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(); |
80 |
|
|
81 |
|
MakeStamps *the_stamps; |
82 |
|
Globals* the_globals; |
83 |
< |
int i, j; |
83 |
> |
int i, j, k, globalAtomIndex; |
84 |
> |
|
85 |
> |
// gather all of the information from the Bass file |
86 |
> |
|
87 |
> |
gatherInfo(); |
88 |
|
|
89 |
< |
// get the stamps and globals; |
72 |
< |
the_stamps = stamps; |
73 |
< |
the_globals = globals; |
89 |
> |
// creation of complex system objects |
90 |
|
|
91 |
< |
// 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(); |
91 |
> |
sysObjectsCreation(); |
92 |
|
|
80 |
– |
// get the ones we know are there, yet still may need some work. |
81 |
– |
n_components = the_globals->getNComponents(); |
82 |
– |
strcpy( force_field, the_globals->getForceField() ); |
83 |
– |
strcpy( ensemble, the_globals->getEnsemble() ); |
84 |
– |
strcpy( simnfo->ensemble, ensemble ); |
93 |
|
|
86 |
– |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
87 |
– |
simnfo->usePBC = the_globals->getPBC(); |
88 |
– |
|
94 |
|
|
95 |
+ |
// initialize the arrays |
96 |
|
|
97 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
98 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
99 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
100 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
101 |
< |
else{ |
102 |
< |
sprintf( painCave.errMsg, |
97 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
98 |
< |
force_field ); |
99 |
< |
painCave.isFatal = 1; |
100 |
< |
simError(); |
97 |
> |
|
98 |
> |
|
99 |
> |
makeMolecules(); |
100 |
> |
info->identArray = new int[info->n_atoms]; |
101 |
> |
for(i=0; i<info->n_atoms; i++){ |
102 |
> |
info->identArray[i] = the_atoms[i]->getIdent(); |
103 |
|
} |
104 |
+ |
|
105 |
|
|
106 |
< |
#ifdef IS_MPI |
104 |
< |
strcpy( checkPointMsg, "ForceField creation successful" ); |
105 |
< |
MPIcheckPoint(); |
106 |
< |
#endif // is_mpi |
107 |
< |
|
106 |
> |
// check on the post processing info |
107 |
|
|
108 |
+ |
finalInfoCheck(); |
109 |
|
|
110 |
– |
// 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]; |
110 |
|
|
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 |
111 |
|
|
119 |
– |
tot_nmol = 0; |
120 |
– |
for( i=0; i<n_components; i++ ){ |
112 |
|
|
113 |
< |
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 |
< |
} |
113 |
> |
// initialize the system coordinates |
114 |
|
|
115 |
< |
tot_nmol += the_components[i]->getNMol(); |
116 |
< |
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 |
< |
} |
115 |
> |
initSystemCoords(); |
116 |
> |
|
117 |
|
|
118 |
< |
#ifdef IS_MPI |
161 |
< |
strcpy( checkPointMsg, "Have the number of components" ); |
162 |
< |
MPIcheckPoint(); |
163 |
< |
#endif // is_mpi |
118 |
> |
// make the output filenames |
119 |
|
|
120 |
< |
// make an array of molecule stamps that match the components used. |
121 |
< |
// also extract the used stamps out into a separate linked list |
120 |
> |
makeOutNames(); |
121 |
> |
|
122 |
> |
|
123 |
> |
|
124 |
|
|
168 |
– |
simnfo->nComponents = n_components; |
169 |
– |
simnfo->componentsNmol = components_nmol; |
170 |
– |
simnfo->compStamps = comp_stamps; |
171 |
– |
simnfo->headStamp = new LinkedMolStamp(); |
125 |
|
|
173 |
– |
char* id; |
174 |
– |
LinkedMolStamp* headStamp = simnfo->headStamp; |
175 |
– |
LinkedMolStamp* currentStamp = NULL; |
176 |
– |
for( i=0; i<n_components; i++ ){ |
126 |
|
|
127 |
< |
id = the_components[i]->getType(); |
179 |
< |
comp_stamps[i] = NULL; |
180 |
< |
|
181 |
< |
// check to make sure the component isn't already in the list |
127 |
> |
|
128 |
|
|
183 |
– |
comp_stamps[i] = headStamp->match( id ); |
184 |
– |
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 |
– |
} |
129 |
|
|
130 |
< |
#ifdef IS_MPI |
204 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
205 |
< |
MPIcheckPoint(); |
206 |
< |
#endif // is_mpi |
130 |
> |
// make the integrator |
131 |
|
|
132 |
+ |
|
133 |
+ |
NVT* myNVT = NULL; |
134 |
+ |
NPTi* myNPTi = NULL; |
135 |
+ |
NPTf* myNPTf = NULL; |
136 |
+ |
NPTim* myNPTim = NULL; |
137 |
+ |
NPTfm* myNPTfm = NULL; |
138 |
|
|
139 |
+ |
switch( ensembleCase ){ |
140 |
|
|
141 |
+ |
case NVE_ENS: |
142 |
+ |
new NVE( info, the_ff ); |
143 |
+ |
break; |
144 |
|
|
145 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
145 |
> |
case NVT_ENS: |
146 |
> |
myNVT = new NVT( info, the_ff ); |
147 |
> |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
148 |
|
|
149 |
< |
tot_atoms = 0; |
150 |
< |
tot_bonds = 0; |
215 |
< |
tot_bends = 0; |
216 |
< |
tot_torsions = 0; |
217 |
< |
for( i=0; i<n_components; i++ ){ |
218 |
< |
|
219 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
220 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
221 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
222 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
223 |
< |
} |
149 |
> |
if (the_globals->haveTauThermostat()) |
150 |
> |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
151 |
|
|
152 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
152 |
> |
else { |
153 |
> |
sprintf( painCave.errMsg, |
154 |
> |
"SimSetup error: If you use the NVT\n" |
155 |
> |
" ensemble, you must set tauThermostat.\n"); |
156 |
> |
painCave.isFatal = 1; |
157 |
> |
simError(); |
158 |
> |
} |
159 |
> |
break; |
160 |
|
|
161 |
< |
simnfo->n_atoms = tot_atoms; |
162 |
< |
simnfo->n_bonds = tot_bonds; |
163 |
< |
simnfo->n_bends = tot_bends; |
230 |
< |
simnfo->n_torsions = tot_torsions; |
231 |
< |
simnfo->n_SRI = tot_SRI; |
232 |
< |
simnfo->n_mol = tot_nmol; |
161 |
> |
case NPTi_ENS: |
162 |
> |
myNPTi = new NPTi( info, the_ff ); |
163 |
> |
myNPTi->setTargetTemp( the_globals->getTargetTemp() ); |
164 |
|
|
165 |
< |
|
166 |
< |
#ifdef IS_MPI |
165 |
> |
if (the_globals->haveTargetPressure()) |
166 |
> |
myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
167 |
> |
else { |
168 |
> |
sprintf( painCave.errMsg, |
169 |
> |
"SimSetup error: If you use a constant pressure\n" |
170 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
171 |
> |
painCave.isFatal = 1; |
172 |
> |
simError(); |
173 |
> |
} |
174 |
> |
|
175 |
> |
if( the_globals->haveTauThermostat() ) |
176 |
> |
myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
177 |
> |
else{ |
178 |
> |
sprintf( painCave.errMsg, |
179 |
> |
"SimSetup error: If you use an NPT\n" |
180 |
> |
" ensemble, you must set tauThermostat.\n"); |
181 |
> |
painCave.isFatal = 1; |
182 |
> |
simError(); |
183 |
> |
} |
184 |
|
|
185 |
< |
// divide the molecules among processors here. |
186 |
< |
|
187 |
< |
mpiSim = new mpiSimulation( simnfo ); |
188 |
< |
|
189 |
< |
|
185 |
> |
if( the_globals->haveTauBarostat() ) |
186 |
> |
myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
187 |
> |
else{ |
188 |
> |
sprintf( painCave.errMsg, |
189 |
> |
"SimSetup error: If you use an NPT\n" |
190 |
> |
" ensemble, you must set tauBarostat.\n"); |
191 |
> |
painCave.isFatal = 1; |
192 |
> |
simError(); |
193 |
> |
} |
194 |
> |
break; |
195 |
|
|
196 |
< |
globalIndex = mpiSim->divideLabor(); |
196 |
> |
case NPTf_ENS: |
197 |
> |
myNPTf = new NPTf( info, the_ff ); |
198 |
> |
myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
199 |
> |
|
200 |
> |
if (the_globals->haveTargetPressure()) |
201 |
> |
myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
202 |
> |
else { |
203 |
> |
sprintf( painCave.errMsg, |
204 |
> |
"SimSetup error: If you use a constant pressure\n" |
205 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
206 |
> |
painCave.isFatal = 1; |
207 |
> |
simError(); |
208 |
> |
} |
209 |
|
|
210 |
< |
|
211 |
< |
|
212 |
< |
// set up the local variables |
213 |
< |
|
214 |
< |
int localMol, allMol; |
215 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
216 |
< |
|
217 |
< |
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++ ){ |
