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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 "SimSetup.hpp" |
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#include "parse_me.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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#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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#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(); |
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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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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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// 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++){ |
168 |
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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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|
172 |
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molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
173 |
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molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
174 |
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molInfo.nBends = comp_stamps[stampID]->getNBends(); |
175 |
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molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
176 |
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molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
172 |
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atomOffset = 0; |
173 |
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excludeOffset = 0; |
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for(i=0; i<info[k].n_mol; i++){ |
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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]; |
179 |
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molInfo.myExcludes = &the_excludes[excludeOffset]; |
180 |
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molInfo.myBonds = new Bond*[molInfo.nBonds]; |
181 |
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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(); |
179 |
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molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
180 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
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> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
182 |
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molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
183 |
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|
184 |
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molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
185 |
> |
molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
186 |
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molInfo.myBonds = new Bond*[molInfo.nBonds]; |
187 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
188 |
> |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
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|
190 |
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theBonds = new bond_pair[molInfo.nBonds]; |
191 |
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theBends = new bend_set[molInfo.nBends]; |
192 |
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theTorsions = new torsion_set[molInfo.nTorsions]; |
190 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
191 |
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theBends = new bend_set[molInfo.nBends]; |
192 |
> |
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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|
196 |
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for(j=0; j<molInfo.nAtoms; j++){ |
172 |
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|
173 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
174 |
< |
if( currentAtom->haveOrientation() ){ |
196 |
> |
for(j=0; j<molInfo.nAtoms; j++){ |
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|
198 |
< |
dAtom = new DirectionalAtom(j + atomOffset); |
199 |
< |
info->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 |
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|
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 |
< |
} |
220 |
< |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
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() ); |
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|
