# | Line 1 | Line 1 | |
---|---|---|
1 | #include <algorithm> | |
2 | < | #include <cstdlib> |
2 | > | #include <stdlib.h> |
3 | #include <iostream> | |
4 | < | #include <cmath> |
4 | > | #include <math.h> |
5 | #include <string> | |
6 | < | |
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 21 | Line 25 | |
25 | #define NVT_ENS 1 | |
26 | #define NPTi_ENS 2 | |
27 | #define NPTf_ENS 3 | |
28 | < | #define NPTim_ENS 4 |
25 | < | #define NPTfm_ENS 5 |
28 | > | #define NPTxyz_ENS 4 |
29 | ||
27 | – | #define FF_DUFF 0 |
28 | – | #define FF_LJ 1 |
29 | – | #define FF_EAM 2 |
30 | ||
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 | < | |
67 | > | |
68 | stamps = new MakeStamps(); | |
69 | globals = new Globals(); | |
70 | < | |
71 | < | |
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 50 | Line 80 | SimSetup::~SimSetup(){ | |
80 | delete globals; | |
81 | } | |
82 | ||
83 | < | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
84 | < | info = the_info; |
85 | < | nInfo = theNinfo; |
86 | < | isInfoArray = 1; |
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 ){ |
61 | < | |
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(); |
89 | < | mpiEventLoop(); |
90 | < | |
117 | > | set_interface_stamps(stamps, globals); |
118 | > | mpiEventInit(); |
119 | > | MPIcheckPoint(); |
120 | > | mpiEventLoop(); |
121 | } | |
122 | ||
123 | #endif // is_mpi | |
124 | ||
125 | void SimSetup::createSim(void){ | |
126 | ||
97 | – | int i, j, k, globalAtomIndex; |
98 | – | |
127 | // gather all of the information from the Bass file | |
128 | ||
101 | – | std::cerr << "gathering info\n"; |
102 | – | |
129 | gatherInfo(); | |
130 | ||
131 | // creation of complex system objects | |
132 | ||
107 | – | std::cerr << "creating system objects\n"; |
108 | – | |
133 | sysObjectsCreation(); | |
134 | ||
135 | // check on the post processing info | |
112 | – | |
113 | – | std::cerr << "performing final info check.\n"; |
136 | ||
137 | finalInfoCheck(); | |
138 | ||
139 | // initialize the system coordinates | |
140 | ||
141 | < | std::cerr << "about to init coords\n"; |
141 | > | if ( !initSuspend ){ |
142 | > | initSystemCoords(); |
143 | ||
144 | < | if( !isInfoArray ) initSystemCoords(); |
144 | > | if( !(globals->getUseInitTime()) ) |
145 | > | info[0].currentTime = 0.0; |
146 | > | } |
147 | ||
148 | // make the output filenames | |
149 | ||
150 | makeOutNames(); | |
126 | – | |
127 | – | // make the integrator |
151 | ||
129 | – | makeIntegrator(); |
130 | – | |
152 | #ifdef IS_MPI | |
153 | mpiSim->mpiRefresh(); | |
154 | #endif | |
# | Line 136 | Line 157 | void SimSetup::createSim(void){ | |
157 | ||
158 | initFortran(); | |
159 | ||
160 | + | if (globals->haveMinimizer()) |
161 | + | // make minimizer |
162 | + | makeMinimizer(); |
163 | + | else |
164 | + | // make the integrator |
165 | + | makeIntegrator(); |
166 | ||
140 | – | |
167 | } | |
168 | ||
169 | ||
170 | < | void SimSetup::makeMolecules( void ){ |
171 | < | |
172 | < | int k,l; |
173 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
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; |
175 | > | int stampID, atomOffset, rbOffset; |
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 | ||
166 | – | |
212 | // init the atoms | |
213 | ||
214 | < | double ux, uy, uz, u, uSqr; |
170 | < | |
171 | < | for(k=0; k<nInfo; k++){ |
172 | < | |
173 | < | the_ff->setSimInfo( &(info[k]) ); |
214 | > | int nMembers, nNew, rb1, rb2; |
215 | ||
216 | + | for (k = 0; k < nInfo; k++){ |
217 | + | the_ff->setSimInfo(&(info[k])); |
218 | + | |
219 | atomOffset = 0; | |
220 | < | excludeOffset = 0; |
221 | < | for(i=0; i<info[k].n_mol; i++){ |
222 | < | |
220 | > | groupOffset = 0; |
221 | > | |
222 | > | for (i = 0; i < info[k].n_mol; i++){ |
223 | stampID = info[k].molecules[i].getStampID(); | |
224 | + | molName = comp_stamps[stampID]->getID(); |