261 |
< |
|
262 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
264 |
< |
|
265 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
266 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
267 |
< |
local_bends += comp_stamps[i]->getNBends(); |
268 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
269 |
< |
localMol++; |
270 |
< |
} |
271 |
< |
allMol++; |
210 |
> |
if( the_globals->haveTauThermostat() ) |
211 |
> |
myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
212 |
> |
else{ |
213 |
> |
sprintf( painCave.errMsg, |
214 |
> |
"SimSetup error: If you use an NPT\n" |
215 |
> |
" ensemble, you must set tauThermostat.\n"); |
216 |
> |
painCave.isFatal = 1; |
217 |
> |
simError(); |
218 |
|
} |
273 |
– |
} |
274 |
– |
local_SRI = local_bonds + local_bends + local_torsions; |
275 |
– |
|
219 |
|
|
220 |
< |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
221 |
< |
|
222 |
< |
if( local_atoms != simnfo->n_atoms ){ |
280 |
< |
sprintf( painCave.errMsg, |
281 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
282 |
< |
" localAtom (%d) are note equal.\n", |
283 |
< |
simnfo->n_atoms, |
284 |
< |
local_atoms ); |
285 |
< |
painCave.isFatal = 1; |
286 |
< |
simError(); |
287 |
< |
} |
288 |
< |
|
289 |
< |
simnfo->n_bonds = local_bonds; |
290 |
< |
simnfo->n_bends = local_bends; |
291 |
< |
simnfo->n_torsions = local_torsions; |
292 |
< |
simnfo->n_SRI = local_SRI; |
293 |
< |
simnfo->n_mol = localMol; |
294 |
< |
|
295 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
296 |
< |
MPIcheckPoint(); |
297 |
< |
|
298 |
< |
|
299 |
< |
#endif // is_mpi |
300 |
< |
|
301 |
< |
|
302 |
< |
// create the atom and short range interaction arrays |
303 |
< |
|
304 |
< |
Atom::createArrays(simnfo->n_atoms); |
305 |
< |
the_atoms = new Atom*[simnfo->n_atoms]; |
306 |
< |
the_molecules = new Molecule[simnfo->n_mol]; |
307 |
< |
|
308 |
< |
|
309 |
< |
if( simnfo->n_SRI ){ |
310 |
< |
Exclude::createArray(simnfo->n_SRI); |
311 |
< |
the_excludes = new Exclude*[simnfo->n_SRI]; |
312 |
< |
simnfo->globalExcludes = new int; |
313 |
< |
simnfo->n_exclude = tot_SRI; |
314 |
< |
} |
315 |
< |
else{ |
316 |
< |
|
317 |
< |
Exclude::createArray( 1 ); |
318 |
< |
the_excludes = new Exclude*; |
319 |
< |
the_excludes[0] = new Exclude(0); |
320 |
< |
the_excludes[0]->setPair( 0,0 ); |
321 |
< |
simnfo->globalExcludes = new int; |
322 |
< |
simnfo->globalExcludes[0] = 0; |
323 |
< |
simnfo->n_exclude = 0; |
324 |
< |
} |
325 |
< |
|
326 |
< |
// set the arrays into the SimInfo object |
327 |
< |
|
328 |
< |
simnfo->atoms = the_atoms; |
329 |
< |
simnfo->sr_interactions = the_sris; |
330 |
< |
simnfo->nGlobalExcludes = 0; |
331 |
< |
simnfo->excludes = the_excludes; |
332 |
< |
|
333 |
< |
|
334 |
< |
// get some of the tricky things that may still be in the globals |
335 |
< |
|
336 |
< |
|
337 |
< |
if( the_globals->haveBox() ){ |
338 |
< |
simnfo->box_x = the_globals->getBox(); |
339 |
< |
simnfo->box_y = the_globals->getBox(); |
340 |
< |
simnfo->box_z = the_globals->getBox(); |
341 |
< |
} |
342 |
< |
else if( the_globals->haveDensity() ){ |
343 |
< |
|
344 |
< |
double vol; |
345 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
346 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
347 |
< |
simnfo->box_y = simnfo->box_x; |
348 |
< |
simnfo->box_z = simnfo->box_x; |
349 |
< |
} |
350 |
< |
else{ |
351 |
< |
if( !the_globals->haveBoxX() ){ |
220 |
> |
if( the_globals->haveTauBarostat() ) |
221 |
> |
myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
222 |
> |
else{ |
223 |
|
sprintf( painCave.errMsg, |
224 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
224 |
> |
"SimSetup error: If you use an NPT\n" |
225 |
> |
" ensemble, you must set tauBarostat.\n"); |
226 |
|
painCave.isFatal = 1; |
227 |
|
simError(); |
228 |
|
} |
229 |
< |
simnfo->box_x = the_globals->getBoxX(); |
229 |
> |
break; |
230 |
> |
|
231 |
> |
case NPTim_ENS: |
232 |
> |
myNPTim = new NPTim( info, the_ff ); |
233 |
> |
myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
234 |
|
|
235 |
< |
if( !the_globals->haveBoxY() ){ |
235 |
> |
if (the_globals->haveTargetPressure()) |
236 |
> |
myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
237 |
> |
else { |
238 |
|
sprintf( painCave.errMsg, |
239 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
239 |
> |
"SimSetup error: If you use a constant pressure\n" |
240 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
241 |
|
painCave.isFatal = 1; |
242 |
|
simError(); |
243 |
|
} |
244 |
< |
simnfo->box_y = the_globals->getBoxY(); |
245 |
< |
|
246 |
< |
if( !the_globals->haveBoxZ() ){ |
244 |
> |
|
245 |
> |
if( the_globals->haveTauThermostat() ) |
246 |
> |
myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
247 |
> |
else{ |
248 |
|
sprintf( painCave.errMsg, |
249 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
249 |
> |
"SimSetup error: If you use an NPT\n" |
250 |
> |
" ensemble, you must set tauThermostat.\n"); |
251 |
|
painCave.isFatal = 1; |
252 |
|
simError(); |
253 |
|
} |
373 |
– |
simnfo->box_z = the_globals->getBoxZ(); |
374 |
– |
} |
254 |
|
|
255 |
< |
#ifdef IS_MPI |
256 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
257 |
< |
MPIcheckPoint(); |
379 |
< |
#endif // is_mpi |
380 |
< |
|
381 |
< |
|
382 |
< |
// initialize the arrays |
383 |
< |
|
384 |
< |
the_ff->setSimInfo( simnfo ); |
385 |
< |
|
386 |
< |
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 |
< |
} |
391 |
< |
|
392 |
< |
if( tot_bonds ){ |
393 |
< |
makeBonds(); |
394 |
< |
} |
395 |
< |
|
396 |
< |
if( tot_bends ){ |
397 |
< |
makeBends(); |
398 |
< |
} |
399 |
< |
|
400 |
< |
if( tot_torsions ){ |
401 |
< |
makeTorsions(); |
402 |
< |
} |
403 |
< |
|
404 |
< |
|
405 |
< |
if (the_globals->getUseRF() ) { |
406 |
< |
simnfo->useReactionField = 1; |
407 |
< |
|
408 |
< |
if( !the_globals->haveECR() ){ |
255 |
> |
if( the_globals->haveTauBarostat() ) |
256 |
> |
myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
257 |
> |
else{ |
258 |
|
sprintf( painCave.errMsg, |
259 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
260 |
< |
"box length for the electrostaticCutoffRadius.\n" |
261 |
< |
"I hope you have a very fast processor!\n"); |
413 |
< |
painCave.isFatal = 0; |
259 |
> |
"SimSetup error: If you use an NPT\n" |
260 |
> |
" ensemble, you must set tauBarostat.\n"); |
261 |
> |
painCave.isFatal = 1; |
262 |
|
simError(); |
415 |
– |
double smallest; |
416 |
– |
smallest = simnfo->box_x; |
417 |
– |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
418 |
– |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
419 |
– |
simnfo->ecr = 0.5 * smallest; |
420 |
– |
} else { |
421 |
– |
simnfo->ecr = the_globals->getECR(); |
263 |
|
} |
264 |
+ |
break; |
265 |
|
|
266 |
< |
if( !the_globals->haveEST() ){ |
266 |
> |
case NPTfm_ENS: |
267 |
> |
myNPTfm = new NPTfm( info, the_ff ); |
268 |
> |
myNPTfm->setTargetTemp( the_globals->getTargetTemp()); |
269 |
> |
|
270 |
> |
if (the_globals->haveTargetPressure()) |
271 |
> |
myNPTfm->setTargetPressure(the_globals->getTargetPressure()); |
272 |
> |
else { |
273 |
|
sprintf( painCave.errMsg, |
274 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
275 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
276 |
< |
); |
429 |
< |
painCave.isFatal = 0; |
274 |
> |
"SimSetup error: If you use a constant pressure\n" |
275 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
276 |
> |
painCave.isFatal = 1; |
277 |
|
simError(); |
431 |
– |
simnfo->est = 0.05 * simnfo->ecr; |
432 |
– |
} else { |
433 |
– |
simnfo->est = the_globals->getEST(); |
278 |
|
} |
279 |
|
|
280 |
< |
if(!the_globals->haveDielectric() ){ |
280 |
> |
if( the_globals->haveTauThermostat() ) |
281 |
> |
myNPTfm->setTauThermostat( the_globals->getTauThermostat() ); |
282 |
> |
else{ |
