12 |
|
#include "mpiSimulation.hpp" |
13 |
|
#endif |
14 |
|
|
15 |
+ |
// some defines for ensemble and Forcefield cases |
16 |
+ |
|
17 |
+ |
#define NVE_ENS 0 |
18 |
+ |
#define NVT_ENS 1 |
19 |
+ |
#define NPTi_ENS 2 |
20 |
+ |
#define NPTf_ENS 3 |
21 |
+ |
#define NPTim_ENS 4 |
22 |
+ |
#define NPTfm_ENS 5 |
23 |
+ |
|
24 |
+ |
|
25 |
+ |
#define FF_DUFF 0 |
26 |
+ |
#define FF_LJ 1 |
27 |
+ |
|
28 |
+ |
|
29 |
|
SimSetup::SimSetup(){ |
30 |
|
stamps = new MakeStamps(); |
31 |
|
globals = new Globals(); |
78 |
|
|
79 |
|
void SimSetup::createSim( void ){ |
80 |
|
|
81 |
< |
MakeStamps *the_stamps; |
82 |
< |
Globals* the_globals; |
83 |
< |
int i, j; |
81 |
> |
int i, j, k, globalAtomIndex; |
82 |
> |
|
83 |
> |
// gather all of the information from the Bass file |
84 |
> |
|
85 |
> |
gatherInfo(); |
86 |
|
|
87 |
< |
// get the stamps and globals; |
72 |
< |
the_stamps = stamps; |
73 |
< |
the_globals = globals; |
87 |
> |
// creation of complex system objects |
88 |
|
|
89 |
< |
// set the easy ones first |
76 |
< |
simnfo->target_temp = the_globals->getTargetTemp(); |
77 |
< |
simnfo->dt = the_globals->getDt(); |
78 |
< |
simnfo->run_time = the_globals->getRunTime(); |
89 |
> |
sysObjectsCreation(); |
90 |
|
|
91 |
< |
// get the ones we know are there, yet still may need some work. |
92 |
< |
n_components = the_globals->getNComponents(); |
93 |
< |
strcpy( force_field, the_globals->getForceField() ); |
83 |
< |
strcpy( ensemble, the_globals->getEnsemble() ); |
84 |
< |
strcpy( simnfo->ensemble, ensemble ); |
91 |
> |
// check on the post processing info |
92 |
> |
|
93 |
> |
finalInfoCheck(); |
94 |
|
|
95 |
< |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
87 |
< |
simnfo->usePBC = the_globals->getPBC(); |
88 |
< |
|
95 |
> |
// initialize the system coordinates |
96 |
|
|
97 |
+ |
initSystemCoords(); |
98 |
+ |
|
99 |
|
|
100 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
92 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
93 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
94 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
95 |
< |
else{ |
96 |
< |
sprintf( painCave.errMsg, |
97 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
98 |
< |
force_field ); |
99 |
< |
painCave.isFatal = 1; |
100 |
< |
simError(); |
101 |
< |
} |
100 |
> |
// make the output filenames |
101 |
|
|
102 |
+ |
makeOutNames(); |
103 |
+ |
|
104 |
+ |
// make the integrator |
105 |
+ |
|
106 |
+ |
makeIntegrator(); |
107 |
+ |
|
108 |
|
#ifdef IS_MPI |
109 |
< |
strcpy( checkPointMsg, "ForceField creation successful" ); |
110 |
< |
MPIcheckPoint(); |
106 |
< |
#endif // is_mpi |
109 |
> |
mpiSim->mpiRefresh(); |
110 |
> |
#endif |
111 |
|
|
112 |
< |
|
112 |
> |
// initialize the Fortran |
113 |
|
|
114 |
< |
// get the components and calculate the tot_nMol and indvidual n_mol |
111 |
< |
the_components = the_globals->getComponents(); |
112 |
< |
components_nmol = new int[n_components]; |
113 |
< |
comp_stamps = new MoleculeStamp*[n_components]; |
114 |
> |
initFortran(); |
115 |
|
|
115 |
– |
if( !the_globals->haveNMol() ){ |
116 |
– |
// we don't have the total number of molecules, so we assume it is |
117 |
– |
// given in each component |
116 |
|
|
119 |
– |
tot_nmol = 0; |
120 |
– |
for( i=0; i<n_components; i++ ){ |
117 |
|
|
118 |
< |
if( !the_components[i]->haveNMol() ){ |
123 |
< |
// we have a problem |
124 |
< |
sprintf( painCave.errMsg, |
125 |
< |
"SimSetup Error. No global NMol or component NMol" |
126 |
< |
" given. Cannot calculate the number of atoms.\n" ); |
127 |
< |
painCave.isFatal = 1; |
128 |
< |
simError(); |
129 |
< |
} |
118 |
> |
} |
119 |
|
|
131 |
– |
tot_nmol += the_components[i]->getNMol(); |
132 |
– |
components_nmol[i] = the_components[i]->getNMol(); |
133 |
– |
} |
134 |
– |
} |
135 |
– |
else{ |
136 |
– |
sprintf( painCave.errMsg, |
137 |
– |
"SimSetup error.\n" |
138 |
– |
"\tSorry, the ability to specify total" |
139 |
– |
" nMols and then give molfractions in the components\n" |
140 |
– |
"\tis not currently supported." |
141 |
– |
" Please give nMol in the components.\n" ); |
142 |
– |
painCave.isFatal = 1; |
143 |
– |
simError(); |
144 |
– |
|
145 |
– |
|
146 |
– |
// tot_nmol = the_globals->getNMol(); |
147 |
– |
|
148 |
– |
// //we have the total number of molecules, now we check for molfractions |
149 |
– |
// for( i=0; i<n_components; i++ ){ |
150 |
– |
|
151 |
– |
// if( !the_components[i]->haveMolFraction() ){ |
152 |
– |
|
153 |
– |
// if( !the_components[i]->haveNMol() ){ |
154 |
– |
// //we have a problem |
155 |
– |
// std::cerr << "SimSetup error. Neither molFraction nor " |
156 |
– |
// << " nMol was given in component |
157 |
– |
|
158 |
– |
} |
120 |
|
|
121 |
< |
#ifdef IS_MPI |
161 |
< |
strcpy( checkPointMsg, "Have the number of components" ); |
162 |
< |
MPIcheckPoint(); |
163 |
< |
#endif // is_mpi |
121 |
> |
void SimSetup::makeMolecules( void ){ |
122 |
|
|
123 |
< |
// make an array of molecule stamps that match the components used. |
124 |
< |
// also extract the used stamps out into a separate linked list |
123 |
> |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
124 |
> |
molInit molInfo; |
125 |
> |
DirectionalAtom* dAtom; |
126 |
> |
LinkedAssign* extras; |
127 |
> |
LinkedAssign* current_extra; |
128 |
> |
AtomStamp* currentAtom; |
129 |
> |
BondStamp* currentBond; |
130 |
> |
BendStamp* currentBend; |
131 |
> |
TorsionStamp* currentTorsion; |
132 |
|
|
133 |
< |
simnfo->nComponents = n_components; |
134 |
< |
simnfo->componentsNmol = components_nmol; |
135 |
< |
simnfo->compStamps = comp_stamps; |
136 |
< |
simnfo->headStamp = new LinkedMolStamp(); |
133 |
> |
bond_pair* theBonds; |
134 |
> |
bend_set* theBends; |
135 |
> |
torsion_set* theTorsions; |
136 |
> |
|
137 |
|
|
138 |
< |
char* id; |
174 |
< |
LinkedMolStamp* headStamp = simnfo->headStamp; |
175 |
< |
LinkedMolStamp* currentStamp = NULL; |
176 |
< |
for( i=0; i<n_components; i++ ){ |
138 |
> |
//init the forceField paramters |
139 |
|
|
140 |
< |
id = the_components[i]->getType(); |
179 |
< |
comp_stamps[i] = NULL; |
180 |
< |
|
181 |
< |
// check to make sure the component isn't already in the list |
140 |
> |
the_ff->readParams(); |
141 |
|
|
142 |
< |
comp_stamps[i] = headStamp->match( id ); |
143 |
< |
if( comp_stamps[i] == NULL ){ |
185 |
< |
|
186 |
< |
// extract the component from the list; |
187 |
< |
|
188 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
189 |
< |
if( currentStamp == NULL ){ |
190 |
< |
sprintf( painCave.errMsg, |
191 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
192 |
< |
"list of declared molecules\n", |
193 |
< |
id ); |
194 |
< |
painCave.isFatal = 1; |
195 |
< |
simError(); |
196 |
< |
} |
197 |
< |
|
198 |
< |
headStamp->add( currentStamp ); |
199 |
< |
comp_stamps[i] = headStamp->match( id ); |
200 |
< |
} |
201 |
< |
} |
142 |
> |
|
143 |
> |
// init the atoms |
144 |
|
|
145 |
< |
#ifdef IS_MPI |
204 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
205 |
< |
MPIcheckPoint(); |
206 |
< |
#endif // is_mpi |
145 |
> |
double ux, uy, uz, u, uSqr; |
146 |
|
|
147 |
+ |
atomOffset = 0; |
148 |
+ |
excludeOffset = 0; |
149 |
+ |
for(i=0; i<info->n_mol; i++){ |
150 |
+ |
|
151 |
+ |
stampID = the_molecules[i].getStampID(); |
152 |
|
|
153 |
+ |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
154 |
+ |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
155 |
+ |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
156 |
+ |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
157 |
+ |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
158 |
|
|
159 |
+ |
molInfo.myAtoms = &the_atoms[atomOffset]; |
160 |
+ |
molInfo.myExcludes = &the_excludes[excludeOffset]; |
161 |
+ |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
162 |
+ |
molInfo.myBends = new Bend*[molInfo.nBends]; |
163 |
+ |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
164 |
|
|
165 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
166 |
< |
|
167 |
< |
tot_atoms = 0; |
214 |
< |
tot_bonds = 0; |
215 |
< |
tot_bends = 0; |
216 |
< |
tot_torsions = 0; |
217 |
< |
for( i=0; i<n_components; i++ ){ |
165 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
166 |
> |
theBends = new bend_set[molInfo.nBends]; |
167 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
168 |
|
|
169 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
170 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
171 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
172 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
173 |
< |
} |
169 |
> |
// make the Atoms |
170 |
> |
|
171 |
> |
for(j=0; j<molInfo.nAtoms; j++){ |
172 |
> |
|
173 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
174 |
> |
if( currentAtom->haveOrientation() ){ |
175 |
> |
|
176 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