227 |
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#ifdef IS_MPI |
228 |
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|
229 |
< |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
229 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
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|
231 |
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#endif // is_mpi |
232 |
< |
} |
232 |
> |
} |
233 |
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|
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// make the bonds |
235 |
< |
for(j=0; j<molInfo.nBonds; j++){ |
235 |
> |
for(j=0; j<molInfo.nBonds; j++){ |
236 |
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|
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 |
< |
} |
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 = the_atoms[tempEx]->getGlobalIndex() + 1; |
253 |
< |
tempEx = exJ; |
254 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
255 |
< |
|
256 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
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 |
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#else // isn't MPI |
258 |
< |
|
259 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
258 |
> |
|
259 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
260 |
|
#endif //is_mpi |
261 |
< |
} |
262 |
< |
excludeOffset += molInfo.nBonds; |
236 |
< |
|
237 |
< |
//make the bends |
238 |
< |
for(j=0; j<molInfo.nBends; j++){ |
261 |
> |
} |
262 |
> |
excludeOffset += molInfo.nBonds; |
263 |
|
|
264 |
< |
currentBend = comp_stamps[stampID]->getBend( j ); |
265 |
< |
theBends[j].a = currentBend->getA() + atomOffset; |
266 |
< |
theBends[j].b = currentBend->getB() + atomOffset; |
267 |
< |
theBends[j].c = currentBend->getC() + atomOffset; |
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 |
< |
if( currentBend->haveExtras() ){ |
275 |
< |
|
276 |
< |
extras = currentBend->getExtras(); |
277 |
< |
current_extra = extras; |
278 |
< |
|
250 |
< |
while( current_extra != NULL ){ |
251 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
252 |
< |
|
253 |
< |
switch( current_extra->getType() ){ |
274 |
> |
extras = currentBend->getExtras(); |
275 |
> |
current_extra = extras; |
276 |
> |
|
277 |
> |
while( current_extra != NULL ){ |
278 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
279 |
|
|
280 |
< |
case 0: |
281 |
< |
theBends[j].ghost = |
282 |
< |
current_extra->getInt() + atomOffset; |
283 |
< |
theBends[j].isGhost = 1; |
284 |
< |
break; |
285 |
< |
|
286 |
< |
case 1: |
287 |
< |
theBends[j].ghost = |
288 |
< |
(int)current_extra->getDouble() + atomOffset; |
289 |
< |
theBends[j].isGhost = 1; |
290 |
< |
break; |
291 |
< |
|
292 |
< |
default: |
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: ghostVectorSource was neither a " |
309 |
< |
"double nor an int.\n" |
310 |
< |
"-->Bend[%d] in %s\n", |
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 |
|
} |
276 |
– |
} |
277 |
– |
|
278 |
– |
else{ |
315 |
|
|
316 |
< |
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(); |
316 |
> |
current_extra = current_extra->getNext(); |
317 |
|
} |
318 |
+ |
} |
319 |
+ |
|
320 |
+ |
if( !theBends[j].isGhost ){ |
321 |
|
|
322 |
< |
current_extra = current_extra->getNext(); |
322 |
> |
exI = theBends[j].a; |
323 |
> |
exJ = theBends[j].c; |
324 |
|
} |
325 |
< |
} |
325 |
> |
else{ |
326 |
|
|
327 |
< |
if( !theBends[j].isGhost ){ |
328 |
< |
|
329 |
< |
exI = theBends[j].a; |
296 |
< |
exJ = theBends[j].c; |
297 |
< |
} |
298 |
< |
else{ |
327 |
> |
exI = theBends[j].a; |
328 |
> |
exJ = theBends[j].b; |
329 |
> |
} |
330 |
|
|
331 |
< |
exI = theBends[j].a; |
332 |
< |
exJ = theBends[j].b; |
333 |
< |
} |
334 |
< |
|
335 |
< |
// exclude_I must always be the smaller of the pair |
336 |
< |
if( exI > exJ ){ |
306 |
< |
tempEx = exI; |
307 |
< |
exI = exJ; |
308 |
< |
exJ = tempEx; |
309 |
< |
} |
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 = the_atoms[tempEx]->getGlobalIndex() + 1; |
340 |
< |
tempEx = exJ; |
341 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
338 |
> |
tempEx = exI; |
339 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
340 |
> |
tempEx = exJ; |
341 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
342 |
|
|
343 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
343 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
344 |
|
#else // isn't MPI |
345 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
345 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