283 |
|
sprintf( painCave.errMsg, |
284 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
285 |
< |
"setting a dielectric constant!\n" |
440 |
< |
); |
284 |
> |
"SimSetup error: If you use an NPT\n" |
285 |
> |
" ensemble, you must set tauThermostat.\n"); |
286 |
|
painCave.isFatal = 1; |
287 |
|
simError(); |
288 |
|
} |
444 |
– |
simnfo->dielectric = the_globals->getDielectric(); |
445 |
– |
} else { |
446 |
– |
if (simnfo->n_dipoles) { |
447 |
– |
|
448 |
– |
if( !the_globals->haveECR() ){ |
449 |
– |
sprintf( painCave.errMsg, |
450 |
– |
"SimSetup Warning: using default value of 1/2 the smallest" |
451 |
– |
"box length for the electrostaticCutoffRadius.\n" |
452 |
– |
"I hope you have a very fast processor!\n"); |
453 |
– |
painCave.isFatal = 0; |
454 |
– |
simError(); |
455 |
– |
double smallest; |
456 |
– |
smallest = simnfo->box_x; |
457 |
– |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
458 |
– |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
459 |
– |
simnfo->ecr = 0.5 * smallest; |
460 |
– |
} else { |
461 |
– |
simnfo->ecr = the_globals->getECR(); |
462 |
– |
} |
463 |
– |
|
464 |
– |
if( !the_globals->haveEST() ){ |
465 |
– |
sprintf( painCave.errMsg, |
466 |
– |
"SimSetup Warning: using default value of 5% of the" |
467 |
– |
"electrostaticCutoffRadius for the " |
468 |
– |
"electrostaticSkinThickness\n" |
469 |
– |
); |
470 |
– |
painCave.isFatal = 0; |
471 |
– |
simError(); |
472 |
– |
simnfo->est = 0.05 * simnfo->ecr; |
473 |
– |
} else { |
474 |
– |
simnfo->est = the_globals->getEST(); |
475 |
– |
} |
476 |
– |
} |
477 |
– |
} |
289 |
|
|
290 |
< |
#ifdef IS_MPI |
291 |
< |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
481 |
< |
MPIcheckPoint(); |
482 |
< |
#endif // is_mpi |
483 |
< |
|
484 |
< |
if( the_globals->haveInitialConfig() ){ |
485 |
< |
|
486 |
< |
InitializeFromFile* fileInit; |
487 |
< |
#ifdef IS_MPI // is_mpi |
488 |
< |
if( worldRank == 0 ){ |
489 |
< |
#endif //is_mpi |
490 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
491 |
< |
#ifdef IS_MPI |
492 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
493 |
< |
#endif |
494 |
< |
fileInit->read_xyz( simnfo ); // default velocities on |
495 |
< |
|
496 |
< |
delete fileInit; |
497 |
< |
} |
498 |
< |
else{ |
499 |
< |
|
500 |
< |
#ifdef IS_MPI |
501 |
< |
|
502 |
< |
// no init from bass |
503 |
< |
|
504 |
< |
sprintf( painCave.errMsg, |
505 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
506 |
< |
painCave.isFatal; |
507 |
< |
simError(); |
508 |
< |
|
509 |
< |
#else |
510 |
< |
|
511 |
< |
initFromBass(); |
512 |
< |
|
513 |
< |
|
514 |
< |
#endif |
515 |
< |
} |
516 |
< |
|
517 |
< |
#ifdef IS_MPI |
518 |
< |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
519 |
< |
MPIcheckPoint(); |
520 |
< |
#endif // is_mpi |
521 |
< |
|
522 |
< |
|
523 |
< |
|
524 |
< |
|
525 |
< |
|
526 |
< |
|
527 |
< |
|
528 |
< |
#ifdef IS_MPI |
529 |
< |
if( worldRank == 0 ){ |
530 |
< |
#endif // is_mpi |
531 |
< |
|
532 |
< |
if( the_globals->haveFinalConfig() ){ |
533 |
< |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
534 |
< |
} |
290 |
> |
if( the_globals->haveTauBarostat() ) |
291 |
> |
myNPTfm->setTauBarostat( the_globals->getTauBarostat() ); |
292 |
|
else{ |
293 |
< |
strcpy( simnfo->finalName, inFileName ); |
294 |
< |
char* endTest; |
295 |
< |
int nameLength = strlen( simnfo->finalName ); |
296 |
< |
endTest = &(simnfo->finalName[nameLength - 5]); |
297 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
541 |
< |
strcpy( endTest, ".eor" ); |
542 |
< |
} |
543 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
544 |
< |
strcpy( endTest, ".eor" ); |
545 |
< |
} |
546 |
< |
else{ |
547 |
< |
endTest = &(simnfo->finalName[nameLength - 4]); |
548 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
549 |
< |
strcpy( endTest, ".eor" ); |
550 |
< |
} |
551 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
552 |
< |
strcpy( endTest, ".eor" ); |
553 |
< |
} |
554 |
< |
else{ |
555 |
< |
strcat( simnfo->finalName, ".eor" ); |
556 |
< |
} |
557 |
< |
} |
293 |
> |
sprintf( painCave.errMsg, |
294 |
> |
"SimSetup error: If you use an NPT\n" |
295 |
> |
" ensemble, you must set tauBarostat.\n"); |
296 |
> |
painCave.isFatal = 1; |
297 |
> |
simError(); |
298 |
|
} |
299 |
< |
|
560 |
< |
// make the sample and status out names |
561 |
< |
|
562 |
< |
strcpy( simnfo->sampleName, inFileName ); |
563 |
< |
char* endTest; |
564 |
< |
int nameLength = strlen( simnfo->sampleName ); |
565 |
< |
endTest = &(simnfo->sampleName[nameLength - 5]); |
566 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
567 |
< |
strcpy( endTest, ".dump" ); |
568 |
< |
} |
569 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
570 |
< |
strcpy( endTest, ".dump" ); |
571 |
< |
} |
572 |
< |
else{ |
573 |
< |
endTest = &(simnfo->sampleName[nameLength - 4]); |
574 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
575 |
< |
strcpy( endTest, ".dump" ); |
576 |
< |
} |
577 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
578 |
< |
strcpy( endTest, ".dump" ); |
579 |
< |
} |
580 |
< |
else{ |
581 |
< |
strcat( simnfo->sampleName, ".dump" ); |
582 |
< |
} |
583 |
< |
} |
584 |
< |
|
585 |
< |
strcpy( simnfo->statusName, inFileName ); |
586 |
< |
nameLength = strlen( simnfo->statusName ); |
587 |
< |
endTest = &(simnfo->statusName[nameLength - 5]); |
588 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
589 |
< |
strcpy( endTest, ".stat" ); |
590 |
< |
} |
591 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
592 |
< |
strcpy( endTest, ".stat" ); |
593 |
< |
} |
594 |
< |
else{ |
595 |
< |
endTest = &(simnfo->statusName[nameLength - 4]); |
596 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
597 |
< |
strcpy( endTest, ".stat" ); |
598 |
< |
} |
599 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
600 |
< |
strcpy( endTest, ".stat" ); |
601 |
< |
} |
602 |
< |
else{ |
603 |
< |
strcat( simnfo->statusName, ".stat" ); |
604 |
< |
} |
605 |
< |
} |
606 |
< |
|
607 |
< |
#ifdef IS_MPI |
608 |
< |
} |
609 |
< |
#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 |
< |
} |
299 |
> |
break; |
300 |
|
|
301 |
< |
if( the_globals->haveStatusTime() ){ |
302 |
< |
simnfo->statusTime = the_globals->getStatusTime(); |
301 |
> |
default: |
302 |
> |
sprintf( painCave.errMsg, |
303 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
304 |
> |
painCave.isFatal = 1; |
305 |
> |
simError(); |
306 |
|
} |
307 |
|
|
628 |
– |
if( the_globals->haveThermalTime() ){ |
629 |
– |
simnfo->thermalTime = the_globals->getThermalTime(); |
630 |
– |
} |
308 |
|
|
309 |
< |
// check for the temperature set flag |
309 |
> |
#ifdef IS_MPI |
310 |
> |
mpiSim->mpiRefresh(); |
311 |
> |
#endif |
312 |
|
|
313 |
< |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
313 |
> |
// initialize the Fortran |
314 |
|
|
315 |
|
|
316 |
< |
// // make the longe range forces and the integrator |
638 |
< |
|
639 |
< |
// new AllLong( simnfo ); |
640 |
< |
|
641 |
< |
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 ); |
645 |
< |
|
646 |
< |
|
647 |
< |
|
648 |
< |
// initialize the Fortran |
649 |
< |
|
650 |
< |
simnfo->refreshSim(); |
316 |
> |
info->refreshSim(); |
317 |
|
|
318 |
< |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
318 |
> |
if( !strcmp( info->mixingRule, "standard") ){ |
319 |
|
the_ff->initForceField( LB_MIXING_RULE ); |
320 |
|
} |
321 |
< |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
321 |
> |
else if( !strcmp( info->mixingRule, "explicit") ){ |
322 |
|
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
323 |
|
} |
324 |
|
else{ |
325 |
|
sprintf( painCave.errMsg, |
326 |
|
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
327 |
< |
simnfo->mixingRule ); |
327 |
> |
info->mixingRule ); |
328 |
|
painCave.isFatal = 1; |
329 |
|