177 |
> |
info->n_oriented++; |
178 |
> |
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() ); |
199 |
> |
|
200 |
> |
#ifdef IS_MPI |
201 |
> |
|
202 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
203 |
> |
|
204 |
> |
#endif // is_mpi |
205 |
> |
} |
206 |
> |
|
207 |
> |
// make the bonds |
208 |
> |
for(j=0; j<molInfo.nBonds; j++){ |
209 |
> |
|
210 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
211 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
212 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
213 |
|
|
214 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
214 |
> |
exI = theBonds[j].a; |
215 |
> |
exJ = theBonds[j].b; |
216 |
|
|
217 |
< |
simnfo->n_atoms = tot_atoms; |
218 |
< |
simnfo->n_bonds = tot_bonds; |
219 |
< |
simnfo->n_bends = tot_bends; |
220 |
< |
simnfo->n_torsions = tot_torsions; |
221 |
< |
simnfo->n_SRI = tot_SRI; |
222 |
< |
simnfo->n_mol = tot_nmol; |
233 |
< |
|
234 |
< |
|
217 |
> |
// exclude_I must always be the smaller of the pair |
218 |
> |
if( exI > exJ ){ |
219 |
> |
tempEx = exI; |
220 |
> |
exI = exJ; |
221 |
> |
exJ = tempEx; |
222 |
> |
} |
223 |
|
#ifdef IS_MPI |
224 |
+ |
tempEx = exI; |
225 |
+ |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
226 |
+ |
tempEx = exJ; |
227 |
+ |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
228 |
+ |
|
229 |
+ |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
230 |
+ |
#else // isn't MPI |
231 |
|
|
232 |
< |
// divide the molecules among processors here. |
233 |
< |
|
234 |
< |
mpiSim = new mpiSimulation( simnfo ); |
235 |
< |
|
241 |
< |
|
232 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
233 |
> |
#endif //is_mpi |
234 |
> |
} |
235 |
> |
excludeOffset += molInfo.nBonds; |
236 |
|
|
237 |
< |
globalIndex = mpiSim->divideLabor(); |
238 |
< |
|
245 |
< |
|
246 |
< |
|
247 |
< |
// set up the local variables |
248 |
< |
|
249 |
< |
int localMol, allMol; |
250 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
251 |
< |
|
252 |
< |
allMol = 0; |
253 |
< |
localMol = 0; |
254 |
< |
local_atoms = 0; |
255 |
< |
local_bonds = 0; |
256 |
< |
local_bends = 0; |
257 |
< |
local_torsions = 0; |
258 |
< |
for( i=0; i<n_components; i++ ){ |
259 |
< |
|
260 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
237 |
> |
//make the bends |
238 |
> |
for(j=0; j<molInfo.nBends; j++){ |
239 |
|
|
240 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
241 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
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 |
> |
} |
291 |
> |
} |
292 |
> |
|
293 |
> |
if( !theBends[j].isGhost ){ |
294 |
> |
|
295 |
> |
exI = theBends[j].a; |
296 |
> |
exJ = theBends[j].c; |
297 |
> |
} |
298 |
> |
else{ |
299 |
|
|
300 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
301 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
302 |
< |
local_bends += comp_stamps[i]->getNBends(); |
303 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
304 |
< |
localMol++; |
305 |
< |
} |
306 |
< |
allMol++; |
300 |
> |
exI = theBends[j].a; |
301 |
> |
exJ = theBends[j].b; |
302 |
> |
} |
303 |
> |
|
304 |
> |
// exclude_I must always be the smaller of the pair |
305 |
> |
if( exI > exJ ){ |
306 |
> |
tempEx = exI; |
307 |
> |
exI = exJ; |
308 |
> |
exJ = tempEx; |
309 |
> |
} |
310 |
> |
#ifdef IS_MPI |
311 |
> |
tempEx = exI; |
312 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
313 |
> |
tempEx = exJ; |
314 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
315 |
> |
|
316 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
317 |
> |
#else // isn't MPI |
318 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
319 |
> |
#endif //is_mpi |
320 |
|
} |
321 |
< |
} |
274 |
< |
local_SRI = local_bonds + local_bends + local_torsions; |
275 |
< |
|
321 |
> |
excludeOffset += molInfo.nBends; |
322 |
|
|
323 |
< |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
324 |
< |
|
325 |
< |
if( local_atoms != simnfo->n_atoms ){ |
326 |
< |
sprintf( painCave.errMsg, |
327 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
328 |
< |
" localAtom (%d) are note equal.\n", |
329 |
< |
simnfo->n_atoms, |
330 |
< |
local_atoms ); |
331 |
< |
painCave.isFatal = 1; |
332 |
< |
simError(); |
287 |
< |
} |
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 |
< |
simnfo->n_bonds = local_bonds; |
335 |
< |
simnfo->n_bends = local_bends; |
336 |
< |
simnfo->n_torsions = local_torsions; |
337 |
< |
simnfo->n_SRI = local_SRI; |
338 |
< |
simnfo->n_mol = localMol; |
334 |
> |
// exclude_I must always be the smaller of the pair |
335 |
> |
if( exI > exJ ){ |
336 |
> |
tempEx = exI; |
337 |
> |
exI = exJ; |
338 |
> |
exJ = tempEx; |
339 |
> |
} |
340 |
> |
#ifdef IS_MPI |
341 |
> |
tempEx = exI; |
342 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
343 |
> |
tempEx = exJ; |
344 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
345 |
> |
|
346 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
347 |
> |
#else // isn't MPI |
348 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
349 |
> |
#endif //is_mpi |
350 |
> |
} |
351 |
> |
excludeOffset += molInfo.nTorsions; |
352 |
|
|
353 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
353 |
> |
|
354 |
> |
// send the arrays off to the forceField for init. |
355 |
> |
|
356 |
> |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
357 |
> |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
358 |
> |
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; |
369 |
> |
} |
370 |
> |
|
371 |
> |
#ifdef IS_MPI |
372 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
373 |
|
MPIcheckPoint(); |
297 |
– |
|
298 |
– |
|
374 |
|
#endif // is_mpi |
300 |
– |
|
375 |
|
|
376 |
< |
// create the atom and short range interaction arrays |
376 |
> |
// clean up the forcefield |
377 |
> |
the_ff->calcRcut(); |
378 |
> |
the_ff->cleanMe(); |
379 |
|
|
380 |
< |
Atom::createArrays(simnfo->n_atoms); |
305 |
< |
the_atoms = new Atom*[simnfo->n_atoms]; |
306 |
< |
the_molecules = new Molecule[simnfo->n_mol]; |
380 |
> |
} |
381 |
|
|
382 |
+ |
void SimSetup::initFromBass( void ){ |
383 |
|
|
384 |
< |
if( simnfo->n_SRI ){ |
385 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
386 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
387 |
< |
simnfo->globalExcludes = new int; |
388 |
< |
simnfo->n_exclude = tot_SRI; |
384 |
> |
int i, j, k; |
385 |
> |
int n_cells; |
386 |
> |
double cellx, celly, cellz; |
387 |
> |
double temp1, temp2, temp3; |
388 |
> |
int n_per_extra; |
389 |
> |
int n_extra; |
390 |
> |
int have_extra, done; |
391 |
> |
|
392 |
> |
temp1 = (double)tot_nmol / 4.0; |
393 |
> |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
394 |
> |
temp3 = ceil( temp2 ); |
395 |
> |
|
396 |
> |
have_extra =0; |
397 |
> |
if( temp2 < temp3 ){ // we have a non-complete lattice |
398 |
> |
have_extra =1; |
399 |
> |
|
400 |
> |
n_cells = (int)temp3 - 1; |
401 |
> |
cellx = info->boxL[0] / temp3; |
402 |
> |
celly = info->boxL[1] / temp3; |
403 |
> |
cellz = info->boxL[2] / temp3; |
404 |
> |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
405 |
> |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
406 |
> |
n_per_extra = (int)ceil( temp1 ); |
407 |
> |
|
408 |
> |
if( n_per_extra > 4){ |
409 |
> |
sprintf( painCave.errMsg, |
410 |
> |
"SimSetup error. There has been an error in constructing" |
411 |
> |
" the non-complete lattice.\n" ); |
412 |
> |
painCave.isFatal = 1; |
413 |
> |
simError(); |
414 |
> |
} |
415 |
|
} |
416 |
|
else{ |
417 |
< |
|
418 |
< |
the_excludes = new int[2]; |
419 |
< |
the_excludes[0] = 0; |
420 |
< |
the_excludes[1] = 0; |
421 |
< |
simnfo->globalExcludes = new int; |
321 |
< |
simnfo->globalExcludes[0] = 0; |
417 |
> |
n_cells = (int)temp3; |
418 |
> |
cellx = info->boxL[0] / temp3; |
419 |
> |
celly = info->boxL[1] / temp3; |
420 |
> |
cellz = info->boxL[2] / temp3; |
421 |
> |
} |
422 |
|
|
423 |
< |
simnfo->n_exclude = 1; |
423 |
> |
current_mol = 0; |
424 |
> |
current_comp_mol = 0; |
425 |
> |
current_comp = 0; |
426 |
> |
current_atom_ndx = 0; |
427 |
> |
|
428 |
> |
for( i=0; i < n_cells ; i++ ){ |
429 |
> |
for( j=0; j < n_cells; j++ ){ |
430 |
> |
for( k=0; k < n_cells; k++ ){ |
431 |
> |
|
432 |
> |
makeElement( i * cellx, |
433 |
> |
j * celly, |
434 |
> |
k * cellz ); |
435 |
> |
|
436 |
> |
makeElement( i * cellx + 0.5 * cellx, |
437 |
> |
j * celly + 0.5 * celly, |
438 |
> |
k * cellz ); |
439 |
> |
|
440 |
> |
makeElement( i * cellx, |
441 |
> |
j * celly + 0.5 * celly, |
442 |
> |
k * cellz + 0.5 * cellz ); |
443 |
> |
|
444 |
> |
makeElement( i * cellx + 0.5 * cellx, |
445 |
> |
j * celly, |
446 |
> |
k * cellz + 0.5 * cellz ); |
447 |
> |
} |
448 |
> |
} |
449 |
|
} |
450 |
|
|
451 |
< |
// set the arrays into the SimInfo object |
451 |
> |
if( have_extra ){ |
452 |
> |
done = 0; |
453 |
|
