# | Line 1 | Line 1 | |
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1 | < | #include <cstdlib> |
1 | > | #include <algorithm> |
2 | > | #include <stdlib.h> |
3 | #include <iostream> | |
4 | < | #include <cmath> |
5 | < | |
4 | > | #include <math.h> |
5 | > | #include <string> |
6 | > | #include <sprng.h> |
7 | #include "SimSetup.hpp" | |
8 | + | #include "ReadWrite.hpp" |
9 | #include "parse_me.h" | |
10 | #include "Integrator.hpp" | |
11 | #include "simError.h" | |
12 | + | #include "RigidBody.hpp" |
13 | + | #include "OOPSEMinimizer.hpp" |
14 | + | //#include "ConstraintElement.hpp" |
15 | + | //#include "ConstraintPair.hpp" |
16 | ||
17 | #ifdef IS_MPI | |
18 | #include "mpiBASS.h" | |
# | Line 14 | Line 21 | |
21 | ||
22 | // some defines for ensemble and Forcefield cases | |
23 | ||
24 | < | #define NVE_ENS 0 |
25 | < | #define NVT_ENS 1 |
26 | < | #define NPTi_ENS 2 |
27 | < | #define NPTf_ENS 3 |
28 | < | #define NPTim_ENS 4 |
22 | < | #define NPTfm_ENS 5 |
24 | > | #define NVE_ENS 0 |
25 | > | #define NVT_ENS 1 |
26 | > | #define NPTi_ENS 2 |
27 | > | #define NPTf_ENS 3 |
28 | > | #define NPTxyz_ENS 4 |
29 | ||
30 | ||
31 | < | #define FF_DUFF 0 |
32 | < | #define FF_LJ 1 |
31 | > | #define FF_DUFF 0 |
32 | > | #define FF_LJ 1 |
33 | > | #define FF_EAM 2 |
34 | > | #define FF_H2O 3 |
35 | ||
36 | + | using namespace std; |
37 | ||
38 | + | /** |
39 | + | * Check whether dividend is divisble by divisor or not |
40 | + | */ |
41 | + | bool isDivisible(double dividend, double divisor){ |
42 | + | double tolerance = 0.000001; |
43 | + | double quotient; |
44 | + | double diff; |
45 | + | int intQuotient; |
46 | + | |
47 | + | quotient = dividend / divisor; |
48 | + | |
49 | + | if (quotient < 0) |
50 | + | quotient = -quotient; |
51 | + | |
52 | + | intQuotient = int (quotient + tolerance); |
53 | + | |
54 | + | diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
55 | + | |
56 | + | if (diff <= tolerance) |
57 | + | return true; |
58 | + | else |
59 | + | return false; |
60 | + | } |
61 | + | |
62 | SimSetup::SimSetup(){ | |
63 | + | |
64 | + | initSuspend = false; |
65 | + | isInfoArray = 0; |
66 | + | nInfo = 1; |
67 | + | |
68 | stamps = new MakeStamps(); | |
69 | globals = new Globals(); | |
70 | < | |
70 | > | |
71 | > | |
72 | #ifdef IS_MPI | |
73 | < | strcpy( checkPointMsg, "SimSetup creation successful" ); |
73 | > | strcpy(checkPointMsg, "SimSetup creation successful"); |
74 | MPIcheckPoint(); | |
75 | #endif // IS_MPI | |
76 | } | |
# | Line 41 | Line 80 | SimSetup::~SimSetup(){ | |
80 | delete globals; | |
81 | } | |
82 | ||
83 | < | void SimSetup::parseFile( char* fileName ){ |
83 | > | void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
84 | > | info = the_info; |
85 | > | nInfo = theNinfo; |
86 | > | isInfoArray = 1; |
87 | > | initSuspend = true; |
88 | > | } |
89 | ||
90 | + | |
91 | + | void SimSetup::parseFile(char* fileName){ |
92 | #ifdef IS_MPI | |
93 | < | if( worldRank == 0 ){ |
93 | > | if (worldRank == 0){ |
94 | #endif // is_mpi | |
95 | < | |
95 | > | |
96 | inFileName = fileName; | |
97 | < | set_interface_stamps( stamps, globals ); |
98 | < | |
97 | > | set_interface_stamps(stamps, globals); |
98 | > | |
99 | #ifdef IS_MPI | |
100 | mpiEventInit(); | |
101 | #endif | |
102 | ||
103 | < | yacc_BASS( fileName ); |
103 | > | yacc_BASS(fileName); |
104 | ||
105 | #ifdef IS_MPI | |
106 | throwMPIEvent(NULL); | |
107 | } | |
108 | < | else receiveParse(); |
108 | > | else{ |
109 | > | receiveParse(); |
110 | > | } |
111 | #endif | |
112 | ||
113 | } | |
114 | ||
115 | #ifdef IS_MPI | |
116 | void SimSetup::receiveParse(void){ | |
117 | < | |
118 | < | set_interface_stamps( stamps, globals ); |
119 | < | mpiEventInit(); |
120 | < | MPIcheckPoint(); |
73 | < | mpiEventLoop(); |
74 | < | |
117 | > | set_interface_stamps(stamps, globals); |
118 | > | mpiEventInit(); |
119 | > | MPIcheckPoint(); |
120 | > | mpiEventLoop(); |
121 | } | |
122 | ||
123 | #endif // is_mpi | |
124 | ||
125 | < | void SimSetup::createSim( void ){ |
125 | > | void SimSetup::createSim(void){ |
126 | ||
81 | – | MakeStamps *the_stamps; |
82 | – | Globals* the_globals; |
83 | – | int i, j, k, globalAtomIndex; |
84 | – | |
127 | // gather all of the information from the Bass file | |
128 | < | |
128 | > | |
129 | gatherInfo(); | |
130 | ||
131 | // creation of complex system objects | |
132 | ||
133 | sysObjectsCreation(); | |
134 | ||
93 | – | |
94 | – | |
95 | – | // initialize the arrays |
96 | – | |
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 | – | |
135 | // check on the post processing info | |
136 | < | |
136 | > | |
137 | finalInfoCheck(); | |
138 | ||
110 | – | |
111 | – | |
112 | – | |
139 | // initialize the system coordinates | |
140 | ||
141 | < | initSystemCoords(); |
142 | < | |
141 | > | if ( !initSuspend ){ |
142 | > | initSystemCoords(); |
143 | ||
144 | + | if( !(globals->getUseInitTime()) ) |
145 | + | info[0].currentTime = 0.0; |
146 | + | } |
147 | + | |
148 | // make the output filenames | |
149 | ||
150 | makeOutNames(); | |
121 | – | |
122 | – | |
151 | ||
124 | – | |
125 | – | |
126 | – | |
127 | – | |
128 | – | |
129 | – | |
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 | – | case NVT_ENS: |
146 | – | myNVT = new NVT( info, the_ff ); |
147 | – | myNVT->setTargetTemp(the_globals->getTargetTemp()); |
148 | – | |
149 | – | if (the_globals->haveTauThermostat()) |
150 | – | myNVT->setTauThermostat(the_globals->getTauThermostat()); |
151 | – | |
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 | – | case NPTi_ENS: |
162 | – | myNPTi = new NPTi( info, the_ff ); |
163 | – | myNPTi->setTargetTemp( the_globals->getTargetTemp() ); |
164 | – | |
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 | – | 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 | – | 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 | – | 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 | – | } |
219 | – | |
220 | – | if( the_globals->haveTauBarostat() ) |
221 | – | myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
222 | – | else{ |
223 | – | sprintf( painCave.errMsg, |
224 | – | "SimSetup error: If you use an NPT\n" |
225 | – | " ensemble, you must set tauBarostat.\n"); |
226 | – | painCave.isFatal = 1; |
227 | – | simError(); |
228 | – | } |
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->haveTargetPressure()) |
236 | – | myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
237 | – | else { |
238 | – | sprintf( painCave.errMsg, |
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 | – | |
245 | – | if( the_globals->haveTauThermostat() ) |
246 | – | myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
247 | – | else{ |
248 | – | sprintf( painCave.errMsg, |
249 | – | "SimSetup error: If you use an NPT\n" |
250 | – | " ensemble, you must set tauThermostat.\n"); |
251 | – | painCave.isFatal = 1; |
252 | – | simError(); |
253 | – | } |
254 | – | |
255 | – | if( the_globals->haveTauBarostat() ) |
256 | – | myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
257 | – | else{ |
258 | – | sprintf( painCave.errMsg, |
259 | – | "SimSetup error: If you use an NPT\n" |
260 | – | " ensemble, you must set tauBarostat.\n"); |
261 | – | painCave.isFatal = 1; |
262 | – | simError(); |
263 | – | } |
264 | – | break; |
265 | – | |
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 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(); |
278 | – | } |
279 | – | |
280 | – | if( the_globals->haveTauThermostat() ) |
281 | – | myNPTfm->setTauThermostat( the_globals->getTauThermostat() ); |
282 | – | else{ |
283 | – | sprintf( painCave.errMsg, |
284 | – | "SimSetup error: If you use an NPT\n" |
285 | – | " ensemble, you must set tauThermostat.\n"); |
286 | – | painCave.isFatal = 1; |
287 | – | simError(); |
288 | – | } |
289 | – | |
290 | – | if( the_globals->haveTauBarostat() ) |
291 | – | myNPTfm->setTauBarostat( the_globals->getTauBarostat() ); |
292 | – | else{ |
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 | – | break; |
300 | – | |
301 | – | default: |
302 | – | sprintf( painCave.errMsg, |
303 | – | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
304 | – | painCave.isFatal = 1; |
305 | – | simError(); |
306 | – | } |
307 | – | |
308 | – | |
152 | #ifdef IS_MPI | |
153 | mpiSim->mpiRefresh(); | |
154 | #endif | |
155 | ||
156 | // initialize the Fortran | |
157 | ||
158 | + | initFortran(); |
159 | ||
160 | < | info->refreshSim(); |
161 | < | |
162 | < | if( !strcmp( info->mixingRule, "standard") ){ |
163 | < | the_ff->initForceField( LB_MIXING_RULE ); |
164 | < | } |
165 | < | 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 | < | info->mixingRule ); |
328 | < | painCave.isFatal = 1; |
329 | < | simError(); |
330 | < | } |
160 | > | if (globals->haveMinimizer()) |
161 | > | // make minimizer |
162 | > | makeMinimizer(); |
163 | > | else |
164 | > | // make the integrator |
165 | > | makeIntegrator(); |
166 | ||
332 | – | |
333 | – | #ifdef IS_MPI |
334 | – | strcpy( checkPointMsg, |
335 | – | "Successfully intialized the mixingRule for Fortran." ); |
336 | – | MPIcheckPoint(); |
337 | – | #endif // is_mpi |
167 | } | |
168 | ||
169 | ||
170 | < | void SimSetup::makeMolecules( void ){ |
171 | < | |
172 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
173 | < | molInit info; |
170 | > | void SimSetup::makeMolecules(void){ |
171 | > | int i, j, k; |
172 | > | int exI, exJ, exK, exL, slI, slJ; |
173 | > | int tempI, tempJ, tempK, tempL; |
174 | > | int molI, globalID; |
175 | > | int stampID, atomOffset, rbOffset, groupOffset; |
176 | > | molInit molInfo; |
177 | DirectionalAtom* dAtom; | |
178 | + | RigidBody* myRB; |
179 | + | StuntDouble* mySD; |
180 | LinkedAssign* extras; | |
181 | LinkedAssign* current_extra; | |
182 | AtomStamp* currentAtom; | |
183 | BondStamp* currentBond; | |
184 | BendStamp* currentBend; | |
185 | TorsionStamp* currentTorsion; | |
186 | + | RigidBodyStamp* currentRigidBody; |
187 | + | CutoffGroupStamp* currentCutoffGroup; |
188 | + | CutoffGroup* myCutoffGroup; |
189 | + | int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file |
190 | + | set<int> cutoffAtomSet; //atoms belong to cutoffgroup defined at mdl file |
191 | ||
192 | bond_pair* theBonds; | |
193 | bend_set* theBends; | |
194 | torsion_set* theTorsions; | |
195 | ||
196 | < | |
196 | > | set<int> skipList; |
197 | > | |
198 | > | double phi, theta, psi; |
199 | > | char* molName; |
200 | > | char rbName[100]; |
201 | > | |
202 | > | //ConstraintPair* consPair; //constraint pair |
203 | > | //ConstraintElement* consElement1; //first element of constraint pair |
204 | > | //ConstraintElement* consElement2; //second element of constraint pair |
205 | > | //int whichRigidBody; |
206 | > | //int consAtomIndex; //index of constraint atom in rigid body's atom array |
207 | > | //vector<pair<int, int> > jointAtoms; |
208 | //init the forceField paramters | |
209 | ||
210 | the_ff->readParams(); | |
211 | ||
362 | – | |
212 | // init the atoms | |
213 | ||
214 | < | double ux, uy, uz, u, uSqr; |
366 | < | |
367 | < | atomOffset = 0; |
368 | < | excludeOffset = 0; |
369 | < | for(i=0; i<info->n_mol; i++){ |
370 | < | |
371 | < | stampID = the_molecules[i].getStampID(); |
214 | > | int nMembers, nNew, rb1, rb2; |
215 | ||
216 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
217 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
375 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
376 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
377 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
216 | > | for (k = 0; k < nInfo; k++){ |
217 | > | the_ff->setSimInfo(&(info[k])); |
218 | ||
219 | < | info.myAtoms = &the_atoms[atomOffset]; |
220 | < | info.myExcludes = &the_excludes[excludeOffset]; |
221 | < | info.myBonds = new Bond*[info.nBonds]; |
222 | < | info.myBends = new Bend*[info.nBends]; |
223 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
219 | > | #ifdef IS_MPI |
220 | > | info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()]; |
221 | > | for (i = 0; i < mpiSim->getNAtomsGlobal(); i++) |
222 | > | info[k].globalGroupMembership[i] = 0; |
223 | > | #else |
224 | > | info[k].globalGroupMembership = new int[info[k].n_atoms]; |
225 | > | for (i = 0; i < info[k].n_atoms; i++) |
226 | > | info[k].globalGroupMembership[i] = 0; |
227 | > | #endif |
228 | ||
229 | < | theBonds = new bond_pair[info.nBonds]; |
230 | < | theBends = new bend_set[info.nBends]; |
231 | < | theTorsions = new torsion_set[info.nTorsions]; |
232 | < | |
233 | < | // make the Atoms |
234 | < | |
235 | < | for(j=0; j<info.nAtoms; j++){ |
229 | > | atomOffset = 0; |
230 | > | groupOffset = 0; |
231 | > | |
232 | > | for (i = 0; i < info[k].n_mol; i++){ |
233 | > | stampID = info[k].molecules[i].getStampID(); |
234 | > | molName = comp_stamps[stampID]->getID(); |
235 | > | |
236 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
237 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
238 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
239 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
240 | > | molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); |
241 | > | |