simError(); |
330 |
|
} |
349 |
|
BondStamp* currentBond; |
350 |
|
BendStamp* currentBend; |
351 |
|
TorsionStamp* currentTorsion; |
352 |
+ |
|
353 |
+ |
bond_pair* theBonds; |
354 |
+ |
bend_set* theBends; |
355 |
+ |
torsion_set* theTorsions; |
356 |
+ |
|
357 |
|
|
358 |
|
//init the forceField paramters |
359 |
|
|
360 |
|
the_ff->readParams(); |
361 |
|
|
362 |
|
|
363 |
< |
// init the molecules |
363 |
> |
// init the atoms |
364 |
|
|
365 |
+ |
double ux, uy, uz, u, uSqr; |
366 |
+ |
|
367 |
|
atomOffset = 0; |
368 |
|
excludeOffset = 0; |
369 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
369 |
> |
for(i=0; i<info->n_mol; i++){ |
370 |
|
|
371 |
|
stampID = the_molecules[i].getStampID(); |
372 |
|
|
380 |
|
info.myExcludes = &the_excludes[excludeOffset]; |
381 |
|
info.myBonds = new Bond*[info.nBonds]; |
382 |
|
info.myBends = new Bend*[info.nBends]; |
383 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
383 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
384 |
|
|
385 |
|
theBonds = new bond_pair[info.nBonds]; |
386 |
|
theBends = new bend_set[info.nBends]; |
390 |
|
|
391 |
|
for(j=0; j<info.nAtoms; j++){ |
392 |
|
|
393 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
393 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
394 |
|
if( currentAtom->haveOrientation() ){ |
395 |
|
|
396 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
397 |
< |
simnfo->n_oriented++; |
397 |
> |
info->n_oriented++; |
398 |
|
info.myAtoms[j] = dAtom; |
399 |
|
|
400 |
|
ux = currentAtom->getOrntX(); |
431 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
432 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
433 |
|
|
434 |
< |
exI = theBonds[i].a; |
435 |
< |
exJ = theBonds[i].b; |
434 |
> |
exI = theBonds[j].a; |
435 |
> |
exJ = theBonds[j].b; |
436 |
|
|
437 |
|
// exclude_I must always be the smaller of the pair |
438 |
|
if( exI > exJ ){ |
448 |
|
|
449 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
450 |
|
#else // isn't MPI |
451 |
+ |
|
452 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
453 |
|
#endif //is_mpi |
454 |
|
} |
464 |
|
|
465 |
|
if( currentBend->haveExtras() ){ |
466 |
|
|
467 |
< |
extras = current_bend->getExtras(); |
467 |
> |
extras = currentBend->getExtras(); |
468 |
|
current_extra = extras; |
469 |
|
|
470 |
|
while( current_extra != NULL ){ |
486 |
|
|
487 |
|
default: |
488 |
|
sprintf( painCave.errMsg, |
489 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
489 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
490 |
|
"double nor an int.\n" |
491 |
|
"-->Bend[%d] in %s\n", |
492 |
|
j, comp_stamps[stampID]->getID() ); |
571 |
|
excludeOffset += info.nTorsions; |
572 |
|
|
573 |
|
|
574 |
< |
|
901 |
< |
|
902 |
< |
|
903 |
< |
|
904 |
< |
|
905 |
< |
|
906 |
< |
void SimSetup::makeAtoms( void ){ |
907 |
< |
|
908 |
< |
int i, j, k, index; |
909 |
< |
double ux, uy, uz, uSqr, u; |
910 |
< |
AtomStamp* current_atom; |
911 |
< |
|
912 |
< |
DirectionalAtom* dAtom; |
913 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
914 |
< |
|
915 |
< |
lMolIndex = 0; |
916 |
< |
molIndex = 0; |
917 |
< |
index = 0; |
918 |
< |
for( i=0; i<n_components; i++ ){ |
919 |
< |
|
920 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
921 |
< |
|
922 |
< |
#ifdef IS_MPI |
923 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
924 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
925 |
< |
#endif // is_mpi |
574 |
> |
// send the arrays off to the forceField for init. |
575 |
|
|
576 |
< |
molStart = index; |
577 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
578 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
579 |
< |
|
931 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
932 |
< |
if( current_atom->haveOrientation() ){ |
933 |
< |
|
934 |
< |
dAtom = new DirectionalAtom(index); |
935 |
< |
simnfo->n_oriented++; |
936 |
< |
the_atoms[index] = dAtom; |
937 |
< |
|
938 |
< |
ux = current_atom->getOrntX(); |
939 |
< |
uy = current_atom->getOrntY(); |
940 |
< |
uz = current_atom->getOrntZ(); |
941 |
< |
|
942 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
943 |
< |
|
944 |
< |
u = sqrt( uSqr ); |
945 |
< |
ux = ux / u; |
946 |
< |
uy = uy / u; |
947 |
< |
uz = uz / u; |
948 |
< |
|
949 |
< |
dAtom->setSUx( ux ); |
950 |
< |
dAtom->setSUy( uy ); |
951 |
< |
dAtom->setSUz( uz ); |
952 |
< |
} |
953 |
< |
else{ |
954 |
< |
the_atoms[index] = new GeneralAtom(index); |
955 |
< |
} |
956 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
957 |
< |
the_atoms[index]->setIndex( index ); |
958 |
< |
|
959 |
< |
// increment the index and repeat; |
960 |
< |
index++; |
961 |
< |
} |
962 |
< |
|
963 |
< |
molEnd = index -1; |
964 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
965 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
966 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
967 |
< |
the_molecules[lMolIndex].setStampID( i ); |
968 |
< |
lMolIndex++; |
969 |
< |
|
970 |
< |
#ifdef IS_MPI |
971 |
< |
} |
972 |
< |
#endif //is_mpi |
973 |
< |
|
974 |
< |
molIndex++; |
975 |
< |
} |
976 |
< |
} |
977 |
< |
|
978 |
< |
#ifdef IS_MPI |
979 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
980 |
< |
|
981 |
< |
delete[] globalIndex; |
576 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
577 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
578 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
579 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
580 |
|
|
983 |
– |
mpiSim->mpiRefresh(); |
984 |
– |
#endif //IS_MPI |
985 |
– |
|
986 |
– |
the_ff->initializeAtoms(); |
987 |
– |
} |
581 |
|
|
582 |
< |
void SimSetup::makeBonds( void ){ |
990 |
< |
|
991 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
992 |
< |
bond_pair* the_bonds; |
993 |
< |
BondStamp* current_bond; |
994 |
< |
|
995 |
< |
the_bonds = new bond_pair[tot_bonds]; |
996 |
< |
index = 0; |
997 |
< |
offset = 0; |
998 |
< |
molIndex = 0; |
999 |
< |
|
1000 |
< |
for( i=0; i<n_components; i++ ){ |
1001 |
< |
|
1002 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1003 |
< |
|
1004 |
< |
#ifdef IS_MPI |
1005 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
1006 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
1007 |
< |
#endif // is_mpi |
1008 |
< |
|
1009 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
1010 |
< |
|
1011 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
1012 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
1013 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
1014 |
< |
|
1015 |
< |
exI = the_bonds[index].a; |
1016 |
< |
exJ = the_bonds[index].b; |
1017 |
< |
|
1018 |
< |
// exclude_I must always be the smaller of the pair |
1019 |
< |
if( exI > exJ ){ |
1020 |
< |
tempEx = exI; |
1021 |
< |
exI = exJ; |
1022 |
< |
exJ = tempEx; |
1023 |
< |
} |
1024 |
< |
|
1025 |
< |
|
1026 |
< |
#ifdef IS_MPI |
1027 |
< |
|
1028 |
< |
the_excludes[index*2] = |
1029 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1030 |
< |
the_excludes[index*2 + 1] = |
1031 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1032 |
< |
|
1033 |
< |
#else // isn't MPI |
1034 |
< |
|
1035 |
< |
the_excludes[index*2] = exI + 1; |
1036 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
1037 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
1038 |
< |
#endif //is_mpi |
1039 |
< |
|
1040 |
< |
// increment the index and repeat; |
1041 |
< |
index++; |
1042 |
< |
} |
1043 |
< |
offset += comp_stamps[i]->getNAtoms(); |
1044 |
< |
|
1045 |
< |
#ifdef IS_MPI |
1046 |
< |
} |
1047 |
< |
#endif //is_mpi |
1048 |
< |
|
1049 |
< |
molIndex++; |
1050 |
< |
} |
1051 |
< |
} |
1052 |
< |
|
1053 |
< |
the_ff->initializeBonds( the_bonds ); |
1054 |
< |
} |
1055 |
< |
|
1056 |
< |
void SimSetup::makeBends( void ){ |
1057 |
< |
|
1058 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1059 |