|
454 |
< |
simnfo->atoms = the_atoms; |
455 |
< |
simnfo->sr_interactions = the_sris; |
456 |
< |
simnfo->nGlobalExcludes = 0; |
331 |
< |
simnfo->excludes = the_excludes; |
454 |
> |
int start_ndx; |
455 |
> |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
456 |
> |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
457 |
|
|
458 |
+ |
if( i < n_cells ){ |
459 |
|
|
460 |
< |
// get some of the tricky things that may still be in the globals |
460 |
> |
if( j < n_cells ){ |
461 |
> |
start_ndx = n_cells; |
462 |
> |
} |
463 |
> |
else start_ndx = 0; |
464 |
> |
} |
465 |
> |
else start_ndx = 0; |
466 |
|
|
467 |
+ |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
468 |
+ |
|
469 |
+ |
makeElement( i * cellx, |
470 |
+ |
j * celly, |
471 |
+ |
k * cellz ); |
472 |
+ |
done = ( current_mol >= tot_nmol ); |
473 |
+ |
|
474 |
+ |
if( !done && n_per_extra > 1 ){ |
475 |
+ |
makeElement( i * cellx + 0.5 * cellx, |
476 |
+ |
j * celly + 0.5 * celly, |
477 |
+ |
k * cellz ); |
478 |
+ |
done = ( current_mol >= tot_nmol ); |
479 |
+ |
} |
480 |
+ |
|
481 |
+ |
if( !done && n_per_extra > 2){ |
482 |
+ |
makeElement( i * cellx, |
483 |
+ |
j * celly + 0.5 * celly, |
484 |
+ |
k * cellz + 0.5 * cellz ); |
485 |
+ |
done = ( current_mol >= tot_nmol ); |
486 |
+ |
} |
487 |
+ |
|
488 |
+ |
if( !done && n_per_extra > 3){ |
489 |
+ |
makeElement( i * cellx + 0.5 * cellx, |
490 |
+ |
j * celly, |
491 |
+ |
k * cellz + 0.5 * cellz ); |
492 |
+ |
done = ( current_mol >= tot_nmol ); |
493 |
+ |
} |
494 |
+ |
} |
495 |
+ |
} |
496 |
+ |
} |
497 |
+ |
} |
498 |
+ |
|
499 |
+ |
|
500 |
+ |
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 ); |
504 |
+ |
} |
505 |
+ |
} |
506 |
+ |
|
507 |
+ |
void SimSetup::makeElement( double x, double y, double z ){ |
508 |
+ |
|
509 |
+ |
int k; |
510 |
+ |
AtomStamp* current_atom; |
511 |
+ |
DirectionalAtom* dAtom; |
512 |
+ |
double rotMat[3][3]; |
513 |
+ |
|
514 |
+ |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
515 |
+ |
|
516 |
+ |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
517 |
+ |
if( !current_atom->havePosition() ){ |
518 |
+ |
sprintf( painCave.errMsg, |
519 |
+ |
"SimSetup:initFromBass error.\n" |
520 |
+ |
"\tComponent %s, atom %s does not have a position specified.\n" |
521 |
+ |
"\tThe initialization routine is unable to give a start" |
522 |
+ |
" position.\n", |
523 |
+ |
comp_stamps[current_comp]->getID(), |
524 |
+ |
current_atom->getType() ); |
525 |
+ |
painCave.isFatal = 1; |
526 |
+ |
simError(); |
527 |
+ |
} |
528 |
+ |
|
529 |
+ |
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() ); |
532 |
+ |
|
533 |
+ |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
534 |
+ |
|
535 |
+ |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
536 |
+ |
|
537 |
+ |
rotMat[0][0] = 1.0; |
538 |
+ |
rotMat[0][1] = 0.0; |
539 |
+ |
rotMat[0][2] = 0.0; |
540 |
+ |
|
541 |
+ |
rotMat[1][0] = 0.0; |
542 |
+ |
rotMat[1][1] = 1.0; |
543 |
+ |
rotMat[1][2] = 0.0; |
544 |
+ |
|
545 |
+ |
rotMat[2][0] = 0.0; |
546 |
+ |
rotMat[2][1] = 0.0; |
547 |
+ |
rotMat[2][2] = 1.0; |
548 |
+ |
|
549 |
+ |
dAtom->setA( rotMat ); |
550 |
+ |
} |
551 |
+ |
|
552 |
+ |
current_atom_ndx++; |
553 |
+ |
} |
554 |
+ |
|
555 |
+ |
current_mol++; |
556 |
+ |
current_comp_mol++; |
557 |
+ |
|
558 |
+ |
if( current_comp_mol >= components_nmol[current_comp] ){ |
559 |
+ |
|
560 |
+ |
current_comp_mol = 0; |
561 |
+ |
current_comp++; |
562 |
+ |
} |
563 |
+ |
} |
564 |
+ |
|
565 |
+ |
|
566 |
+ |
void SimSetup::gatherInfo( void ){ |
567 |
+ |
int i,j,k; |
568 |
+ |
|
569 |
+ |
ensembleCase = -1; |
570 |
+ |
ffCase = -1; |
571 |
+ |
|
572 |
+ |
// get the stamps and globals; |
573 |
+ |
stamps = stamps; |
574 |
+ |
globals = globals; |
575 |
+ |
|
576 |
+ |
// set the easy ones first |
577 |
+ |
info->target_temp = globals->getTargetTemp(); |
578 |
+ |
info->dt = globals->getDt(); |
579 |
+ |
info->run_time = globals->getRunTime(); |
580 |
+ |
n_components = globals->getNComponents(); |
581 |
+ |
|
582 |
+ |
|
583 |
+ |
// get the forceField |
584 |
+ |
|
585 |
+ |
strcpy( force_field, globals->getForceField() ); |
586 |
+ |
|
587 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
588 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
589 |
+ |
else{ |
590 |
+ |
sprintf( painCave.errMsg, |
591 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
592 |
+ |
force_field ); |
593 |
+ |
painCave.isFatal = 1; |
594 |
+ |
simError(); |
595 |
+ |
} |
596 |
+ |
|
597 |
+ |
// get the ensemble |
598 |
+ |
|
599 |
+ |
strcpy( ensemble, globals->getEnsemble() ); |
600 |
+ |
|
601 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
602 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
603 |
+ |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
604 |
+ |
ensembleCase = NPTi_ENS; |
605 |
+ |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
606 |
+ |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
607 |
+ |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
608 |
+ |
else{ |
609 |
+ |
sprintf( painCave.errMsg, |
610 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
611 |
+ |
"reverting to NVE for this simulation.\n", |
612 |
+ |
ensemble ); |
613 |
+ |
painCave.isFatal = 0; |
614 |
+ |
simError(); |
615 |
+ |
strcpy( ensemble, "NVE" ); |
616 |
+ |
ensembleCase = NVE_ENS; |
617 |
+ |
} |
618 |
+ |
strcpy( info->ensemble, ensemble ); |
619 |
+ |
|
620 |
+ |
// get the mixing rule |
621 |
+ |
|
622 |
+ |
strcpy( info->mixingRule, globals->getMixingRule() ); |
623 |
+ |
info->usePBC = globals->getPBC(); |
624 |
+ |
|
625 |
|
|
626 |
< |
if( the_globals->haveBox() ){ |
627 |
< |
simnfo->box_x = the_globals->getBox(); |
628 |
< |
simnfo->box_y = the_globals->getBox(); |
629 |
< |
simnfo->box_z = the_globals->getBox(); |
626 |
> |
// get the components and calculate the tot_nMol and indvidual n_mol |
627 |
> |
|
628 |
> |
the_components = globals->getComponents(); |
629 |
> |
components_nmol = new int[n_components]; |
630 |
> |
|
631 |
> |
|
632 |
> |
if( !globals->haveNMol() ){ |
633 |
> |
// we don't have the total number of molecules, so we assume it is |
634 |
> |
// given in each component |
635 |
> |
|
636 |
> |
tot_nmol = 0; |
637 |
> |
for( i=0; i<n_components; i++ ){ |
638 |
> |
|
639 |
> |
if( !the_components[i]->haveNMol() ){ |
640 |
> |
// we have a problem |
641 |
> |
sprintf( painCave.errMsg, |
642 |
> |
"SimSetup Error. No global NMol or component NMol" |
643 |
> |
" given. Cannot calculate the number of atoms.\n" ); |
644 |
> |
painCave.isFatal = 1; |
645 |
> |
simError(); |
646 |
> |
} |
647 |
> |
|
648 |
> |
tot_nmol += the_components[i]->getNMol(); |
649 |
> |
components_nmol[i] = the_components[i]->getNMol(); |
650 |
> |
} |
651 |
|
} |
652 |
< |
else if( the_globals->haveDensity() ){ |
652 |
> |
else{ |
653 |
> |
sprintf( painCave.errMsg, |
654 |
> |
"SimSetup error.\n" |
655 |
> |
"\tSorry, the ability to specify total" |
656 |
> |
" nMols and then give molfractions in the components\n" |
657 |
> |
"\tis not currently supported." |
658 |
> |
" Please give nMol in the components.\n" ); |
659 |
> |
painCave.isFatal = 1; |
660 |
> |
simError(); |
661 |
> |
} |
662 |
|
|
663 |
+ |
// set the status, sample, and thermal kick times |
664 |
+ |
|
665 |
+ |
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 |
+ |
} |
675 |
+ |
|
676 |
+ |
if( globals->haveStatusTime() ){ |
677 |
+ |
info->statusTime = globals->getStatusTime(); |
678 |
+ |
} |
679 |
+ |
|
680 |
+ |
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(); |
695 |
+ |
|
696 |
+ |
info->setBox( boxVector ); |
697 |
+ |
} |
698 |
+ |
else if( globals->haveDensity() ){ |
699 |
+ |
|
700 |
|
double vol; |
701 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
702 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
703 |
< |
simnfo->box_y = simnfo->box_x; |
704 |
< |
simnfo->box_z = simnfo->box_x; |
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( !the_globals->haveBoxX() ){ |
709 |
> |
if( !globals->haveBoxX() ){ |
710 |
|
sprintf( painCave.errMsg, |
711 |
|
"SimSetup error, no periodic BoxX size given.\n" ); |
712 |
|
painCave.isFatal = 1; |
713 |
|
simError(); |
714 |
|
} |
715 |
< |
simnfo->box_x = the_globals->getBoxX(); |
715 |
> |
boxVector[0] = globals->getBoxX(); |
716 |
|
|
717 |
< |
if( !the_globals->haveBoxY() ){ |
717 |
> |
if( !globals->haveBoxY() ){ |
718 |
|
sprintf( painCave.errMsg, |
719 |
|
"SimSetup error, no periodic BoxY size given.\n" ); |
720 |
|
painCave.isFatal = 1; |
721 |
|
simError(); |
722 |
|
} |
723 |
< |
simnfo->box_y = the_globals->getBoxY(); |
723 |
> |
boxVector[1] = globals->getBoxY(); |
724 |
|
|
725 |
< |
if( !the_globals->haveBoxZ() ){ |
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 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
731 |
> |
boxVector[2] = globals->getBoxZ(); |