242 | > | nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups(); |
243 | ||
244 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
394 | < | if( currentAtom->haveOrientation() ){ |
395 | < | |
396 | < | dAtom = new DirectionalAtom(j + atomOffset); |
397 | < | info->n_oriented++; |
398 | < | info.myAtoms[j] = dAtom; |
399 | < | |
400 | < | ux = currentAtom->getOrntX(); |
401 | < | uy = currentAtom->getOrntY(); |
402 | < | uz = currentAtom->getOrntZ(); |
403 | < | |
404 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
405 | < | |
406 | < | u = sqrt( uSqr ); |
407 | < | ux = ux / u; |
408 | < | uy = uy / u; |
409 | < | uz = uz / u; |
410 | < | |
411 | < | dAtom->setSUx( ux ); |
412 | < | dAtom->setSUy( uy ); |
413 | < | dAtom->setSUz( uz ); |
414 | < | } |
415 | < | else{ |
416 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
417 | < | } |
418 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
419 | < | |
420 | < | #ifdef IS_MPI |
421 | < | |
422 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
423 | < | |
424 | < | #endif // is_mpi |
425 | < | } |
426 | < | |
427 | < | // make the bonds |
428 | < | for(j=0; j<info.nBonds; j++){ |
429 | < | |
430 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
431 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
432 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
244 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
245 | ||
246 | < | exI = theBonds[j].a; |
247 | < | exJ = theBonds[j].b; |
246 | > | if (molInfo.nBonds > 0) |
247 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
248 | > | else |
249 | > | molInfo.myBonds = NULL; |
250 | ||
251 | < | // exclude_I must always be the smaller of the pair |
252 | < | if( exI > exJ ){ |
253 | < | tempEx = exI; |
254 | < | exI = exJ; |
255 | < | exJ = tempEx; |
256 | < | } |
257 | < | #ifdef IS_MPI |
258 | < | tempEx = exI; |
259 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
260 | < | tempEx = exJ; |
261 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
251 | > | if (molInfo.nBends > 0) |
252 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
253 | > | else |
254 | > | molInfo.myBends = NULL; |
255 | > | |
256 | > | if (molInfo.nTorsions > 0) |
257 | > | molInfo.myTorsions = new Torsion *[molInfo.nTorsions]; |
258 | > | else |
259 | > | molInfo.myTorsions = NULL; |
260 | > | |
261 | > | theBonds = new bond_pair[molInfo.nBonds]; |
262 | > | theBends = new bend_set[molInfo.nBends]; |
263 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
264 | ||
265 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
450 | < | #else // isn't MPI |
265 | > | // make the Atoms |
266 | ||
267 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
268 | < | #endif //is_mpi |
454 | < | } |
455 | < | excludeOffset += info.nBonds; |
267 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
268 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
269 | ||
270 | < | //make the bends |
271 | < | for(j=0; j<info.nBends; j++){ |
272 | < | |
273 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
274 | < | theBends[j].a = currentBend->getA() + atomOffset; |
275 | < | theBends[j].b = currentBend->getB() + atomOffset; |
276 | < | theBends[j].c = currentBend->getC() + atomOffset; |
277 | < | |
278 | < | if( currentBend->haveExtras() ){ |
279 | < | |
280 | < | extras = currentBend->getExtras(); |
281 | < | current_extra = extras; |
282 | < | |
283 | < | while( current_extra != NULL ){ |
284 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
285 | < | |
286 | < | switch( current_extra->getType() ){ |
287 | < | |
288 | < | case 0: |
289 | < | theBends[j].ghost = |
290 | < | current_extra->getInt() + atomOffset; |
291 | < | theBends[j].isGhost = 1; |
292 | < | break; |
293 | < | |
294 | < | case 1: |
295 | < | theBends[j].ghost = |
296 | < | (int)current_extra->getDouble() + atomOffset; |
297 | < | theBends[j].isGhost = 1; |
298 | < | break; |
299 | < | |
300 | < | default: |
301 | < | sprintf( painCave.errMsg, |
302 | < | "SimSetup Error: ghostVectorSource was neither a " |
303 | < | "double nor an int.\n" |
304 | < | "-->Bend[%d] in %s\n", |
305 | < | j, comp_stamps[stampID]->getID() ); |
306 | < | painCave.isFatal = 1; |
307 | < | simError(); |
308 | < | } |
309 | < | } |
310 | < | |
311 | < | else{ |
312 | < | |
313 | < | sprintf( painCave.errMsg, |
314 | < | "SimSetup Error: unhandled bend assignment:\n" |
315 | < | " -->%s in Bend[%d] in %s\n", |
316 | < | current_extra->getlhs(), |
504 | < | j, comp_stamps[stampID]->getID() ); |
505 | < | painCave.isFatal = 1; |
506 | < | simError(); |
507 | < | } |
508 | < | |
509 | < | current_extra = current_extra->getNext(); |
510 | < | } |
270 | > | if (currentAtom->haveOrientation()){ |
271 | > | dAtom = new DirectionalAtom((j + atomOffset), |
272 | > | info[k].getConfiguration()); |
273 | > | info[k].n_oriented++; |
274 | > | molInfo.myAtoms[j] = dAtom; |
275 | > | |
276 | > | // Directional Atoms have standard unit vectors which are oriented |
277 | > | // in space using the three Euler angles. We assume the standard |
278 | > | // unit vector was originally along the z axis below. |
279 | > | |
280 | > | phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
281 | > | theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
282 | > | psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
283 | > | |
284 | > | dAtom->setUnitFrameFromEuler(phi, theta, psi); |
285 | > | |
286 | > | } |
287 | > | else{ |
288 | > | |
289 | > | molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); |
290 | > | |
291 | > | } |
292 | > | |
293 | > | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
294 | > | #ifdef IS_MPI |
295 | > | molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); |
296 | > | #endif // is_mpi |
297 | > | } |
298 | > | |
299 | > | // make the bonds |
300 | > | for (j = 0; j < molInfo.nBonds; j++){ |
301 | > | currentBond = comp_stamps[stampID]->getBond(j); |
302 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
303 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
304 | > | |
305 | > | tempI = theBonds[j].a; |
306 | > | tempJ = theBonds[j].b; |
307 | > | |
308 | > | #ifdef IS_MPI |
309 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
310 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
311 | > | #else |
312 | > | exI = tempI + 1; |
313 | > | exJ = tempJ + 1; |
314 | > | #endif |
315 | > | |
316 | > | info[k].excludes->addPair(exI, exJ); |
317 | } | |
318 | < | |
319 | < | if( !theBends[j].isGhost ){ |
320 | < | |
321 | < | exI = theBends[j].a; |
322 | < | exJ = theBends[j].c; |
318 | > | |
319 | > | //make the bends |
320 | > | for (j = 0; j < molInfo.nBends; j++){ |
321 | > | currentBend = comp_stamps[stampID]->getBend(j); |
322 | > | theBends[j].a = currentBend->getA() + atomOffset; |
323 | > | theBends[j].b = currentBend->getB() + atomOffset; |
324 | > | theBends[j].c = currentBend->getC() + atomOffset; |
325 | > | |
326 | > | if (currentBend->haveExtras()){ |
327 | > | extras = currentBend->getExtras(); |
328 | > | current_extra = extras; |
329 | > | |
330 | > | while (current_extra != NULL){ |
331 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
332 | > | switch (current_extra->getType()){ |
333 | > | case 0: |
334 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
335 | > | theBends[j].isGhost = 1; |
336 | > | break; |
337 | > | |
338 | > | case 1: |
339 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
340 | > | atomOffset; |
341 | > | theBends[j].isGhost = 1; |
342 | > | break; |
343 | > | |
344 | > | default: |
345 | > | sprintf(painCave.errMsg, |
346 | > | "SimSetup Error: ghostVectorSource was neither a " |
347 | > | "double nor an int.\n" |
348 | > | "-->Bend[%d] in %s\n", |
349 | > | j, comp_stamps[stampID]->getID()); |
350 | > | painCave.isFatal = 1; |
351 | > | simError(); |
352 | > | } |
353 | > | } |
354 | > | else{ |
355 | > | sprintf(painCave.errMsg, |
356 | > | "SimSetup Error: unhandled bend assignment:\n" |
357 | > | " -->%s in Bend[%d] in %s\n", |
358 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
359 | > | painCave.isFatal = 1; |
360 | > | simError(); |
361 | > | } |
362 | > | |
363 | > | current_extra = current_extra->getNext(); |
364 | > | } |
365 | > | } |
366 | > | |
367 | > | if (theBends[j].isGhost) { |
368 | > | |
369 | > | tempI = theBends[j].a; |
370 | > | tempJ = theBends[j].b; |
371 | > | |
372 | > | #ifdef IS_MPI |
373 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
374 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
375 | > | #else |
376 | > | exI = tempI + 1; |
377 | > | exJ = tempJ + 1; |
378 | > | #endif |
379 | > | info[k].excludes->addPair(exI, exJ); |
380 | > | |
381 | > | } else { |
382 | > | |
383 | > | tempI = theBends[j].a; |
384 | > | tempJ = theBends[j].b; |
385 | > | tempK = theBends[j].c; |
386 | > | |
387 | > | #ifdef IS_MPI |
388 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
389 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
390 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
391 | > | #else |
392 | > | exI = tempI + 1; |
393 | > | exJ = tempJ + 1; |
394 | > | exK = tempK + 1; |
395 | > | #endif |
396 | > | |
397 | > | info[k].excludes->addPair(exI, exK); |
398 | > | info[k].excludes->addPair(exI, exJ); |
399 | > | info[k].excludes->addPair(exJ, exK); |
400 | > | } |
401 | } | |
402 | < | else{ |
403 | < | |
404 | < | exI = theBends[j].a; |
405 | < | exJ = theBends[j].b; |
406 | < | } |
407 | < | |
408 | < | // exclude_I must always be the smaller of the pair |
409 | < | if( exI > exJ ){ |
410 | < | tempEx = exI; |
411 | < | exI = exJ; |
412 | < | exJ = tempEx; |
413 | < | } |
402 | > | |
403 | > | for (j = 0; j < molInfo.nTorsions; j++){ |
404 | > | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
405 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
406 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
407 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
408 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
409 | > | |
410 | > | tempI = theTorsions[j].a; |
411 | > | tempJ = theTorsions[j].b; |
412 | > | tempK = theTorsions[j].c; |
413 | > | tempL = theTorsions[j].d; |
414 | > | |
415 | #ifdef IS_MPI | |
416 | < | tempEx = exI; |
417 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
418 | < | tempEx = exJ; |
419 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
420 | < | |
421 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
422 | < | #else // isn't MPI |
423 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
424 | < | #endif //is_mpi |
425 | < | } |
541 | < | excludeOffset += info.nBends; |
416 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
417 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
418 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
419 | > | exL = info[k].atoms[tempL]->getGlobalIndex() + 1; |
420 | > | #else |
421 | > | exI = tempI + 1; |
422 | > | exJ = tempJ + 1; |
423 | > | exK = tempK + 1; |
424 | > | exL = tempL + 1; |
425 | > | #endif |
426 | ||
427 | < | for(j=0; j<info.nTorsions; j++){ |
427 | > | info[k].excludes->addPair(exI, exJ); |
428 | > | info[k].excludes->addPair(exI, exK); |
429 | > | info[k].excludes->addPair(exI, exL); |
430 | > | info[k].excludes->addPair(exJ, exK); |
431 | > | info[k].excludes->addPair(exJ, exL); |
432 | > | info[k].excludes->addPair(exK, exL); |
433 | > | } |
434 | > | |
435 | ||
436 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
546 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
547 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
548 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
549 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
436 | > | molInfo.myRigidBodies.clear(); |
437 | ||
438 | < | exI = theTorsions[j].a; |
552 | < | exJ = theTorsions[j].d; |
438 | > | for (j = 0; j < molInfo.nRigidBodies; j++){ |
439 | ||
440 | < | // exclude_I must always be the smaller of the pair |
441 | < | if( exI > exJ ){ |
442 | < | tempEx = exI; |
443 | < | exI = exJ; |
444 | < | exJ = tempEx; |
445 | < | } |
440 | > | currentRigidBody = comp_stamps[stampID]->getRigidBody(j); |
441 | > | nMembers = currentRigidBody->getNMembers(); |
442 | > | |
443 | > | // Create the Rigid Body: |
444 | > | |
445 | > | myRB = new RigidBody(); |
446 | > | |
447 | > | sprintf(rbName,"%s_RB_%d", molName, j); |
448 | > | myRB->setType(rbName); |
449 | > | |
450 | > | for (rb1 = 0; rb1 < nMembers; rb1++) { |
451 | > | |
452 | > | // molI is atom numbering inside this molecule |
453 | > | molI = currentRigidBody->getMember(rb1); |
454 | > | |
455 | > | // tempI is atom numbering on local processor |
456 | > | tempI = molI + atomOffset; |
457 | > | |
458 | > | // currentAtom is the AtomStamp (which we need for |
459 | > | // rigid body reference positions) |
460 | > | currentAtom = comp_stamps[stampID]->getAtom(molI); |
461 | > | |
462 | > | // When we add to the rigid body, add the atom itself and |
463 | > | // the stamp info: |
464 | > | |
465 | > | myRB->addAtom(info[k].atoms[tempI], currentAtom); |
466 | > | |
467 | > | // Add this atom to the Skip List for the integrators |
468 | #ifdef IS_MPI | |
469 | < | tempEx = exI; |
470 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