346 |
|
#endif //is_mpi |
320 |
– |
} |
321 |
– |
excludeOffset += molInfo.nBends; |
322 |
– |
|
323 |
– |
for(j=0; j<molInfo.nTorsions; j++){ |
324 |
– |
|
325 |
– |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
326 |
– |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
327 |
– |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
328 |
– |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
329 |
– |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
330 |
– |
|
331 |
– |
exI = theTorsions[j].a; |
332 |
– |
exJ = theTorsions[j].d; |
333 |
– |
|
334 |
– |
// exclude_I must always be the smaller of the pair |
335 |
– |
if( exI > exJ ){ |
336 |
– |
tempEx = exI; |
337 |
– |
exI = exJ; |
338 |
– |
exJ = tempEx; |
347 |
|
} |
348 |
< |
#ifdef IS_MPI |
341 |
< |
tempEx = exI; |
342 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
343 |
< |
tempEx = exJ; |
344 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
348 |
> |
excludeOffset += molInfo.nBends; |
349 |
|
|
350 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
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 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
375 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
376 |
|
#endif //is_mpi |
377 |
< |
} |
378 |
< |
excludeOffset += molInfo.nTorsions; |
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 |
< |
// send the arrays off to the forceField for init. |
393 |
< |
|
394 |
< |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
395 |
< |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
396 |
< |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
359 |
< |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
360 |
< |
|
361 |
< |
|
362 |
< |
the_molecules[i].initialize( molInfo ); |
363 |
< |
|
364 |
< |
|
365 |
< |
atomOffset += molInfo.nAtoms; |
366 |
< |
delete[] theBonds; |
367 |
< |
delete[] theBends; |
368 |
< |
delete[] theTorsions; |
391 |
> |
|
392 |
> |
atomOffset += molInfo.nAtoms; |
393 |
> |
delete[] theBonds; |
394 |
> |
delete[] theBends; |
395 |
> |
delete[] theTorsions; |
396 |
> |
} |
397 |
|
} |
398 |
< |
|
398 |
> |
|
399 |
|
#ifdef IS_MPI |
400 |
|
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
401 |
|
MPIcheckPoint(); |
402 |
|
#endif // is_mpi |
403 |
< |
|
403 |
> |
|
404 |
|
// clean up the forcefield |
405 |
+ |
|
406 |
|
the_ff->calcRcut(); |
407 |
|
the_ff->cleanMe(); |
408 |
< |
|
408 |
> |
|
409 |
|
} |
410 |
|
|
411 |
|
void SimSetup::initFromBass( void ){ |
418 |
|
int n_extra; |
419 |
|
int have_extra, done; |
420 |
|
|
421 |
+ |
double vel[3]; |
422 |
+ |
vel[0] = 0.0; |
423 |
+ |
vel[1] = 0.0; |
424 |
+ |
vel[2] = 0.0; |
425 |
+ |
|
426 |
|
temp1 = (double)tot_nmol / 4.0; |
427 |
|
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
428 |
|
temp3 = ceil( temp2 ); |
432 |
|
have_extra =1; |
433 |
|
|
434 |
|
n_cells = (int)temp3 - 1; |
435 |
< |
cellx = info->boxL[0] / temp3; |
436 |
< |
celly = info->boxL[1] / temp3; |
437 |
< |
cellz = info->boxL[2] / temp3; |
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 ); |
449 |
|
} |
450 |
|
else{ |
451 |
|
n_cells = (int)temp3; |
452 |
< |
cellx = info->boxL[0] / temp3; |
453 |
< |
celly = info->boxL[1] / temp3; |
454 |
< |
cellz = info->boxL[2] / 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 |
|
current_mol = 0; |
530 |
|
} |
531 |
|
} |
532 |
|
|
533 |
< |
|
534 |
< |
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 ); |
533 |
> |
for( i=0; i<info[0].n_atoms; i++ ){ |
534 |
> |
info[0].atoms[i]->setVel( vel ); |
535 |
|
} |
536 |
|
} |
537 |
|
|
541 |
|
AtomStamp* current_atom; |
542 |
|
DirectionalAtom* dAtom; |
543 |
|
double rotMat[3][3]; |
544 |
+ |
double pos[3]; |
545 |
|
|
546 |
|
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
547 |
|
|
557 |
|
painCave.isFatal = 1; |
558 |
|
simError(); |
559 |
|
} |
560 |
+ |
|
561 |
+ |
pos[0] = x + current_atom->getPosX(); |
562 |
+ |
pos[1] = y + current_atom->getPosY(); |
563 |
+ |
pos[2] = z + current_atom->getPosZ(); |
564 |
+ |
|
565 |
+ |
info[0].atoms[current_atom_ndx]->setPos( pos ); |
566 |
|
|
567 |
< |
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() ); |
567 |
> |
if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
568 |
|
|
569 |
< |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
569 |
> |
dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
570 |
|
|
535 |
– |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
536 |
– |
|
571 |
|
rotMat[0][0] = 1.0; |
572 |
|
rotMat[0][1] = 0.0; |