225 | ||
226 | < | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
227 | < | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
228 | < | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
226 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
227 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
228 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
229 | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
230 | < | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
230 | > | molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); |
231 | > | |
232 | > | nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups(); |
233 | ||
234 | molInfo.myAtoms = &(info[k].atoms[atomOffset]); | |
188 | – | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
189 | – | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
190 | – | molInfo.myBends = new Bend*[molInfo.nBends]; |
191 | – | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
235 | ||
236 | + | if (molInfo.nBonds > 0) |
237 | + | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
238 | + | else |
239 | + | molInfo.myBonds = NULL; |
240 | + | |
241 | + | if (molInfo.nBends > 0) |
242 | + | molInfo.myBends = new Bend*[molInfo.nBends]; |
243 | + | else |
244 | + | molInfo.myBends = NULL; |
245 | + | |
246 | + | if (molInfo.nTorsions > 0) |
247 | + | molInfo.myTorsions = new Torsion *[molInfo.nTorsions]; |
248 | + | else |
249 | + | molInfo.myTorsions = NULL; |
250 | + | |
251 | theBonds = new bond_pair[molInfo.nBonds]; | |
252 | theBends = new bend_set[molInfo.nBends]; | |
253 | theTorsions = new torsion_set[molInfo.nTorsions]; | |
254 | < | |
254 | > | |
255 | // make the Atoms | |
256 | < | |
257 | < | for(j=0; j<molInfo.nAtoms; j++){ |
258 | < | |
259 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
260 | < | if( currentAtom->haveOrientation() ){ |
261 | < | |
262 | < | dAtom = new DirectionalAtom( (j + atomOffset), |
263 | < | info[k].getConfiguration() ); |
264 | < | info[k].n_oriented++; |
265 | < | molInfo.myAtoms[j] = dAtom; |
266 | < | |
267 | < | ux = currentAtom->getOrntX(); |
268 | < | uy = currentAtom->getOrntY(); |
269 | < | uz = currentAtom->getOrntZ(); |
270 | < | |
271 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
272 | < | |
273 | < | u = sqrt( uSqr ); |
274 | < | ux = ux / u; |
275 | < | uy = uy / u; |
276 | < | uz = uz / u; |
277 | < | |
278 | < | dAtom->setSUx( ux ); |
279 | < | dAtom->setSUy( uy ); |
280 | < | dAtom->setSUz( uz ); |
281 | < | } |
282 | < | else{ |
283 | < | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
226 | < | info[k].getConfiguration() ); |
227 | < | } |
228 | < | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
229 | < | |
256 | > | |
257 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
258 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
259 | > | |
260 | > | if (currentAtom->haveOrientation()){ |
261 | > | dAtom = new DirectionalAtom((j + atomOffset), |
262 | > | info[k].getConfiguration()); |
263 | > | info[k].n_oriented++; |
264 | > | molInfo.myAtoms[j] = dAtom; |
265 | > | |
266 | > | // Directional Atoms have standard unit vectors which are oriented |
267 | > | // in space using the three Euler angles. We assume the standard |
268 | > | // unit vector was originally along the z axis below. |
269 | > | |
270 | > | phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
271 | > | theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
272 | > | psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
273 | > | |
274 | > | dAtom->setUnitFrameFromEuler(phi, theta, psi); |
275 | > | |
276 | > | } |
277 | > | else{ |
278 | > | |
279 | > | molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); |
280 | > | |
281 | > | } |
282 | > | |
283 | > | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
284 | #ifdef IS_MPI | |
285 | < | |
286 | < | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