471 | < | tempEx = exJ; |
472 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
469 | > | slI = info[k].atoms[tempI]->getGlobalIndex(); |
470 | > | #else |
471 | > | slI = tempI; |
472 | > | #endif |
473 | > | skipList.insert(slI); |
474 | > | |
475 | > | } |
476 | > | |
477 | > | for(rb1 = 0; rb1 < nMembers - 1; rb1++) { |
478 | > | for(rb2 = rb1+1; rb2 < nMembers; rb2++) { |
479 | > | |
480 | > | tempI = currentRigidBody->getMember(rb1); |
481 | > | tempJ = currentRigidBody->getMember(rb2); |
482 | > | |
483 | > | // Some explanation is required here. |
484 | > | // Fortran indexing starts at 1, while c indexing starts at 0 |
485 | > | // Also, in parallel computations, the GlobalIndex is |
486 | > | // used for the exclude list: |
487 | > | |
488 | > | #ifdef IS_MPI |
489 | > | exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1; |
490 | > | exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1; |
491 | > | #else |
492 | > | exI = molInfo.myAtoms[tempI]->getIndex() + 1; |
493 | > | exJ = molInfo.myAtoms[tempJ]->getIndex() + 1; |
494 | > | #endif |
495 | > | |
496 | > | info[k].excludes->addPair(exI, exJ); |
497 | > | |
498 | > | } |
499 | > | } |
500 | > | |
501 | > | molInfo.myRigidBodies.push_back(myRB); |
502 | > | info[k].rigidBodies.push_back(myRB); |
503 | > | } |
504 | ||
505 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
506 | < | #else // isn't MPI |
507 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
508 | < | #endif //is_mpi |
505 | > | |
506 | > | //create cutoff group for molecule |
507 | > | |
508 | > | cutoffAtomSet.clear(); |
509 | > | molInfo.myCutoffGroups.clear(); |
510 | > | |
511 | > | for (j = 0; j < nCutoffGroups; j++){ |
512 | > | |
513 | > | currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j); |
514 | > | nMembers = currentCutoffGroup->getNMembers(); |
515 | > | |
516 | > | myCutoffGroup = new CutoffGroup(); |
517 | > | |
518 | > | #ifdef IS_MPI |
519 | > | myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]); |
520 | > | #else |
521 | > | myCutoffGroup->setGlobalIndex(groupOffset); |
522 | > | #endif |
523 | > | |
524 | > | for (int cg = 0; cg < nMembers; cg++) { |
525 | > | |
526 | > | // molI is atom numbering inside this molecule |
527 | > | molI = currentCutoffGroup->getMember(cg); |
528 | > | |
529 | > | // tempI is atom numbering on local processor |
530 | > | tempI = molI + atomOffset; |
531 | > | |
532 | > | #ifdef IS_MPI |
533 | > | globalID = info[k].atoms[tempI]->getGlobalIndex(); |
534 | > | info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset]; |
535 | > | #else |
536 | > | globalID = info[k].atoms[tempI]->getIndex(); |
537 | > | info[k].globalGroupMembership[globalID] = groupOffset; |
538 | > | #endif |
539 | > | myCutoffGroup->addAtom(info[k].atoms[tempI]); |
540 | > | cutoffAtomSet.insert(tempI); |
541 | > | } |
542 | > | |
543 | > | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
544 | > | groupOffset++; |
545 | > | |
546 | > | }//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
547 | > | |
548 | > | |
549 | > | // create a cutoff group for every atom in current molecule which |
550 | > | // does not belong to cutoffgroup defined at mdl file |
551 | > | |
552 | > | for(j = 0; j < molInfo.nAtoms; j++){ |
553 | > | |
554 | > | if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){ |
555 | > | myCutoffGroup = new CutoffGroup(); |
556 | > | myCutoffGroup->addAtom(molInfo.myAtoms[j]); |
557 | > | |
558 | > | #ifdef IS_MPI |
559 | > | myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]); |
560 | > | globalID = info[k].atoms[atomOffset + j]->getGlobalIndex(); |
561 | > | info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset]; |
562 | > | #else |
563 | > | myCutoffGroup->setGlobalIndex(groupOffset); |
564 | > | globalID = info[k].atoms[atomOffset + j]->getIndex(); |
565 | > | info[k].globalGroupMembership[globalID] = groupOffset; |
566 | > | #endif |
567 | > | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
568 | > | groupOffset++; |
569 | > | } |
570 | > | } |
571 | > | |
572 | > | // After this is all set up, scan through the atoms to |
573 | > | // see if they can be added to the integrableObjects: |
574 | > | |
575 | > | molInfo.myIntegrableObjects.clear(); |
576 | > | |
577 | > | |
578 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
579 | > | |
580 | > | #ifdef IS_MPI |
581 | > | slJ = molInfo.myAtoms[j]->getGlobalIndex(); |
582 | > | #else |
583 | > | slJ = j+atomOffset; |
584 | > | #endif |
585 | > | |
586 | > | // if they aren't on the skip list, then they can be integrated |
587 | > | |
588 | > | if (skipList.find(slJ) == skipList.end()) { |
589 | > | mySD = (StuntDouble *) molInfo.myAtoms[j]; |
590 | > | info[k].integrableObjects.push_back(mySD); |
591 | > | molInfo.myIntegrableObjects.push_back(mySD); |
592 | > | } |
593 | > | } |
594 | > | |
595 | > | // all rigid bodies are integrated: |
596 | > | |
597 | > | for (j = 0; j < molInfo.nRigidBodies; j++) { |
598 | > | mySD = (StuntDouble *) molInfo.myRigidBodies[j]; |
599 | > | info[k].integrableObjects.push_back(mySD); |
600 | > | molInfo.myIntegrableObjects.push_back(mySD); |
601 | > | } |
602 | > | |
603 | > | |
604 | > | /* |
605 | > | |
606 | > | //creat ConstraintPair. |
607 | > | molInfo.myConstraintPair.clear(); |
608 | > | |
609 | > | for (j = 0; j < molInfo.nBonds; j++){ |
610 | > | |
611 | > | //if both atoms are in the same rigid body, just skip it |
612 | > | currentBond = comp_stamps[stampID]->getBond(j); |
613 | > | if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){ |
614 | > | |
615 | > | tempI = currentBond->getA() + atomOffset; |
616 | > | if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex)) |
617 | > | consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
618 | > | else |
619 | > | consElement1 = new ConstraintAtom(info[k].atoms[tempI]); |
620 | > | |
621 | > | tempJ = currentBond->getB() + atomOffset; |
622 | > | if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex)) |
623 | > | consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
624 | > | else |
625 | > | consElement2 = new ConstraintAtom(info[k].atoms[tempJ]); |
626 | > | |
627 | > | consPair = new DistanceConstraintPair(consElement1, consElement2); |
628 | > | molInfo.myConstraintPairs.push_back(consPair); |
629 | > | } |
630 | > | } |
631 | > | |
632 | > | //loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair |
633 | > | for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){ |
634 | > | for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){ |
635 | > | |
636 | > | jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2); |
637 | > | |
638 | > | for(size_t m = 0; m < jointAtoms.size(); m++){ |
639 | > | consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first); |
640 | > | consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second); |
641 | > | |
642 | > | consPair = new JointConstraintPair(consElement1, consElement2); |
643 | > | molInfo.myConstraintPairs.push_back(consPair); |
644 | > | } |
645 | > | |
646 | > | } |
647 | > | } |
648 | > | |
649 | > | */ |
650 | > | // send the arrays off to the forceField for init. |
651 | > | |
652 | > | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
653 | > | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
654 | > | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
655 | > | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
656 | > | theTorsions); |
657 | > | |
658 | > | info[k].molecules[i].initialize(molInfo); |
659 | > | |
660 | > | |
661 | > | atomOffset += molInfo.nAtoms; |
662 | > | delete[] theBonds; |
663 | > | delete[] theBends; |
664 | > | delete[] theTorsions; |
665 | } | |
571 | – | excludeOffset += info.nTorsions; |
666 | ||
573 | – | |
574 | – | // send the arrays off to the forceField for init. |
667 | ||
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 ); |
668 | ||
669 | + | #ifdef IS_MPI |
670 | + | // Since the globalGroupMembership has been zero filled and we've only |
671 | + | // poked values into the atoms we know, we can do an Allreduce |
672 | + | // to get the full globalGroupMembership array (We think). |
673 | + | // This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
674 | + | // docs said we could. |
675 | ||
676 | < | the_molecules[i].initialize( info ); |
676 | > | int* ggMjunk = new int[mpiSim->getNAtomsGlobal()]; |
677 | ||
678 | + | MPI_Allreduce(info[k].globalGroupMembership, |
679 | + | ggMjunk, |
680 | + | mpiSim->getNAtomsGlobal(), |
681 | + | MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
682 | ||
683 | < | atomOffset += info.nAtoms; |
684 | < | delete[] theBonds; |
685 | < | delete[] theBends; |
686 | < | delete[] theTorsions; |
683 | > | for (i = 0; i < mpiSim->getNAtomsGlobal(); i++) |
684 | > | info[k].globalGroupMembership[i] = ggMjunk[i]; |
685 | > | |
686 | > | delete[] ggMjunk; |
687 | > | |
688 | > | #endif |
689 | > | |
690 | > | |
691 | > | |
692 | } | |
693 | ||
694 | #ifdef IS_MPI | |
695 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
695 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
696 | MPIcheckPoint(); | |
697 | #endif // is_mpi | |
698 | ||
596 | – | // clean up the forcefield |
597 | – | the_ff->calcRcut(); |
598 | – | the_ff->cleanMe(); |
599 | – | |
699 | } | |
700 | ||
701 | < | void SimSetup::initFromBass( void ){ |
603 | < | |
701 | > | void SimSetup::initFromBass(void){ |
702 | int i, j, k; | |
703 | int n_cells; | |
704 | double cellx, celly, cellz; | |
# | Line 609 | Line 707 | void SimSetup::initFromBass( void ){ | |
707 | int n_extra; | |
708 | int have_extra, done; | |
709 | ||
710 | < | temp1 = (double)tot_nmol / 4.0; |
711 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
712 | < | temp3 = ceil( temp2 ); |
710 | > | double vel[3]; |
711 | > | vel[0] = 0.0; |
712 | > | vel[1] = 0.0; |
713 | > | vel[2] = 0.0; |
714 | ||
715 | < | have_extra =0; |
716 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
717 | < | have_extra =1; |
715 | > | temp1 = (double) tot_nmol / 4.0; |
716 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
717 | > | temp3 = ceil(temp2); |
718 | ||
719 | < | n_cells = (int)temp3 - 1; |
720 | < | cellx = info->boxLx / temp3; |
721 | < | celly = info->boxLy / temp3; |
722 | < | cellz = info->boxLz / temp3; |
723 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
724 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
725 | < | n_per_extra = (int)ceil( temp1 ); |
726 | < | |
727 | < | if( n_per_extra > 4){ |
728 | < | sprintf( painCave.errMsg, |
729 | < | "SimSetup error. There has been an error in constructing" |
730 | < | " the non-complete lattice.\n" ); |
719 | > | have_extra = 0; |
720 | > | if (temp2 < temp3){ |
721 | > | // we have a non-complete lattice |
722 | > | have_extra = 1; |
723 | > | |
724 | > | n_cells = (int) temp3 - 1; |
725 | > | cellx = info[0].boxL[0] / temp3; |
726 | > | celly = info[0].boxL[1] / temp3; |
727 | > | cellz = info[0].boxL[2] / temp3; |
728 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
729 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
730 | > | n_per_extra = (int) ceil(temp1); |
731 | > | |
732 | > | if (n_per_extra > 4){ |
733 | > | sprintf(painCave.errMsg, |
734 | > | "SimSetup error. There has been an error in constructing" |
735 | > | " the non-complete lattice.\n"); |
736 | painCave.isFatal = 1; | |
737 | simError(); | |
738 | } | |
739 | } | |
740 | else{ | |
741 | < | n_cells = (int)temp3; |
742 | < | cellx = info->boxLx / temp3; |
743 | < | celly = info->boxLy / temp3; |
744 | < | cellz = info->boxLz / temp3; |
741 | > | n_cells = (int) temp3; |
742 | > | cellx = info[0].boxL[0] / temp3; |
743 | > | celly = info[0].boxL[1] / temp3; |
744 | > | cellz = info[0].boxL[2] / temp3; |
745 | } | |
746 | ||
747 | current_mol = 0; | |
# | Line 645 | Line 749 | void SimSetup::initFromBass( void ){ | |
749 | current_comp = 0; | |
750 | current_atom_ndx = 0; | |
751 | ||
752 | < | for( i=0; i < n_cells ; i++ ){ |
753 | < | for( j=0; j < n_cells; j++ ){ |
754 | < | for( k=0; k < n_cells; k++ ){ |
752 | > | for (i = 0; i < n_cells ; i++){ |
753 | > | for (j = 0; j < n_cells; j++){ |
754 | > | for (k = 0; k < n_cells; k++){ |
755 | > | makeElement(i * cellx, j * celly, k * cellz); |
756 | ||
757 | < | makeElement( i * cellx, |
653 | < | j * celly, |
654 | < | k * cellz ); |
757 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
758 | ||
759 | < | makeElement( i * cellx + 0.5 * cellx, |
657 | < | j * celly + 0.5 * celly, |
658 | < | k * cellz ); |
759 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
760 | ||
761 | < | makeElement( i * cellx, |
661 | < | j * celly + 0.5 * celly, |
662 | < | k * cellz + 0.5 * cellz ); |
663 | < | |
664 | < | makeElement( i * cellx + 0.5 * cellx, |
665 | < | j * celly, |
666 | < | k * cellz + 0.5 * cellz ); |
761 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
762 | } | |
763 | } | |
764 | } | |
765 | ||
766 | < | if( have_extra ){ |
766 | > | if (have_extra){ |
767 | done = 0; | |
768 | ||
769 | int start_ndx; | |
770 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
771 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
770 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