732 |
> |
|
733 |
> |
info->setBox( boxVector ); |
734 |
|
} |
735 |
|
|
736 |
+ |
|
737 |
+ |
|
738 |
|
#ifdef IS_MPI |
739 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
739 |
> |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
740 |
|
MPIcheckPoint(); |
741 |
|
#endif // is_mpi |
742 |
|
|
743 |
+ |
} |
744 |
|
|
382 |
– |
// initialize the arrays |
745 |
|
|
746 |
< |
the_ff->setSimInfo( simnfo ); |
746 |
> |
void SimSetup::finalInfoCheck( void ){ |
747 |
> |
int index; |
748 |
> |
int usesDipoles; |
749 |
> |
|
750 |
|
|
751 |
< |
makeAtoms(); |
387 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
388 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
389 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
390 |
< |
} |
751 |
> |
// check electrostatic parameters |
752 |
|
|
753 |
< |
if( tot_bonds ){ |
754 |
< |
makeBonds(); |
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 |
< |
if( tot_bends ){ |
397 |
< |
makeBends(); |
398 |
< |
} |
765 |
> |
double theEcr, theEst; |
766 |
|
|
767 |
< |
if( tot_torsions ){ |
768 |
< |
makeTorsions(); |
769 |
< |
} |
770 |
< |
|
404 |
< |
|
405 |
< |
if (the_globals->getUseRF() ) { |
406 |
< |
simnfo->useReactionField = 1; |
407 |
< |
|
408 |
< |
if( !the_globals->haveECR() ){ |
767 |
> |
if (globals->getUseRF() ) { |
768 |
> |
info->useReactionField = 1; |
769 |
> |
|
770 |
> |
if( !globals->haveECR() ){ |
771 |
|
sprintf( painCave.errMsg, |
772 |
|
"SimSetup Warning: using default value of 1/2 the smallest " |
773 |
|
"box length for the electrostaticCutoffRadius.\n" |
775 |
|
painCave.isFatal = 0; |
776 |
|
simError(); |
777 |
|
double smallest; |
778 |
< |
smallest = simnfo->box_x; |
779 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
780 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
781 |
< |
simnfo->ecr = 0.5 * 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 |
< |
simnfo->ecr = the_globals->getECR(); |
783 |
> |
theEcr = globals->getECR(); |
784 |
|
} |
785 |
|
|
786 |
< |
if( !the_globals->haveEST() ){ |
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 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
793 |
> |
theEst = 0.05 * theEcr; |
794 |
|
} else { |
795 |
< |
simnfo->est = the_globals->getEST(); |
795 |
> |
theEst= globals->getEST(); |
796 |
|
} |
797 |
+ |
|
798 |
+ |
info->setEcr( theEcr, theEst ); |
799 |
|
|
800 |
< |
if(!the_globals->haveDielectric() ){ |
800 |
> |
if(!globals->haveDielectric() ){ |
801 |
|
sprintf( painCave.errMsg, |
802 |
|
"SimSetup Error: You are trying to use Reaction Field without" |
803 |
|
"setting a dielectric constant!\n" |
805 |
|
painCave.isFatal = 1; |
806 |
|
simError(); |
807 |
|
} |
808 |
< |
simnfo->dielectric = the_globals->getDielectric(); |
809 |
< |
} else { |
810 |
< |
if (simnfo->n_dipoles) { |
808 |
> |
info->dielectric = globals->getDielectric(); |
809 |
> |
} |
810 |
> |
else { |
811 |
> |
if (usesDipoles) { |
812 |
|
|
813 |
< |
if( !the_globals->haveECR() ){ |
814 |
< |
sprintf( painCave.errMsg, |
815 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
816 |
< |
"box length for the electrostaticCutoffRadius.\n" |
817 |
< |
"I hope you have a very fast processor!\n"); |
818 |
< |
painCave.isFatal = 0; |
819 |
< |
simError(); |
820 |
< |
double smallest; |
821 |
< |
smallest = simnfo->box_x; |
822 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
823 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
824 |
< |
simnfo->ecr = 0.5 * smallest; |
813 |
> |
if( !globals->haveECR() ){ |
814 |
> |
sprintf( painCave.errMsg, |
815 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
816 |
> |
"box length for the electrostaticCutoffRadius.\n" |
817 |
> |
"I hope you have a very fast processor!\n"); |
818 |
> |
painCave.isFatal = 0; |
819 |
> |
simError(); |
820 |
> |
double smallest; |
821 |
> |
smallest = info->boxL[0]; |
822 |
> |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
823 |
> |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
824 |
> |
theEcr = 0.5 * smallest; |
825 |
|
} else { |
826 |
< |
simnfo->ecr = the_globals->getECR(); |
826 |
> |
theEcr = globals->getECR(); |
827 |
|
} |
828 |
|
|
829 |
< |
if( !the_globals->haveEST() ){ |
830 |
< |
sprintf( painCave.errMsg, |
831 |
< |
"SimSetup Warning: using default value of 5% of the" |
832 |
< |
"electrostaticCutoffRadius for the " |
833 |
< |
"electrostaticSkinThickness\n" |
834 |
< |
); |
835 |
< |
painCave.isFatal = 0; |
836 |
< |
simError(); |
837 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
829 |
> |
if( !globals->haveEST() ){ |
830 |
> |
sprintf( painCave.errMsg, |
831 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
832 |
> |
"electrostaticCutoffRadius for the " |
833 |
> |
"electrostaticSkinThickness\n" |
834 |
> |
); |
835 |
> |
painCave.isFatal = 0; |
836 |
> |
simError(); |
837 |
> |
theEst = 0.05 * theEcr; |
838 |
|
} else { |
839 |
< |
simnfo->est = the_globals->getEST(); |
839 |
> |
theEst= globals->getEST(); |
840 |
|
} |
841 |
+ |
|
842 |
+ |
info->setEcr( theEcr, theEst ); |
843 |
|
} |
844 |
|
} |
845 |
|
|
846 |
|
#ifdef IS_MPI |
847 |
< |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
847 |
> |
strcpy( checkPointMsg, "post processing checks out" ); |
848 |
|
MPIcheckPoint(); |
849 |
|
#endif // is_mpi |
850 |
|
|
851 |
< |
if( the_globals->haveInitialConfig() ){ |
851 |
> |
} |
852 |
> |
|
853 |
> |
void SimSetup::initSystemCoords( void ){ |
854 |
> |
|
855 |
> |
if( globals->haveInitialConfig() ){ |
856 |
|
|
857 |
|
InitializeFromFile* fileInit; |
858 |
|
#ifdef IS_MPI // is_mpi |
859 |
|
if( worldRank == 0 ){ |
860 |
|
#endif //is_mpi |
861 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
861 |
> |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
862 |
|
#ifdef IS_MPI |
863 |
|
}else fileInit = new InitializeFromFile( NULL ); |
864 |
|
#endif |
865 |
< |
fileInit->read_xyz( simnfo ); // default velocities on |
865 |
> |
fileInit->read_xyz( info ); // default velocities on |
866 |
|
|
867 |
|
delete fileInit; |
868 |
|
} |
890 |
|
MPIcheckPoint(); |
891 |
|
#endif // is_mpi |
892 |
|
|
893 |
+ |
} |
894 |
|
|
895 |
< |
|
896 |
< |
|
525 |
< |
|
895 |
> |
|
896 |
> |
void SimSetup::makeOutNames( void ){ |
897 |
|
|
527 |
– |
|
898 |
|
#ifdef IS_MPI |
899 |
|
if( worldRank == 0 ){ |
900 |
|
#endif // is_mpi |
901 |
|
|
902 |
< |
if( the_globals->haveFinalConfig() ){ |
903 |
< |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
902 |
> |
if( globals->haveFinalConfig() ){ |
903 |
> |
strcpy( info->finalName, globals->getFinalConfig() ); |
904 |
|
} |
905 |
|
else{ |
906 |
< |
strcpy( simnfo->finalName, inFileName ); |
906 |
> |
strcpy( info->finalName, inFileName ); |
907 |
|
char* endTest; |
908 |
< |
int nameLength = strlen( simnfo->finalName ); |
909 |
< |
endTest = &(simnfo->finalName[nameLength - 5]); |
908 |
> |
int nameLength = strlen( info->finalName ); |
909 |
> |
endTest = &(info->finalName[nameLength - 5]); |
910 |
|
if( !strcmp( endTest, ".bass" ) ){ |
911 |
|
strcpy( endTest, ".eor" ); |
912 |
|
} |
914 |
|
strcpy( endTest, ".eor" ); |
915 |
|
} |
916 |
|
else{ |
917 |
< |
endTest = &(simnfo->finalName[nameLength - 4]); |
917 |
> |
endTest = &(info->finalName[nameLength - 4]); |
918 |
|
if( !strcmp( endTest, ".bss" ) ){ |
919 |
|
strcpy( endTest, ".eor" ); |
920 |
|
} |
922 |
|
strcpy( endTest, ".eor" ); |
923 |
|
} |
924 |
|
else{ |
925 |
< |
strcat( simnfo->finalName, ".eor" ); |
925 |
> |
strcat( info->finalName, ".eor" ); |
926 |
|
} |
927 |
|
} |
928 |
|
} |
929 |
|
|
930 |
|
// make the sample and status out names |
931 |
|
|
932 |
< |
strcpy( simnfo->sampleName, inFileName ); |
932 |
> |
strcpy( info->sampleName, inFileName ); |
933 |
|
char* endTest; |
934 |
< |
int nameLength = strlen( simnfo->sampleName ); |
935 |
< |
endTest = &(simnfo->sampleName[nameLength - 5]); |
934 |
> |
int nameLength = strlen( info->sampleName ); |
935 |
> |
endTest = &(info->sampleName[nameLength - 5]); |
936 |
|
if( !strcmp( endTest, ".bass" ) ){ |
937 |
|
strcpy( endTest, ".dump" ); |
938 |
|
} |
940 |
|
strcpy( endTest, ".dump" ); |
941 |
|
} |
942 |
|
else{ |
943 |
< |
endTest = &(simnfo->sampleName[nameLength - 4]); |
943 |
> |
endTest = &(info->sampleName[nameLength - 4]); |
944 |
|
if( !strcmp( endTest, ".bss" ) ){ |
945 |
|
strcpy( endTest, ".dump" ); |
946 |
|
} |
948 |
|
strcpy( endTest, ".dump" ); |
949 |
|
} |
950 |
|
else{ |
951 |
< |
strcat( simnfo->sampleName, ".dump" ); |
951 |
> |
strcat( info->sampleName, ".dump" ); |
952 |
|
} |
953 |
|
} |
954 |
|
|
955 |
< |
strcpy( simnfo->statusName, inFileName ); |
956 |
< |
nameLength = strlen( simnfo->statusName ); |
957 |
< |
endTest = &(simnfo->statusName[nameLength - 5]); |
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 |
|
} |
962 |
|
strcpy( endTest, ".stat" ); |
963 |
|
} |
964 |
|
else{ |
965 |
< |
