
|
1060 |
< |
int i; |
1061 |
< |
|
1059 |
> |
|
1060 |
> |
int i,k; |
1061 |
> |
|
1062 |
|
// create the forceField |
1063 |
|
|
1064 |
|
createFF(); |
1078 |
|
#endif //is_mpi |
1079 |
|
|
1080 |
|
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1081 |
< |
|
1081 |
> |
|
1082 |
|
makeSysArrays(); |
1083 |
|
|
1084 |
|
// make and initialize the molecules (all but atomic coordinates) |
1085 |
< |
|
1085 |
> |
|
1086 |
|
makeMolecules(); |
1013 |
– |
info->identArray = new int[info->n_atoms]; |
1014 |
– |
for(i=0; i<info->n_atoms; i++){ |
1015 |
– |
info->identArray[i] = the_atoms[i]->getIdent(); |
1016 |
– |
} |
1087 |
|
|
1088 |
< |
|
1089 |
< |
|
1088 |
> |
for(k=0; k<nInfo; k++){ |
1089 |
> |
info[k].identArray = new int[info[k].n_atoms]; |
1090 |
> |
for(i=0; i<info[k].n_atoms; i++){ |
1091 |
> |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1092 |
> |
} |
1093 |
> |
} |
1094 |
|
} |
1095 |
|
|
1096 |
|
|
1106 |
|
the_ff = new LJFF(); |
1107 |
|
break; |
1108 |
|
|
1109 |
+ |
case FF_EAM: |
1110 |
+ |
the_ff = new EAM_FF(); |
1111 |
+ |
break; |
1112 |
+ |
|
1113 |
|
default: |
1114 |
|
sprintf( painCave.errMsg, |
1115 |
< |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1115 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1116 |
|
painCave.isFatal = 1; |
1117 |
|
simError(); |
1118 |
|
} |
1128 |
|
void SimSetup::compList( void ){ |
1129 |
|
|
1130 |
|
int i; |
1131 |
< |
|
1131 |
> |
char* id; |
1132 |
> |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1133 |
> |
LinkedMolStamp* currentStamp = NULL; |
1134 |
|
comp_stamps = new MoleculeStamp*[n_components]; |
1135 |
< |
|
1135 |
> |
|
1136 |
|
// make an array of molecule stamps that match the components used. |
1137 |
|
// also extract the used stamps out into a separate linked list |
1058 |
– |
|
1059 |
– |
info->nComponents = n_components; |
1060 |
– |
info->componentsNmol = components_nmol; |
1061 |
– |
info->compStamps = comp_stamps; |
1062 |
– |
info->headStamp = new LinkedMolStamp(); |
1138 |
|
|
1139 |
< |
char* id; |
1140 |
< |
LinkedMolStamp* headStamp = info->headStamp; |
1141 |
< |
LinkedMolStamp* currentStamp = NULL; |
1139 |
> |
for(i=0; i<nInfo; i++){ |
1140 |
> |
info[i].nComponents = n_components; |
1141 |
> |
info[i].componentsNmol = components_nmol; |
1142 |
> |
info[i].compStamps = comp_stamps; |
1143 |
> |
info[i].headStamp = headStamp; |
1144 |
> |
} |
1145 |
> |
|
1146 |
> |
|
1147 |
|
for( i=0; i<n_components; i++ ){ |
1148 |
|
|
1149 |
|
id = the_components[i]->getType(); |
1158 |
|
|
1159 |
|
currentStamp = stamps->extractMolStamp( id ); |
1160 |
|
if( currentStamp == NULL ){ |
1161 |
< |
sprintf( painCave.errMsg, |
1162 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
1163 |
< |
"list of declared molecules\n", |
1164 |
< |
id ); |
1165 |
< |
painCave.isFatal = 1; |
1166 |
< |
simError(); |
1161 |
> |
sprintf( painCave.errMsg, |
1162 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
1163 |
> |
"list of declared molecules\n", |
1164 |
> |
id ); |
1165 |
> |
painCave.isFatal = 1; |
1166 |
> |
simError(); |
1167 |
|
} |
1168 |
|
|
1169 |
|
headStamp->add( currentStamp ); |
1181 |
|
|
1182 |
|
void SimSetup::calcSysValues( void ){ |
1183 |
|
int i, j, k; |
1184 |
< |
|
1185 |
< |
|
1184 |
> |
|
1185 |
> |
int *molMembershipArray; |
1186 |
> |
|
1187 |
|
tot_atoms = 0; |
1188 |
|
tot_bonds = 0; |
1189 |
|
tot_bends = 0; |
1195 |
|
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1196 |
|
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1197 |
|
} |
1198 |
< |
|
1199 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1200 |
< |
|
1120 |
< |
info->n_atoms = tot_atoms; |
1121 |
< |
info->n_bonds = tot_bonds; |
1122 |
< |
info->n_bends = tot_bends; |
1123 |
< |
info->n_torsions = tot_torsions; |
1124 |
< |
info->n_SRI = tot_SRI; |
1125 |
< |