573 |
|
rotMat[0][2] = 0.0; |
603 |
|
ensembleCase = -1; |
604 |
|
ffCase = -1; |
605 |
|
|
572 |
– |
// get the stamps and globals; |
573 |
– |
stamps = stamps; |
574 |
– |
globals = globals; |
575 |
– |
|
606 |
|
// set the easy ones first |
607 |
< |
info->target_temp = globals->getTargetTemp(); |
608 |
< |
info->dt = globals->getDt(); |
609 |
< |
info->run_time = globals->getRunTime(); |
607 |
> |
|
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 |
|
n_components = globals->getNComponents(); |
614 |
|
|
615 |
|
|
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", |
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 |
+ |
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, " |
658 |
|
strcpy( ensemble, "NVE" ); |
659 |
|
ensembleCase = NVE_ENS; |
660 |
|
} |
661 |
< |
strcpy( info->ensemble, ensemble ); |
661 |
> |
|
662 |
> |
for(i=0; i<nInfo; i++){ |
663 |
> |
|
664 |
> |
strcpy( info[i].ensemble, ensemble ); |
665 |
|
|
666 |
< |
// get the mixing rule |
666 |
> |
// get the mixing rule |
667 |
|
|
668 |
< |
strcpy( info->mixingRule, globals->getMixingRule() ); |
669 |
< |
info->usePBC = globals->getPBC(); |
670 |
< |
|
668 |
> |
strcpy( info[i].mixingRule, globals->getMixingRule() ); |
669 |
> |
info[i].usePBC = globals->getPBC(); |
670 |
> |
} |
671 |
|
|
672 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
673 |
|
|
708 |
|
|
709 |
|
// set the status, sample, and thermal kick times |
710 |
|
|
711 |
< |
if( globals->haveSampleTime() ){ |
666 |
< |
info->sampleTime = globals->getSampleTime(); |
667 |
< |
info->statusTime = info->sampleTime; |
668 |
< |
info->thermalTime = info->sampleTime; |
669 |
< |
} |
670 |
< |
else{ |
671 |
< |
info->sampleTime = globals->getRunTime(); |
672 |
< |
info->statusTime = info->sampleTime; |
673 |
< |
info->thermalTime = info->sampleTime; |
674 |
< |
} |
711 |
> |
for(i=0; i<nInfo; i++){ |
712 |
|
|
713 |
< |
if( globals->haveStatusTime() ){ |
714 |
< |
info->statusTime = globals->getStatusTime(); |
715 |
< |
} |
716 |
< |
|
717 |
< |
if( globals->haveThermalTime() ){ |
718 |
< |
info->thermalTime = globals->getThermalTime(); |
719 |
< |
} |
720 |
< |
|
721 |
< |
// check for the temperature set flag |
722 |
< |
|
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(); |
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 |
> |
info[i].sampleTime = globals->getRunTime(); |
720 |
> |
info[i].statusTime = info[i].sampleTime; |
721 |
> |
info[i].thermalTime = info[i].sampleTime; |
722 |
> |
} |
723 |
|
|
724 |
< |
info->setBox( boxVector ); |
725 |
< |
} |
698 |
< |
else if( globals->haveDensity() ){ |
699 |
< |
|
700 |
< |
double vol; |
701 |
< |
vol = (double)tot_nmol / globals->getDensity(); |
702 |
< |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
703 |
< |
boxVector[1] = boxVector[0]; |
704 |
< |
boxVector[2] = boxVector[0]; |
705 |
< |
|
706 |
< |
info->setBox( boxVector ); |
707 |
< |
} |
708 |
< |
else{ |
709 |
< |
if( !globals->haveBoxX() ){ |
710 |
< |
sprintf( painCave.errMsg, |
711 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
712 |
< |
painCave.isFatal = 1; |
713 |
< |
simError(); |
724 |
> |
if( globals->haveStatusTime() ){ |
725 |
> |
info[i].statusTime = globals->getStatusTime(); |
726 |
|
} |
727 |
< |
boxVector[0] = globals->getBoxX(); |
728 |
< |
|
729 |
< |
if( !globals->haveBoxY() ){ |
718 |
< |
sprintf( painCave.errMsg, |
719 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
720 |
< |
painCave.isFatal = 1; |
721 |
< |
simError(); |
727 |
> |
|
728 |
> |
if( globals->haveThermalTime() ){ |
729 |
> |
info[i].thermalTime = globals->getThermalTime(); |
730 |
|
} |
723 |
– |
boxVector[1] = globals->getBoxY(); |
731 |
|
|
732 |
< |
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 |
> |
// check for the temperature set flag |
733 |
|
|
734 |
< |
info->setBox( boxVector ); |
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 |
+ |
if( !globals->haveBoxX() ){ |
758 |
+ |
sprintf( painCave.errMsg, |
759 |
+ |
"SimSetup error, no periodic BoxX size given.\n" ); |
760 |
+ |
painCave.isFatal = 1; |
761 |
+ |
simError(); |
762 |
+ |
} |
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 |
+ |
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 |
+ |
boxVector[2] = globals->getBoxZ(); |
780 |
+ |
|
781 |
+ |
info[i].setBox( boxVector ); |
782 |
+ |
} |
783 |
|
|
784 |
< |
|
784 |
> |
} |
785 |
|
|
786 |
|
#ifdef IS_MPI |
787 |
|
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
794 |
|
void SimSetup::finalInfoCheck( void ){ |