endTest = &(simnfo->statusName[nameLength - 4]); |
965 |
> |
endTest = &(info->statusName[nameLength - 4]); |
966 |
|
if( !strcmp( endTest, ".bss" ) ){ |
967 |
|
strcpy( endTest, ".stat" ); |
968 |
|
} |
970 |
|
strcpy( endTest, ".stat" ); |
971 |
|
} |
972 |
|
else{ |
973 |
< |
strcat( simnfo->statusName, ".stat" ); |
973 |
> |
strcat( info->statusName, ".stat" ); |
974 |
|
} |
975 |
|
} |
976 |
|
|
977 |
|
#ifdef IS_MPI |
978 |
|
} |
979 |
|
#endif // is_mpi |
610 |
– |
|
611 |
– |
// set the status, sample, and themal kick times |
612 |
– |
|
613 |
– |
if( the_globals->haveSampleTime() ){ |
614 |
– |
simnfo->sampleTime = the_globals->getSampleTime(); |
615 |
– |
simnfo->statusTime = simnfo->sampleTime; |
616 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
617 |
– |
} |
618 |
– |
else{ |
619 |
– |
simnfo->sampleTime = the_globals->getRunTime(); |
620 |
– |
simnfo->statusTime = simnfo->sampleTime; |
621 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
622 |
– |
} |
980 |
|
|
981 |
< |
if( the_globals->haveStatusTime() ){ |
625 |
< |
simnfo->statusTime = the_globals->getStatusTime(); |
626 |
< |
} |
981 |
> |
} |
982 |
|
|
628 |
– |
if( the_globals->haveThermalTime() ){ |
629 |
– |
simnfo->thermalTime = the_globals->getThermalTime(); |
630 |
– |
} |
983 |
|
|
984 |
< |
// check for the temperature set flag |
984 |
> |
void SimSetup::sysObjectsCreation( void ){ |
985 |
|
|
986 |
< |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
986 |
> |
int i; |
987 |
|
|
988 |
+ |
// create the forceField |
989 |
|
|
990 |
< |
// // make the longe range forces and the integrator |
990 |
> |
createFF(); |
991 |
|
|
992 |
< |
// new AllLong( simnfo ); |
992 |
> |
// extract componentList |
993 |
|
|
994 |
< |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 |
< |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
643 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
644 |
< |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
994 |
> |
compList(); |
995 |
|
|
996 |
+ |
// calc the number of atoms, bond, bends, and torsions |
997 |
|
|
998 |
+ |
calcSysValues(); |
999 |
|
|
1000 |
< |
// initialize the Fortran |
1000 |
> |
#ifdef IS_MPI |
1001 |
> |
// divide the molecules among the processors |
1002 |
|
|
1003 |
< |
simnfo->refreshSim(); |
1003 |
> |
mpiMolDivide(); |
1004 |
> |
#endif //is_mpi |
1005 |
|
|
1006 |
< |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
1007 |
< |
the_ff->initForceField( LB_MIXING_RULE ); |
1006 |
> |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1007 |
> |
|
1008 |
> |
makeSysArrays(); |
1009 |
> |
|
1010 |
> |
// make and initialize the molecules (all but atomic coordinates) |
1011 |
> |
|
1012 |
> |
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 |
|
} |
1017 |
< |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
1018 |
< |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1019 |
< |
} |
1020 |
< |
else{ |
1017 |
> |
|
1018 |
> |
|
1019 |
> |
|
1020 |
> |
} |
1021 |
> |
|
1022 |
> |
|
1023 |
> |
void SimSetup::createFF( void ){ |
1024 |
> |
|
1025 |
> |
switch( ffCase ){ |
1026 |
> |
|
1027 |
> |
case FF_DUFF: |
1028 |
> |
the_ff = new DUFF(); |
1029 |
> |
break; |
1030 |
> |
|
1031 |
> |
case FF_LJ: |
1032 |
> |
the_ff = new LJFF(); |
1033 |
> |
break; |
1034 |
> |
|
1035 |
> |
default: |
1036 |
|
sprintf( painCave.errMsg, |
1037 |
< |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
661 |
< |
simnfo->mixingRule ); |
1037 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1038 |
|
painCave.isFatal = 1; |
1039 |
|
simError(); |
1040 |
|
} |
1041 |
|
|
666 |
– |
|
1042 |
|
#ifdef IS_MPI |
1043 |
< |
strcpy( checkPointMsg, |
669 |
< |
"Successfully intialized the mixingRule for Fortran." ); |
1043 |
> |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1044 |
|
MPIcheckPoint(); |
1045 |
|
#endif // is_mpi |
1046 |
+ |
|
1047 |
|
} |
1048 |
|
|
1049 |
|
|
1050 |
< |
void SimSetup::makeMolecules( void ){ |
1050 |
> |
void SimSetup::compList( void ){ |
1051 |
|
|
1052 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset; |
678 |
< |
molInit info; |
679 |
< |
DirectionalAtom* dAtom; |
680 |
< |
AtomStamp* currentAtom; |
681 |
< |
BondStamp* currentBond; |
682 |
< |
BendStamp* currentBend; |
683 |
< |
TorsionStamp* currentTorsion; |
684 |
< |
|
685 |
< |
//init the forceField paramters |
1052 |
> |
int i; |
1053 |
|
|
1054 |
< |
the_ff->readParams(); |
1054 |
> |
comp_stamps = new MoleculeStamp*[n_components]; |
1055 |
|
|
1056 |
+ |
// make an array of molecule stamps that match the components used. |
1057 |
+ |
// 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(); |
1063 |
|
|
1064 |
< |
// init the molecules |
1064 |
> |
char* id; |
1065 |
> |
LinkedMolStamp* headStamp = info->headStamp; |
1066 |
> |
LinkedMolStamp* currentStamp = NULL; |
1067 |
> |
for( i=0; i<n_components; i++ ){ |
1068 |
|
|
1069 |
< |
atomOffset = 0; |
1070 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
1069 |
> |
id = the_components[i]->getType(); |
1070 |
> |
comp_stamps[i] = NULL; |
1071 |
|
|
1072 |
< |
stampID = the_molecules[i].getStampID(); |
1072 |
> |
// check to make sure the component isn't already in the list |
1073 |
|
|
1074 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
1075 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
699 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
700 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
701 |
< |
|
702 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
703 |
< |
info.myBonds = new Bond*[info.nBonds]; |
704 |
< |
info.myBends = new Bend*[info.nBends]; |
705 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
706 |
< |
|
707 |
< |
theBonds = new bond_pair[info.nBonds]; |
708 |
< |
theBends = new bend_set[info.nBends]; |
709 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
710 |
< |
|
711 |
< |
// make the Atoms |
712 |
< |
|
713 |
< |
for(j=0; j<info.nAtoms; j++){ |
1074 |
> |
comp_stamps[i] = headStamp->match( id ); |
1075 |
> |
if( comp_stamps[i] == NULL ){ |
1076 |
|
|
1077 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
1078 |
< |
if( currentAtom->haveOrientation() ){ |
1079 |
< |
|
1080 |
< |
dAtom = new DirectionalAtom(j + atomOffset); |
1081 |
< |
simnfo->n_oriented++; |
1082 |
< |
info.myAtoms[j] = dAtom; |
1083 |
< |
|
1084 |
< |
ux = currentAtom->getOrntX(); |
1085 |
< |
uy = currentAtom->getOrntY(); |
1086 |
< |
uz = currentAtom->getOrntZ(); |
725 |
< |
|
726 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
727 |
< |
|
728 |
< |
u = sqrt( uSqr ); |
729 |
< |
ux = ux / u; |
730 |
< |
uy = uy / u; |
731 |
< |
uz = uz / u; |
732 |
< |
|
733 |
< |
dAtom->setSUx( ux ); |
734 |
< |
dAtom->setSUy( uy ); |
735 |
< |
dAtom->setSUz( uz ); |
1077 |
> |
// extract the component from the list; |
1078 |
> |
|
1079 |
> |
currentStamp = stamps->extractMolStamp( id ); |
1080 |
> |
if( currentStamp == NULL ){ |
1081 |
> |
sprintf( painCave.errMsg, |
1082 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
1083 |
> |
"list of declared molecules\n", |
1084 |
> |
id ); |
1085 |
> |
painCave.isFatal = 1; |
1086 |
> |
simError(); |
1087 |
|
} |
737 |
– |
else{ |
738 |
– |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
739 |
– |
} |
740 |
– |
info.myAtoms[j]->setType( currentAtom->getType() ); |
741 |
– |
|
742 |
– |
#ifdef IS_MPI |
1088 |
|
|
1089 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
1090 |
< |
|
1089 |
> |
headStamp->add( currentStamp ); |
1090 |
> |
comp_stamps[i] = headStamp->match( id ); |
1091 |
> |
} |
1092 |
> |
} |
1093 |
> |
|
1094 |
> |
#ifdef IS_MPI |
1095 |
> |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1096 |
> |
MPIcheckPoint(); |
1097 |
|
#endif // is_mpi |
747 |
– |
} |
748 |
– |
|
749 |
– |
// make the bonds |
750 |
– |
for(j=0; j<nBonds; j++){ |
751 |
– |
|
752 |
– |
currentBond = comp_stamps[stampID]->getBond( j ); |
753 |
– |
theBonds[j].a = currentBond->getA() + atomOffset; |
754 |
– |
theBonds[j].b = currentBond->getB() + atomOffset; |
1098 |
|
|
756 |
– |
exI = theBonds[i].a; |
757 |
– |
exJ = theBonds[i].b; |
1099 |
|
|
1100 |
< |
// exclude_I must always be the smaller of the pair |
760 |
< |
if( exI > exJ ){ |
761 |
< |
tempEx = exI; |
762 |
< |
exI = exJ; |
763 |
< |
exJ = tempEx; |
764 |
< |
} |
765 |
< |
#ifdef IS_MPI |
766 |
< |
|
767 |
< |
the_excludes[index*2] = |
768 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
769 |
< |
the_excludes[index*2 + 1] = |
770 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
771 |
< |
|
772 |
< |
#else // isn't MPI |
773 |
< |
|
774 |
< |
the_excludes[index*2] = exI + 1; |
775 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
776 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
1100 |
> |
} |
1101 |
|
|
1102 |
< |
#endif //is_mpi |
1102 |
> |
void SimSetup::calcSysValues( void ){ |
1103 |
> |
int i, j, k; |