< |
bend_set* the_bends; |
1060 |
< |
BendStamp* current_bend; |
1061 |
< |
LinkedAssign* extras; |
1062 |
< |
LinkedAssign* current_extra; |
1063 |
< |
|
1064 |
< |
|
1065 |
< |
the_bends = new bend_set[tot_bends]; |
1066 |
< |
index = 0; |
1067 |
< |
offset = 0; |
1068 |
< |
molIndex = 0; |
1069 |
< |
for( i=0; i<n_components; i++ ){ |
1070 |
< |
|
1071 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1072 |
< |
|
1073 |
< |
#ifdef IS_MPI |
1074 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
1075 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
1076 |
< |
#endif // is_mpi |
1077 |
< |
|
1078 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
1079 |
< |
|
1080 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
1081 |
< |
the_bends[index].a = current_bend->getA() + offset; |
1082 |
< |
the_bends[index].b = current_bend->getB() + offset; |
1083 |
< |
the_bends[index].c = current_bend->getC() + offset; |
1084 |
< |
|
1085 |
< |
if( current_bend->haveExtras() ){ |
1086 |
< |
|
1087 |
< |
extras = current_bend->getExtras(); |
1088 |
< |
current_extra = extras; |
1089 |
< |
|
1090 |
< |
while( current_extra != NULL ){ |
1091 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1092 |
< |
|
1093 |
< |
switch( current_extra->getType() ){ |
1094 |
< |
|
1095 |
< |
case 0: |
1096 |
< |
the_bends[index].ghost = |
1097 |
< |
current_extra->getInt() + offset; |
1098 |
< |
the_bends[index].isGhost = 1; |
1099 |
< |
break; |
1100 |
< |
|
1101 |
< |
case 1: |
1102 |
< |
the_bends[index].ghost = |
1103 |
< |
(int)current_extra->getDouble() + offset; |
1104 |
< |
the_bends[index].isGhost = 1; |
1105 |
< |
break; |
1106 |
< |
|
1107 |
< |
default: |
1108 |
< |
sprintf( painCave.errMsg, |
1109 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
1110 |
< |
"double nor an int.\n" |
1111 |
< |
"-->Bend[%d] in %s\n", |
1112 |
< |
k, comp_stamps[i]->getID() ); |
1113 |
< |
painCave.isFatal = 1; |
1114 |
< |
simError(); |
1115 |
< |
} |
1116 |
< |
} |
1117 |
< |
|
1118 |
< |
else{ |
1119 |
< |
|
1120 |
< |
sprintf( painCave.errMsg, |
1121 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
1122 |
< |
" -->%s in Bend[%d] in %s\n", |
1123 |
< |
current_extra->getlhs(), |
1124 |
< |
k, comp_stamps[i]->getID() ); |
1125 |
< |
painCave.isFatal = 1; |
1126 |
< |
simError(); |
1127 |
< |
} |
1128 |
< |
|
1129 |
< |
current_extra = current_extra->getNext(); |
1130 |
< |
} |
1131 |
< |
} |
1132 |
< |
|
1133 |
< |
if( !the_bends[index].isGhost ){ |
1134 |
< |
|
1135 |
< |
exI = the_bends[index].a; |
1136 |
< |
exJ = the_bends[index].c; |
1137 |
< |
} |
1138 |
< |
else{ |
1139 |
< |
|
1140 |
< |
exI = the_bends[index].a; |
1141 |
< |
exJ = the_bends[index].b; |
1142 |
< |
} |
1143 |
< |
|
1144 |
< |
// exclude_I must always be the smaller of the pair |
1145 |
< |
if( exI > exJ ){ |
1146 |
< |
tempEx = exI; |
1147 |
< |
exI = exJ; |
1148 |
< |
exJ = tempEx; |
1149 |
< |
} |
582 |
> |
the_molecules[i].initialize( info ); |
583 |
|
|
584 |
|
|
585 |
< |
#ifdef IS_MPI |
586 |
< |
|
587 |
< |
the_excludes[(index + tot_bonds)*2] = |
588 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1156 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
1157 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1158 |
< |
|
1159 |
< |
#else // isn't MPI |
1160 |
< |
|
1161 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
1162 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
1163 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
1164 |
< |
#endif //is_mpi |
1165 |
< |
|
1166 |
< |
|
1167 |
< |
// increment the index and repeat; |
1168 |
< |
index++; |
1169 |
< |
} |
1170 |
< |
offset += comp_stamps[i]->getNAtoms(); |
1171 |
< |
|
1172 |
< |
#ifdef IS_MPI |
1173 |
< |
} |
1174 |
< |
#endif //is_mpi |
1175 |
< |
|
1176 |
< |
molIndex++; |
1177 |
< |
} |
585 |
> |
atomOffset += info.nAtoms; |
586 |
> |
delete[] theBonds; |
587 |
> |
delete[] theBends; |
588 |
> |
delete[] theTorsions; |
589 |
|
} |
590 |
|
|
591 |
|
#ifdef IS_MPI |
592 |
< |
sprintf( checkPointMsg, |
1182 |
< |
"Successfully created the bends list.\n" ); |
592 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
593 |
|
MPIcheckPoint(); |
594 |
|
#endif // is_mpi |
1185 |
– |
|
595 |
|
|
596 |
< |
the_ff->initializeBends( the_bends ); |
597 |
< |
} |
598 |
< |
|
1190 |
< |
void SimSetup::makeTorsions( void ){ |
1191 |
< |
|
1192 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1193 |
< |
torsion_set* the_torsions; |
1194 |
< |
TorsionStamp* current_torsion; |
1195 |
< |
|
1196 |
< |
the_torsions = new torsion_set[tot_torsions]; |
1197 |
< |
index = 0; |
1198 |
< |
offset = 0; |
1199 |
< |
molIndex = 0; |
1200 |
< |
for( i=0; i<n_components; i++ ){ |
596 |
> |
// clean up the forcefield |
597 |
> |
the_ff->calcRcut(); |
598 |
> |
the_ff->cleanMe(); |
599 |
|
|
1202 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
1203 |
– |
|
1204 |
– |
#ifdef IS_MPI |
1205 |
– |
if( mpiSim->getMyMolStart() <= molIndex && |
1206 |
– |
molIndex <= mpiSim->getMyMolEnd() ){ |
1207 |
– |
#endif // is_mpi |
1208 |
– |
|
1209 |
– |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1210 |
– |
|
1211 |
– |
current_torsion = comp_stamps[i]->getTorsion( k ); |
1212 |
– |
the_torsions[index].a = current_torsion->getA() + offset; |
1213 |
– |
the_torsions[index].b = current_torsion->getB() + offset; |
1214 |
– |
the_torsions[index].c = current_torsion->getC() + offset; |
1215 |
– |
the_torsions[index].d = current_torsion->getD() + offset; |
1216 |
– |
|
1217 |
– |
exI = the_torsions[index].a; |
1218 |
– |
exJ = the_torsions[index].d; |
1219 |
– |
|
1220 |
– |
|
1221 |
– |
// exclude_I must always be the smaller of the pair |
1222 |
– |
if( exI > exJ ){ |
1223 |
– |
tempEx = exI; |
1224 |
– |
exI = exJ; |
1225 |
– |
exJ = tempEx; |
1226 |
– |
} |
1227 |
– |
|
1228 |
– |
|
1229 |
– |
#ifdef IS_MPI |
1230 |
– |
|
1231 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
1232 |
– |
the_atoms[exI]->getGlobalIndex() + 1; |
1233 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1234 |
– |
the_atoms[exJ]->getGlobalIndex() + 1; |
1235 |
– |
|
1236 |
– |
#else // isn't MPI |
1237 |
– |
|
1238 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1239 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1240 |
– |
// fortran indexes from 1 (hence the +1 in the indexing) |
1241 |
– |
#endif //is_mpi |
1242 |
– |
|
1243 |
– |
|
1244 |
– |
// increment the index and repeat; |
1245 |
– |
index++; |
1246 |
– |
} |
1247 |
– |
offset += comp_stamps[i]->getNAtoms(); |
1248 |
– |
|
1249 |
– |
#ifdef IS_MPI |
1250 |
– |
} |
1251 |
– |
#endif //is_mpi |
1252 |
– |
|
1253 |
– |
molIndex++; |
1254 |
– |
} |
1255 |
– |
} |
1256 |
– |
|
1257 |
– |
the_ff->initializeTorsions( the_torsions ); |
600 |
|
} |
601 |
|
|
602 |
|
void SimSetup::initFromBass( void ){ |
618 |
|
have_extra =1; |
619 |
|
|
620 |
|
n_cells = (int)temp3 - 1; |
621 |
< |
cellx = simnfo->box_x / temp3; |
622 |
< |
celly = simnfo->box_y / temp3; |
623 |
< |
cellz = simnfo->box_z / temp3; |
621 |
> |
cellx = info->boxLx / temp3; |
622 |
> |
celly = info->boxLy / temp3; |
623 |
> |
cellz = info->boxLz / temp3; |
624 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
625 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
626 |
|
n_per_extra = (int)ceil( temp1 ); |
635 |
|
} |
636 |
|
else{ |
637 |
|
n_cells = (int)temp3; |
638 |
< |
cellx = simnfo->box_x / temp3; |
639 |
< |
celly = simnfo->box_y / temp3; |
640 |
< |
cellz = simnfo->box_z / temp3; |
638 |
> |
cellx = info->boxLx / temp3; |
639 |
> |
celly = info->boxLy / temp3; |
640 |
> |
cellz = info->boxLz / temp3; |
641 |
|
} |
642 |
|
|
643 |
|
current_mol = 0; |
717 |
|
} |
718 |
|
|
719 |
|
|
720 |
< |
for( i=0; i<simnfo->n_atoms; i++ ){ |
721 |
< |
simnfo->atoms[i]->set_vx( 0.0 ); |
722 |
< |