795 |
|
int index; |
796 |
|
int usesDipoles; |
797 |
< |
|
797 |
> |
int i; |
798 |
|
|
799 |
< |
// check electrostatic parameters |
800 |
< |
|
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; |
799 |
> |
for(i=0; i<nInfo; i++){ |
800 |
> |
// check electrostatic parameters |
801 |
|
|
802 |
< |
if( !globals->haveECR() ){ |
803 |
< |
sprintf( painCave.errMsg, |
804 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
805 |
< |
"box length for the electrostaticCutoffRadius.\n" |
806 |
< |
"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(); |
802 |
> |
index = 0; |
803 |
> |
usesDipoles = 0; |
804 |
> |
while( (index < info[i].n_atoms) && !usesDipoles ){ |
805 |
> |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
806 |
> |
index++; |
807 |
|
} |
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 ); |
808 |
|
|
809 |
< |
if(!globals->haveDielectric() ){ |
810 |
< |
sprintf( painCave.errMsg, |
811 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
812 |
< |
"setting a dielectric constant!\n" |
813 |
< |
); |
814 |
< |
painCave.isFatal = 1; |
815 |
< |
simError(); |
816 |
< |
} |
817 |
< |
info->dielectric = globals->getDielectric(); |
809 |
< |
} |
810 |
< |
else { |
811 |
< |
if (usesDipoles) { |
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, |
824 |
|
painCave.isFatal = 0; |
825 |
|
simError(); |
826 |
|
double smallest; |
827 |
< |
smallest = info->boxL[0]; |
828 |
< |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
829 |
< |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
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(); |
835 |
|
if( !globals->haveEST() ){ |
836 |
|
sprintf( painCave.errMsg, |
837 |
|
"SimSetup Warning: using default value of 0.05 * the " |
838 |
< |
"electrostaticCutoffRadius for the " |
833 |
< |
"electrostaticSkinThickness\n" |
838 |
> |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
839 |
|
); |
840 |
|
painCave.isFatal = 0; |
841 |
|
simError(); |
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 |
|
|
842 |
– |
info->setEcr( theEcr, theEst ); |
843 |
– |
} |
844 |
– |
} |
845 |
– |
|
896 |
|
#ifdef IS_MPI |
897 |
|
strcpy( checkPointMsg, "post processing checks out" ); |
898 |
|
MPIcheckPoint(); |
901 |
|
} |
902 |
|
|
903 |
|
void SimSetup::initSystemCoords( void ){ |
904 |
+ |
int i; |
905 |
+ |
|
906 |
+ |
std::cerr << "Setting atom Coords\n"; |
907 |
|
|
908 |
< |
if( globals->haveInitialConfig() ){ |
909 |
< |
|
910 |
< |
InitializeFromFile* fileInit; |
908 |
> |
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
909 |
> |
|
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 ){ |
916 |
> |
if( worldRank == 0 ){ |
917 |
|
#endif //is_mpi |
918 |
< |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
918 |
> |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
919 |
|
#ifdef IS_MPI |
920 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
920 |
> |
}else fileInit = new InitializeFromFile( NULL ); |
921 |
|
#endif |
922 |
< |
fileInit->readInit( info ); // default velocities on |
923 |
< |
|
924 |
< |
delete fileInit; |
925 |
< |
} |
926 |
< |
else{ |
927 |
< |
|
922 |
> |
fileInit->readInit( info ); // default velocities on |
923 |
> |
|
924 |
> |
delete fileInit; |
925 |
> |
} |
926 |
> |
else{ |
927 |
> |
|
928 |
|
#ifdef IS_MPI |
929 |
< |
|
930 |
< |
// no init from bass |
931 |
< |
|
932 |
< |
sprintf( painCave.errMsg, |
933 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
934 |
< |
painCave.isFatal; |
935 |
< |
simError(); |
936 |
< |
|
929 |
> |
|
930 |
> |
// no init from bass |
931 |
> |
|
932 |
> |
sprintf( painCave.errMsg, |
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 |
< |
|
938 |
> |
|
939 |
> |
initFromBass(); |
940 |
> |
|
941 |
> |
|
942 |
|
#endif |
943 |
< |
} |
944 |
< |
|
943 |
> |
} |
944 |
> |
|
945 |
|
#ifdef IS_MPI |
946 |
|
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
947 |
|
MPIcheckPoint(); |
948 |
|
#endif // is_mpi |
949 |
< |
|
949 |
> |
|
950 |
|
} |
951 |
|
|
952 |
|
|
953 |
|
void SimSetup::makeOutNames( void ){ |
954 |
+ |
|
955 |
+ |
int k; |
956 |
|
|
957 |
+ |
|
958 |
+ |
for(k=0; k<nInfo; k++){ |
959 |
+ |
|
960 |
|
#ifdef IS_MPI |
961 |
< |
if( worldRank == 0 ){ |
961 |
> |
if( worldRank == 0 ){ |
962 |
|
#endif // is_mpi |
963 |
< |
|
964 |
< |
if( globals->haveFinalConfig() ){ |
965 |
< |
strcpy( info->finalName, globals->getFinalConfig() ); |
904 |
< |
} |
905 |
< |
else{ |
906 |
< |
strcpy( info->finalName, inFileName ); |
907 |
< |
char* endTest; |
908 |
< |