771 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
772 | > | if (i < n_cells){ |
773 | > | if (j < n_cells){ |
774 | > | start_ndx = n_cells; |
775 | > | } |
776 | > | else |
777 | > | start_ndx = 0; |
778 | > | } |
779 | > | else |
780 | > | start_ndx = 0; |
781 | ||
782 | < | if( i < n_cells ){ |
782 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
783 | > | makeElement(i * cellx, j * celly, k * cellz); |
784 | > | done = (current_mol >= tot_nmol); |
785 | ||
786 | < | if( j < n_cells ){ |
787 | < | start_ndx = n_cells; |
788 | < | } |
789 | < | else start_ndx = 0; |
790 | < | } |
685 | < | else start_ndx = 0; |
786 | > | if (!done && n_per_extra > 1){ |
787 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
788 | > | k * cellz); |
789 | > | done = (current_mol >= tot_nmol); |
790 | > | } |
791 | ||
792 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
792 | > | if (!done && n_per_extra > 2){ |
793 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
794 | > | k * cellz + 0.5 * cellz); |
795 | > | done = (current_mol >= tot_nmol); |
796 | > | } |
797 | ||
798 | < | makeElement( i * cellx, |
799 | < | j * celly, |
800 | < | k * cellz ); |
801 | < | done = ( current_mol >= tot_nmol ); |
802 | < | |
803 | < | if( !done && n_per_extra > 1 ){ |
695 | < | makeElement( i * cellx + 0.5 * cellx, |
696 | < | j * celly + 0.5 * celly, |
697 | < | k * cellz ); |
698 | < | done = ( current_mol >= tot_nmol ); |
699 | < | } |
700 | < | |
701 | < | if( !done && n_per_extra > 2){ |
702 | < | makeElement( i * cellx, |
703 | < | j * celly + 0.5 * celly, |
704 | < | k * cellz + 0.5 * cellz ); |
705 | < | done = ( current_mol >= tot_nmol ); |
706 | < | } |
707 | < | |
708 | < | if( !done && n_per_extra > 3){ |
709 | < | makeElement( i * cellx + 0.5 * cellx, |
710 | < | j * celly, |
711 | < | k * cellz + 0.5 * cellz ); |
712 | < | done = ( current_mol >= tot_nmol ); |
713 | < | } |
714 | < | } |
798 | > | if (!done && n_per_extra > 3){ |
799 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
800 | > | k * cellz + 0.5 * cellz); |
801 | > | done = (current_mol >= tot_nmol); |
802 | > | } |
803 | > | } |
804 | } | |
805 | } | |
806 | } | |
807 | ||
808 | < | |
809 | < | 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 ); |
808 | > | for (i = 0; i < info[0].n_atoms; i++){ |
809 | > | info[0].atoms[i]->setVel(vel); |
810 | } | |
811 | } | |
812 | ||
813 | < | void SimSetup::makeElement( double x, double y, double z ){ |
728 | < | |
813 | > | void SimSetup::makeElement(double x, double y, double z){ |
814 | int k; | |
815 | AtomStamp* current_atom; | |
816 | DirectionalAtom* dAtom; | |
817 | double rotMat[3][3]; | |
818 | + | double pos[3]; |
819 | ||
820 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
821 | < | |
822 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
823 | < | if( !current_atom->havePosition() ){ |
824 | < | sprintf( painCave.errMsg, |
825 | < | "SimSetup:initFromBass error.\n" |
826 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
827 | < | "\tThe initialization routine is unable to give a start" |
828 | < | " position.\n", |
743 | < | comp_stamps[current_comp]->getID(), |
744 | < | current_atom->getType() ); |
820 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
821 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
822 | > | if (!current_atom->havePosition()){ |
823 | > | sprintf(painCave.errMsg, |
824 | > | "SimSetup:initFromBass error.\n" |
825 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
826 | > | "\tThe initialization routine is unable to give a start" |
827 | > | " position.\n", |
828 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
829 | painCave.isFatal = 1; | |
830 | simError(); | |
831 | } | |
832 | ||
833 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
834 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
835 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
833 | > | pos[0] = x + current_atom->getPosX(); |
834 | > | pos[1] = y + current_atom->getPosY(); |
835 | > | pos[2] = z + current_atom->getPosZ(); |
836 | ||
837 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
837 | > | info[0].atoms[current_atom_ndx]->setPos(pos); |
838 | ||
839 | < | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
839 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
840 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
841 | ||
842 | rotMat[0][0] = 1.0; | |
843 | rotMat[0][1] = 0.0; | |
# | Line 766 | Line 851 | void SimSetup::makeElement( double x, double y, double | |
851 | rotMat[2][1] = 0.0; | |
852 | rotMat[2][2] = 1.0; | |
853 | ||
854 | < | dAtom->setA( rotMat ); |
854 | > | dAtom->setA(rotMat); |
855 | } | |
856 | ||
857 | current_atom_ndx++; | |
# | Line 775 | Line 860 | void SimSetup::makeElement( double x, double y, double | |
860 | current_mol++; | |
861 | current_comp_mol++; | |
862 | ||
863 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
779 | < | |
863 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
864 | current_comp_mol = 0; | |
865 | current_comp++; | |
866 | } | |
867 | } | |
868 | ||
869 | ||
870 | < | void SimSetup::gatherInfo( void ){ |
870 | > | void SimSetup::gatherInfo(void){ |
871 | > | int i; |
872 | ||
873 | ensembleCase = -1; | |
874 | ffCase = -1; | |
875 | ||
791 | – | // get the stamps and globals; |
792 | – | the_stamps = stamps; |
793 | – | the_globals = globals; |
794 | – | |
876 | // 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(); |
877 | ||
878 | + | for (i = 0; i < nInfo; i++){ |
879 | + | info[i].target_temp = globals->getTargetTemp(); |
880 | + | info[i].dt = globals->getDt(); |
881 | + | info[i].run_time = globals->getRunTime(); |
882 | + | } |
883 | + | n_components = globals->getNComponents(); |
884 | ||
885 | + | |
886 | // get the forceField | |
887 | ||
888 | < | strcpy( force_field, the_globals->getForceField() ); |
888 | > | strcpy(force_field, globals->getForceField()); |
889 | ||
890 | < | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
891 | < | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
890 | > | if (!strcasecmp(force_field, "DUFF")){ |
891 | > | ffCase = FF_DUFF; |
892 | > | } |
893 | > | else if (!strcasecmp(force_field, "LJ")){ |
894 | > | ffCase = FF_LJ; |
895 | > | } |
896 | > | else if (!strcasecmp(force_field, "EAM")){ |
897 | > | ffCase = FF_EAM; |
898 | > | } |
899 | > | else if (!strcasecmp(force_field, "WATER")){ |
900 | > | ffCase = FF_H2O; |
901 | > | } |
902 | else{ | |
903 | < | sprintf( painCave.errMsg, |
904 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
905 | < | force_field ); |
906 | < | painCave.isFatal = 1; |
813 | < | simError(); |
903 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
904 | > | force_field); |
905 | > | painCave.isFatal = 1; |
906 | > | simError(); |
907 | } | |
908 | ||
909 | < | // get the ensemble |
909 | > | // get the ensemble |
910 | ||
911 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
911 | > | strcpy(ensemble, globals->getEnsemble()); |
912 | ||
913 | < | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
914 | < | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
915 | < | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
913 | > | if (!strcasecmp(ensemble, "NVE")){ |
914 | > | ensembleCase = NVE_ENS; |
915 | > | } |
916 | > | else if (!strcasecmp(ensemble, "NVT")){ |
917 | > | ensembleCase = NVT_ENS; |
918 | > | } |
919 | > | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
920 | ensembleCase = NPTi_ENS; | |
921 | < | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
922 | < | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
923 | < | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
921 | > | } |
922 | > | else if (!strcasecmp(ensemble, "NPTf")){ |
923 | > | ensembleCase = NPTf_ENS; |
924 | > | } |
925 | > | else if (!strcasecmp(ensemble, "NPTxyz")){ |
926 | > | ensembleCase = NPTxyz_ENS; |
927 | > | } |
928 | else{ | |
929 | < | sprintf( painCave.errMsg, |
930 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
931 | < | "reverting to NVE for this simulation.\n", |
932 | < | ensemble ); |
933 | < | painCave.isFatal = 0; |
934 | < | simError(); |
935 | < | strcpy( ensemble, "NVE" ); |
936 | < | ensembleCase = NVE_ENS; |
937 | < | } |
938 | < | strcpy( info->ensemble, ensemble ); |
939 | < | |
940 | < | // get the mixing rule |
941 | < | |
942 | < | strcpy( info->mixingRule, the_globals->getMixingRule() ); |
943 | < | info->usePBC = the_globals->getPBC(); |
944 | < | |
945 | < | |
929 | > | sprintf(painCave.errMsg, |
930 | > | "SimSetup Warning. Unrecognized Ensemble -> %s \n" |
931 | > | "\treverting to NVE for this simulation.\n", |
932 | > | ensemble); |
933 | > | painCave.isFatal = 0; |
934 | > | simError(); |
935 | > | strcpy(ensemble, "NVE"); |
936 | > | ensembleCase = NVE_ENS; |
937 | > | } |
938 | > | |
939 | > | for (i = 0; i < nInfo; i++){ |
940 | > | strcpy(info[i].ensemble, ensemble); |
941 | > | |
942 | > | // get the mixing rule |
943 | > | |
944 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
945 | > | info[i].usePBC = globals->getPBC(); |
946 | > | } |
947 | > | |
948 | // get the components and calculate the tot_nMol and indvidual n_mol | |
949 | < | |
950 | < | the_components = the_globals->getComponents(); |
949 | > | |
950 | > | the_components = globals->getComponents(); |
951 | components_nmol = new int[n_components]; | |
952 | ||
953 | ||
954 | < | if( !the_globals->haveNMol() ){ |
954 | > | if (!globals->haveNMol()){ |
955 | // we don't have the total number of molecules, so we assume it is | |
956 | // given in each component | |
957 | ||
958 | tot_nmol = 0; | |
959 | < | for( i=0; i<n_components; i++ ){ |
960 | < | |
961 | < | if( !the_components[i]->haveNMol() ){ |
962 | < | // we have a problem |
963 | < | sprintf( painCave.errMsg, |
964 | < | "SimSetup Error. No global NMol or component NMol" |
965 | < | " given. Cannot calculate the number of atoms.\n" ); |
966 | < | painCave.isFatal = 1; |
864 | < | simError(); |
959 | > | for (i = 0; i < n_components; i++){ |
960 | > | if (!the_components[i]->haveNMol()){ |
961 | > | // we have a problem |
962 | > | sprintf(painCave.errMsg, |
963 | > | "SimSetup Error. No global NMol or component NMol given.\n" |
964 | > | "\tCannot calculate the number of atoms.\n"); |
965 | > | painCave.isFatal = 1; |
966 | > | simError(); |
967 | } | |
968 | ||
969 | tot_nmol += the_components[i]->getNMol(); | |
# | Line 869 | Line 971 | void SimSetup::gatherInfo( void ){ | |
971 | } | |
972 | } | |
973 | else{ | |
974 | < | sprintf( painCave.errMsg, |
975 | < | "SimSetup error.\n" |
976 | < | "\tSorry, the ability to specify total" |
977 | < | " nMols and then give molfractions in the components\n" |
978 | < | "\tis not currently supported." |
979 | < | " Please give nMol in the components.\n" ); |
974 | > | sprintf(painCave.errMsg, |
975 | > | "SimSetup error.\n" |
976 | > | "\tSorry, the ability to specify total" |
977 | > | " nMols and then give molfractions in the components\n" |
978 | > | "\tis not currently supported." |
979 | > | " Please give nMol in the components.\n"); |
980 | painCave.isFatal = 1; | |
981 | simError(); | |
982 | } | |
983 | ||
984 | < | // set the status, sample, and thermal kick times |
985 | < | |
986 | < | if( the_globals->haveSampleTime() ){ |
987 | < | info->sampleTime = the_globals->getSampleTime(); |
988 | < | info->statusTime = info->sampleTime; |
989 | < | info->thermalTime = info->sampleTime; |
984 | > | //check whether sample time, status time, thermal time and reset time are divisble by dt |
985 | > | if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
986 | > | sprintf(painCave.errMsg, |
987 | > | "Sample time is not divisible by dt.\n" |
988 | > | "\tThis will result in samples that are not uniformly\n" |
989 | > | "\tdistributed in time. If this is a problem, change\n" |
990 | > | "\tyour sampleTime variable.\n"); |
991 | > | painCave.isFatal = 0; |
992 | > | simError(); |
993 | } | |
889 | – | else{ |
890 | – | info->sampleTime = the_globals->getRunTime(); |
891 | – | info->statusTime = info->sampleTime; |
892 | – | info->thermalTime = info->sampleTime; |
893 | – | } |
994 | ||
995 | < | if( the_globals->haveStatusTime() ){ |
996 | < | info->statusTime = the_globals->getStatusTime(); |
995 | > | if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){ |
996 | > | sprintf(painCave.errMsg, |
997 | > | "Status time is not divisible by dt.\n" |
998 | > | "\tThis will result in status reports that are not uniformly\n" |
999 | > | "\tdistributed in time. If this is a problem, change \n" |
1000 | > | "\tyour statusTime variable.\n"); |
1001 | > | painCave.isFatal = 0; |
1002 | > | simError(); |
1003 | } | |
1004 | ||
1005 | < | if( the_globals->haveThermalTime() ){ |
1006 | < | info->thermalTime = the_globals->getThermalTime(); |
1007 | < | } |
1005 | > | if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
1006 | > | sprintf(painCave.errMsg, |
1007 | > | "Thermal time is not divisible by dt.\n" |
1008 | > | "\tThis will result in thermalizations that are not uniformly\n" |
1009 | > | "\tdistributed in time. If this is a problem, change \n" |
1010 | > | "\tyour thermalTime variable.\n"); |