info->n_mol = tot_nmol; |
1198 |
> |
|
1199 |
> |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1200 |
> |
molMembershipArray = new int[tot_atoms]; |
1201 |
|
|
1202 |
< |
info->molMembershipArray = new int[tot_atoms]; |
1202 |
> |
for(i=0; i<nInfo; i++){ |
1203 |
> |
info[i].n_atoms = tot_atoms; |
1204 |
> |
info[i].n_bonds = tot_bonds; |
1205 |
> |
info[i].n_bends = tot_bends; |
1206 |
> |
info[i].n_torsions = tot_torsions; |
1207 |
> |
info[i].n_SRI = tot_SRI; |
1208 |
> |
info[i].n_mol = tot_nmol; |
1209 |
> |
|
1210 |
> |
info[i].molMembershipArray = molMembershipArray; |
1211 |
> |
} |
1212 |
|
} |
1213 |
|
|
1130 |
– |
|
1214 |
|
#ifdef IS_MPI |
1215 |
|
|
1216 |
|
void SimSetup::mpiMolDivide( void ){ |
1242 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
1243 |
|
|
1244 |
|
if( mol2proc[allMol] == worldRank ){ |
1245 |
< |
|
1246 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
1247 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
1248 |
< |
local_bends += comp_stamps[i]->getNBends(); |
1249 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
1250 |
< |
localMol++; |
1245 |
> |
|
1246 |
> |
local_atoms += comp_stamps[i]->getNAtoms(); |
1247 |
> |
local_bonds += comp_stamps[i]->getNBonds(); |
1248 |
> |
local_bends += comp_stamps[i]->getNBends(); |
1249 |
> |
local_torsions += comp_stamps[i]->getNTorsions(); |
1250 |
> |
localMol++; |
1251 |
|
} |
1252 |
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1253 |
< |
info->molMembershipArray[globalAtomIndex] = allMol; |
1253 |
> |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1254 |
|
globalAtomIndex++; |
1255 |
|
} |
1256 |
|
|
1259 |
|
} |
1260 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
1261 |
|
|
1262 |
< |
info->n_atoms = mpiSim->getMyNlocal(); |
1262 |
> |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1263 |
|
|
1264 |
< |
if( local_atoms != info->n_atoms ){ |
1264 |
> |
if( local_atoms != info[0].n_atoms ){ |
1265 |
|
sprintf( painCave.errMsg, |
1266 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1267 |
< |
" localAtom (%d) are not equal.\n", |
1268 |
< |
info->n_atoms, |
1269 |
< |
local_atoms ); |
1266 |
> |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1267 |
> |
" localAtom (%d) are not equal.\n", |
1268 |
> |
info[0].n_atoms, |
1269 |
> |
local_atoms ); |
1270 |
|
painCave.isFatal = 1; |
1271 |
|
simError(); |
1272 |
|
} |
1273 |
|
|
1274 |
< |
info->n_bonds = local_bonds; |
1275 |
< |
info->n_bends = local_bends; |
1276 |
< |
info->n_torsions = local_torsions; |
1277 |
< |
info->n_SRI = local_SRI; |
1278 |
< |
info->n_mol = localMol; |
1274 |
> |
info[0].n_bonds = local_bonds; |
1275 |
> |
info[0].n_bends = local_bends; |
1276 |
> |
info[0].n_torsions = local_torsions; |
1277 |
> |
info[0].n_SRI = local_SRI; |
1278 |
> |
info[0].n_mol = localMol; |
1279 |
|
|
1280 |
|
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1281 |
|
MPIcheckPoint(); |
1282 |
|
} |
1283 |
< |
|
1283 |
> |
|
1284 |
|
#endif // is_mpi |
1285 |
|
|
1286 |
|
|
1287 |
|
void SimSetup::makeSysArrays( void ){ |
1288 |
< |
int i, j, k; |
1288 |
> |
int i, j, k, l; |
1289 |
|
|
1290 |
+ |
Atom** the_atoms; |
1291 |
+ |
Molecule* the_molecules; |
1292 |
+ |
Exclude** the_excludes; |
1293 |
|
|
1208 |
– |
// create the atom and short range interaction arrays |
1209 |
– |
|
1210 |
– |
Atom::createArrays(info->n_atoms); |
1211 |
– |
the_atoms = new Atom*[info->n_atoms]; |
1212 |
– |
the_molecules = new Molecule[info->n_mol]; |
1213 |
– |
int molIndex; |
1214 |
– |
|
1215 |
– |
// initialize the molecule's stampID's |
1216 |
– |
|
1217 |
– |
#ifdef IS_MPI |
1294 |
|
|
1295 |
+ |
for(l=0; l<nInfo; l++){ |
1296 |
+ |
|
1297 |
+ |
// create the atom and short range interaction arrays |
1298 |
+ |
|
1299 |
+ |
the_atoms = new Atom*[info[l].n_atoms]; |
1300 |
+ |