int nameLength = strlen( info->finalName ); |
909 |
< |
endTest = &(info->finalName[nameLength - 5]); |
910 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
911 |
< |
strcpy( endTest, ".eor" ); |
963 |
> |
|
964 |
> |
if( globals->haveFinalConfig() ){ |
965 |
> |
strcpy( info[k].finalName, globals->getFinalConfig() ); |
966 |
|
} |
913 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
914 |
– |
strcpy( endTest, ".eor" ); |
915 |
– |
} |
967 |
|
else{ |
968 |
< |
endTest = &(info->finalName[nameLength - 4]); |
969 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
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, ".mdl" ) ){ |
975 |
> |
else if( !strcmp( endTest, ".BASS" ) ){ |
976 |
|
strcpy( endTest, ".eor" ); |
977 |
|
} |
978 |
|
else{ |
979 |
< |
strcat( info->finalName, ".eor" ); |
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 |
|
} |
991 |
< |
} |
992 |
< |
|
993 |
< |
// make the sample and status out names |
994 |
< |
|
995 |
< |
strcpy( info->sampleName, inFileName ); |
996 |
< |
char* endTest; |
997 |
< |
int nameLength = strlen( info->sampleName ); |
998 |
< |
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" ) ){ |
991 |
> |
|
992 |
> |
// make the sample and status out names |
993 |
> |
|
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 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
1001 |
> |
else if( !strcmp( endTest, ".BASS" ) ){ |
1002 |
|
strcpy( endTest, ".dump" ); |
1003 |
|
} |
1004 |
|
else{ |
1005 |
< |
strcat( info->sampleName, ".dump" ); |
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 |
< |
|
1018 |
< |
strcpy( info->statusName, inFileName ); |
1019 |
< |
nameLength = strlen( info->statusName ); |
1020 |
< |
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" ) ){ |
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, ".mdl" ) ){ |
1023 |
> |
else if( !strcmp( endTest, ".BASS" ) ){ |
1024 |
|
strcpy( endTest, ".stat" ); |
1025 |
|
} |
1026 |
|
else{ |
1027 |
< |
strcat( info->statusName, ".stat" ); |
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 |
< |
} |
976 |
< |
|
1038 |
> |
|
1039 |
|
#ifdef IS_MPI |
1040 |
< |
} |
1040 |
> |
} |
1041 |
|
#endif // is_mpi |
1042 |
< |
|
1042 |
> |
} |
1043 |
|
} |
1044 |
|
|
1045 |
|
|
1046 |
|
void SimSetup::sysObjectsCreation( void ){ |
1047 |
< |
|
1048 |
< |
int i; |
1049 |
< |
|
1047 |
> |
|
1048 |
> |
int i,k; |
1049 |
> |
|
1050 |
|
// create the forceField |
1051 |
< |
|
1051 |
> |
|
1052 |
|
createFF(); |
1053 |
|
|
1054 |
|
// extract componentList |
1072 |
|
// make and initialize the molecules (all but atomic coordinates) |
1073 |
|
|
1074 |
|
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 |
– |
} |
1075 |
|
|
1076 |
< |
|
1077 |
< |
|
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 |
> |
} |
1082 |
|
} |
1083 |
|
|
1084 |
|
|
1094 |
|
the_ff = new LJFF(); |
1095 |
|
break; |
1096 |
|
|
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"); |
1116 |
|
void SimSetup::compList( void ){ |
1117 |
|
|
1118 |
|
int i; |
1119 |
< |
|
1119 |
> |
char* id; |
1120 |
> |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1121 |
> |
LinkedMolStamp* currentStamp = NULL; |
1122 |
|
comp_stamps = new MoleculeStamp*[n_components]; |
1123 |
< |
|
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 |
1058 |
– |
|
1059 |
– |
info->nComponents = n_components; |
1060 |
– |
info->componentsNmol = components_nmol; |
1061 |
– |
info->compStamps = comp_stamps; |
1062 |
– |
info->headStamp = new LinkedMolStamp(); |
1126 |
|
|
1127 |
< |
char* id; |
1128 |
< |
LinkedMolStamp* headStamp = info->headStamp; |
1129 |
< |
LinkedMolStamp* currentStamp = NULL; |
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 |
> |
|
1134 |
> |
|
1135 |
|
for( i=0; i<n_components; i++ ){ |
1136 |
|
|
1137 |
|
id = the_components[i]->getType(); |
1169 |
|
|
1170 |
|
void SimSetup::calcSysValues( void ){ |
1171 |
|
int i, j, k; |
1172 |
< |
|
1173 |
< |
|
1172 |
> |
|
1173 |
> |
int *molMembershipArray; |
1174 |
> |
|
1175 |
|
tot_atoms = 0; |
1176 |
|
tot_bonds = 0; |
1177 |
|
tot_bends = 0; |
1183 |
|
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1184 |
|
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1185 |
|
} |
1186 |
< |
|
1186 |
> |
|
1187 |
|
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1188 |
< |
|
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; |
1188 |
> |
molMembershipArray = new int[tot_atoms]; |
1189 |
|
|
1190 |
< |
info->molMembershipArray = new int[tot_atoms]; |