1104 |
> |
|
1105 |
> |
|
1106 |
> |
tot_atoms = 0; |
1107 |
> |
tot_bonds = 0; |
1108 |
> |
tot_bends = 0; |
1109 |
> |
tot_torsions = 0; |
1110 |
> |
for( i=0; i<n_components; i++ ){ |
1111 |
|
|
1112 |
+ |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1113 |
+ |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1114 |
+ |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1115 |
+ |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1116 |
|
} |
1117 |
|
|
1118 |
+ |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1119 |
|
|
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; |
1126 |
+ |
|
1127 |
+ |
info->molMembershipArray = new int[tot_atoms]; |
1128 |
+ |
} |
1129 |
|
|
1130 |
|
|
1131 |
+ |
#ifdef IS_MPI |
1132 |
|
|
1133 |
+ |
void SimSetup::mpiMolDivide( void ){ |
1134 |
+ |
|
1135 |
+ |
int i, j, k; |
1136 |
+ |
int localMol, allMol; |
1137 |
+ |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1138 |
|
|
1139 |
+ |
mpiSim = new mpiSimulation( info ); |
1140 |
+ |
|
1141 |
+ |
globalIndex = mpiSim->divideLabor(); |
1142 |
|
|
1143 |
+ |
// set up the local variables |
1144 |
+ |
|
1145 |
+ |
mol2proc = mpiSim->getMolToProcMap(); |
1146 |
+ |
molCompType = mpiSim->getMolComponentType(); |
1147 |
+ |
|
1148 |
+ |
allMol = 0; |
1149 |
+ |
localMol = 0; |
1150 |
+ |
local_atoms = 0; |
1151 |
+ |
local_bonds = 0; |
1152 |
+ |
local_bends = 0; |
1153 |
+ |
local_torsions = 0; |
1154 |
+ |
globalAtomIndex = 0; |
1155 |
|
|
1156 |
|
|
1157 |
+ |
for( i=0; i<n_components; i++ ){ |
1158 |
|
|
1159 |
+ |
for( j=0; j<components_nmol[i]; j++ ){ |
1160 |
+ |
|
1161 |
+ |
if( mol2proc[allMol] == worldRank ){ |
1162 |
+ |
|
1163 |
+ |
local_atoms += comp_stamps[i]->getNAtoms(); |
1164 |
+ |
local_bonds += comp_stamps[i]->getNBonds(); |
1165 |
+ |
local_bends += comp_stamps[i]->getNBends(); |
1166 |
+ |
local_torsions += comp_stamps[i]->getNTorsions(); |
1167 |
+ |
localMol++; |
1168 |
+ |
} |
1169 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1170 |
+ |
info->molMembershipArray[globalAtomIndex] = allMol; |
1171 |
+ |
globalAtomIndex++; |
1172 |
+ |
} |
1173 |
|
|
1174 |
+ |
allMol++; |
1175 |
+ |
} |
1176 |
+ |
} |
1177 |
+ |
local_SRI = local_bonds + local_bends + local_torsions; |
1178 |
+ |
|
1179 |
+ |
info->n_atoms = mpiSim->getMyNlocal(); |
1180 |
+ |
|
1181 |
+ |
if( local_atoms != info->n_atoms ){ |
1182 |
+ |
sprintf( painCave.errMsg, |
1183 |
+ |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1184 |
+ |
" localAtom (%d) are not equal.\n", |
1185 |
+ |
info->n_atoms, |
1186 |
+ |
local_atoms ); |
1187 |
+ |
painCave.isFatal = 1; |
1188 |
+ |
simError(); |
1189 |
+ |
} |
1190 |
|
|
1191 |
+ |
info->n_bonds = local_bonds; |
1192 |
+ |
info->n_bends = local_bends; |
1193 |
+ |
info->n_torsions = local_torsions; |
1194 |
+ |
info->n_SRI = local_SRI; |
1195 |
+ |
info->n_mol = localMol; |
1196 |
|
|
1197 |
+ |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1198 |
+ |
MPIcheckPoint(); |
1199 |
+ |
} |
1200 |
+ |
|
1201 |
+ |
#endif // is_mpi |
1202 |
|
|
1203 |
|
|
1204 |
< |
void SimSetup::makeAtoms( void ){ |
1204 |
> |
void SimSetup::makeSysArrays( void ){ |
1205 |
> |
int i, j, k; |
1206 |
|
|
798 |
– |
int i, j, k, index; |
799 |
– |
double ux, uy, uz, uSqr, u; |
800 |
– |
AtomStamp* current_atom; |
1207 |
|
|
1208 |
< |
DirectionalAtom* dAtom; |
803 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
1208 |
> |
// create the atom and short range interaction arrays |
1209 |
|
|
1210 |
< |
lMolIndex = 0; |
1211 |
< |
molIndex = 0; |
1212 |
< |
index = 0; |
1213 |
< |
for( i=0; i<n_components; i++ ){ |
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 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1215 |
> |
// initialize the molecule's stampID's |
1216 |
|
|
1217 |
|
#ifdef IS_MPI |
1218 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
814 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
815 |
< |
#endif // is_mpi |
1218 |
> |
|
1219 |
|
|
1220 |
< |
molStart = index; |
1221 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
1222 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
1223 |
< |
|
1224 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
1225 |
< |
if( current_atom->haveOrientation() ){ |
1226 |
< |
|
1227 |
< |
dAtom = new DirectionalAtom(index); |
1228 |
< |
simnfo->n_oriented++; |
1229 |
< |
the_atoms[index] = dAtom; |
827 |
< |
|
828 |
< |
ux = current_atom->getOrntX(); |
829 |
< |
uy = current_atom->getOrntY(); |
830 |
< |
uz = current_atom->getOrntZ(); |
831 |
< |
|
832 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
833 |
< |
|
834 |
< |
u = sqrt( uSqr ); |
835 |
< |
ux = ux / u; |
836 |
< |
uy = uy / u; |
837 |
< |
uz = uz / u; |
838 |
< |
|
839 |
< |
dAtom->setSUx( ux ); |
840 |
< |
dAtom->setSUy( uy ); |
841 |
< |
dAtom->setSUz( uz ); |
842 |
< |
} |
843 |
< |
else{ |
844 |
< |
the_atoms[index] = new GeneralAtom(index); |
845 |
< |
} |
846 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
847 |
< |
the_atoms[index]->setIndex( index ); |
848 |
< |
|
849 |
< |
// increment the index and repeat; |
850 |
< |
index++; |
851 |
< |
} |
852 |
< |
|
853 |
< |
molEnd = index -1; |
854 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
855 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
856 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
857 |
< |
the_molecules[lMolIndex].setStampID( i ); |
858 |
< |
lMolIndex++; |
1220 |
> |
molIndex = 0; |
1221 |
> |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1222 |
> |
|
1223 |
> |
if(mol2proc[i] == worldRank ){ |
1224 |
> |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1225 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
1226 |
> |
the_molecules[molIndex].setGlobalIndex( i ); |
1227 |
> |
molIndex++; |
1228 |
> |
} |
1229 |
> |
} |
1230 |
|
|
1231 |
< |
#ifdef IS_MPI |
1231 |
> |
#else // is_mpi |
1232 |
> |
|
1233 |
> |
molIndex = 0; |
1234 |
> |
globalAtomIndex = 0; |
1235 |
> |
for(i=0; i<n_components; i++){ |
1236 |
> |
for(j=0; j<components_nmol[i]; j++ ){ |
1237 |
> |
the_molecules[molIndex].setStampID( i ); |
1238 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
1239 |
> |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1240 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1241 |
> |
info->molMembershipArray[globalAtomIndex] = molIndex; |
1242 |
> |
globalAtomIndex++; |
1243 |
|
} |
862 |
– |
#endif //is_mpi |
863 |
– |
|
1244 |
|
molIndex++; |
1245 |
|
} |
1246 |
|
} |
867 |
– |
|
868 |
– |
#ifdef IS_MPI |
869 |
– |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
1247 |
|
|
871 |
– |
delete[] globalIndex; |
1248 |
|
|
1249 |
< |
mpiSim->mpiRefresh(); |
874 |
< |
#endif //IS_MPI |
875 |
< |
|
876 |
< |
the_ff->initializeAtoms(); |
877 |
< |
} |
1249 |
> |
#endif // is_mpi |
1250 |
|
|
879 |
– |
void SimSetup::makeBonds( void ){ |
1251 |
|
|
1252 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1253 |
< |
bond_pair* the_bonds; |
1254 |
< |
BondStamp* current_bond; |
1252 |
> |
if( info->n_SRI ){ |
1253 |
> |
|
1254 |
> |
Exclude::createArray(info->n_SRI); |
1255 |
> |
the_excludes = new Exclude*[info->n_SRI]; |
1256 |
> |
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1257 |
> |
info->globalExcludes = new int; |
1258 |
> |
info->n_exclude = info->n_SRI; |
1259 |
> |
} |
1260 |
> |
else{ |
1261 |
> |
|
1262 |
> |
Exclude::createArray( 1 ); |
1263 |
> |
the_excludes = new Exclude*; |
1264 |
> |
the_excludes[0] = new Exclude(0); |
1265 |
> |
the_excludes[0]->setPair( 0,0 ); |
1266 |
> |
info->globalExcludes = new int; |
1267 |
> |
info->globalExcludes[0] = 0; |
1268 |
> |
info->n_exclude = 0; |
1269 |
> |
} |
1270 |
|
|
1271 |
< |
the_bonds = new bond_pair[tot_bonds]; |
886 |
< |
index = 0; |
887 |
< |
offset = 0; |
888 |
< |
molIndex = 0; |
1271 |
> |
// set the arrays into the SimInfo object |
1272 |
|
|
1273 |
< |
for( i=0; i<n_components; i++ ){ |
1273 |
> |
info->atoms = the_atoms; |
1274 |
> |
info->molecules = the_molecules; |
1275 |
> |
info->nGlobalExcludes = 0; |
1276 |
> |
info->excludes = the_excludes; |
1277 |
|
|
1278 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1278 |
> |
the_ff->setSimInfo( info ); |
1279 |
|
|
1280 |
< |
#ifdef IS_MPI |
895 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
896 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
897 |
< |
#endif // is_mpi |
898 |
< |
|
899 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
900 |
< |
|
901 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
902 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
903 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
1280 |
> |
} |
1281 |
|
|
1282 |
< |
exI = the_bonds[index].a; |
906 |
< |
exJ = the_bonds[index].b; |
1282 |
> |
void SimSetup::makeIntegrator( void ){ |
1283 |
|
|
1284 |
< |
// exclude_I must always be the smaller of the pair |