the_molecules = new Molecule[info[l].n_mol]; |
1301 |
+ |
int molIndex; |
1302 |
|
|
1303 |
< |
molIndex = 0; |
1221 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1303 |
> |
// initialize the molecule's stampID's |
1304 |
|
|
1305 |
< |
if(mol2proc[i] == worldRank ){ |
1306 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1307 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
1308 |
< |
the_molecules[molIndex].setGlobalIndex( i ); |
1309 |
< |
molIndex++; |
1305 |
> |
#ifdef IS_MPI |
1306 |
> |
|
1307 |
> |
|
1308 |
> |
molIndex = 0; |
1309 |
> |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1310 |
> |
|
1311 |
> |
if(mol2proc[i] == worldRank ){ |
1312 |
> |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1313 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
1314 |
> |
the_molecules[molIndex].setGlobalIndex( i ); |
1315 |
> |
molIndex++; |
1316 |
> |
} |
1317 |
|
} |
1318 |
< |
} |
1230 |
< |
|
1318 |
> |
|
1319 |
|
#else // is_mpi |
1320 |
< |
|
1321 |
< |
molIndex = 0; |
1322 |
< |
globalAtomIndex = 0; |
1323 |
< |
for(i=0; i<n_components; i++){ |
1324 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
1325 |
< |
the_molecules[molIndex].setStampID( i ); |
1326 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
1327 |
< |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1328 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1329 |
< |
info->molMembershipArray[globalAtomIndex] = molIndex; |
1330 |
< |
globalAtomIndex++; |
1320 |
> |
|
1321 |
> |
molIndex = 0; |
1322 |
> |
globalAtomIndex = 0; |
1323 |
> |
for(i=0; i<n_components; i++){ |
1324 |
> |
for(j=0; j<components_nmol[i]; j++ ){ |
1325 |
> |
the_molecules[molIndex].setStampID( i ); |
1326 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
1327 |
> |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1328 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1329 |
> |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1330 |
> |
globalAtomIndex++; |
1331 |
> |
} |
1332 |
> |
molIndex++; |
1333 |
|
} |
1244 |
– |
molIndex++; |
1334 |
|
} |
1246 |
– |
} |
1335 |
|
|
1336 |
< |
|
1336 |
> |
|
1337 |
|
#endif // is_mpi |
1338 |
|
|
1339 |
|
|
1340 |
< |
if( info->n_SRI ){ |
1340 |
> |
if( info[l].n_SRI ){ |
1341 |
|
|
1342 |
< |
Exclude::createArray(info->n_SRI); |
1343 |
< |
the_excludes = new Exclude*[info->n_SRI]; |
1344 |
< |
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1345 |
< |
info->globalExcludes = new int; |
1346 |
< |
info->n_exclude = info->n_SRI; |
1347 |
< |
} |
1348 |
< |
else{ |
1342 |
> |
Exclude::createArray(info[l].n_SRI); |
1343 |
> |
the_excludes = new Exclude*[info[l].n_SRI]; |
1344 |
> |
for( int ex=0; ex<info[l].n_SRI; ex++){ |
1345 |
> |
the_excludes[ex] = new Exclude(ex); |
1346 |
> |
} |
1347 |
> |
info[l].globalExcludes = new int; |
1348 |
> |
info[l].n_exclude = info[l].n_SRI; |
1349 |
> |
} |
1350 |
> |
else{ |
1351 |
|
|
1352 |
< |
Exclude::createArray( 1 ); |
1353 |
< |
the_excludes = new Exclude*; |
1354 |
< |
the_excludes[0] = new Exclude(0); |
1355 |
< |
the_excludes[0]->setPair( 0,0 ); |
1356 |
< |
info->globalExcludes = new int; |
1357 |
< |
info->globalExcludes[0] = 0; |
1358 |
< |
info->n_exclude = 0; |
1359 |
< |
} |
1352 |
> |
Exclude::createArray( 1 ); |
1353 |
> |
the_excludes = new Exclude*; |
1354 |
> |
the_excludes[0] = new Exclude(0); |
1355 |
> |
the_excludes[0]->setPair( 0,0 ); |
1356 |
> |
info[l].globalExcludes = new int; |
1357 |
> |
info[l].globalExcludes[0] = 0; |
1358 |
> |
info[l].n_exclude = 0; |
1359 |
> |
} |
1360 |
|
|
1361 |
< |
// set the arrays into the SimInfo object |
1361 |
> |
// set the arrays into the SimInfo object |
1362 |
|
|
1363 |
< |
info->atoms = the_atoms; |
1364 |
< |
info->molecules = the_molecules; |
1365 |
< |
info->nGlobalExcludes = 0; |
1366 |
< |
info->excludes = the_excludes; |
1363 |
> |