simnfo->atoms[i]->set_vy( 0.0 ); |
723 |
< |
simnfo->atoms[i]->set_vz( 0.0 ); |
720 |
> |
for( i=0; i<info->n_atoms; i++ ){ |
721 |
> |
info->atoms[i]->set_vx( 0.0 ); |
722 |
> |
info->atoms[i]->set_vy( 0.0 ); |
723 |
> |
info->atoms[i]->set_vz( 0.0 ); |
724 |
|
} |
725 |
|
} |
726 |
|
|
781 |
|
current_comp++; |
782 |
|
} |
783 |
|
} |
784 |
+ |
|
785 |
+ |
|
786 |
+ |
void SimSetup::gatherInfo( void ){ |
787 |
+ |
|
788 |
+ |
ensembleCase = -1; |
789 |
+ |
ffCase = -1; |
790 |
+ |
|
791 |
+ |
// get the stamps and globals; |
792 |
+ |
the_stamps = stamps; |
793 |
+ |
the_globals = globals; |
794 |
+ |
|
795 |
+ |
// set the easy ones first |
796 |
+ |
info->target_temp = the_globals->getTargetTemp(); |
797 |
+ |
info->dt = the_globals->getDt(); |
798 |
+ |
info->run_time = the_globals->getRunTime(); |
799 |
+ |
n_components = the_globals->getNComponents(); |
800 |
+ |
|
801 |
+ |
|
802 |
+ |
// get the forceField |
803 |
+ |
|
804 |
+ |
strcpy( force_field, the_globals->getForceField() ); |
805 |
+ |
|
806 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
807 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
808 |
+ |
else{ |
809 |
+ |
sprintf( painCave.errMsg, |
810 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
811 |
+ |
force_field ); |
812 |
+ |
painCave.isFatal = 1; |
813 |
+ |
simError(); |
814 |
+ |
} |
815 |
+ |
|
816 |
+ |
// get the ensemble |
817 |
+ |
|
818 |
+ |
strcpy( ensemble, the_globals->getEnsemble() ); |
819 |
+ |
|
820 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
821 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
822 |
+ |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
823 |
+ |
ensembleCase = NPTi_ENS; |
824 |
+ |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
825 |
+ |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
826 |
+ |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
827 |
+ |
else{ |
828 |
+ |
sprintf( painCave.errMsg, |
829 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
830 |
+ |
"reverting to NVE for this simulation.\n", |
831 |
+ |
ensemble ); |
832 |
+ |
painCave.isFatal = 0; |
833 |
+ |
simError(); |
834 |
+ |
strcpy( ensemble, "NVE" ); |
835 |
+ |
ensembleCase = NVE_ENS; |
836 |
+ |
} |
837 |
+ |
strcpy( info->ensemble, ensemble ); |
838 |
+ |
|
839 |
+ |
// get the mixing rule |
840 |
+ |
|
841 |
+ |
strcpy( info->mixingRule, the_globals->getMixingRule() ); |
842 |
+ |
info->usePBC = the_globals->getPBC(); |
843 |
+ |
|
844 |
+ |
|
845 |
+ |
// get the components and calculate the tot_nMol and indvidual n_mol |
846 |
+ |
|
847 |
+ |
the_components = the_globals->getComponents(); |
848 |
+ |
components_nmol = new int[n_components]; |
849 |
+ |
|
850 |
+ |
|
851 |
+ |
if( !the_globals->haveNMol() ){ |
852 |
+ |
// we don't have the total number of molecules, so we assume it is |
853 |
+ |
// given in each component |
854 |
+ |
|
855 |
+ |
tot_nmol = 0; |
856 |
+ |
for( i=0; i<n_components; i++ ){ |
857 |
+ |
|
858 |
+ |
if( !the_components[i]->haveNMol() ){ |
859 |
+ |
// we have a problem |
860 |
+ |
sprintf( painCave.errMsg, |
861 |
+ |
"SimSetup Error. No global NMol or component NMol" |
862 |
+ |
" given. Cannot calculate the number of atoms.\n" ); |
863 |
+ |
painCave.isFatal = 1; |
864 |
+ |
simError(); |
865 |
+ |
} |
866 |
+ |
|
867 |
+ |
tot_nmol += the_components[i]->getNMol(); |
868 |
+ |
components_nmol[i] = the_components[i]->getNMol(); |
869 |
+ |
} |
870 |
+ |
} |
871 |
+ |
else{ |
872 |
+ |
sprintf( painCave.errMsg, |
873 |
+ |
"SimSetup error.\n" |
874 |
+ |
"\tSorry, the ability to specify total" |
875 |
+ |
" nMols and then give molfractions in the components\n" |
876 |
+ |
"\tis not currently supported." |
877 |
+ |
" Please give nMol in the components.\n" ); |
878 |
+ |
painCave.isFatal = 1; |
879 |
+ |
simError(); |
880 |
+ |
} |
881 |
+ |
|
882 |
+ |
// set the status, sample, and thermal kick times |
883 |
+ |
|
884 |
+ |
if( the_globals->haveSampleTime() ){ |
885 |
+ |
info->sampleTime = the_globals->getSampleTime(); |
886 |
+ |
info->statusTime = info->sampleTime; |
887 |
+ |
info->thermalTime = info->sampleTime; |
888 |
+ |
} |
889 |
+ |
else{ |
890 |
+ |
info->sampleTime = the_globals->getRunTime(); |
891 |
+ |
info->statusTime = info->sampleTime; |
892 |
+ |
info->thermalTime = info->sampleTime; |
893 |
+ |
} |
894 |
+ |
|
895 |
+ |
if( the_globals->haveStatusTime() ){ |
896 |
+ |
info->statusTime = the_globals->getStatusTime(); |
897 |
+ |
} |
898 |
+ |
|
899 |
+ |
if( the_globals->haveThermalTime() ){ |
900 |
+ |
info->thermalTime = the_globals->getThermalTime(); |
901 |
+ |
} |
902 |
+ |
|
903 |
+ |
// check for the temperature set flag |
904 |
+ |
|
905 |
+ |
if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet(); |
906 |
+ |
|
907 |
+ |
// get some of the tricky things that may still be in the globals |
908 |
+ |
|
909 |
+ |
double boxVector[3]; |
910 |
+ |
if( the_globals->haveBox() ){ |
911 |
+ |
boxVector[0] = the_globals->getBox(); |
912 |
+ |
boxVector[1] = the_globals->getBox(); |
913 |
+ |
boxVector[2] = the_globals->getBox(); |
914 |
+ |
|
915 |
+ |
info->setBox( boxVector ); |
916 |
+ |
} |
917 |
+ |
else if( the_globals->haveDensity() ){ |
918 |
+ |
|
919 |
+ |
double vol; |
920 |
+ |
vol = (double)tot_nmol / the_globals->getDensity(); |
921 |
+ |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
922 |
+ |
boxVector[1] = boxVector[0]; |
923 |
+ |
boxVector[2] = boxVector[0]; |
924 |
+ |
|
925 |
+ |
info->setBox( boxVector ); |
926 |
+ |
} |
927 |
+ |
else{ |
928 |
+ |
if( !the_globals->haveBoxX() ){ |
929 |
+ |
sprintf( painCave.errMsg, |
930 |
+ |
"SimSetup error, no periodic BoxX size given.\n" ); |
931 |
+ |
painCave.isFatal = 1; |
932 |
+ |
simError(); |
933 |
+ |
} |
934 |
+ |
boxVector[0] = the_globals->getBoxX(); |
935 |
+ |
|
936 |
+ |
if( !the_globals->haveBoxY() ){ |
937 |
+ |
sprintf( painCave.errMsg, |
938 |
+ |
"SimSetup error, no periodic BoxY size given.\n" ); |
939 |
+ |
painCave.isFatal = 1; |
940 |
+ |
simError(); |
941 |
+ |
} |
942 |
+ |
boxVector[1] = the_globals->getBoxY(); |
943 |
+ |
|
944 |
+ |
if( !the_globals->haveBoxZ() ){ |
945 |
+ |
sprintf( painCave.errMsg, |
946 |
+ |
"SimSetup error, no periodic BoxZ size given.\n" ); |
947 |
+ |
painCave.isFatal = 1; |
948 |
+ |
simError(); |
949 |
+ |
} |
950 |
+ |
boxVector[2] = the_globals->getBoxZ(); |
951 |
+ |
|
952 |
+ |
info->setBox( boxVector ); |
953 |
+ |
} |
954 |
+ |
|
955 |
+ |
|
956 |
+ |
|
957 |
+ |
#ifdef IS_MPI |
958 |
+ |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
959 |
+ |
MPIcheckPoint(); |
960 |
+ |
#endif // is_mpi |
961 |
+ |
|
962 |
+ |
} |
963 |
+ |
|
964 |
+ |
|
965 |
+ |
void SimSetup::finalInfoCheck( void ){ |
966 |
+ |
int index; |
967 |
+ |
int usesDipoles; |
968 |
+ |
|
969 |
+ |
|
970 |
+ |
// check electrostatic parameters |
971 |
+ |
|
972 |
+ |
index = 0; |
973 |
+ |
usesDipoles = 0; |
974 |
+ |
while( (index < info->n_atoms) && !usesDipoles ){ |
975 |
+ |
usesDipoles = ((info->atoms)[index])->hasDipole(); |
976 |
+ |
index++; |
977 |
+ |
} |
978 |
+ |
|
979 |
+ |
#ifdef IS_MPI |
980 |
+ |
int myUse = usesDipoles |
981 |
+ |
MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
982 |
+ |
#endif //is_mpi |
983 |
+ |
|
984 |
+ |
|
985 |
+ |
if (the_globals->getUseRF() ) { |
986 |
+ |
info->useReactionField = 1; |
987 |
+ |
|
988 |
+ |
if( !the_globals->haveECR() ){ |
989 |
+ |
sprintf( painCave.errMsg, |
990 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
991 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
992 |
+ |
"I hope you have a very fast processor!\n"); |
993 |
+ |
painCave.isFatal = 0; |
994 |
+ |
simError(); |
995 |
+ |
double smallest; |
996 |
+ |
smallest = info->boxLx; |
997 |
+ |
if (info->boxLy <= smallest) smallest = info->boxLy; |
998 |
+ |
if (info->boxLz <= smallest) smallest = info->boxLz; |