1011 | > | painCave.isFatal = 0; |
1012 | > | simError(); |
1013 | > | } |
1014 | ||
1015 | < | // check for the temperature set flag |
1015 | > | if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
1016 | > | sprintf(painCave.errMsg, |
1017 | > | "Reset time is not divisible by dt.\n" |
1018 | > | "\tThis will result in integrator resets that are not uniformly\n" |
1019 | > | "\tdistributed in time. If this is a problem, change\n" |
1020 | > | "\tyour resetTime variable.\n"); |
1021 | > | painCave.isFatal = 0; |
1022 | > | simError(); |
1023 | > | } |
1024 | ||
1025 | < | if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet(); |
1025 | > | // set the status, sample, and thermal kick times |
1026 | ||
1027 | < | // get some of the tricky things that may still be in the globals |
1027 | > | for (i = 0; i < nInfo; i++){ |
1028 | > | if (globals->haveSampleTime()){ |
1029 | > | info[i].sampleTime = globals->getSampleTime(); |
1030 | > | info[i].statusTime = info[i].sampleTime; |
1031 | > | } |
1032 | > | else{ |
1033 | > | info[i].sampleTime = globals->getRunTime(); |
1034 | > | info[i].statusTime = info[i].sampleTime; |
1035 | > | } |
1036 | ||
1037 | < | double boxVector[3]; |
1038 | < | 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(); |
1037 | > | if (globals->haveStatusTime()){ |
1038 | > | info[i].statusTime = globals->getStatusTime(); |
1039 | } | |
934 | – | boxVector[0] = the_globals->getBoxX(); |
1040 | ||
1041 | < | if( !the_globals->haveBoxY() ){ |
1042 | < | sprintf( painCave.errMsg, |
1043 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
1044 | < | painCave.isFatal = 1; |
940 | < | simError(); |
1041 | > | if (globals->haveThermalTime()){ |
1042 | > | info[i].thermalTime = globals->getThermalTime(); |
1043 | > | } else { |
1044 | > | info[i].thermalTime = globals->getRunTime(); |
1045 | } | |
942 | – | boxVector[1] = the_globals->getBoxY(); |
1046 | ||
1047 | < | if( !the_globals->haveBoxZ() ){ |
1048 | < | sprintf( painCave.errMsg, |
1049 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
1050 | < | painCave.isFatal = 1; |
948 | < | simError(); |
1047 | > | info[i].resetIntegrator = 0; |
1048 | > | if( globals->haveResetTime() ){ |
1049 | > | info[i].resetTime = globals->getResetTime(); |
1050 | > | info[i].resetIntegrator = 1; |
1051 | } | |
950 | – | boxVector[2] = the_globals->getBoxZ(); |
1052 | ||
1053 | < | info->setBox( boxVector ); |
1053 | > | // check for the temperature set flag |
1054 | > | |
1055 | > | if (globals->haveTempSet()) |
1056 | > | info[i].setTemp = globals->getTempSet(); |
1057 | > | |
1058 | > | // check for the extended State init |
1059 | > | |
1060 | > | info[i].useInitXSstate = globals->getUseInitXSstate(); |
1061 | > | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
1062 | > | |
1063 | > | // check for thermodynamic integration |
1064 | > | if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) { |
1065 | > | if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
1066 | > | info[i].useSolidThermInt = globals->getUseSolidThermInt(); |
1067 | > | info[i].thermIntLambda = globals->getThermIntLambda(); |
1068 | > | info[i].thermIntK = globals->getThermIntK(); |
1069 | > | |
1070 | > | Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK); |
1071 | > | info[i].restraint = myRestraint; |
1072 | > | } |
1073 | > | else { |
1074 | > | sprintf(painCave.errMsg, |
1075 | > | "SimSetup Error:\n" |
1076 | > | "\tKeyword useSolidThermInt was set to 'true' but\n" |
1077 | > | "\tthermodynamicIntegrationLambda (and/or\n" |
1078 | > | "\tthermodynamicIntegrationK) was not specified.\n" |
1079 | > | "\tPlease provide a lambda value and k value in your .bass file.\n"); |
1080 | > | painCave.isFatal = 1; |
1081 | > | simError(); |
1082 | > | } |
1083 | > | } |
1084 | > | else if(globals->getUseLiquidThermInt()) { |
1085 | > | if (globals->getUseSolidThermInt()) { |
1086 | > | sprintf( painCave.errMsg, |
1087 | > | "SimSetup Warning: It appears that you have both solid and\n" |
1088 | > | "\tliquid thermodynamic integration activated in your .bass\n" |
1089 | > | "\tfile. To avoid confusion, specify only one technique in\n" |
1090 | > | "\tyour .bass file. Liquid-state thermodynamic integration\n" |
1091 | > | "\twill be assumed for the current simulation. If this is not\n" |
1092 | > | "\twhat you desire, set useSolidThermInt to 'true' and\n" |
1093 | > | "\tuseLiquidThermInt to 'false' in your .bass file.\n"); |
1094 | > | painCave.isFatal = 0; |
1095 | > | simError(); |
1096 | > | } |
1097 | > | if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
1098 | > | info[i].useLiquidThermInt = globals->getUseLiquidThermInt(); |
1099 | > | info[i].thermIntLambda = globals->getThermIntLambda(); |
1100 | > | info[i].thermIntK = globals->getThermIntK(); |
1101 | > | } |
1102 | > | else { |
1103 | > | sprintf(painCave.errMsg, |
1104 | > | "SimSetup Error:\n" |
1105 | > | "\tKeyword useLiquidThermInt was set to 'true' but\n" |
1106 | > | "\tthermodynamicIntegrationLambda (and/or\n" |
1107 | > | "\tthermodynamicIntegrationK) was not specified.\n" |
1108 | > | "\tPlease provide a lambda value and k value in your .bass file.\n"); |
1109 | > | painCave.isFatal = 1; |
1110 | > | simError(); |
1111 | > | } |
1112 | > | } |
1113 | > | else if(globals->haveThermIntLambda() || globals->haveThermIntK()){ |
1114 | > | sprintf(painCave.errMsg, |
1115 | > | "SimSetup Warning: If you want to use Thermodynamic\n" |
1116 | > | "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n" |
1117 | > | "\t'true' in your .bass file. These keywords are set to\n" |
1118 | > | "\t'false' by default, so your lambda and/or k values are\n" |
1119 | > | "\tbeing ignored.\n"); |
1120 | > | painCave.isFatal = 0; |
1121 | > | simError(); |
1122 | > | } |
1123 | } | |
1124 | + | |
1125 | + | //setup seed for random number generator |
1126 | + | int seedValue; |
1127 | ||
1128 | + | if (globals->haveSeed()){ |
1129 | + | seedValue = globals->getSeed(); |
1130 | ||
1131 | + | if(seedValue / 1E9 == 0){ |
1132 | + | sprintf(painCave.errMsg, |
1133 | + | "Seed for sprng library should contain at least 9 digits\n" |
1134 | + | "OOPSE will generate a seed for user\n"); |
1135 | + | painCave.isFatal = 0; |
1136 | + | simError(); |
1137 | + | |
1138 | + | //using seed generated by system instead of invalid seed set by user |
1139 | + | #ifndef IS_MPI |
1140 | + | seedValue = make_sprng_seed(); |
1141 | + | #else |
1142 | + | if (worldRank == 0){ |
1143 | + | seedValue = make_sprng_seed(); |
1144 | + | } |
1145 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
1146 | + | #endif |
1147 | + | } |
1148 | + | }//end of if branch of globals->haveSeed() |
1149 | + | else{ |
1150 | ||
1151 | + | #ifndef IS_MPI |
1152 | + | seedValue = make_sprng_seed(); |
1153 | + | #else |
1154 | + | if (worldRank == 0){ |
1155 | + | seedValue = make_sprng_seed(); |
1156 | + | } |
1157 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
1158 | + | #endif |
1159 | + | }//end of globals->haveSeed() |
1160 | + | |
1161 | + | for (int i = 0; i < nInfo; i++){ |
1162 | + | info[i].setSeed(seedValue); |
1163 | + | } |
1164 | + | |
1165 | #ifdef IS_MPI | |
1166 | < | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
1166 | > | strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
1167 | MPIcheckPoint(); | |
1168 | #endif // is_mpi | |
961 | – | |
1169 | } | |
1170 | ||
1171 | ||
1172 | < | void SimSetup::finalInfoCheck( void ){ |
1172 | > | void SimSetup::finalInfoCheck(void){ |
1173 | int index; | |
1174 | int usesDipoles; | |
1175 | < | |
1175 | > | int usesCharges; |
1176 | > | int i; |
1177 | ||
1178 | < | // check electrostatic parameters |
1179 | < | |
1180 | < | index = 0; |
1181 | < | usesDipoles = 0; |
1182 | < | while( (index < info->n_atoms) && !usesDipoles ){ |
1183 | < | usesDipoles = ((info->atoms)[index])->hasDipole(); |
1184 | < | index++; |
1185 | < | } |
1186 | < | |
1178 | > | for (i = 0; i < nInfo; i++){ |
1179 | > | // check electrostatic parameters |
1180 | > | |
1181 | > | index = 0; |
1182 | > | usesDipoles = 0; |
1183 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
1184 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
1185 | > | index++; |
1186 | > | } |
1187 | > | index = 0; |
1188 | > | usesCharges = 0; |
1189 | > | while ((index < info[i].n_atoms) && !usesCharges){ |
1190 | > | usesCharges= (info[i].atoms[index])->hasCharge(); |
1191 | > | index++; |
1192 | > | } |
1193 | #ifdef IS_MPI | |
1194 | < | int myUse = usesDipoles |
1195 | < | MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
1194 | > | int myUse = usesDipoles; |
1195 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
1196 | #endif //is_mpi | |
1197 | ||
1198 | + | double theRcut, theRsw; |
1199 | ||
1200 | < | if (the_globals->getUseRF() ) { |
1201 | < | 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 | < | } |
1200 | > | if (globals->haveRcut()) { |
1201 | > | theRcut = globals->getRcut(); |
1202 | ||
1203 | < | if( !the_globals->haveEST() ){ |
1204 | < | sprintf( painCave.errMsg, |
1205 | < | "SimSetup Warning: using default value of 0.05 * the " |
1206 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
1207 | < | ); |
1208 | < | painCave.isFatal = 0; |
1209 | < | simError(); |
1011 | < | info->est = 0.05 * info->ecr; |
1203 | > | if (globals->haveRsw()) |
1204 | > | theRsw = globals->getRsw(); |
1205 | > | else |
1206 | > | theRsw = theRcut; |
1207 | > | |
1208 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1209 | > | |
1210 | } else { | |
1211 | < | info->est = the_globals->getEST(); |
1211 | > | |
1212 | > | the_ff->calcRcut(); |
1213 | > | theRcut = info[i].getRcut(); |
1214 | > | |
1215 | > | if (globals->haveRsw()) |
1216 | > | theRsw = globals->getRsw(); |
1217 | > | else |
1218 | > | theRsw = theRcut; |
1219 | > | |
1220 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1221 | } | |
1222 | < | |
1223 | < | if(!the_globals->haveDielectric() ){ |
1224 | < | 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) { |
1222 | > | |
1223 | > | if (globals->getUseRF()){ |
1224 | > | info[i].useReactionField = 1; |
1225 | ||
1226 | < | if( !the_globals->haveECR() ){ |
1227 | < | sprintf( painCave.errMsg, |
1228 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
1229 | < | "box length for the electrostaticCutoffRadius.\n" |
1230 | < | "I hope you have a very fast processor!\n"); |
1226 | > | if (!globals->haveRcut()){ |
1227 | > | sprintf(painCave.errMsg, |
1228 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1229 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
1230 | > | "\tfor the cutoffRadius.\n"); |
1231 | painCave.isFatal = 0; | |
1232 | simError(); | |
1233 | < | 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(); |
1233 | > | theRcut = 15.0; |
1234 | } | |
1235 | < | |
1236 | < | if( !the_globals->haveEST() ){ |
1237 | < | sprintf( painCave.errMsg, |
1238 | < | "SimSetup Warning: using default value of 5%% of the " |
1239 | < | "electrostaticCutoffRadius for the " |
1240 | < | "electrostaticSkinThickness\n" |
1241 | < | ); |
1235 | > | else{ |
1236 | > | theRcut = globals->getRcut(); |
1237 | > | } |
1238 | > | |
1239 | > | if (!globals->haveRsw()){ |
1240 | > | sprintf(painCave.errMsg, |
1241 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1242 | > | "\tOOPSE will use a default value of\n" |
1243 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1244 | painCave.isFatal = 0; | |
1245 | simError(); | |
1246 | < | info->est = 0.05 * info->ecr; |
1054 | < | } else { |
1055 | < | info->est = the_globals->getEST(); |
1246 | > | theRsw = 0.95 * theRcut; |
1247 | } | |
1248 | < | } |
1249 | < | } |
1248 | > | else{ |
1249 | > | theRsw = globals->getRsw(); |
1250 | > | } |
1251 | ||
1252 | < | #ifdef IS_MPI |
1061 | < | strcpy( checkPointMsg, "post processing checks out" ); |
1062 | < | MPIcheckPoint(); |
1063 | < | #endif // is_mpi |
1252 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1253 | ||
1254 | < | } |
1255 | < | |
1256 | < | void SimSetup::initSystemCoords( void ){ |
1257 | < | |
1258 | < | if( the_globals->haveInitialConfig() ){ |
1259 | < | |
1260 | < | InitializeFromFile* fileInit; |
1261 | < | #ifdef IS_MPI // is_mpi |
1262 | < | if( worldRank == 0 ){ |
1263 | < | #endif //is_mpi |
1264 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
1265 | < | #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(); |
1254 | > | if (!globals->haveDielectric()){ |
1255 | > | sprintf(painCave.errMsg, |
1256 | > | "SimSetup Error: No Dielectric constant was set.\n" |
1257 | > | "\tYou are trying to use Reaction Field without" |
1258 | > | "\tsetting a dielectric constant!\n"); |
1259 | > | painCave.isFatal = 1; |
1260 | > | simError(); |
1261 | > | } |
1262 | > | info[i].dielectric = globals->getDielectric(); |
1263 | > | } |
1264 | > | else{ |
1265 | > | if (usesDipoles || usesCharges){ |
1266 | ||
1267 | + | if (!globals->haveRcut()){ |
1268 | + | sprintf(painCave.errMsg, |
1269 | + | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1270 | + | "\tOOPSE will use a default value of 15.0 angstroms" |
1271 | + | "\tfor the cutoffRadius.\n"); |
1272 | + | painCave.isFatal = 0; |
1273 | + | simError(); |