info[l].atoms = the_atoms; |
1364 |
> |
info[l].molecules = the_molecules; |
1365 |
> |
info[l].nGlobalExcludes = 0; |
1366 |
> |
info[l].excludes = the_excludes; |
1367 |
|
|
1368 |
< |
the_ff->setSimInfo( info ); |
1369 |
< |
|
1368 |
> |
the_ff->setSimInfo( info ); |
1369 |
> |
|
1370 |
> |
} |
1371 |
|
} |
1372 |
|
|
1373 |
|
void SimSetup::makeIntegrator( void ){ |
1374 |
|
|
1375 |
< |
NVT* myNVT = NULL; |
1285 |
< |
NPTi* myNPTi = NULL; |
1286 |
< |
NPTf* myNPTf = NULL; |
1287 |
< |
NPTim* myNPTim = NULL; |
1288 |
< |
NPTfm* myNPTfm = NULL; |
1375 |
> |
int k; |
1376 |
|
|
1377 |
< |
switch( ensembleCase ){ |
1377 |
> |
NVT<RealIntegrator>* myNVT = NULL; |
1378 |
> |
NPTi<RealIntegrator>* myNPTi = NULL; |
1379 |
> |
NPTf<RealIntegrator>* myNPTf = NULL; |
1380 |
> |
NPTim<RealIntegrator>* myNPTim = NULL; |
1381 |
> |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1382 |
> |
|
1383 |
> |
for(k=0; k<nInfo; k++){ |
1384 |
> |
|
1385 |
> |
switch( ensembleCase ){ |
1386 |
> |
|
1387 |
> |
case NVE_ENS: |
1388 |
> |
if (globals->haveZconstraints()){ |
1389 |
> |
setupZConstraint(info[k]); |
1390 |
> |
new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1391 |
> |
} |
1392 |
|
|
1393 |
< |
case NVE_ENS: |
1394 |
< |
new NVE( info, the_ff ); |
1395 |
< |
break; |
1396 |
< |
|
1397 |
< |
case NVT_ENS: |
1398 |
< |
myNVT = new NVT( info, the_ff ); |
1399 |
< |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1400 |
< |
|
1401 |
< |
if (globals->haveTauThermostat()) |
1402 |
< |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1403 |
< |
|
1303 |
< |
else { |
1304 |
< |
sprintf( painCave.errMsg, |
1305 |
< |
"SimSetup error: If you use the NVT\n" |
1306 |
< |
" ensemble, you must set tauThermostat.\n"); |
1307 |
< |
painCave.isFatal = 1; |
1308 |
< |
simError(); |
1309 |
< |
} |
1310 |
< |
break; |
1393 |
> |
else |
1394 |
> |
new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1395 |
> |
break; |
1396 |
> |
|
1397 |
> |
case NVT_ENS: |
1398 |
> |
if (globals->haveZconstraints()){ |
1399 |
> |
setupZConstraint(info[k]); |
1400 |
> |
myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1401 |
> |
} |
1402 |
> |
else |
1403 |
> |
myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1404 |
|
|
1405 |
< |
case NPTi_ENS: |
1406 |
< |
myNPTi = new NPTi( info, the_ff ); |
1407 |
< |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1405 |
> |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1406 |
> |
|
1407 |
> |
if (globals->haveTauThermostat()) |
1408 |
> |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1409 |
> |
|
1410 |
> |
else { |
1411 |
> |
sprintf( painCave.errMsg, |
1412 |
> |
"SimSetup error: If you use the NVT\n" |
1413 |
> |
" ensemble, you must set tauThermostat.\n"); |
1414 |
> |
painCave.isFatal = 1; |
1415 |
> |
simError(); |
1416 |
> |
} |
1417 |
> |
break; |
1418 |
> |
|
1419 |
> |
case NPTi_ENS: |
1420 |
> |
if (globals->haveZconstraints()){ |
1421 |
> |
setupZConstraint(info[k]); |
1422 |
> |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1423 |
> |
} |
1424 |
> |
else |
1425 |
> |
myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1426 |
|
|
1427 |
< |
if (globals->haveTargetPressure()) |
1428 |
< |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1429 |
< |
else { |
1430 |
< |
sprintf( painCave.errMsg, |
1431 |
< |
"SimSetup error: If you use a constant pressure\n" |
1432 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1433 |
< |
painCave.isFatal = 1; |
1434 |
< |
simError(); |
1435 |
< |
} |
1436 |
< |
|
1437 |
< |
if( globals->haveTauThermostat() ) |
1438 |
< |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1439 |
< |
else{ |
1440 |
< |
sprintf( painCave.errMsg, |
1441 |
< |
"SimSetup error: If you use an NPT\n" |
1442 |
< |
" ensemble, you must set tauThermostat.\n"); |
1443 |
< |
painCave.isFatal = 1; |