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 |
|
|
1130 |
– |
|
1202 |
|
#ifdef IS_MPI |
1203 |
|
|
1204 |
|
void SimSetup::mpiMolDivide( void ){ |
1238 |
|
localMol++; |
1239 |
|
} |
1240 |
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1241 |
< |
info->molMembershipArray[globalAtomIndex] = allMol; |
1241 |
> |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1242 |
|
globalAtomIndex++; |
1243 |
|
} |
1244 |
|
|
1247 |
|
} |
1248 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
1249 |
|
|
1250 |
< |
info->n_atoms = mpiSim->getMyNlocal(); |
1250 |
> |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1251 |
|
|
1252 |
< |
if( local_atoms != info->n_atoms ){ |
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->n_atoms, |
1256 |
> |
info[0].n_atoms, |
1257 |
|
local_atoms ); |
1258 |
|
painCave.isFatal = 1; |
1259 |
|
simError(); |
1260 |
|
} |
1261 |
|
|
1262 |
< |
info->n_bonds = local_bonds; |
1263 |
< |
info->n_bends = local_bends; |
1264 |
< |
info->n_torsions = local_torsions; |
1265 |
< |
info->n_SRI = local_SRI; |
1266 |
< |
info->n_mol = localMol; |
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 |
|
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1269 |
|
MPIcheckPoint(); |
1270 |
|
} |
1271 |
< |
|
1271 |
> |
|
1272 |
|
#endif // is_mpi |
1273 |
|
|
1274 |
|
|
1275 |
|
void SimSetup::makeSysArrays( void ){ |
1276 |
< |
int i, j, k; |
1276 |
> |
int i, j, k, l; |
1277 |
|
|
1278 |
+ |
Atom** the_atoms; |
1279 |
+ |
Molecule* the_molecules; |
1280 |
+ |
Exclude** the_excludes; |
1281 |
|
|
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 |
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 |
< |
molIndex = 0; |
1221 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1291 |
> |
// initialize the molecule's stampID's |
1292 |
|
|
1293 |
< |
if(mol2proc[i] == worldRank ){ |
1294 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1295 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
1296 |
< |
the_molecules[molIndex].setGlobalIndex( i ); |
1297 |
< |
molIndex++; |
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 |
< |
} |
1230 |
< |
|
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->molMembershipArray[globalAtomIndex] = molIndex; |
1318 |
< |
globalAtomIndex++; |
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 |
|
} |
1244 |
– |
molIndex++; |
1322 |
|
} |
1246 |
– |
} |
1323 |
|
|
1324 |
< |
|
1324 |
> |
|
1325 |
|
#endif // is_mpi |
1326 |
|
|
1327 |
|
|
1328 |
< |
if( info->n_SRI ){ |
1328 |
> |
if( info[l].n_SRI ){ |
1329 |
|
|
1330 |
< |
Exclude::createArray(info->n_SRI); |
1331 |
< |
the_excludes = new Exclude*[info->n_SRI]; |
1332 |
< |
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1333 |
< |
info->globalExcludes = new int; |
1334 |
< |
info->n_exclude = info->n_SRI; |
1335 |
< |
} |
1336 |
< |
else{ |
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->globalExcludes = new int; |
1345 |
< |
info->globalExcludes[0] = 0; |
1346 |
< |
info->n_exclude = 0; |
1347 |
< |
} |
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 |
< |
// set the arrays into the SimInfo object |
1349 |
> |
// set the arrays into the SimInfo object |
1350 |
|
|
1351 |
< |
info->atoms = the_atoms; |
1352 |
< |
info->molecules = the_molecules; |
1353 |
< |
info->nGlobalExcludes = 0; |
1354 |
< |
info->excludes = the_excludes; |
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 |
< |
the_ff->setSimInfo( info ); |
1357 |
< |
|
1356 |
> |
the_ff->setSimInfo( info ); |
1357 |
> |
|
1358 |
> |
} |
1359 |
|
} |
1360 |
|
|
1361 |
|
void SimSetup::makeIntegrator( void ){ |
1362 |
|
|
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 |
< |
|
1371 |
< |
switch( ensembleCase ){ |
1372 |
< |
|
1373 |
< |
case NVE_ENS: |
1374 |
< |
new NVE<RealIntegrator>( info, the_ff ); |
1375 |
< |
break; |
1376 |
< |
|
1377 |
< |
case NVT_ENS: |
1297 |
< |
myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1298 |
< |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1299 |
< |
|
1300 |
< |
if (globals->haveTauThermostat()) |
1301 |
< |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1302 |
< |
|
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; |
1311 |
< |
|
1312 |
< |
case NPTi_ENS: |
1313 |
< |
myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1314 |
< |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1315 |
< |
|
1316 |
< |
if (globals->haveTargetPressure()) |
1317 |
< |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1318 |
< |
else { |
1319 |
< |
sprintf( painCave.errMsg, |