287 | < | |
285 | > | |
286 | > | molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); |
287 | > | |
288 | #endif // is_mpi | |
289 | } | |
290 | < | |
291 | < | // make the bonds |
292 | < | for(j=0; j<molInfo.nBonds; j++){ |
293 | < | |
294 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
295 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
296 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
297 | < | |
298 | < | exI = theBonds[j].a; |
299 | < | exJ = theBonds[j].b; |
246 | < | |
247 | < | // exclude_I must always be the smaller of the pair |
248 | < | if( exI > exJ ){ |
249 | < | tempEx = exI; |
250 | < | exI = exJ; |
251 | < | exJ = tempEx; |
252 | < | } |
290 | > | |
291 | > | // make the bonds |
292 | > | for (j = 0; j < molInfo.nBonds; j++){ |
293 | > | currentBond = comp_stamps[stampID]->getBond(j); |
294 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
295 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
296 | > | |
297 | > | tempI = theBonds[j].a; |
298 | > | tempJ = theBonds[j].b; |
299 | > | |
300 | #ifdef IS_MPI | |
301 | < | tempEx = exI; |
302 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
303 | < | tempEx = exJ; |
304 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
305 | < | |
306 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
307 | < | #else // isn't MPI |
308 | < | |
262 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
263 | < | #endif //is_mpi |
301 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
302 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
303 | > | #else |
304 | > | exI = tempI + 1; |
305 | > | exJ = tempJ + 1; |
306 | > | #endif |
307 | > | |
308 | > | info[k].excludes->addPair(exI, exJ); |
309 | } | |
310 | < | excludeOffset += molInfo.nBonds; |
266 | < | |
310 | > | |
311 | //make the bends | |
312 | < | for(j=0; j<molInfo.nBends; j++){ |
313 | < | |
314 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
315 | < | theBends[j].a = currentBend->getA() + atomOffset; |
316 | < | theBends[j].b = currentBend->getB() + atomOffset; |
317 | < | theBends[j].c = currentBend->getC() + atomOffset; |
318 | < | |
319 | < | if( currentBend->haveExtras() ){ |
320 | < | |
321 | < | extras = currentBend->getExtras(); |
322 | < | current_extra = extras; |
323 | < | |
324 | < | while( current_extra != NULL ){ |
325 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
326 | < | |
327 | < | switch( current_extra->getType() ){ |
328 | < | |
329 | < | case 0: |
330 | < | theBends[j].ghost = |
331 | < | current_extra->getInt() + atomOffset; |
332 | < | theBends[j].isGhost = 1; |
333 | < | break; |
334 | < | |
335 | < | case 1: |
336 | < | theBends[j].ghost = |
337 | < | (int)current_extra->getDouble() + atomOffset; |
338 | < | theBends[j].isGhost = 1; |
339 | < | break; |
340 | < | |
341 | < | default: |
342 | < | sprintf( painCave.errMsg, |
343 | < | "SimSetup Error: ghostVectorSource was neither a " |
344 | < | "double nor an int.\n" |
345 | < | "-->Bend[%d] in %s\n", |
346 | < | j, comp_stamps[stampID]->getID() ); |
347 | < | painCave.isFatal = 1; |
348 | < | simError(); |
349 | < | } |
350 | < | } |
351 | < | |
352 | < | else{ |
353 | < | |
354 | < | sprintf( painCave.errMsg, |
355 | < | "SimSetup Error: unhandled bend assignment:\n" |
356 | < | " -->%s in Bend[%d] in %s\n", |
357 | < | current_extra->getlhs(), |
358 | < | j, comp_stamps[stampID]->getID() ); |
359 | < | painCave.isFatal = 1; |
360 | < | simError(); |
361 | < | } |
362 | < | |
363 | < | current_extra = current_extra->getNext(); |
320 | < | } |
321 | < | } |
322 | < | |
323 | < | if( !theBends[j].isGhost ){ |
324 | < | |
325 | < | exI = theBends[j].a; |
326 | < | exJ = theBends[j].c; |
327 | < | } |
328 | < | else{ |
329 | < | |
330 | < | exI = theBends[j].a; |
331 | < | exJ = theBends[j].b; |
332 | < | } |
333 | < | |