1444 |
< |
simError(); |
1445 |
< |
} |
1427 |
> |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1428 |
> |
|
1429 |
> |
if (globals->haveTargetPressure()) |
1430 |
> |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1431 |
> |
else { |
1432 |
> |
sprintf( painCave.errMsg, |
1433 |
> |
"SimSetup error: If you use a constant pressure\n" |
1434 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1435 |
> |
painCave.isFatal = 1; |
1436 |
> |
simError(); |
1437 |
> |
} |
1438 |
> |
|
1439 |
> |
if( globals->haveTauThermostat() ) |
1440 |
> |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1441 |
> |
else{ |
1442 |
> |
sprintf( painCave.errMsg, |
1443 |
> |
"SimSetup error: If you use an NPT\n" |
1444 |
> |
" ensemble, you must set tauThermostat.\n"); |
1445 |
> |
painCave.isFatal = 1; |
1446 |
> |
simError(); |
1447 |
> |
} |
1448 |
> |
|
1449 |
> |
if( globals->haveTauBarostat() ) |
1450 |
> |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1451 |
> |
else{ |
1452 |
> |
sprintf( painCave.errMsg, |
1453 |
> |
"SimSetup error: If you use an NPT\n" |
1454 |
> |
" ensemble, you must set tauBarostat.\n"); |
1455 |
> |
painCave.isFatal = 1; |
1456 |
> |
simError(); |
1457 |
> |
} |
1458 |
> |
break; |
1459 |
> |
|
1460 |
> |
case NPTf_ENS: |
1461 |
> |
if (globals->haveZconstraints()){ |
1462 |
> |
setupZConstraint(info[k]); |
1463 |
> |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1464 |
> |
} |
1465 |
> |
else |
1466 |
> |
myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1467 |
|
|
1468 |
< |
if( globals->haveTauBarostat() ) |
1469 |
< |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1470 |
< |
else{ |
1471 |
< |
sprintf( painCave.errMsg, |
1472 |
< |
"SimSetup error: If you use an NPT\n" |
1473 |
< |
" ensemble, you must set tauBarostat.\n"); |
1474 |
< |
painCave.isFatal = 1; |
1475 |
< |
simError(); |
1476 |
< |
} |
1477 |
< |
break; |
1468 |
> |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1469 |
> |
|
1470 |
> |
if (globals->haveTargetPressure()) |
1471 |
> |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1472 |
> |
else { |
1473 |
> |
sprintf( painCave.errMsg, |
1474 |
> |
"SimSetup error: If you use a constant pressure\n" |
1475 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1476 |
> |
painCave.isFatal = 1; |
1477 |
> |
simError(); |
1478 |
> |
} |
1479 |
> |
|
1480 |
> |
if( globals->haveTauThermostat() ) |
1481 |
> |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1482 |
> |
else{ |
1483 |
> |
sprintf( painCave.errMsg, |
1484 |
> |
"SimSetup error: If you use an NPT\n" |
1485 |
> |
" ensemble, you must set tauThermostat.\n"); |
1486 |
> |
painCave.isFatal = 1; |
1487 |
> |
simError(); |
1488 |
> |
} |
1489 |
> |
|
1490 |
> |
if( globals->haveTauBarostat() ) |
1491 |
> |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1492 |
> |
else{ |
1493 |
> |
sprintf( painCave.errMsg, |
1494 |
> |
"SimSetup error: If you use an NPT\n" |
1495 |
> |
" ensemble, you must set tauBarostat.\n"); |
1496 |
> |
painCave.isFatal = 1; |
1497 |
> |
simError(); |
1498 |
> |
} |
1499 |
> |
break; |
1500 |
> |
|
1501 |
> |
case NPTim_ENS: |
1502 |
> |
if (globals->haveZconstraints()){ |
1503 |
> |
setupZConstraint(info[k]); |
1504 |
> |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1505 |
> |
} |
1506 |
> |
else |
1507 |
> |
myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1508 |
|
|
1509 |
< |
case NPTf_ENS: |
1510 |
< |
myNPTf = new NPTf( info, the_ff ); |
1511 |
< |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1509 |
> |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1510 |
> |
|
1511 |
> |
if (globals->haveTargetPressure()) |
1512 |
> |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1513 |
> |
else { |
1514 |
> |
sprintf( painCave.errMsg, |
1515 |
> |
"SimSetup error: If you use a constant pressure\n" |