1285 |
< |
if( exI > exJ ){ |
1286 |
< |
tempEx = exI; |
1287 |
< |
exI = exJ; |
1288 |
< |
exJ = tempEx; |
913 |
< |
} |
1284 |
> |
NVT* myNVT = NULL; |
1285 |
> |
NPTi* myNPTi = NULL; |
1286 |
> |
NPTf* myNPTf = NULL; |
1287 |
> |
NPTim* myNPTim = NULL; |
1288 |
> |
NPTfm* myNPTfm = NULL; |
1289 |
|
|
1290 |
< |
|
916 |
< |
#ifdef IS_MPI |
1290 |
> |
switch( ensembleCase ){ |
1291 |
|
|
1292 |
< |
the_excludes[index*2] = |
1293 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1294 |
< |
the_excludes[index*2 + 1] = |
921 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1292 |
> |
case NVE_ENS: |
1293 |
> |
new NVE( info, the_ff ); |
1294 |
> |
break; |
1295 |
|
|
1296 |
< |
#else // isn't MPI |
1297 |
< |
|
1298 |
< |
the_excludes[index*2] = exI + 1; |
926 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
927 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
928 |
< |
#endif //is_mpi |
929 |
< |
|
930 |
< |
// increment the index and repeat; |
931 |
< |
index++; |
932 |
< |
} |
933 |
< |
offset += comp_stamps[i]->getNAtoms(); |
934 |
< |
|
935 |
< |
#ifdef IS_MPI |
936 |
< |
} |
937 |
< |
#endif //is_mpi |
938 |
< |
|
939 |
< |
molIndex++; |
940 |
< |
} |
941 |
< |
} |
1296 |
> |
case NVT_ENS: |
1297 |
> |
myNVT = new NVT( info, the_ff ); |
1298 |
> |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1299 |
|
|
1300 |
< |
the_ff->initializeBonds( the_bonds ); |
1301 |
< |
} |
1300 |
> |
if (globals->haveTauThermostat()) |
1301 |
> |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1302 |
|
|
1303 |
< |
void SimSetup::makeBends( void ){ |
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 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1313 |
< |
bend_set* the_bends; |
1314 |
< |
BendStamp* current_bend; |
951 |
< |
LinkedAssign* extras; |
952 |
< |
LinkedAssign* current_extra; |
953 |
< |
|
1312 |
> |
case NPTi_ENS: |
1313 |
> |
myNPTi = new NPTi( info, the_ff ); |
1314 |
> |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1315 |
|
|
1316 |
< |
the_bends = new bend_set[tot_bends]; |
1317 |
< |
index = 0; |
1318 |
< |
offset = 0; |
1319 |
< |
molIndex = 0; |
1320 |
< |
for( i=0; i<n_components; i++ ){ |
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 |
> |
} |
1325 |
> |
|
1326 |
> |
if( globals->haveTauThermostat() ) |
1327 |
> |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1328 |
> |
else{ |
1329 |
> |
sprintf( painCave.errMsg, |
1330 |
> |
"SimSetup error: If you use an NPT\n" |
1331 |
> |
" ensemble, you must set tauThermostat.\n"); |
1332 |
> |
painCave.isFatal = 1; |
1333 |
> |
simError(); |
1334 |
> |
} |
1335 |
|
|
1336 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1337 |
< |
|
1338 |
< |
#ifdef IS_MPI |
1339 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
1340 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
1341 |
< |
#endif // is_mpi |
1336 |
> |
if( globals->haveTauBarostat() ) |
1337 |
> |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1338 |
> |
else{ |
1339 |
> |
sprintf( painCave.errMsg, |
1340 |
> |
"SimSetup error: If you use an NPT\n" |
1341 |
> |
" ensemble, you must set tauBarostat.\n"); |
1342 |
> |
painCave.isFatal = 1; |
1343 |
> |
simError(); |
1344 |
> |
} |
1345 |
> |
break; |
1346 |
|
|
1347 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
1348 |
< |
|
1349 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
971 |
< |
the_bends[index].a = current_bend->getA() + offset; |
972 |
< |
the_bends[index].b = current_bend->getB() + offset; |
973 |
< |
the_bends[index].c = current_bend->getC() + offset; |
974 |
< |
|
975 |
< |
if( current_bend->haveExtras() ){ |
976 |
< |
|
977 |
< |
extras = current_bend->getExtras(); |
978 |
< |
current_extra = extras; |
979 |
< |
|
980 |
< |
while( current_extra != NULL ){ |
981 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
982 |
< |
|
983 |
< |
switch( current_extra->getType() ){ |
984 |
< |
|
985 |
< |
case 0: |
986 |
< |
the_bends[index].ghost = |
987 |
< |
current_extra->getInt() + offset; |
988 |
< |
the_bends[index].isGhost = 1; |
989 |
< |
break; |
990 |
< |
|
991 |
< |
case 1: |
992 |
< |
the_bends[index].ghost = |
993 |
< |
(int)current_extra->getDouble() + offset; |
994 |
< |
the_bends[index].isGhost = 1; |
995 |
< |
break; |
996 |
< |
|
997 |
< |
default: |
998 |
< |
sprintf( painCave.errMsg, |
999 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
1000 |
< |
"double nor an int.\n" |
1001 |
< |
"-->Bend[%d] in %s\n", |
1002 |
< |
k, comp_stamps[i]->getID() ); |
1003 |
< |
painCave.isFatal = 1; |
1004 |
< |
simError(); |
1005 |
< |
} |
1006 |
< |
} |
1007 |
< |
|
1008 |
< |
else{ |
1009 |
< |
|
1010 |
< |
sprintf( painCave.errMsg, |
1011 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
1012 |
< |
" -->%s in Bend[%d] in %s\n", |
1013 |
< |
current_extra->getlhs(), |
1014 |
< |
k, comp_stamps[i]->getID() ); |
1015 |
< |
painCave.isFatal = 1; |
1016 |
< |
simError(); |
1017 |
< |
} |
1018 |
< |
|
1019 |
< |
current_extra = current_extra->getNext(); |
1020 |
< |
} |
1021 |
< |
} |
1022 |
< |
|
1023 |
< |
if( !the_bends[index].isGhost ){ |
1024 |
< |
|
1025 |
< |
exI = the_bends[index].a; |
1026 |
< |
exJ = the_bends[index].c; |
1027 |
< |
} |
1028 |
< |
else{ |
1029 |
< |
|
1030 |
< |
exI = the_bends[index].a; |
1031 |
< |
exJ = the_bends[index].b; |
1032 |
< |
} |
1033 |
< |
|
1034 |
< |
// exclude_I must always be the smaller of the pair |
1035 |
< |
if( exI > exJ ){ |
1036 |
< |
tempEx = exI; |
1037 |
< |
exI = exJ; |
1038 |
< |
exJ = tempEx; |
1039 |
< |
} |
1347 |
> |
case NPTf_ENS: |
1348 |
> |
myNPTf = new NPTf( info, the_ff ); |
1349 |
> |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1350 |
|
|
1351 |
+ |
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 |
+ |
} |
1360 |
|
|
1361 |
< |
#ifdef IS_MPI |
1362 |
< |
|
1363 |
< |
the_excludes[(index + tot_bonds)*2] = |
1364 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1365 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
1366 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1367 |
< |
|
1368 |
< |
#else // isn't MPI |
1050 |
< |
|
1051 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
1052 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
1053 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
1054 |
< |
#endif //is_mpi |
1055 |
< |
|
1056 |
< |
|
1057 |
< |
// increment the index and repeat; |
1058 |
< |
index++; |
1059 |
< |
} |
1060 |
< |
offset += comp_stamps[i]->getNAtoms(); |
1061 |
< |
|
1062 |
< |
#ifdef IS_MPI |
1063 |
< |
} |
1064 |
< |
#endif //is_mpi |
1065 |
< |
|
1066 |
< |
molIndex++; |
1361 |
> |
if( globals->haveTauThermostat() ) |
1362 |
> |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1363 |
> |
else{ |
1364 |
> |
sprintf( painCave.errMsg, |
1365 |
> |
"SimSetup error: If you use an NPT\n" |
1366 |
> |
" ensemble, you must set tauThermostat.\n"); |
1367 |
> |
painCave.isFatal = 1; |
1368 |
> |
simError(); |
1369 |
|
} |
1068 |
– |
} |
1370 |
|
|
1371 |
< |
#ifdef IS_MPI |
1372 |
< |
sprintf( checkPointMsg, |
1373 |
< |
"Successfully created the bends list.\n" ); |
1374 |
< |
MPIcheckPoint(); |
1375 |
< |
#endif // is_mpi |
1376 |
< |
|
1377 |
< |
|
1378 |
< |
the_ff->initializeBends( the_bends ); |
1078 |
< |
} |
1079 |
< |
|
1080 |
< |
void SimSetup::makeTorsions( void ){ |
1081 |
< |
|
1082 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1083 |
< |
torsion_set* the_torsions; |
1084 |
< |
TorsionStamp* current_torsion; |
1085 |
< |
|
1086 |
< |
the_torsions = new torsion_set[tot_torsions]; |
1087 |
< |
index = 0; |
1088 |
< |
offset = 0; |
1089 |
< |
molIndex = 0; |
1090 |
< |
for( i=0; i<n_components; i++ ){ |
1091 |
< |
|
1092 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1093 |
< |
|
1094 |
< |
#ifdef IS_MPI |
1095 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
1096 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
1097 |
< |
#endif // is_mpi |
1098 |
< |
|
1099 |
< |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1100 |
< |
|
1101 |
< |
current_torsion = comp_stamps[i]->getTorsion( k ); |
1102 |
< |
the_torsions[index].a = current_torsion->getA() + offset; |
1103 |
< |
the_torsions[index].b = current_torsion->getB() + offset; |
1104 |
< |
the_torsions[index].c = current_torsion->getC() + offset; |
1105 |
< |
the_torsions[index].d = current_torsion->getD() + offset; |
1106 |
< |
|
1107 |
< |
exI = the_torsions[index].a; |
1108 |
< |
exJ = the_torsions[index].d; |
1109 |
< |
|
1110 |
< |
|
1111 |
< |
// exclude_I must always be the smaller of the pair |
1112 |
< |
if( exI > exJ ){ |
1113 |
< |
tempEx = exI; |
1114 |
< |
exI = exJ; |
1115 |
< |
exJ = tempEx; |
1116 |
< |
} |
1117 |
< |
|
1118 |
< |
|
1119 |
< |
#ifdef IS_MPI |
1120 |
< |
|
1121 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