334 | < | // exclude_I must always be the smaller of the pair |
335 | < | if( exI > exJ ){ |
336 | < | tempEx = exI; |
337 | < | exI = exJ; |
338 | < | exJ = tempEx; |
339 | < | } |
312 | > | for (j = 0; j < molInfo.nBends; j++){ |
313 | > | currentBend = comp_stamps[stampID]->getBend(j); |
314 | > | theBends[j].a = currentBend->getA() + atomOffset; |
315 | > | theBends[j].b = currentBend->getB() + atomOffset; |
316 | > | theBends[j].c = currentBend->getC() + atomOffset; |
317 | > | |
318 | > | if (currentBend->haveExtras()){ |
319 | > | extras = currentBend->getExtras(); |
320 | > | current_extra = extras; |
321 | > | |
322 | > | while (current_extra != NULL){ |
323 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
324 | > | switch (current_extra->getType()){ |
325 | > | case 0: |
326 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
327 | > | theBends[j].isGhost = 1; |
328 | > | break; |
329 | > | |
330 | > | case 1: |
331 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
332 | > | atomOffset; |
333 | > | theBends[j].isGhost = 1; |
334 | > | break; |
335 | > | |
336 | > | default: |
337 | > | sprintf(painCave.errMsg, |
338 | > | "SimSetup Error: ghostVectorSource was neither a " |
339 | > | "double nor an int.\n" |
340 | > | "-->Bend[%d] in %s\n", |
341 | > | j, comp_stamps[stampID]->getID()); |
342 | > | painCave.isFatal = 1; |
343 | > | simError(); |
344 | > | } |
345 | > | } |
346 | > | else{ |
347 | > | sprintf(painCave.errMsg, |
348 | > | "SimSetup Error: unhandled bend assignment:\n" |
349 | > | " -->%s in Bend[%d] in %s\n", |
350 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
351 | > | painCave.isFatal = 1; |
352 | > | simError(); |
353 | > | } |
354 | > | |
355 | > | current_extra = current_extra->getNext(); |
356 | > | } |
357 | > | } |
358 | > | |
359 | > | if (theBends[j].isGhost) { |
360 | > | |
361 | > | tempI = theBends[j].a; |
362 | > | tempJ = theBends[j].b; |
363 | > | |
364 | #ifdef IS_MPI | |
365 | < | tempEx = exI; |
366 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
367 | < | tempEx = exJ; |
368 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
369 | < | |
370 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
371 | < | #else // isn't MPI |
372 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
373 | < | #endif //is_mpi |
365 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
366 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
367 | > | #else |
368 | > | exI = tempI + 1; |
369 | > | exJ = tempJ + 1; |
370 | > | #endif |
371 | > | info[k].excludes->addPair(exI, exJ); |
372 | > | |
373 | > | } else { |
374 | > | |
375 | > | tempI = theBends[j].a; |
376 | > | tempJ = theBends[j].b; |
377 | > | tempK = theBends[j].c; |
378 | > | |
379 | > | #ifdef IS_MPI |
380 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
381 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
382 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
383 | > | #else |
384 | > | exI = tempI + 1; |
385 | > | exJ = tempJ + 1; |
386 | > | exK = tempK + 1; |
387 | > | #endif |
388 | > | |
389 | > | info[k].excludes->addPair(exI, exK); |
390 | > | info[k].excludes->addPair(exI, exJ); |
391 | > | info[k].excludes->addPair(exJ, exK); |
392 | > | } |
393 | } | |
394 | < | excludeOffset += molInfo.nBends; |
395 | < | |
396 | < | for(j=0; j<molInfo.nTorsions; j++){ |
397 | < | |
398 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
399 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
400 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
401 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
402 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
403 | < | |
404 | < | exI = theTorsions[j].a; |
405 | < | exJ = theTorsions[j].d; |
406 | < | |
364 | < | // exclude_I must always be the smaller of the pair |
365 | < | if( exI > exJ ){ |
366 | < | tempEx = exI; |
367 | < | exI = exJ; |