1516 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1517 |
> |
painCave.isFatal = 1; |
1518 |
> |
simError(); |
1519 |
> |
} |
1520 |
> |
|
1521 |
> |
if( globals->haveTauThermostat() ) |
1522 |
> |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1523 |
> |
else{ |
1524 |
> |
sprintf( painCave.errMsg, |
1525 |
> |
"SimSetup error: If you use an NPT\n" |
1526 |
> |
" ensemble, you must set tauThermostat.\n"); |
1527 |
> |
painCave.isFatal = 1; |
1528 |
> |
simError(); |
1529 |
> |
} |
1530 |
> |
|
1531 |
> |
if( globals->haveTauBarostat() ) |
1532 |
> |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1533 |
> |
else{ |
1534 |
> |
sprintf( painCave.errMsg, |
1535 |
> |
"SimSetup error: If you use an NPT\n" |
1536 |
> |
" ensemble, you must set tauBarostat.\n"); |
1537 |
> |
painCave.isFatal = 1; |
1538 |
> |
simError(); |
1539 |
> |
} |
1540 |
> |
break; |
1541 |
> |
|
1542 |
> |
case NPTfm_ENS: |
1543 |
> |
if (globals->haveZconstraints()){ |
1544 |
> |
setupZConstraint(info[k]); |
1545 |
> |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1546 |
> |
} |
1547 |
> |
else |
1548 |
> |
myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1549 |
|
|
1550 |
< |
if (globals->haveTargetPressure()) |
1352 |
< |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1353 |
< |
else { |
1354 |
< |
sprintf( painCave.errMsg, |
1355 |
< |
"SimSetup error: If you use a constant pressure\n" |
1356 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1357 |
< |
painCave.isFatal = 1; |
1358 |
< |
simError(); |
1359 |
< |
} |
1550 |
> |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1551 |
|
|
1552 |
< |
if( globals->haveTauThermostat() ) |
1553 |
< |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1554 |
< |
else{ |
1555 |
< |
sprintf( painCave.errMsg, |
1556 |
< |
"SimSetup error: If you use an NPT\n" |
1557 |
< |
" ensemble, you must set tauThermostat.\n"); |
1558 |
< |
painCave.isFatal = 1; |
1559 |
< |
simError(); |
1560 |
< |
} |
1552 |
> |
if (globals->haveTargetPressure()) |
1553 |
> |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1554 |
> |
else { |
1555 |
> |
sprintf( painCave.errMsg, |
1556 |
> |
"SimSetup error: If you use a constant pressure\n" |
1557 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1558 |
> |
painCave.isFatal = 1; |
1559 |
> |
simError(); |
1560 |
> |
} |
1561 |
|
|
1562 |
< |
if( globals->haveTauBarostat() ) |
1563 |
< |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1564 |
< |
else{ |
1565 |
< |
sprintf( painCave.errMsg, |
1566 |
< |
"SimSetup error: If you use an NPT\n" |
1567 |
< |
" ensemble, you must set tauBarostat.\n"); |
1568 |
< |
painCave.isFatal = 1; |
1569 |
< |
simError(); |
1570 |
< |
} |
1380 |
< |
break; |
1381 |
< |
|
1382 |
< |
case NPTim_ENS: |
1383 |
< |
myNPTim = new NPTim( info, the_ff ); |
1384 |
< |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1562 |
> |
if( globals->haveTauThermostat() ) |
1563 |
> |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1564 |
> |
else{ |
1565 |
> |
sprintf( painCave.errMsg, |
1566 |
> |
"SimSetup error: If you use an NPT\n" |
1567 |
> |
" ensemble, you must set tauThermostat.\n"); |
1568 |
> |
painCave.isFatal = 1; |
1569 |
> |
simError(); |
1570 |
> |
} |
1571 |
|
|
1572 |
< |
if (globals->haveTargetPressure()) |
1573 |
< |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1574 |
< |
else { |
1572 |
> |
if( globals->haveTauBarostat() ) |
1573 |
> |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1574 |
> |
else{ |
1575 |
> |
sprintf( painCave.errMsg, |
1576 |
> |
"SimSetup error: If you use an NPT\n" |
1577 |
> |
" ensemble, you must set tauBarostat.\n"); |
1578 |
> |
painCave.isFatal = 1; |
1579 |
> |
simError(); |
1580 |
> |
} |
1581 |
> |
break; |
1582 |
> |
|
1583 |
> |
default: |
1584 |
|
sprintf( painCave.errMsg, |
1585 |
< |