1274 | + | theRcut = 15.0; |
1275 | + | } |
1276 | + | else{ |
1277 | + | theRcut = globals->getRcut(); |
1278 | + | } |
1279 | + | |
1280 | + | if (!globals->haveRsw()){ |
1281 | + | sprintf(painCave.errMsg, |
1282 | + | "SimSetup Warning: No value was set for switchingRadius.\n" |
1283 | + | "\tOOPSE will use a default value of\n" |
1284 | + | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1285 | + | painCave.isFatal = 0; |
1286 | + | simError(); |
1287 | + | theRsw = 0.95 * theRcut; |
1288 | + | } |
1289 | + | else{ |
1290 | + | theRsw = globals->getRsw(); |
1291 | + | } |
1292 | + | |
1293 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1294 | + | |
1295 | + | } |
1296 | + | } |
1297 | + | } |
1298 | + | #ifdef IS_MPI |
1299 | + | strcpy(checkPointMsg, "post processing checks out"); |
1300 | + | MPIcheckPoint(); |
1301 | + | #endif // is_mpi |
1302 | ||
1303 | + | // clean up the forcefield |
1304 | + | the_ff->cleanMe(); |
1305 | + | } |
1306 | + | |
1307 | + | void SimSetup::initSystemCoords(void){ |
1308 | + | int i; |
1309 | + | |
1310 | + | char* inName; |
1311 | + | |
1312 | + | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
1313 | + | |
1314 | + | for (i = 0; i < info[0].n_atoms; i++) |
1315 | + | info[0].atoms[i]->setCoords(); |
1316 | + | |
1317 | + | if (globals->haveInitialConfig()){ |
1318 | + | InitializeFromFile* fileInit; |
1319 | + | #ifdef IS_MPI // is_mpi |
1320 | + | if (worldRank == 0){ |
1321 | + | #endif //is_mpi |
1322 | + | inName = globals->getInitialConfig(); |
1323 | + | fileInit = new InitializeFromFile(inName); |
1324 | + | #ifdef IS_MPI |
1325 | + | } |
1326 | + | else |
1327 | + | fileInit = new InitializeFromFile(NULL); |
1328 | #endif | |
1329 | < | } |
1329 | > | fileInit->readInit(info); // default velocities on |
1330 | ||
1331 | + | delete fileInit; |
1332 | + | } |
1333 | + | else{ |
1334 | + | |
1335 | + | // no init from bass |
1336 | + | |
1337 | + | sprintf(painCave.errMsg, |
1338 | + | "Cannot intialize a simulation without an initial configuration file.\n"); |
1339 | + | painCave.isFatal = 1;; |
1340 | + | simError(); |
1341 | + | |
1342 | + | } |
1343 | + | |
1344 | #ifdef IS_MPI | |
1345 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
1345 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
1346 | MPIcheckPoint(); | |
1347 | #endif // is_mpi | |
1106 | – | |
1348 | } | |
1349 | ||
1350 | ||
1351 | < | void SimSetup::makeOutNames( void ){ |
1351 | > | void SimSetup::makeOutNames(void){ |
1352 | > | int k; |
1353 | ||
1354 | + | |
1355 | + | for (k = 0; k < nInfo; k++){ |
1356 | #ifdef IS_MPI | |
1357 | < | if( worldRank == 0 ){ |
1357 | > | if (worldRank == 0){ |
1358 | #endif // is_mpi | |
1359 | < | |
1360 | < | if( the_globals->haveFinalConfig() ){ |
1361 | < | strcpy( info->finalName, the_globals->getFinalConfig() ); |
1362 | < | } |
1363 | < | else{ |
1364 | < | strcpy( info->finalName, inFileName ); |
1359 | > | |
1360 | > | if (globals->haveFinalConfig()){ |
1361 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
1362 | > | } |
1363 | > | else{ |
1364 | > | strcpy(info[k].finalName, inFileName); |
1365 | > | char* endTest; |
1366 | > | int nameLength = strlen(info[k].finalName); |
1367 | > | endTest = &(info[k].finalName[nameLength - 5]); |
1368 | > | if (!strcmp(endTest, ".bass")){ |
1369 | > | strcpy(endTest, ".eor"); |
1370 | > | } |
1371 | > | else if (!strcmp(endTest, ".BASS")){ |
1372 | > | strcpy(endTest, ".eor"); |
1373 | > | } |
1374 | > | else{ |
1375 | > | endTest = &(info[k].finalName[nameLength - 4]); |
1376 | > | if (!strcmp(endTest, ".bss")){ |
1377 | > | strcpy(endTest, ".eor"); |
1378 | > | } |
1379 | > | else if (!strcmp(endTest, ".mdl")){ |
1380 | > | strcpy(endTest, ".eor"); |
1381 | > | } |
1382 | > | else{ |
1383 | > | strcat(info[k].finalName, ".eor"); |
1384 | > | } |
1385 | > | } |
1386 | > | } |
1387 | > | |
1388 | > | // make the sample and status out names |
1389 | > | |
1390 | > | strcpy(info[k].sampleName, inFileName); |
1391 | char* endTest; | |
1392 | < | int nameLength = strlen( info->finalName ); |
1393 | < | endTest = &(info->finalName[nameLength - 5]); |
1394 | < | if( !strcmp( endTest, ".bass" ) ){ |
1395 | < | strcpy( endTest, ".eor" ); |
1392 | > | int nameLength = strlen(info[k].sampleName); |
1393 | > | endTest = &(info[k].sampleName[nameLength - 5]); |
1394 | > | if (!strcmp(endTest, ".bass")){ |
1395 | > | strcpy(endTest, ".dump"); |
1396 | } | |
1397 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1398 | < | strcpy( endTest, ".eor" ); |
1397 | > | else if (!strcmp(endTest, ".BASS")){ |
1398 | > | strcpy(endTest, ".dump"); |
1399 | } | |
1400 | else{ | |
1401 | < | endTest = &(info->finalName[nameLength - 4]); |
1402 | < | if( !strcmp( endTest, ".bss" ) ){ |
1403 | < | strcpy( endTest, ".eor" ); |
1404 | < | } |
1405 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1406 | < | strcpy( endTest, ".eor" ); |
1407 | < | } |
1408 | < | else{ |
1409 | < | strcat( info->finalName, ".eor" ); |
1410 | < | } |
1401 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1402 | > | if (!strcmp(endTest, ".bss")){ |
1403 | > | strcpy(endTest, ".dump"); |
1404 | > | } |
1405 | > | else if (!strcmp(endTest, ".mdl")){ |
1406 | > | strcpy(endTest, ".dump"); |
1407 | > | } |
1408 | > | else{ |
1409 | > | strcat(info[k].sampleName, ".dump"); |
1410 | > | } |
1411 | } | |
1412 | < | } |
1413 | < | |
1414 | < | // make the sample and status out names |
1415 | < | |
1416 | < | strcpy( info->sampleName, inFileName ); |
1417 | < | 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" ); |
1412 | > | |
1413 | > | strcpy(info[k].statusName, inFileName); |
1414 | > | nameLength = strlen(info[k].statusName); |
1415 | > | endTest = &(info[k].statusName[nameLength - 5]); |
1416 | > | if (!strcmp(endTest, ".bass")){ |
1417 | > | strcpy(endTest, ".stat"); |
1418 | } | |
1419 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1420 | < | strcpy( endTest, ".dump" ); |
1419 | > | else if (!strcmp(endTest, ".BASS")){ |
1420 | > | strcpy(endTest, ".stat"); |
1421 | } | |
1422 | else{ | |
1423 | < | strcat( info->sampleName, ".dump" ); |
1424 | < | } |
1425 | < | } |
1426 | < | |
1427 | < | strcpy( info->statusName, inFileName ); |
1428 | < | nameLength = strlen( info->statusName ); |
1429 | < | endTest = &(info->statusName[nameLength - 5]); |
1430 | < | if( !strcmp( endTest, ".bass" ) ){ |
1431 | < | strcpy( endTest, ".stat" ); |
1432 | < | } |
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" ); |
1423 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1424 | > | if (!strcmp(endTest, ".bss")){ |
1425 | > | strcpy(endTest, ".stat"); |
1426 | > | } |
1427 | > | else if (!strcmp(endTest, ".mdl")){ |
1428 | > | strcpy(endTest, ".stat"); |
1429 | > | } |
1430 | > | else{ |
1431 | > | strcat(info[k].statusName, ".stat"); |
1432 | > | } |
1433 | } | |
1434 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1435 | < | strcpy( endTest, ".stat" ); |
1434 | > | |
1435 | > | strcpy(info[k].rawPotName, inFileName); |
1436 | > | nameLength = strlen(info[k].rawPotName); |
1437 | > | endTest = &(info[k].rawPotName[nameLength - 5]); |
1438 | > | if (!strcmp(endTest, ".bass")){ |
1439 | > | strcpy(endTest, ".raw"); |
1440 | } | |
1441 | + | else if (!strcmp(endTest, ".BASS")){ |
1442 | + | strcpy(endTest, ".raw"); |
1443 | + | } |
1444 | else{ | |
1445 | < | strcat( info->statusName, ".stat" ); |
1445 | > | endTest = &(info[k].rawPotName[nameLength - 4]); |
1446 | > | if (!strcmp(endTest, ".bss")){ |
1447 | > | strcpy(endTest, ".raw"); |
1448 | > | } |
1449 | > | else if (!strcmp(endTest, ".mdl")){ |
1450 | > | strcpy(endTest, ".raw"); |
1451 | > | } |
1452 | > | else{ |
1453 | > | strcat(info[k].rawPotName, ".raw"); |
1454 | > | } |
1455 | } | |
1456 | < | } |
1190 | < | |
1456 | > | |
1457 | #ifdef IS_MPI | |
1192 | – | } |
1193 | – | #endif // is_mpi |
1458 | ||
1459 | + | } |
1460 | + | #endif // is_mpi |
1461 | + | } |
1462 | } | |
1463 | ||
1464 | ||
1465 | < | void SimSetup::sysObjectsCreation( void ){ |
1465 | > | void SimSetup::sysObjectsCreation(void){ |
1466 | > | int i, k; |
1467 | ||
1468 | // create the forceField | |
1469 | ||
# | Line 1211 | Line 1479 | void SimSetup::sysObjectsCreation( void ){ | |
1479 | ||
1480 | #ifdef IS_MPI | |
1481 | // divide the molecules among the processors | |
1482 | < | |
1482 | > | |
1483 | mpiMolDivide(); | |
1484 | #endif //is_mpi | |
1485 | < | |
1485 | > | |
1486 | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's | |
1487 | < | |
1487 | > | |
1488 | makeSysArrays(); | |
1489 | ||
1490 | < | |
1490 | > | // make and initialize the molecules (all but atomic coordinates) |
1491 | ||
1492 | + | makeMolecules(); |
1493 | ||
1494 | + | for (k = 0; k < nInfo; k++){ |
1495 | + | info[k].identArray = new int[info[k].n_atoms]; |
1496 | + | for (i = 0; i < info[k].n_atoms; i++){ |
1497 | + | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1498 | + | } |
1499 | + | } |
1500 | } | |
1501 | ||
1502 | ||
1503 | < | void SimSetup::createFF( void ){ |
1503 | > | void SimSetup::createFF(void){ |
1504 | > | switch (ffCase){ |
1505 | > | case FF_DUFF: |
1506 | > | the_ff = new DUFF(); |
1507 | > | break; |
1508 | ||
1509 | < | switch( ffCase ){ |
1509 | > | case FF_LJ: |
1510 | > | the_ff = new LJFF(); |
1511 | > | break; |
1512 | ||
1513 | < | case FF_DUFF: |
1514 | < | the_ff = new DUFF(); |
1515 | < | break; |
1513 | > | case FF_EAM: |
1514 | > | the_ff = new EAM_FF(); |
1515 | > | break; |
1516 | ||
1517 | < | case FF_LJ: |
1518 | < | the_ff = new LJFF(); |
1519 | < | break; |
1517 | > | case FF_H2O: |
1518 | > | the_ff = new WATER(); |
1519 | > | break; |
1520 | ||
1521 | < | default: |
1522 | < | sprintf( painCave.errMsg, |
1523 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1524 | < | painCave.isFatal = 1; |
1525 | < | simError(); |
1521 | > | default: |
1522 | > | sprintf(painCave.errMsg, |
1523 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1524 | > | painCave.isFatal = 1; |
1525 | > | simError(); |
1526 | } | |
1527 | ||
1528 | #ifdef IS_MPI | |
1529 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
1529 | > | strcpy(checkPointMsg, "ForceField creation successful"); |
1530 | MPIcheckPoint(); | |
1531 | #endif // is_mpi | |
1251 | – | |
1532 | } | |
1533 | ||
1534 | ||
1535 | < | void SimSetup::compList( void ){ |
1535 | > | void SimSetup::compList(void){ |
1536 | > | int i; |
1537 | > | char* id; |
1538 | > | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1539 | > | LinkedMolStamp* currentStamp = NULL; |
1540 | > | comp_stamps = new MoleculeStamp * [n_components]; |
1541 | > | bool haveCutoffGroups; |
1542 | ||
1543 | < | comp_stamps = new MoleculeStamp*[n_components]; |
1544 | < | |
1543 | > | haveCutoffGroups = false; |
1544 | > | |
1545 | // make an array of molecule stamps that match the components used. | |
1546 | // also extract the used stamps out into a separate linked list | |
1547 | ||
1548 | < | info->nComponents = n_components; |
1549 | < | info->componentsNmol = components_nmol; |
1550 | < | info->compStamps = comp_stamps; |
1551 | < | info->headStamp = new LinkedMolStamp(); |
1552 | < | |
1553 | < | char* id; |
1268 | < | LinkedMolStamp* headStamp = info->headStamp; |
1269 | < | LinkedMolStamp* currentStamp = NULL; |
1270 | < | for( i=0; i<n_components; i++ ){ |
1548 | > | for (i = 0; i < nInfo; i++){ |
1549 | > | info[i].nComponents = n_components; |
1550 | > | info[i].componentsNmol = components_nmol; |
1551 | > | info[i].compStamps = comp_stamps; |
1552 | > | info[i].headStamp = headStamp; |
1553 | > | } |
1554 | ||
1555 | + | |
1556 | + | for (i = 0; i < n_components; i++){ |
1557 | id = the_components[i]->getType(); | |
1558 | comp_stamps[i] = NULL; | |
1559 | < | |
1559 | > | |
1560 | // check to make sure the component isn't already in the list | |
1561 | ||
1562 | < | comp_stamps[i] = headStamp->match( id ); |
1563 | < | if( comp_stamps[i] == NULL ){ |
1279 | < | |
1562 | > | comp_stamps[i] = headStamp->match(id); |
1563 | > | if (comp_stamps[i] == NULL){ |
1564 | // extract the component from the list; | |
1565 | < | |
1566 | < | currentStamp = the_stamps->extractMolStamp( id ); |
1567 | < | if( currentStamp == NULL ){ |
1568 | < | sprintf( painCave.errMsg, |
1569 | < | "SimSetup error: Component \"%s\" was not found in the " |
1570 | < | "list of declared molecules\n", |
1571 | < | id ); |
1572 | < | painCave.isFatal = 1; |
1573 | < | simError(); |
1565 | > | |
1566 | > | currentStamp = stamps->extractMolStamp(id); |
1567 | > | if (currentStamp == NULL){ |
1568 | > | sprintf(painCave.errMsg, |
1569 | > | "SimSetup error: Component \"%s\" was not found in the " |
1570 | > | "list of declared molecules\n", |
1571 | > | id); |
1572 | > | painCave.isFatal = 1; |
1573 | > | simError(); |
1574 | } | |
1575 | < | |
1576 | < | headStamp->add( currentStamp ); |
1577 | < | comp_stamps[i] = headStamp->match( id ); |
1575 | > | |
1576 | > | headStamp->add(currentStamp); |
1577 | > | comp_stamps[i] = headStamp->match(id); |
1578 | } | |
1579 | + | |
1580 | + | if(comp_stamps[i]->getNCutoffGroups() > 0) |
1581 | + | haveCutoffGroups = true; |
1582 | } | |
1583 | + | |