368 | < | exJ = tempEx; |
369 | < | } |
394 | > | |
395 | > | for (j = 0; j < molInfo.nTorsions; j++){ |
396 | > | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
397 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
398 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
399 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
400 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
401 | > | |
402 | > | tempI = theTorsions[j].a; |
403 | > | tempJ = theTorsions[j].b; |
404 | > | tempK = theTorsions[j].c; |
405 | > | tempL = theTorsions[j].d; |
406 | > | |
407 | #ifdef IS_MPI | |
408 | < | tempEx = exI; |
409 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
410 | < | tempEx = exJ; |
411 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
412 | < | |
413 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
414 | < | #else // isn't MPI |
415 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
416 | < | #endif //is_mpi |
408 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
409 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
410 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
411 | > | exL = info[k].atoms[tempL]->getGlobalIndex() + 1; |
412 | > | #else |
413 | > | exI = tempI + 1; |
414 | > | exJ = tempJ + 1; |
415 | > | exK = tempK + 1; |
416 | > | exL = tempL + 1; |
417 | > | #endif |
418 | > | |
419 | > | info[k].excludes->addPair(exI, exJ); |
420 | > | info[k].excludes->addPair(exI, exK); |
421 | > | info[k].excludes->addPair(exI, exL); |
422 | > | info[k].excludes->addPair(exJ, exK); |
423 | > | info[k].excludes->addPair(exJ, exL); |
424 | > | info[k].excludes->addPair(exK, exL); |
425 | } | |
426 | < | excludeOffset += molInfo.nTorsions; |
426 | > | |
427 | ||
428 | + | molInfo.myRigidBodies.clear(); |
429 | ||
430 | < | // send the arrays off to the forceField for init. |
431 | < | |
432 | < | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
433 | < | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
434 | < | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
435 | < | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
430 | > | for (j = 0; j < molInfo.nRigidBodies; j++){ |
431 | > | |
432 | > | currentRigidBody = comp_stamps[stampID]->getRigidBody(j); |
433 | > | nMembers = currentRigidBody->getNMembers(); |
434 | > | |
435 | > | // Create the Rigid Body: |
436 | > | |
437 | > | myRB = new RigidBody(); |
438 | > | |
439 | > | sprintf(rbName,"%s_RB_%d", molName, j); |
440 | > | myRB->setType(rbName); |
441 | > | |
442 | > | for (rb1 = 0; rb1 < nMembers; rb1++) { |
443 | > | |
444 | > | // molI is atom numbering inside this molecule |
445 | > | molI = currentRigidBody->getMember(rb1); |
446 | > | |
447 | > | // tempI is atom numbering on local processor |
448 | > | tempI = molI + atomOffset; |
449 | > | |
450 | > | // currentAtom is the AtomStamp (which we need for |
451 | > | // rigid body reference positions) |
452 | > | currentAtom = comp_stamps[stampID]->getAtom(molI); |
453 | > | |
454 | > | // When we add to the rigid body, add the atom itself and |
455 | > | // the stamp info: |
456 | > | |
457 | > | myRB->addAtom(info[k].atoms[tempI], currentAtom); |
458 | > | |
459 | > | // Add this atom to the Skip List for the integrators |
460 | > | #ifdef IS_MPI |
461 | > | slI = info[k].atoms[tempI]->getGlobalIndex(); |
462 | > | #else |
463 | > | slI = tempI; |
464 | > | #endif |
465 | > | skipList.insert(slI); |
466 | > | |
467 | > | } |
468 | > | |
469 | > | for(rb1 = 0; rb1 < nMembers - 1; rb1++) { |
470 | > | for(rb2 = rb1+1; rb2 < nMembers; rb2++) { |
471 | > | |
472 | > | tempI = currentRigidBody->getMember(rb1); |
473 | > | tempJ = currentRigidBody->getMember(rb2); |
474 | > | |
475 | > | // Some explanation is required here. |
476 | > | // Fortran indexing starts at 1, while c indexing starts at 0 |
477 | > | // Also, in parallel computations, the GlobalIndex is |