"SimSetup error: If you use a constant pressure\n" |
1391 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1585 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1586 |
|
painCave.isFatal = 1; |
1587 |
|
simError(); |
1588 |
|
} |
1395 |
– |
|
1396 |
– |
if( globals->haveTauThermostat() ) |
1397 |
– |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1398 |
– |
else{ |
1399 |
– |
sprintf( painCave.errMsg, |
1400 |
– |
"SimSetup error: If you use an NPT\n" |
1401 |
– |
" ensemble, you must set tauThermostat.\n"); |
1402 |
– |
painCave.isFatal = 1; |
1403 |
– |
simError(); |
1404 |
– |
} |
1405 |
– |
|
1406 |
– |
if( globals->haveTauBarostat() ) |
1407 |
– |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1408 |
– |
else{ |
1409 |
– |
sprintf( painCave.errMsg, |
1410 |
– |
"SimSetup error: If you use an NPT\n" |
1411 |
– |
" ensemble, you must set tauBarostat.\n"); |
1412 |
– |
painCave.isFatal = 1; |
1413 |
– |
simError(); |
1414 |
– |
} |
1415 |
– |
break; |
1416 |
– |
|
1417 |
– |
case NPTfm_ENS: |
1418 |
– |
myNPTfm = new NPTfm( info, the_ff ); |
1419 |
– |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1420 |
– |
|
1421 |
– |
if (globals->haveTargetPressure()) |
1422 |
– |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1423 |
– |
else { |
1424 |
– |
sprintf( painCave.errMsg, |
1425 |
– |
"SimSetup error: If you use a constant pressure\n" |
1426 |
– |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1427 |
– |
painCave.isFatal = 1; |
1428 |
– |
simError(); |
1429 |
– |
} |
1430 |
– |
|
1431 |
– |
if( globals->haveTauThermostat() ) |
1432 |
– |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1433 |
– |
else{ |
1434 |
– |
sprintf( painCave.errMsg, |
1435 |
– |
"SimSetup error: If you use an NPT\n" |
1436 |
– |
" ensemble, you must set tauThermostat.\n"); |
1437 |
– |
painCave.isFatal = 1; |
1438 |
– |
simError(); |
1439 |
– |
} |
1440 |
– |
|
1441 |
– |
if( globals->haveTauBarostat() ) |
1442 |
– |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1443 |
– |
else{ |
1444 |
– |
sprintf( painCave.errMsg, |
1445 |
– |
"SimSetup error: If you use an NPT\n" |
1446 |
– |
" ensemble, you must set tauBarostat.\n"); |
1447 |
– |
painCave.isFatal = 1; |
1448 |
– |
simError(); |
1449 |
– |
} |
1450 |
– |
break; |
1451 |
– |
|
1452 |
– |
default: |
1453 |
– |
sprintf( painCave.errMsg, |
1454 |
– |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1455 |
– |
painCave.isFatal = 1; |
1456 |
– |
simError(); |
1589 |
|
} |
1458 |
– |
|
1590 |
|
} |
1591 |
|
|
1592 |
|
void SimSetup::initFortran( void ){ |
1593 |
|
|
1594 |
< |
info->refreshSim(); |
1594 |
> |
info[0].refreshSim(); |
1595 |
|
|
1596 |
< |
if( !strcmp( info->mixingRule, "standard") ){ |
1596 |
> |
if( !strcmp( info[0].mixingRule, "standard") ){ |
1597 |
|
the_ff->initForceField( LB_MIXING_RULE ); |
1598 |
|
} |
1599 |
< |
else if( !strcmp( info->mixingRule, "explicit") ){ |
1599 |
> |
else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1600 |
|
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1601 |
|
} |
1602 |
|
else{ |
1603 |
|
sprintf( painCave.errMsg, |
1604 |
< |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1605 |
< |
info->mixingRule ); |
1604 |
> |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1605 |
> |
info[0].mixingRule ); |
1606 |
|
painCave.isFatal = 1; |
1607 |
|
simError(); |
1608 |
|
} |
1610 |
|
|
1611 |
|
#ifdef IS_MPI |
1612 |
|
strcpy( checkPointMsg, |
1613 |
< |
"Successfully intialized the mixingRule for Fortran." ); |
1613 |
> |
"Successfully intialized the mixingRule for Fortran." ); |
1614 |
|
MPIcheckPoint(); |
1615 |
|
#endif // is_mpi |
1616 |
|
|
1617 |
|
} |
1618 |
+ |
|
1619 |
+ |
void SimSetup::setupZConstraint(SimInfo& theInfo) |
1620 |
+ |
{ |
1621 |
+ |
int nZConstraints; |
1622 |
+ |
ZconStamp** zconStamp; |
1623 |
+ |
|
1624 |
+ |