999 |
+ |
info->ecr = 0.5 * smallest; |
1000 |
+ |
} else { |
1001 |
+ |
info->ecr = the_globals->getECR(); |
1002 |
+ |
} |
1003 |
+ |
|
1004 |
+ |
if( !the_globals->haveEST() ){ |
1005 |
+ |
sprintf( painCave.errMsg, |
1006 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
1007 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
1008 |
+ |
); |
1009 |
+ |
painCave.isFatal = 0; |
1010 |
+ |
simError(); |
1011 |
+ |
info->est = 0.05 * info->ecr; |
1012 |
+ |
} else { |
1013 |
+ |
info->est = the_globals->getEST(); |
1014 |
+ |
} |
1015 |
+ |
|
1016 |
+ |
if(!the_globals->haveDielectric() ){ |
1017 |
+ |
sprintf( painCave.errMsg, |
1018 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
1019 |
+ |
"setting a dielectric constant!\n" |
1020 |
+ |
); |
1021 |
+ |
painCave.isFatal = 1; |
1022 |
+ |
simError(); |
1023 |
+ |
} |
1024 |
+ |
info->dielectric = the_globals->getDielectric(); |
1025 |
+ |
} |
1026 |
+ |
else { |
1027 |
+ |
if (usesDipoles) { |
1028 |
+ |
|
1029 |
+ |
if( !the_globals->haveECR() ){ |
1030 |
+ |
sprintf( painCave.errMsg, |
1031 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
1032 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
1033 |
+ |
"I hope you have a very fast processor!\n"); |
1034 |
+ |
painCave.isFatal = 0; |
1035 |
+ |
simError(); |
1036 |
+ |
double smallest; |
1037 |
+ |
smallest = info->boxLx; |
1038 |
+ |
if (info->boxLy <= smallest) smallest = info->boxLy; |
1039 |
+ |
if (info->boxLz <= smallest) smallest = info->boxLz; |
1040 |
+ |
info->ecr = 0.5 * smallest; |
1041 |
+ |
} else { |
1042 |
+ |
info->ecr = the_globals->getECR(); |
1043 |
+ |
} |
1044 |
+ |
|
1045 |
+ |
if( !the_globals->haveEST() ){ |
1046 |
+ |
sprintf( painCave.errMsg, |
1047 |
+ |
"SimSetup Warning: using default value of 5%% of the " |
1048 |
+ |
"electrostaticCutoffRadius for the " |
1049 |
+ |
"electrostaticSkinThickness\n" |
1050 |
+ |
); |
1051 |
+ |
painCave.isFatal = 0; |
1052 |
+ |
simError(); |
1053 |
+ |
info->est = 0.05 * info->ecr; |
1054 |
+ |
} else { |
1055 |
+ |
info->est = the_globals->getEST(); |
1056 |
+ |
} |
1057 |
+ |
} |
1058 |
+ |
} |
1059 |
+ |
|
1060 |
+ |
#ifdef IS_MPI |
1061 |
+ |
strcpy( checkPointMsg, "post processing checks out" ); |
1062 |
+ |
MPIcheckPoint(); |
1063 |
+ |
#endif // is_mpi |
1064 |
+ |
|
1065 |
+ |
} |
1066 |
+ |
|
1067 |
+ |
void SimSetup::initSystemCoords( void ){ |
1068 |
+ |
|
1069 |
+ |
if( the_globals->haveInitialConfig() ){ |
1070 |
+ |
|
1071 |
+ |
InitializeFromFile* fileInit; |
1072 |
+ |
#ifdef IS_MPI // is_mpi |
1073 |
+ |
if( worldRank == 0 ){ |
1074 |
+ |
#endif //is_mpi |
1075 |
+ |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
1076 |
+ |
#ifdef IS_MPI |
1077 |
+ |
}else fileInit = new InitializeFromFile( NULL ); |
1078 |
+ |
#endif |
1079 |
+ |
fileInit->read_xyz( info ); // default velocities on |
1080 |
+ |
|
1081 |
+ |
delete fileInit; |
1082 |
+ |
} |
1083 |
+ |
else{ |
1084 |
+ |
|
1085 |
+ |
#ifdef IS_MPI |
1086 |
+ |
|
1087 |
+ |
// no init from bass |
1088 |
+ |
|
1089 |
+ |
sprintf( painCave.errMsg, |
1090 |
+ |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
1091 |
+ |
painCave.isFatal; |
1092 |
+ |
simError(); |
1093 |
+ |
|
1094 |
+ |
#else |
1095 |
+ |
|
1096 |
+ |
initFromBass(); |
1097 |
+ |
|
1098 |
+ |
|
1099 |
+ |
#endif |
1100 |
+ |
} |
1101 |
+ |
|
1102 |
+ |
#ifdef IS_MPI |
1103 |
+ |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
1104 |
+ |
MPIcheckPoint(); |
1105 |
+ |
#endif // is_mpi |
1106 |
+ |
|
1107 |
+ |
} |
1108 |
+ |
|
1109 |
+ |
|
1110 |
+ |
void SimSetup::makeOutNames( void ){ |
1111 |
+ |
|
1112 |
+ |
#ifdef IS_MPI |
1113 |
+ |
if( worldRank == 0 ){ |
1114 |
+ |
#endif // is_mpi |
1115 |
+ |
|
1116 |
+ |
if( the_globals->haveFinalConfig() ){ |
1117 |
+ |
strcpy( info->finalName, the_globals->getFinalConfig() ); |
1118 |
+ |
} |
1119 |
+ |
else{ |
1120 |
+ |
strcpy( info->finalName, inFileName ); |
1121 |
+ |
char* endTest; |
1122 |
+ |
int nameLength = strlen( info->finalName ); |
1123 |
+ |
endTest = &(info->finalName[nameLength - 5]); |
1124 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
1125 |
+ |
strcpy( endTest, ".eor" ); |
1126 |
+ |
} |
1127 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
1128 |
+ |
strcpy( endTest, ".eor" ); |
1129 |
+ |
} |
1130 |
+ |
else{ |
1131 |
+ |
endTest = &(info->finalName[nameLength - 4]); |
1132 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
1133 |
+ |
strcpy( endTest, ".eor" ); |
1134 |
+ |
} |
1135 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
1136 |
+ |
strcpy( endTest, ".eor" ); |
1137 |
+ |
} |
1138 |
+ |
else{ |
1139 |
+ |
strcat( info->finalName, ".eor" ); |
1140 |
+ |
} |
1141 |
+ |
} |
1142 |
+ |
} |
1143 |
+ |
|
1144 |
+ |
// make the sample and status out names |
1145 |
+ |
|
1146 |
+ |
strcpy( info->sampleName, inFileName ); |
1147 |
+ |
char* endTest; |
1148 |
+ |
int nameLength = strlen( info->sampleName ); |
1149 |
+ |
endTest = &(info->sampleName[nameLength - 5]); |
1150 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
1151 |
+ |
strcpy( endTest, ".dump" ); |
1152 |
+ |
} |
1153 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
1154 |
+ |
strcpy( endTest, ".dump" ); |
1155 |
+ |
} |
1156 |
+ |
else{ |
1157 |
+ |
endTest = &(info->sampleName[nameLength - 4]); |
1158 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
1159 |
+ |
strcpy( endTest, ".dump" ); |
1160 |
+ |
} |
1161 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
1162 |
+ |
strcpy( endTest, ".dump" ); |
1163 |
+ |
} |
1164 |
+ |
else{ |
1165 |
+ |
strcat( info->sampleName, ".dump" ); |
1166 |
+ |
} |
1167 |
+ |
} |
1168 |
+ |
|
1169 |
+ |
strcpy( info->statusName, inFileName ); |
1170 |
+ |
nameLength = strlen( info->statusName ); |
1171 |
+ |
endTest = &(info->statusName[nameLength - 5]); |
1172 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
1173 |
+ |
strcpy( endTest, ".stat" ); |
1174 |
+ |
} |
1175 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
1176 |
+ |
strcpy( endTest, ".stat" ); |
1177 |
+ |
} |
1178 |
+ |
else{ |
1179 |
+ |
endTest = &(info->statusName[nameLength - 4]); |
1180 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
1181 |
+ |
strcpy( endTest, ".stat" ); |
1182 |
+ |
} |
1183 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
1184 |
+ |
strcpy( endTest, ".stat" ); |
1185 |
+ |
} |
1186 |
+ |
else{ |
1187 |
+ |
strcat( info->statusName, ".stat" ); |
1188 |
+ |
} |
1189 |
+ |
} |
1190 |
+ |
|
1191 |
+ |
#ifdef IS_MPI |
1192 |
+ |
} |
1193 |
+ |
#endif // is_mpi |
1194 |
+ |
|
1195 |
+ |
} |
1196 |
+ |
|
1197 |
+ |
|
1198 |
+ |
void SimSetup::sysObjectsCreation( void ){ |
1199 |
+ |
|
1200 |
+ |
// create the forceField |
1201 |
+ |
|
1202 |
+ |
createFF(); |
1203 |
+ |
|
1204 |
+ |
// extract componentList |
1205 |
+ |
|
1206 |
+ |
compList(); |
1207 |
+ |
|
1208 |
+ |
// calc the number of atoms, bond, bends, and torsions |
1209 |
+ |
|
1210 |
+ |
calcSysValues(); |
1211 |
+ |
|
1212 |
+ |
#ifdef IS_MPI |
1213 |
+ |
// divide the molecules among the processors |
1214 |
+ |
|
1215 |
+ |
mpiMolDivide(); |
1216 |
+ |
#endif //is_mpi |
1217 |
+ |
|
1218 |
+ |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1219 |
+ |
|
1220 |
+ |
makeSysArrays(); |
1221 |
+ |
|
1222 |
+ |
|
1223 |
+ |
|
1224 |
+ |
|
1225 |
+ |
} |
1226 |
+ |
|
1227 |
+ |
|
1228 |
+ |
void SimSetup::createFF( void ){ |
1229 |
+ |
|
1230 |
+ |
switch( ffCase ){ |
1231 |
+ |
|
1232 |
+ |
case FF_DUFF: |
1233 |
+ |
the_ff = new DUFF(); |
1234 |
+ |
break; |
1235 |
+ |
|
1236 |
+ |
case FF_LJ: |
1237 |
+ |
the_ff = new LJFF(); |
1238 |
+ |
break; |
1239 |
+ |
|
1240 |
+ |
default: |
1241 |
+ |
sprintf( painCave.errMsg, |
1242 |
+ |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1243 |
+ |
painCave.isFatal = 1; |
1244 |
+ |
simError(); |
1245 |