478 | > | // used for the exclude list: |
479 | > | |
480 | > | #ifdef IS_MPI |
481 | > | exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1; |
482 | > | exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1; |
483 | > | #else |
484 | > | exI = molInfo.myAtoms[tempI]->getIndex() + 1; |
485 | > | exJ = molInfo.myAtoms[tempJ]->getIndex() + 1; |
486 | > | #endif |
487 | > | |
488 | > | info[k].excludes->addPair(exI, exJ); |
489 | > | |
490 | > | } |
491 | > | } |
492 | > | |
493 | > | molInfo.myRigidBodies.push_back(myRB); |
494 | > | info[k].rigidBodies.push_back(myRB); |
495 | > | } |
496 | ||
497 | + | |
498 | + | //create cutoff group for molecule |
499 | + | |
500 | + | cutoffAtomSet.clear(); |
501 | + | molInfo.myCutoffGroups.clear(); |
502 | ||
503 | < | info[k].molecules[i].initialize( molInfo ); |
503 | > | for (j = 0; j < nCutoffGroups; j++){ |
504 | ||
505 | + | currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j); |
506 | + | nMembers = currentCutoffGroup->getNMembers(); |
507 | + | |
508 | + | myCutoffGroup = new CutoffGroup(); |
509 | + | myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]); |
510 | + | |
511 | + | for (int cg = 0; cg < nMembers; cg++) { |
512 | + | |
513 | + | // molI is atom numbering inside this molecule |
514 | + | molI = currentCutoffGroup->getMember(cg); |
515 | + | |
516 | + | // tempI is atom numbering on local processor |
517 | + | tempI = molI + atomOffset; |
518 | + | |
519 | + | #ifdef IS_MPI |
520 | + | globalID = info[k].atoms[tempI]->getGlobalIndex() |
521 | + | #else |
522 | + | globalID = info[k].atoms[tempI]->getIndex(); |
523 | + | #endif |
524 | + | |
525 | + | globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset]; |
526 | + | |
527 | + | myCutoffGroup->addAtom(info[k].atoms[tempI]); |
528 | + | |
529 | + | cutoffAtomSet.insert(tempI); |
530 | + | } |
531 | + | |
532 | + | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
533 | + | groupOffset++; |
534 | + | |
535 | + | }//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
536 | + | |
537 | + | //creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file |
538 | + | |
539 | + | for(j = 0; j < molInfo.nAtoms; j++){ |
540 | + | |
541 | + | if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){ |
542 | + | myCutoffGroup = new CutoffGroup(); |
543 | + | myCutoffGroup->addAtom(molInfo.myAtoms[j]); |
544 | + | myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]); |
545 | + | #ifdef IS_MPI |
546 | + | globalID = info[k].atoms[atomOffset + j]->getGlobalIndex() |
547 | + | #else |
548 | + | globalID = info[k].atoms[atomOffset + j]->getIndex(); |
549 | + | #endif |
550 | + | globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset]; |
551 | + | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
552 | + | groupOffset++; |
553 | + | } |
554 | + | |
555 | + | } |
556 | + | |
557 | + | // After this is all set up, scan through the atoms to |
558 | + | // see if they can be added to the integrableObjects: |
559 | + | |
560 | + | molInfo.myIntegrableObjects.clear(); |
561 | ||
562 | + | |
563 | + | for (j = 0; j < molInfo.nAtoms; j++){ |
564 | + | |
565 | + | #ifdef IS_MPI |
566 | + | slJ = molInfo.myAtoms[j]->getGlobalIndex(); |
567 | + | #else |
568 | + | slJ = j+atomOffset; |
569 | + | #endif |
570 | + | |
571 | + | // if they aren't on the skip list, then they can be integrated |
572 | + | |
573 | + | if (skipList.find(slJ) == skipList.end()) { |
574 | + | mySD = (StuntDouble *) molInfo.myAtoms[j]; |
575 | + | info[k].integrableObjects.push_back(mySD); |
576 | + | molInfo.myIntegrableObjects.push_back(mySD); |
577 | + | } |
578 | + | } |
579 | + | |
580 | + | // all rigid bodies are integrated: |
581 | + | |
582 | + | for (j = 0; j < molInfo.nRigidBodies; j++) { |
583 | + | mySD = (StuntDouble *) molInfo.myRigidBodies[j]; |
584 | + | info[k].integrableObjects.push_back(mySD); |