if(globals->haveZconstraintTime()){ |
1625 |
+ |
|
1626 |
+ |
//add sample time of z-constraint into SimInfo's property list |
1627 |
+ |
DoubleData* zconsTimeProp = new DoubleData(); |
1628 |
+ |
zconsTimeProp->setID(ZCONSTIME_ID); |
1629 |
+ |
zconsTimeProp->setData(globals->getZconsTime()); |
1630 |
+ |
theInfo.addProperty(zconsTimeProp); |
1631 |
+ |
} |
1632 |
+ |
else{ |
1633 |
+ |
sprintf( painCave.errMsg, |
1634 |
+ |
"ZConstraint error: If you use an ZConstraint\n" |
1635 |
+ |
" , you must set sample time.\n"); |
1636 |
+ |
painCave.isFatal = 1; |
1637 |
+ |
simError(); |
1638 |
+ |
} |
1639 |
+ |
|
1640 |
+ |
//push zconsTol into siminfo, if user does not specify |
1641 |
+ |
//value for zconsTol, a default value will be used |
1642 |
+ |
DoubleData* zconsTol = new DoubleData(); |
1643 |
+ |
zconsTol->setID(ZCONSTOL_ID); |
1644 |
+ |
if(globals->haveZconsTol()){ |
1645 |
+ |
zconsTol->setData(globals->getZconsTol()); |
1646 |
+ |
} |
1647 |
+ |
else{ |
1648 |
+ |
double defaultZConsTol = 0.01; |
1649 |
+ |
sprintf( painCave.errMsg, |
1650 |
+ |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1651 |
+ |
" , default value %f is used.\n", defaultZConsTol); |
1652 |
+ |
painCave.isFatal = 0; |
1653 |
+ |
simError(); |
1654 |
+ |
|
1655 |
+ |
zconsTol->setData(defaultZConsTol); |
1656 |
+ |
} |
1657 |
+ |
theInfo.addProperty(zconsTol); |
1658 |
+ |
|
1659 |
+ |
//set Force Substraction Policy |
1660 |
+ |
StringData* zconsForcePolicy = new StringData(); |
1661 |
+ |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1662 |
+ |
|
1663 |
+ |
if(globals->haveZconsForcePolicy()){ |
1664 |
+ |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1665 |
+ |
} |
1666 |
+ |
else{ |
1667 |
+ |
sprintf( painCave.errMsg, |
1668 |
+ |
"ZConstraint Warning: User does not set force substraction policy, " |
1669 |
+ |
"average force substraction policy is used\n"); |
1670 |
+ |
painCave.isFatal = 0; |
1671 |
+ |
simError(); |
1672 |
+ |
zconsForcePolicy->setData("BYNUMBER"); |
1673 |
+ |
} |
1674 |
+ |
|
1675 |
+ |
theInfo.addProperty(zconsForcePolicy); |
1676 |
+ |
|
1677 |
+ |
//Determine the name of ouput file and add it into SimInfo's property list |
1678 |
+ |
//Be careful, do not use inFileName, since it is a pointer which |
1679 |
+ |
//point to a string at master node, and slave nodes do not contain that string |
1680 |
+ |
|
1681 |
+ |
string zconsOutput(theInfo.finalName); |
1682 |
+ |
|
1683 |
+ |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1684 |
+ |
|
1685 |
+ |
StringData* zconsFilename = new StringData(); |
1686 |
+ |
zconsFilename->setID(ZCONSFILENAME_ID); |
1687 |
+ |
zconsFilename->setData(zconsOutput); |
1688 |
+ |
|
1689 |
+ |
theInfo.addProperty(zconsFilename); |
1690 |
+ |
|
1691 |
+ |
//setup index, pos and other parameters of z-constraint molecules |
1692 |
+ |
nZConstraints = globals->getNzConstraints(); |
1693 |
+ |
theInfo.nZconstraints = nZConstraints; |
1694 |
+ |
|
1695 |
+ |
zconStamp = globals->getZconStamp(); |
1696 |
+ |
ZConsParaItem tempParaItem; |
1697 |
+ |
|
1698 |
+ |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1699 |
+ |
zconsParaData->setID(ZCONSPARADATA_ID); |
1700 |
+ |
|
1701 |
+ |
for(int i = 0; i < nZConstraints; i++){ |
1702 |
+ |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1703 |
+ |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1704 |
+ |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1705 |
+ |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1706 |
+ |
|
1707 |
+ |
zconsParaData->addItem(tempParaItem); |
1708 |
+ |
} |
1709 |
+ |
|
1710 |
+ |
//sort the parameters by index of molecules |
1711 |
+ |
zconsParaData->sortByIndex(); |
1712 |
+ |
|
1713 |
+ |
//push data into siminfo, therefore, we can retrieve later |
1714 |
+ |
theInfo.addProperty(zconsParaData); |
1715 |
+ |
|
1716 |
+ |
} |