1320 |
< |
"SimSetup error: If you use a constant pressure\n" |
1321 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1322 |
< |
painCave.isFatal = 1; |
1323 |
< |
simError(); |
1324 |
< |
} |
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 |
< |
if( globals->haveTauThermostat() ) |
1380 |
< |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1381 |
< |
else{ |
1382 |
< |
sprintf( painCave.errMsg, |
1383 |
< |
"SimSetup error: If you use an NPT\n" |
1384 |
< |
" ensemble, you must set tauThermostat.\n"); |
1385 |
< |
painCave.isFatal = 1; |
1386 |
< |
simError(); |
1387 |
< |
} |
1388 |
< |
|
1389 |
< |
if( globals->haveTauBarostat() ) |
1390 |
< |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1391 |
< |
else{ |
1392 |
< |
sprintf( painCave.errMsg, |
1393 |
< |
"SimSetup error: If you use an NPT\n" |
1394 |
< |
" ensemble, you must set tauBarostat.\n"); |
1395 |
< |
painCave.isFatal = 1; |
1396 |
< |
simError(); |
1397 |
< |
} |
1398 |
< |
break; |
1399 |
< |
|
1400 |
< |
case NPTf_ENS: |
1401 |
< |
myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1402 |
< |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1403 |
< |
|
1404 |
< |
if (globals->haveTargetPressure()) |
1405 |
< |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1406 |
< |
else { |
1407 |
< |
sprintf( painCave.errMsg, |
1408 |
< |
"SimSetup error: If you use a constant pressure\n" |
1409 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1410 |
< |
painCave.isFatal = 1; |
1411 |
< |
simError(); |
1412 |
< |
} |
1413 |
< |
|
1414 |
< |
if( globals->haveTauThermostat() ) |
1415 |
< |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1416 |
< |
else{ |
1417 |
< |
sprintf( painCave.errMsg, |
1418 |
< |
"SimSetup error: If you use an NPT\n" |
1419 |
< |
" ensemble, you must set tauThermostat.\n"); |
1420 |
< |
painCave.isFatal = 1; |
1421 |
< |
simError(); |
1422 |
< |
} |
1423 |
< |
|
1424 |
< |
if( globals->haveTauBarostat() ) |
1425 |
< |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1426 |
< |
else{ |
1427 |
< |
sprintf( painCave.errMsg, |
1428 |
< |
"SimSetup error: If you use an NPT\n" |
1429 |
< |
" ensemble, you must set tauBarostat.\n"); |
1430 |
< |
painCave.isFatal = 1; |
1431 |
< |
simError(); |
1432 |
< |
} |
1433 |
< |
break; |
1434 |
< |
|
1435 |
< |
case NPTim_ENS: |
1436 |
< |
myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1437 |
< |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1438 |
< |
|
1439 |
< |
if (globals->haveTargetPressure()) |
1440 |
< |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1441 |
< |
else { |
1442 |
< |
sprintf( painCave.errMsg, |
1443 |
< |
"SimSetup error: If you use a constant pressure\n" |
1444 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1445 |
< |
painCave.isFatal = 1; |
1446 |
< |
simError(); |
1447 |
< |
} |
1448 |
< |
|
1449 |
< |
if( globals->haveTauThermostat() ) |
1450 |
< |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1451 |
< |
else{ |
1452 |
< |
sprintf( painCave.errMsg, |
1453 |
< |
"SimSetup error: If you use an NPT\n" |
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 |
< |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1462 |
< |
else{ |
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, the_ff ); |
1508 |
< |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1509 |
< |
|
1510 |
< |
if (globals->haveTargetPressure()) |
1511 |
< |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1512 |
< |
else { |
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: If you use a constant pressure\n" |
1426 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1732 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1733 |
|
painCave.isFatal = 1; |
1734 |
|
simError(); |
1735 |
|
} |
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(); |
1736 |
|
} |
1458 |
– |
|
1737 |
|
} |
1738 |
|
|
1739 |
|
void SimSetup::initFortran( void ){ |
1740 |
|
|
1741 |
< |
info->refreshSim(); |
1741 |
> |
info[0].refreshSim(); |
1742 |
|
|
1743 |
< |
if( !strcmp( info->mixingRule, "standard") ){ |
1743 |
> |
if( !strcmp( info[0].mixingRule, "standard") ){ |
1744 |
|
the_ff->initForceField( LB_MIXING_RULE ); |
1745 |
|
} |
1746 |
< |
else if( !strcmp( info->mixingRule, "explicit") ){ |
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->mixingRule ); |
1752 |
> |
info[0].mixingRule ); |
1753 |
|
painCave.isFatal = 1; |
1754 |
|
simError(); |
1755 |
|
} |
1762 |
|
#endif // is_mpi |
1763 |
|
|
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 |
+ |
} |