1584 | + | for (i = 0; i < nInfo; i++) |
1585 | + | info[i].haveCutoffGroups = haveCutoffGroups; |
1586 | ||
1587 | #ifdef IS_MPI | |
1588 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1588 | > | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1589 | MPIcheckPoint(); | |
1590 | #endif // is_mpi | |
1301 | – | |
1302 | – | |
1591 | } | |
1592 | ||
1593 | < | void SimSetup::calcSysValues( void ){ |
1593 | > | void SimSetup::calcSysValues(void){ |
1594 | > | int i, j; |
1595 | > | int ncutgroups, atomsingroups, ngroupsinstamp; |
1596 | ||
1597 | + | int* molMembershipArray; |
1598 | + | CutoffGroupStamp* cg; |
1599 | + | |
1600 | tot_atoms = 0; | |
1601 | tot_bonds = 0; | |
1602 | tot_bends = 0; | |
1603 | tot_torsions = 0; | |
1604 | < | for( i=0; i<n_components; i++ ){ |
1605 | < | |
1606 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1607 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1608 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1604 | > | tot_rigid = 0; |
1605 | > | tot_groups = 0; |
1606 | > | for (i = 0; i < n_components; i++){ |
1607 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1608 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1609 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1610 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1611 | < | } |
1611 | > | tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); |
1612 | ||
1613 | + | ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
1614 | + | atomsingroups = 0; |
1615 | + | for (j=0; j < ncutgroups; j++) { |
1616 | + | cg = comp_stamps[i]->getCutoffGroup(j); |
1617 | + | atomsingroups += cg->getNMembers(); |
1618 | + | } |
1619 | + | ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups; |
1620 | + | tot_groups += components_nmol[i] * ngroupsinstamp; |
1621 | + | } |
1622 | + | |
1623 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1624 | + | molMembershipArray = new int[tot_atoms]; |
1625 | ||
1626 | < | info->n_atoms = tot_atoms; |
1627 | < | info->n_bonds = tot_bonds; |
1628 | < | info->n_bends = tot_bends; |
1629 | < | info->n_torsions = tot_torsions; |
1630 | < | info->n_SRI = tot_SRI; |
1631 | < | info->n_mol = tot_nmol; |
1632 | < | |
1633 | < | info->molMembershipArray = new int[tot_atoms]; |
1626 | > | for (i = 0; i < nInfo; i++){ |
1627 | > | info[i].n_atoms = tot_atoms; |
1628 | > | info[i].n_bonds = tot_bonds; |
1629 | > | info[i].n_bends = tot_bends; |
1630 | > | info[i].n_torsions = tot_torsions; |
1631 | > | info[i].n_SRI = tot_SRI; |
1632 | > | info[i].n_mol = tot_nmol; |
1633 | > | info[i].ngroup = tot_groups; |
1634 | > | info[i].molMembershipArray = molMembershipArray; |
1635 | > | } |
1636 | } | |
1637 | ||
1331 | – | |
1638 | #ifdef IS_MPI | |
1639 | ||
1640 | < | void SimSetup::mpiMolDivide( void ){ |
1641 | < | |
1640 | > | void SimSetup::mpiMolDivide(void){ |
1641 | > | int i, j, k; |
1642 | int localMol, allMol; | |
1643 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1644 | + | int local_rigid, local_groups; |
1645 | + | vector<int> globalMolIndex; |
1646 | + | int ncutgroups, atomsingroups, ngroupsinstamp; |
1647 | + | CutoffGroupStamp* cg; |
1648 | ||
1649 | < | mpiSim = new mpiSimulation( info ); |
1340 | < | |
1341 | < | globalIndex = mpiSim->divideLabor(); |
1649 | > | mpiSim = new mpiSimulation(info); |
1650 | ||
1651 | + | mpiSim->divideLabor(); |
1652 | + | globalAtomIndex = mpiSim->getGlobalAtomIndex(); |
1653 | + | globalGroupIndex = mpiSim->getGlobalGroupIndex(); |
1654 | + | //globalMolIndex = mpiSim->getGlobalMolIndex(); |
1655 | + | |
1656 | // set up the local variables | |
1657 | < | |
1657 | > | |
1658 | mol2proc = mpiSim->getMolToProcMap(); | |
1659 | molCompType = mpiSim->getMolComponentType(); | |
1660 | < | |
1660 | > | |
1661 | allMol = 0; | |
1662 | localMol = 0; | |
1663 | local_atoms = 0; | |
1664 | local_bonds = 0; | |
1665 | local_bends = 0; | |
1666 | local_torsions = 0; | |
1667 | < | globalAtomIndex = 0; |
1667 | > | local_rigid = 0; |
1668 | > | local_groups = 0; |
1669 | > | globalAtomCounter = 0; |
1670 | ||
1671 | + | for (i = 0; i < n_components; i++){ |
1672 | + | for (j = 0; j < components_nmol[i]; j++){ |
1673 | + | if (mol2proc[allMol] == worldRank){ |
1674 | + | local_atoms += comp_stamps[i]->getNAtoms(); |
1675 | + | local_bonds += comp_stamps[i]->getNBonds(); |
1676 | + | local_bends += comp_stamps[i]->getNBends(); |
1677 | + | local_torsions += comp_stamps[i]->getNTorsions(); |
1678 | + | local_rigid += comp_stamps[i]->getNRigidBodies(); |
1679 | ||
1680 | < | for( i=0; i<n_components; i++ ){ |
1680 | > | ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
1681 | > | atomsingroups = 0; |
1682 | > | for (k=0; k < ncutgroups; k++) { |
1683 | > | cg = comp_stamps[i]->getCutoffGroup(k); |
1684 | > | atomsingroups += cg->getNMembers(); |
1685 | > | } |
1686 | > | ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + |
1687 | > | ncutgroups; |
1688 | > | local_groups += ngroupsinstamp; |
1689 | ||
1690 | < | 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++; |
1690 | > | localMol++; |
1691 | } | |
1692 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1693 | < | info->molMembershipArray[globalAtomIndex] = allMol; |
1694 | < | globalAtomIndex++; |
1692 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1693 | > | info[0].molMembershipArray[globalAtomCounter] = allMol; |
1694 | > | globalAtomCounter++; |
1695 | } | |
1696 | ||
1697 | < | allMol++; |
1697 | > | allMol++; |
1698 | } | |
1699 | } | |
1700 | local_SRI = local_bonds + local_bends + local_torsions; | |
1701 | + | |
1702 | + | info[0].n_atoms = mpiSim->getNAtomsLocal(); |
1703 | ||
1704 | < | info->n_atoms = mpiSim->getMyNlocal(); |
1705 | < | |
1706 | < | if( local_atoms != info->n_atoms ){ |
1707 | < | sprintf( painCave.errMsg, |
1708 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1384 | < | " localAtom (%d) are not equal.\n", |
1385 | < | info->n_atoms, |
1386 | < | local_atoms ); |
1704 | > | if (local_atoms != info[0].n_atoms){ |
1705 | > | sprintf(painCave.errMsg, |
1706 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1707 | > | "\tlocalAtom (%d) are not equal.\n", |
1708 | > | info[0].n_atoms, local_atoms); |
1709 | painCave.isFatal = 1; | |
1710 | simError(); | |
1711 | } | |
1712 | ||
1713 | < | info->n_bonds = local_bonds; |
1714 | < | info->n_bends = local_bends; |
1715 | < | info->n_torsions = local_torsions; |
1716 | < | info->n_SRI = local_SRI; |
1717 | < | info->n_mol = localMol; |
1713 | > | info[0].ngroup = mpiSim->getNGroupsLocal(); |
1714 | > | if (local_groups != info[0].ngroup){ |
1715 | > | sprintf(painCave.errMsg, |
1716 | > | "SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n" |
1717 | > | "\tlocalGroups (%d) are not equal.\n", |
1718 | > | info[0].ngroup, local_groups); |
1719 | > | painCave.isFatal = 1; |
1720 | > | simError(); |
1721 | > | } |
1722 | > | |
1723 | > | info[0].n_bonds = local_bonds; |
1724 | > | info[0].n_bends = local_bends; |
1725 | > | info[0].n_torsions = local_torsions; |
1726 | > | info[0].n_SRI = local_SRI; |
1727 | > | info[0].n_mol = localMol; |
1728 | ||
1729 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1729 | > | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1730 | MPIcheckPoint(); | |
1731 | } | |
1732 | < | |
1732 | > | |
1733 | #endif // is_mpi | |
1734 | ||
1735 | ||
1736 | < | void SimSetup::makeSysArrays( void ){ |
1736 | > | void SimSetup::makeSysArrays(void){ |
1737 | > | |
1738 | > | #ifndef IS_MPI |
1739 | > | int k, j; |
1740 | > | #endif // is_mpi |
1741 | > | int i, l; |
1742 | ||
1743 | < | // create the atom and short range interaction arrays |
1743 | > | Atom** the_atoms; |
1744 | > | Molecule* the_molecules; |
1745 | ||
1746 | < | Atom::createArrays(info->n_atoms); |
1747 | < | the_atoms = new Atom*[info->n_atoms]; |
1410 | < | the_molecules = new Molecule[info->n_mol]; |
1411 | < | int molIndex; |
1746 | > | for (l = 0; l < nInfo; l++){ |
1747 | > | // create the atom and short range interaction arrays |
1748 | ||
1749 | < | // initialize the molecule's stampID's |
1749 | > | the_atoms = new Atom * [info[l].n_atoms]; |
1750 | > | the_molecules = new Molecule[info[l].n_mol]; |
1751 | > | int molIndex; |
1752 | ||
1753 | + | // initialize the molecule's stampID's |
1754 | + | |
1755 | #ifdef IS_MPI | |
1416 | – | |
1756 | ||
1757 | < | molIndex = 0; |
1758 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1759 | < | |
1760 | < | if(mol2proc[i] == worldRank ){ |
1761 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
1762 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1763 | < | the_molecules[molIndex].setGlobalIndex( i ); |
1764 | < | molIndex++; |
1757 | > | |
1758 | > | molIndex = 0; |
1759 | > | for (i = 0; i < mpiSim->getNMolGlobal(); i++){ |
1760 | > | if (mol2proc[i] == worldRank){ |
1761 | > | the_molecules[molIndex].setStampID(molCompType[i]); |
1762 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1763 | > | the_molecules[molIndex].setGlobalIndex(i); |
1764 | > | molIndex++; |
1765 | > | } |
1766 | } | |
1427 | – | } |
1767 | ||
1768 | #else // is_mpi | |
1769 | < | |
1770 | < | molIndex = 0; |
1771 | < | globalAtomIndex = 0; |
1772 | < | for(i=0; i<n_components; i++){ |
1773 | < | for(j=0; j<components_nmol[i]; j++ ){ |
1774 | < | the_molecules[molIndex].setStampID( i ); |
1775 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1776 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1777 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1778 | < | info->molMembershipArray[globalAtomIndex] = molIndex; |
1779 | < | globalAtomIndex++; |
1769 | > | |
1770 | > | molIndex = 0; |
1771 | > | globalAtomCounter = 0; |
1772 | > | for (i = 0; i < n_components; i++){ |
1773 | > | for (j = 0; j < components_nmol[i]; j++){ |
1774 | > | the_molecules[molIndex].setStampID(i); |
1775 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1776 | > | the_molecules[molIndex].setGlobalIndex(molIndex); |
1777 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1778 | > | info[l].molMembershipArray[globalAtomCounter] = molIndex; |
1779 | > | globalAtomCounter++; |
1780 | > | } |
1781 | > | molIndex++; |
1782 | } | |
1442 | – | molIndex++; |
1783 | } | |
1444 | – | } |
1445 | – | |
1784 | ||
1785 | + | |
1786 | #endif // is_mpi | |
1787 | ||
1788 | + | info[l].globalExcludes = new int; |
1789 | + | info[l].globalExcludes[0] = 0; |
1790 | + | |
1791 | + | // set the arrays into the SimInfo object |
1792 | ||
1793 | < | if( info->n_SRI ){ |
1793 | > | info[l].atoms = the_atoms; |
1794 | > | info[l].molecules = the_molecules; |
1795 | > | info[l].nGlobalExcludes = 0; |
1796 | ||
1797 | < | 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; |
1797 | > | the_ff->setSimInfo(info); |
1798 | } | |
1799 | < | 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 | < | } |
1799 | > | } |
1800 | ||
1801 | < | // set the arrays into the SimInfo object |
1801 | > | void SimSetup::makeIntegrator(void){ |
1802 | > | int k; |
1803 | ||
1804 | < | info->atoms = the_atoms; |
1805 | < | info->molecules = the_molecules; |
1806 | < | info->nGlobalExcludes = 0; |
1807 | < | info->excludes = the_excludes; |
1804 | > | NVE<RealIntegrator>* myNVE = NULL; |
1805 | > | NVT<RealIntegrator>* myNVT = NULL; |
1806 | > | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1807 | > | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1808 | > | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1809 | > | |
1810 | > | for (k = 0; k < nInfo; k++){ |
1811 | > | switch (ensembleCase){ |
1812 | > | case NVE_ENS: |
1813 | > | if (globals->haveZconstraints()){ |
1814 | > | setupZConstraint(info[k]); |
1815 | > | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1816 | > | } |
1817 | > | else{ |
1818 | > | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1819 | > | } |
1820 | > | |
1821 | > | info->the_integrator = myNVE; |
1822 | > | break; |
1823 | ||
1824 | < | the_ff->setSimInfo( info ); |
1824 | > | case NVT_ENS: |
1825 | > | if (globals->haveZconstraints()){ |
1826 | > | setupZConstraint(info[k]); |
1827 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1828 | > | } |
1829 | > | else |
1830 | > | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1831 | ||
1832 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1833 | + | |
1834 | + | if (globals->haveTauThermostat()) |
1835 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1836 | + | else{ |
1837 | + | sprintf(painCave.errMsg, |
1838 | + | "SimSetup error: If you use the NVT\n" |
1839 | + | "\tensemble, you must set tauThermostat.\n"); |
1840 | + | painCave.isFatal = 1; |
1841 | + | simError(); |
1842 | + | } |
1843 | + | |
1844 | + | info->the_integrator = myNVT; |
1845 | + | break; |
1846 | + | |
1847 | + | case NPTi_ENS: |
1848 | + | if (globals->haveZconstraints()){ |
1849 | + | setupZConstraint(info[k]); |
1850 | + | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1851 | + | } |
1852 | + | else |
1853 | + | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1854 | + | |
1855 | + | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1856 | + | |
1857 | + | if (globals->haveTargetPressure()) |
1858 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1859 | + | else{ |