1122 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1123 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1124 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1125 |
< |
|
1126 |
< |
#else // isn't MPI |
1127 |
< |
|
1128 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1129 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1130 |
< |
// fortran indexes from 1 (hence the +1 in the indexing) |
1131 |
< |
#endif //is_mpi |
1132 |
< |
|
1133 |
< |
|
1134 |
< |
// increment the index and repeat; |
1135 |
< |
index++; |
1136 |
< |
} |
1137 |
< |
offset += comp_stamps[i]->getNAtoms(); |
1138 |
< |
|
1139 |
< |
#ifdef IS_MPI |
1140 |
< |
} |
1141 |
< |
#endif //is_mpi |
1142 |
< |
|
1143 |
< |
molIndex++; |
1371 |
> |
if( globals->haveTauBarostat() ) |
1372 |
> |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1373 |
> |
else{ |
1374 |
> |
sprintf( painCave.errMsg, |
1375 |
> |
"SimSetup error: If you use an NPT\n" |
1376 |
> |
" ensemble, you must set tauBarostat.\n"); |
1377 |
> |
painCave.isFatal = 1; |
1378 |
> |
simError(); |
1379 |
|
} |
1380 |
< |
} |
1380 |
> |
break; |
1381 |
> |
|
1382 |
> |
case NPTim_ENS: |
1383 |
> |
myNPTim = new NPTim( info, the_ff ); |
1384 |
> |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1385 |
|
|
1386 |
< |
the_ff->initializeTorsions( the_torsions ); |
1387 |
< |
} |
1388 |
< |
|
1150 |
< |
void SimSetup::initFromBass( void ){ |
1151 |
< |
|
1152 |
< |
int i, j, k; |
1153 |
< |
int n_cells; |
1154 |
< |
double cellx, celly, cellz; |
1155 |
< |
double temp1, temp2, temp3; |
1156 |
< |
int n_per_extra; |
1157 |
< |
int n_extra; |
1158 |
< |
int have_extra, done; |
1159 |
< |
|
1160 |
< |
temp1 = (double)tot_nmol / 4.0; |
1161 |
< |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1162 |
< |
temp3 = ceil( temp2 ); |
1163 |
< |
|
1164 |
< |
have_extra =0; |
1165 |
< |
if( temp2 < temp3 ){ // we have a non-complete lattice |
1166 |
< |
have_extra =1; |
1167 |
< |
|
1168 |
< |
n_cells = (int)temp3 - 1; |
1169 |
< |
cellx = simnfo->box_x / temp3; |
1170 |
< |
celly = simnfo->box_y / temp3; |
1171 |
< |
cellz = simnfo->box_z / temp3; |
1172 |
< |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1173 |
< |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1174 |
< |
n_per_extra = (int)ceil( temp1 ); |
1175 |
< |
|
1176 |
< |
if( n_per_extra > 4){ |
1386 |
> |
if (globals->haveTargetPressure()) |
1387 |
> |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1388 |
> |
else { |
1389 |
|
sprintf( painCave.errMsg, |
1390 |
< |
"SimSetup error. There has been an error in constructing" |
1391 |
< |
" the non-complete lattice.\n" ); |
1390 |
> |
"SimSetup error: If you use a constant pressure\n" |
1391 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1392 |
|
painCave.isFatal = 1; |
1393 |
|
simError(); |
1394 |
|
} |
1395 |
< |
} |
1396 |
< |
else{ |
1397 |
< |
n_cells = (int)temp3; |
1398 |
< |
cellx = simnfo->box_x / temp3; |
1399 |
< |
celly = simnfo->box_y / temp3; |
1400 |
< |
cellz = simnfo->box_z / temp3; |
1401 |
< |
} |
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 |
< |
current_mol = 0; |
1407 |
< |
current_comp_mol = 0; |
1408 |
< |
current_comp = 0; |
1409 |
< |
current_atom_ndx = 0; |
1410 |
< |
|
1411 |
< |
for( i=0; i < n_cells ; i++ ){ |
1412 |
< |
for( j=0; j < n_cells; j++ ){ |
1413 |
< |
for( k=0; k < n_cells; k++ ){ |
1199 |
< |
|
1200 |
< |
makeElement( i * cellx, |
1201 |
< |
j * celly, |
1202 |
< |
k * cellz ); |
1203 |
< |
|
1204 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1205 |
< |
j * celly + 0.5 * celly, |
1206 |
< |
k * cellz ); |
1207 |
< |
|
1208 |
< |
makeElement( i * cellx, |
1209 |
< |
j * celly + 0.5 * celly, |
1210 |
< |
k * cellz + 0.5 * cellz ); |
1211 |
< |
|
1212 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1213 |
< |
j * celly, |
1214 |
< |
k * cellz + 0.5 * cellz ); |
1215 |
< |
} |
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 |
< |
} |
1415 |
> |
break; |
1416 |
|
|
1417 |
< |
if( have_extra ){ |
1418 |
< |
done = 0; |
1417 |
> |
case NPTfm_ENS: |
1418 |
> |
myNPTfm = new NPTfm( info, the_ff ); |
1419 |
> |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1420 |
|
|
1421 |
< |
int start_ndx; |
1422 |
< |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
1423 |
< |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
1424 |
< |
|
1425 |
< |
if( i < n_cells ){ |
1426 |
< |
|
1427 |
< |
if( j < n_cells ){ |
1428 |
< |
start_ndx = n_cells; |
1230 |
< |
} |
1231 |
< |
else start_ndx = 0; |
1232 |
< |
} |
1233 |
< |
else start_ndx = 0; |
1234 |
< |
|
1235 |
< |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1236 |
< |
|
1237 |
< |
makeElement( i * cellx, |
1238 |
< |
j * celly, |
1239 |
< |
k * cellz ); |
1240 |
< |
done = ( current_mol >= tot_nmol ); |
1241 |
< |
|
1242 |
< |
if( !done && n_per_extra > 1 ){ |
1243 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1244 |
< |
j * celly + 0.5 * celly, |
1245 |
< |
k * cellz ); |
1246 |
< |
done = ( current_mol >= tot_nmol ); |
1247 |
< |
} |
1248 |
< |
|
1249 |
< |
if( !done && n_per_extra > 2){ |
1250 |
< |
makeElement( i * cellx, |
1251 |
< |
j * celly + 0.5 * celly, |
1252 |
< |
k * cellz + 0.5 * cellz ); |
1253 |
< |
done = ( current_mol >= tot_nmol ); |
1254 |
< |
} |
1255 |
< |
|
1256 |
< |
if( !done && n_per_extra > 3){ |
1257 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1258 |
< |
j * celly, |
1259 |
< |
k * cellz + 0.5 * cellz ); |
1260 |
< |
done = ( current_mol >= tot_nmol ); |
1261 |
< |
} |
1262 |
< |
} |
1263 |
< |
} |
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 |
< |
} |
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 |
< |
|
1442 |
< |
for( i=0; i<simnfo->n_atoms; i++ ){ |
1443 |
< |
simnfo->atoms[i]->set_vx( 0.0 ); |
1270 |
< |
simnfo->atoms[i]->set_vy( 0.0 ); |
1271 |
< |
simnfo->atoms[i]->set_vz( 0.0 ); |
1272 |
< |
} |
1273 |
< |
} |
1274 |
< |
|
1275 |
< |
void SimSetup::makeElement( double x, double y, double z ){ |
1276 |
< |
|
1277 |
< |
int k; |
1278 |
< |
AtomStamp* current_atom; |
1279 |
< |
DirectionalAtom* dAtom; |
1280 |
< |
double rotMat[3][3]; |
1281 |
< |
|
1282 |
< |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1283 |
< |
|
1284 |
< |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
1285 |
< |
if( !current_atom->havePosition() ){ |
1441 |
> |
if( globals->haveTauBarostat() ) |
1442 |
> |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1443 |
> |
else{ |
1444 |
|
sprintf( painCave.errMsg, |
1445 |
< |
"SimSetup:initFromBass error.\n" |
1446 |
< |
"\tComponent %s, atom %s does not have a position specified.\n" |
1289 |
< |
"\tThe initialization routine is unable to give a start" |
1290 |
< |
" position.\n", |
1291 |
< |
comp_stamps[current_comp]->getID(), |
1292 |
< |
current_atom->getType() ); |
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 |
< |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1453 |
< |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1454 |
< |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1452 |
> |
default: |
1453 |
> |
sprintf( painCave.errMsg, |
1454 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1455 |
> |
painCave.isFatal = 1; |
1456 |
> |
simError(); |
1457 |
> |
} |
1458 |
|
|
1459 |
< |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1459 |
> |
} |
1460 |
|
|
1461 |
< |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1461 |
> |
void SimSetup::initFortran( void ){ |
1462 |
|
|
1463 |
< |
rotMat[0][0] = 1.0; |
1464 |
< |
rotMat[0][1] = 0.0; |
1465 |
< |
rotMat[0][2] = 0.0; |
1466 |
< |
|
1309 |
< |
rotMat[1][0] = 0.0; |
1310 |
< |
rotMat[1][1] = 1.0; |
1311 |
< |
rotMat[1][2] = 0.0; |
1312 |
< |
|
1313 |
< |
rotMat[2][0] = 0.0; |
1314 |
< |
rotMat[2][1] = 0.0; |
1315 |
< |
rotMat[2][2] = 1.0; |
1316 |
< |
|
1317 |
< |
dAtom->setA( rotMat ); |
1318 |
< |
} |
1319 |
< |
|
1320 |
< |
current_atom_ndx++; |
1463 |
> |
info->refreshSim(); |
1464 |
> |
|
1465 |
> |
if( !strcmp( info->mixingRule, "standard") ){ |
1466 |
> |
the_ff->initForceField( LB_MIXING_RULE ); |
1467 |
|
} |
1468 |
+ |
else if( !strcmp( info->mixingRule, "explicit") ){ |
1469 |
+ |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1470 |
+ |
} |
1471 |
+ |
else{ |
1472 |
+ |
sprintf( painCave.errMsg, |
1473 |
+ |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1474 |
+ |
info->mixingRule ); |
1475 |
+ |
painCave.isFatal = 1; |
1476 |
+ |
simError(); |
1477 |
+ |
} |
1478 |
|
|
1323 |
– |
current_mol++; |
1324 |
– |
current_comp_mol++; |
1479 |
|
|
1480 |
< |
if( current_comp_mol >= components_nmol[current_comp] ){ |
1480 |
> |
#ifdef IS_MPI |
1481 |
> |
strcpy( checkPointMsg, |
1482 |
> |
"Successfully intialized the mixingRule for Fortran." ); |
1483 |
> |
MPIcheckPoint(); |
1484 |
> |
#endif // is_mpi |
1485 |
|
|
1328 |
– |
current_comp_mol = 0; |
1329 |
– |
current_comp++; |
1330 |
– |
} |
1486 |
|
} |