+ |
} |
1246 |
+ |
|
1247 |
+ |
#ifdef IS_MPI |
1248 |
+ |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1249 |
+ |
MPIcheckPoint(); |
1250 |
+ |
#endif // is_mpi |
1251 |
+ |
|
1252 |
+ |
} |
1253 |
+ |
|
1254 |
+ |
|
1255 |
+ |
void SimSetup::compList( void ){ |
1256 |
+ |
|
1257 |
+ |
comp_stamps = new MoleculeStamp*[n_components]; |
1258 |
+ |
|
1259 |
+ |
// make an array of molecule stamps that match the components used. |
1260 |
+ |
// also extract the used stamps out into a separate linked list |
1261 |
+ |
|
1262 |
+ |
info->nComponents = n_components; |
1263 |
+ |
info->componentsNmol = components_nmol; |
1264 |
+ |
info->compStamps = comp_stamps; |
1265 |
+ |
info->headStamp = new LinkedMolStamp(); |
1266 |
+ |
|
1267 |
+ |
char* id; |
1268 |
+ |
LinkedMolStamp* headStamp = info->headStamp; |
1269 |
+ |
LinkedMolStamp* currentStamp = NULL; |
1270 |
+ |
for( i=0; i<n_components; i++ ){ |
1271 |
+ |
|
1272 |
+ |
id = the_components[i]->getType(); |
1273 |
+ |
comp_stamps[i] = NULL; |
1274 |
+ |
|
1275 |
+ |
// check to make sure the component isn't already in the list |
1276 |
+ |
|
1277 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1278 |
+ |
if( comp_stamps[i] == NULL ){ |
1279 |
+ |
|
1280 |
+ |
// extract the component from the list; |
1281 |
+ |
|
1282 |
+ |
currentStamp = the_stamps->extractMolStamp( id ); |
1283 |
+ |
if( currentStamp == NULL ){ |
1284 |
+ |
sprintf( painCave.errMsg, |
1285 |
+ |
"SimSetup error: Component \"%s\" was not found in the " |
1286 |
+ |
"list of declared molecules\n", |
1287 |
+ |
id ); |
1288 |
+ |
painCave.isFatal = 1; |
1289 |
+ |
simError(); |
1290 |
+ |
} |
1291 |
+ |
|
1292 |
+ |
headStamp->add( currentStamp ); |
1293 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1294 |
+ |
} |
1295 |
+ |
} |
1296 |
+ |
|
1297 |
+ |
#ifdef IS_MPI |
1298 |
+ |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1299 |
+ |
MPIcheckPoint(); |
1300 |
+ |
#endif // is_mpi |
1301 |
+ |
|
1302 |
+ |
|
1303 |
+ |
} |
1304 |
+ |
|
1305 |
+ |
void SimSetup::calcSysValues( void ){ |
1306 |
+ |
|
1307 |
+ |
tot_atoms = 0; |
1308 |
+ |
tot_bonds = 0; |
1309 |
+ |
tot_bends = 0; |
1310 |
+ |
tot_torsions = 0; |
1311 |
+ |
for( i=0; i<n_components; i++ ){ |
1312 |
+ |
|
1313 |
+ |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1314 |
+ |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1315 |
+ |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1316 |
+ |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1317 |
+ |
} |
1318 |
+ |
|
1319 |
+ |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1320 |
+ |
|
1321 |
+ |
info->n_atoms = tot_atoms; |
1322 |
+ |
info->n_bonds = tot_bonds; |
1323 |
+ |
info->n_bends = tot_bends; |
1324 |
+ |
info->n_torsions = tot_torsions; |
1325 |
+ |
info->n_SRI = tot_SRI; |
1326 |
+ |
info->n_mol = tot_nmol; |
1327 |
+ |
|
1328 |
+ |
info->molMembershipArray = new int[tot_atoms]; |
1329 |
+ |
} |
1330 |
+ |
|
1331 |
+ |
|
1332 |
+ |
#ifdef IS_MPI |
1333 |
+ |
|
1334 |
+ |
void SimSetup::mpiMolDivide( void ){ |
1335 |
+ |
|
1336 |
+ |
int localMol, allMol; |
1337 |
+ |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1338 |
+ |
|
1339 |
+ |
mpiSim = new mpiSimulation( info ); |
1340 |
+ |
|
1341 |
+ |
globalIndex = mpiSim->divideLabor(); |
1342 |
+ |
|
1343 |
+ |
// set up the local variables |
1344 |
+ |
|
1345 |
+ |
mol2proc = mpiSim->getMolToProcMap(); |
1346 |
+ |
molCompType = mpiSim->getMolComponentType(); |
1347 |
+ |
|
1348 |
+ |
allMol = 0; |
1349 |
+ |
localMol = 0; |
1350 |
+ |
local_atoms = 0; |
1351 |
+ |
local_bonds = 0; |
1352 |
+ |
local_bends = 0; |
1353 |
+ |
local_torsions = 0; |
1354 |
+ |
globalAtomIndex = 0; |
1355 |
+ |
|
1356 |
+ |
|
1357 |
+ |
for( i=0; i<n_components; i++ ){ |
1358 |
+ |
|
1359 |
+ |
for( j=0; j<components_nmol[i]; j++ ){ |
1360 |
+ |
|
1361 |
+ |
if( mol2proc[allMol] == worldRank ){ |
1362 |
+ |
|
1363 |
+ |
local_atoms += comp_stamps[i]->getNAtoms(); |
1364 |
+ |
local_bonds += comp_stamps[i]->getNBonds(); |
1365 |
+ |
local_bends += comp_stamps[i]->getNBends(); |
1366 |
+ |
local_torsions += comp_stamps[i]->getNTorsions(); |
1367 |
+ |
localMol++; |
1368 |
+ |
} |
1369 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1370 |
+ |
info->molMembershipArray[globalAtomIndex] = allMol; |
1371 |
+ |
globalAtomIndex++; |
1372 |
+ |
} |
1373 |
+ |
|
1374 |
+ |
allMol++; |
1375 |
+ |
} |
1376 |
+ |
} |
1377 |
+ |
local_SRI = local_bonds + local_bends + local_torsions; |
1378 |
+ |
|
1379 |
+ |
info->n_atoms = mpiSim->getMyNlocal(); |
1380 |
+ |
|
1381 |
+ |
if( local_atoms != info->n_atoms ){ |
1382 |
+ |
sprintf( painCave.errMsg, |
1383 |
+ |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1384 |
+ |
" localAtom (%d) are not equal.\n", |
1385 |
+ |
info->n_atoms, |
1386 |
+ |
local_atoms ); |
1387 |
+ |
painCave.isFatal = 1; |
1388 |
+ |
simError(); |
1389 |
+ |
} |
1390 |
+ |
|
1391 |
+ |
info->n_bonds = local_bonds; |
1392 |
+ |
info->n_bends = local_bends; |
1393 |
+ |
info->n_torsions = local_torsions; |
1394 |
+ |
info->n_SRI = local_SRI; |
1395 |
+ |
info->n_mol = localMol; |
1396 |
+ |
|
1397 |
+ |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1398 |
+ |
MPIcheckPoint(); |
1399 |
+ |
} |
1400 |
+ |
|
1401 |
+ |
#endif // is_mpi |
1402 |
+ |
|
1403 |
+ |
|
1404 |
+ |
void SimSetup::makeSysArrays( void ){ |
1405 |
+ |
|
1406 |
+ |
// create the atom and short range interaction arrays |
1407 |
+ |
|
1408 |
+ |
Atom::createArrays(info->n_atoms); |
1409 |
+ |
the_atoms = new Atom*[info->n_atoms]; |
1410 |
+ |
the_molecules = new Molecule[info->n_mol]; |
1411 |
+ |
int molIndex; |
1412 |
+ |
|
1413 |
+ |
// initialize the molecule's stampID's |
1414 |
+ |
|
1415 |
+ |
#ifdef IS_MPI |
1416 |
+ |
|
1417 |
+ |
|
1418 |
+ |
molIndex = 0; |
1419 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1420 |
+ |
|
1421 |
+ |
if(mol2proc[i] == worldRank ){ |
1422 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1423 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1424 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
1425 |
+ |
molIndex++; |
1426 |
+ |
} |
1427 |
+ |
} |
1428 |
+ |
|
1429 |
+ |
#else // is_mpi |
1430 |
+ |
|
1431 |
+ |
molIndex = 0; |
1432 |
+ |
globalAtomIndex = 0; |
1433 |
+ |
for(i=0; i<n_components; i++){ |
1434 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
1435 |
+ |
the_molecules[molIndex].setStampID( i ); |
1436 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1437 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1438 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1439 |
+ |
info->molMembershipArray[globalAtomIndex] = molIndex; |
1440 |
+ |
globalAtomIndex++; |
1441 |
+ |
} |
1442 |
+ |
molIndex++; |
1443 |
+ |
} |
1444 |
+ |
} |
1445 |
+ |
|
1446 |
+ |
|
1447 |
+ |
#endif // is_mpi |
1448 |
+ |
|
1449 |
+ |
|
1450 |
+ |
if( info->n_SRI ){ |
1451 |
+ |
|
1452 |
+ |
Exclude::createArray(info->n_SRI); |
1453 |
+ |
the_excludes = new Exclude*[info->n_SRI]; |
1454 |
+ |
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1455 |
+ |
info->globalExcludes = new int; |
1456 |
+ |
info->n_exclude = info->n_SRI; |
1457 |
+ |
} |
1458 |
+ |
else{ |
1459 |
+ |
|
1460 |
+ |
Exclude::createArray( 1 ); |
1461 |
+ |
the_excludes = new Exclude*; |
1462 |
+ |
the_excludes[0] = new Exclude(0); |
1463 |
+ |
the_excludes[0]->setPair( 0,0 ); |
1464 |
+ |
info->globalExcludes = new int; |
1465 |
+ |
info->globalExcludes[0] = 0; |
1466 |
+ |
info->n_exclude = 0; |
1467 |
+ |
} |
1468 |
+ |
|
1469 |
+ |
// set the arrays into the SimInfo object |
1470 |
+ |
|
1471 |
+ |
info->atoms = the_atoms; |
1472 |
+ |
info->molecules = the_molecules; |
1473 |
+ |
info->nGlobalExcludes = 0; |
1474 |
+ |
info->excludes = the_excludes; |
1475 |
+ |
|
1476 |
+ |
the_ff->setSimInfo( info ); |
1477 |
+ |
|
1478 |
+ |
} |