1860 | + | sprintf(painCave.errMsg, |
1861 | + | "SimSetup error: If you use a constant pressure\n" |
1862 | + | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1863 | + | painCave.isFatal = 1; |
1864 | + | simError(); |
1865 | + | } |
1866 | + | |
1867 | + | if (globals->haveTauThermostat()) |
1868 | + | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1869 | + | else{ |
1870 | + | sprintf(painCave.errMsg, |
1871 | + | "SimSetup error: If you use an NPT\n" |
1872 | + | "\tensemble, you must set tauThermostat.\n"); |
1873 | + | painCave.isFatal = 1; |
1874 | + | simError(); |
1875 | + | } |
1876 | + | |
1877 | + | if (globals->haveTauBarostat()) |
1878 | + | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1879 | + | else{ |
1880 | + | sprintf(painCave.errMsg, |
1881 | + | "SimSetup error: If you use an NPT\n" |
1882 | + | "\tensemble, you must set tauBarostat.\n"); |
1883 | + | painCave.isFatal = 1; |
1884 | + | simError(); |
1885 | + | } |
1886 | + | |
1887 | + | info->the_integrator = myNPTi; |
1888 | + | break; |
1889 | + | |
1890 | + | case NPTf_ENS: |
1891 | + | if (globals->haveZconstraints()){ |
1892 | + | setupZConstraint(info[k]); |
1893 | + | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1894 | + | } |
1895 | + | else |
1896 | + | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1897 | + | |
1898 | + | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1899 | + | |
1900 | + | if (globals->haveTargetPressure()) |
1901 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1902 | + | else{ |
1903 | + | sprintf(painCave.errMsg, |
1904 | + | "SimSetup error: If you use a constant pressure\n" |
1905 | + | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1906 | + | painCave.isFatal = 1; |
1907 | + | simError(); |
1908 | + | } |
1909 | + | |
1910 | + | if (globals->haveTauThermostat()) |
1911 | + | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1912 | + | |
1913 | + | else{ |
1914 | + | sprintf(painCave.errMsg, |
1915 | + | "SimSetup error: If you use an NPT\n" |
1916 | + | "\tensemble, you must set tauThermostat.\n"); |
1917 | + | painCave.isFatal = 1; |
1918 | + | simError(); |
1919 | + | } |
1920 | + | |
1921 | + | if (globals->haveTauBarostat()) |
1922 | + | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1923 | + | |
1924 | + | else{ |
1925 | + | sprintf(painCave.errMsg, |
1926 | + | "SimSetup error: If you use an NPT\n" |
1927 | + | "\tensemble, you must set tauBarostat.\n"); |
1928 | + | painCave.isFatal = 1; |
1929 | + | simError(); |
1930 | + | } |
1931 | + | |
1932 | + | info->the_integrator = myNPTf; |
1933 | + | break; |
1934 | + | |
1935 | + | case NPTxyz_ENS: |
1936 | + | if (globals->haveZconstraints()){ |
1937 | + | setupZConstraint(info[k]); |
1938 | + | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1939 | + | } |
1940 | + | else |
1941 | + | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1942 | + | |
1943 | + | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1944 | + | |
1945 | + | if (globals->haveTargetPressure()) |
1946 | + | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1947 | + | else{ |
1948 | + | sprintf(painCave.errMsg, |
1949 | + | "SimSetup error: If you use a constant pressure\n" |
1950 | + | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1951 | + | painCave.isFatal = 1; |
1952 | + | simError(); |
1953 | + | } |
1954 | + | |
1955 | + | if (globals->haveTauThermostat()) |
1956 | + | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1957 | + | else{ |
1958 | + | sprintf(painCave.errMsg, |
1959 | + | "SimSetup error: If you use an NPT\n" |
1960 | + | "\tensemble, you must set tauThermostat.\n"); |
1961 | + | painCave.isFatal = 1; |
1962 | + | simError(); |
1963 | + | } |
1964 | + | |
1965 | + | if (globals->haveTauBarostat()) |
1966 | + | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1967 | + | else{ |
1968 | + | sprintf(painCave.errMsg, |
1969 | + | "SimSetup error: If you use an NPT\n" |
1970 | + | "\tensemble, you must set tauBarostat.\n"); |
1971 | + | painCave.isFatal = 1; |
1972 | + | simError(); |
1973 | + | } |
1974 | + | |
1975 | + | info->the_integrator = myNPTxyz; |
1976 | + | break; |
1977 | + | |
1978 | + | default: |
1979 | + | sprintf(painCave.errMsg, |
1980 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1981 | + | painCave.isFatal = 1; |
1982 | + | simError(); |
1983 | + | } |
1984 | + | } |
1985 | } | |
1986 | + | |
1987 | + | void SimSetup::initFortran(void){ |
1988 | + | info[0].refreshSim(); |
1989 | + | |
1990 | + | if (!strcmp(info[0].mixingRule, "standard")){ |
1991 | + | the_ff->initForceField(LB_MIXING_RULE); |
1992 | + | } |
1993 | + | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1994 | + | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1995 | + | } |
1996 | + | else{ |
1997 | + | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1998 | + | info[0].mixingRule); |
1999 | + | painCave.isFatal = 1; |
2000 | + | simError(); |
2001 | + | } |
2002 | + | |
2003 | + | |
2004 | + | #ifdef IS_MPI |
2005 | + | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
2006 | + | MPIcheckPoint(); |
2007 | + | #endif // is_mpi |
2008 | + | } |
2009 | + | |
2010 | + | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
2011 | + | int nZConstraints; |
2012 | + | ZconStamp** zconStamp; |
2013 | + | |
2014 | + | if (globals->haveZconstraintTime()){ |
2015 | + | //add sample time of z-constraint into SimInfo's property list |
2016 | + | DoubleData* zconsTimeProp = new DoubleData(); |
2017 | + | zconsTimeProp->setID(ZCONSTIME_ID); |
2018 | + | zconsTimeProp->setData(globals->getZconsTime()); |
2019 | + | theInfo.addProperty(zconsTimeProp); |
2020 | + | } |
2021 | + | else{ |
2022 | + | sprintf(painCave.errMsg, |
2023 | + | "ZConstraint error: If you use a ZConstraint,\n" |
2024 | + | "\tyou must set zconsTime.\n"); |
2025 | + | painCave.isFatal = 1; |
2026 | + | simError(); |
2027 | + | } |
2028 | + | |
2029 | + | //push zconsTol into siminfo, if user does not specify |
2030 | + | //value for zconsTol, a default value will be used |
2031 | + | DoubleData* zconsTol = new DoubleData(); |
2032 | + | zconsTol->setID(ZCONSTOL_ID); |
2033 | + | if (globals->haveZconsTol()){ |
2034 | + | zconsTol->setData(globals->getZconsTol()); |
2035 | + | } |
2036 | + | else{ |
2037 | + | double defaultZConsTol = 0.01; |
2038 | + | sprintf(painCave.errMsg, |
2039 | + | "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
2040 | + | "\tOOPSE will use a default value of %f.\n" |
2041 | + | "\tTo set the tolerance, use the zconsTol variable.\n", |
2042 | + | defaultZConsTol); |
2043 | + | painCave.isFatal = 0; |
2044 | + | simError(); |
2045 | + | |
2046 | + | zconsTol->setData(defaultZConsTol); |
2047 | + | } |
2048 | + | theInfo.addProperty(zconsTol); |
2049 | + | |
2050 | + | //set Force Subtraction Policy |
2051 | + | StringData* zconsForcePolicy = new StringData(); |
2052 | + | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
2053 | + | |
2054 | + | if (globals->haveZconsForcePolicy()){ |
2055 | + | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
2056 | + | } |
2057 | + | else{ |
2058 | + | sprintf(painCave.errMsg, |
2059 | + | "ZConstraint Warning: No force subtraction policy was set.\n" |
2060 | + | "\tOOPSE will use PolicyByMass.\n" |
2061 | + | "\tTo set the policy, use the zconsForcePolicy variable.\n"); |
2062 | + | painCave.isFatal = 0; |
2063 | + | simError(); |
2064 | + | zconsForcePolicy->setData("BYMASS"); |
2065 | + | } |
2066 | + | |
2067 | + | theInfo.addProperty(zconsForcePolicy); |
2068 | + | |
2069 | + | //set zcons gap |
2070 | + | DoubleData* zconsGap = new DoubleData(); |
2071 | + | zconsGap->setID(ZCONSGAP_ID); |
2072 | + | |
2073 | + | if (globals->haveZConsGap()){ |
2074 | + | zconsGap->setData(globals->getZconsGap()); |
2075 | + | theInfo.addProperty(zconsGap); |
2076 | + | } |
2077 | + | |
2078 | + | //set zcons fixtime |
2079 | + | DoubleData* zconsFixtime = new DoubleData(); |
2080 | + | zconsFixtime->setID(ZCONSFIXTIME_ID); |
2081 | + | |
2082 | + | if (globals->haveZConsFixTime()){ |
2083 | + | zconsFixtime->setData(globals->getZconsFixtime()); |
2084 | + | theInfo.addProperty(zconsFixtime); |
2085 | + | } |
2086 | + | |
2087 | + | //set zconsUsingSMD |
2088 | + | IntData* zconsUsingSMD = new IntData(); |
2089 | + | zconsUsingSMD->setID(ZCONSUSINGSMD_ID); |
2090 | + | |
2091 | + | if (globals->haveZConsUsingSMD()){ |
2092 | + | zconsUsingSMD->setData(globals->getZconsUsingSMD()); |
2093 | + | theInfo.addProperty(zconsUsingSMD); |
2094 | + | } |
2095 | + | |
2096 | + | //Determine the name of ouput file and add it into SimInfo's property list |
2097 | + | //Be careful, do not use inFileName, since it is a pointer which |
2098 | + | //point to a string at master node, and slave nodes do not contain that string |
2099 | + | |
2100 | + | string zconsOutput(theInfo.finalName); |
2101 | + | |
2102 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
2103 | + | |
2104 | + | StringData* zconsFilename = new StringData(); |
2105 | + | zconsFilename->setID(ZCONSFILENAME_ID); |
2106 | + | zconsFilename->setData(zconsOutput); |
2107 | + | |
2108 | + | theInfo.addProperty(zconsFilename); |
2109 | + | |
2110 | + | //setup index, pos and other parameters of z-constraint molecules |
2111 | + | nZConstraints = globals->getNzConstraints(); |
2112 | + | theInfo.nZconstraints = nZConstraints; |
2113 | + | |
2114 | + | zconStamp = globals->getZconStamp(); |
2115 | + | ZConsParaItem tempParaItem; |
2116 | + | |
2117 | + | ZConsParaData* zconsParaData = new ZConsParaData(); |
2118 | + | zconsParaData->setID(ZCONSPARADATA_ID); |
2119 | + | |
2120 | + | for (int i = 0; i < nZConstraints; i++){ |
2121 | + | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
2122 | + | tempParaItem.zPos = zconStamp[i]->getZpos(); |
2123 | + | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
2124 | + | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
2125 | + | tempParaItem.havingCantVel = zconStamp[i]->haveCantVel(); |
2126 | + | tempParaItem.cantVel = zconStamp[i]->getCantVel(); |
2127 | + | zconsParaData->addItem(tempParaItem); |
2128 | + | } |
2129 | + | |
2130 | + | //check the uniqueness of index |
2131 | + | if(!zconsParaData->isIndexUnique()){ |
2132 | + | sprintf(painCave.errMsg, |
2133 | + | "ZConstraint Error: molIndex is not unique!\n"); |
2134 | + | painCave.isFatal = 1; |
2135 | + | simError(); |
2136 | + | } |
2137 | + | |
2138 | + | //sort the parameters by index of molecules |
2139 | + | zconsParaData->sortByIndex(); |
2140 | + | |
2141 | + | //push data into siminfo, therefore, we can retrieve later |
2142 | + | theInfo.addProperty(zconsParaData); |
2143 | + | } |
2144 | + | |
2145 | + | void SimSetup::makeMinimizer(){ |
2146 | + | |
2147 | + | OOPSEMinimizer* myOOPSEMinimizer; |
2148 | + | MinimizerParameterSet* param; |
2149 | + | char minimizerName[100]; |
2150 | + | |
2151 | + | for (int i = 0; i < nInfo; i++){ |
2152 | + | |
2153 | + | //prepare parameter set for minimizer |
2154 | + | param = new MinimizerParameterSet(); |
2155 | + | param->setDefaultParameter(); |
2156 | + | |
2157 | + | if (globals->haveMinimizer()){ |
2158 | + | param->setFTol(globals->getMinFTol()); |
2159 | + | } |
2160 | + | |
2161 | + | if (globals->haveMinGTol()){ |
2162 | + | param->setGTol(globals->getMinGTol()); |
2163 | + | } |
2164 | + | |
2165 | + | if (globals->haveMinMaxIter()){ |
2166 | + | param->setMaxIteration(globals->getMinMaxIter()); |
2167 | + | } |
2168 | + | |
2169 | + | if (globals->haveMinWriteFrq()){ |
2170 | + | param->setMaxIteration(globals->getMinMaxIter()); |
2171 | + | } |
2172 | + | |
2173 | + | if (globals->haveMinWriteFrq()){ |
2174 | + | param->setWriteFrq(globals->getMinWriteFrq()); |
2175 | + | } |
2176 | + | |
2177 | + | if (globals->haveMinStepSize()){ |
2178 | + | param->setStepSize(globals->getMinStepSize()); |
2179 | + | } |
2180 | + | |
2181 | + | if (globals->haveMinLSMaxIter()){ |
2182 | + | param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
2183 | + | } |
2184 | + | |
2185 | + | if (globals->haveMinLSTol()){ |
2186 | + | param->setLineSearchTol(globals->getMinLSTol()); |
2187 | + | } |
2188 | + | |
2189 | + | strcpy(minimizerName, globals->getMinimizer()); |
2190 | + | |
2191 | + | if (!strcasecmp(minimizerName, "CG")){ |
2192 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
2193 | + | } |
2194 | + | else if (!strcasecmp(minimizerName, "SD")){ |
2195 | + | //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param); |
2196 | + | myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param); |
2197 | + | } |
2198 | + | else{ |
2199 | + | sprintf(painCave.errMsg, |
2200 | + | "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n"); |
2201 | + | painCave.isFatal = 0; |
2202 | + | simError(); |
2203 | + | |
2204 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
2205 | + | } |
2206 | + | info[i].the_integrator = myOOPSEMinimizer; |
2207 | + | |
2208 | + | //store the minimizer into simInfo |
2209 | + | info[i].the_minimizer = myOOPSEMinimizer; |
2210 | + | info[i].has_minimizer = true; |
2211 | + | } |
2212 | + | |
2213 | + | } |
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