585 | + | molInfo.myIntegrableObjects.push_back(mySD); |
586 | + | } |
587 | + | |
588 | + | |
589 | + | /* |
590 | + | |
591 | + | //creat ConstraintPair. |
592 | + | molInfo.myConstraintPair.clear(); |
593 | + | |
594 | + | for (j = 0; j < molInfo.nBonds; j++){ |
595 | + | |
596 | + | //if both atoms are in the same rigid body, just skip it |
597 | + | currentBond = comp_stamps[stampID]->getBond(j); |
598 | + | if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){ |
599 | + | |
600 | + | tempI = currentBond->getA() + atomOffset; |
601 | + | if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex)) |
602 | + | consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
603 | + | else |
604 | + | consElement1 = new ConstraintAtom(info[k].atoms[tempI]); |
605 | + | |
606 | + | tempJ = currentBond->getB() + atomOffset; |
607 | + | if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex)) |
608 | + | consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
609 | + | else |
610 | + | consElement2 = new ConstraintAtom(info[k].atoms[tempJ]); |
611 | + | |
612 | + | consPair = new DistanceConstraintPair(consElement1, consElement2); |
613 | + | molInfo.myConstraintPairs.push_back(consPair); |
614 | + | } |
615 | + | } |
616 | + | |
617 | + | //loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair |
618 | + | for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){ |
619 | + | for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){ |
620 | + | |
621 | + | jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2); |
622 | + | |
623 | + | for(size_t m = 0; m < jointAtoms.size(); m++){ |
624 | + | consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first); |
625 | + | consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second); |
626 | + | |
627 | + | consPair = new JointConstraintPair(consElement1, consElement2); |
628 | + | molInfo.myConstraintPairs.push_back(consPair); |
629 | + | } |
630 | + | |
631 | + | } |
632 | + | } |
633 | + | |
634 | + | */ |
635 | + | // send the arrays off to the forceField for init. |
636 | + | |
637 | + | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
638 | + | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
639 | + | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
640 | + | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
641 | + | theTorsions); |
642 | + | |
643 | + | info[k].molecules[i].initialize(molInfo); |
644 | + | |
645 | + | |
646 | atomOffset += molInfo.nAtoms; | |
647 | delete[] theBonds; | |
648 | delete[] theBends; | |
649 | delete[] theTorsions; | |
650 | < | } |
650 | > | } |
651 | } | |
652 | < | |
652 | > | |
653 | #ifdef IS_MPI | |
654 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
654 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
655 | MPIcheckPoint(); | |
656 | #endif // is_mpi | |
406 | – | |
407 | – | // clean up the forcefield |
657 | ||
409 | – | the_ff->calcRcut(); |
410 | – | the_ff->cleanMe(); |
411 | – | |
658 | } | |
659 | ||
660 | < | void SimSetup::initFromBass( void ){ |
415 | < | |
660 | > | void SimSetup::initFromBass(void){ |
661 | int i, j, k; | |
662 | int n_cells; | |
663 | double cellx, celly, cellz; | |
# | Line 426 | Line 671 | void SimSetup::initFromBass( void ){ | |
671 | vel[1] = 0.0; | |
672 | vel[2] = 0.0; | |
673 | ||
674 | < | temp1 = (double)tot_nmol / 4.0; |
675 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
676 | < | temp3 = ceil( temp2 ); |
674 | > | temp1 = (double) tot_nmol / 4.0; |
675 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
676 | > | temp3 = ceil(temp2); |
677 | ||
678 | < | have_extra =0; |
679 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
680 | < | have_extra =1; |
678 | > | have_extra = 0; |
679 | > | if (temp2 < temp3){ |
680 | > | // we have a non-complete lattice |
681 | > | have_extra = 1; |
682 | ||
683 | < | n_cells = (int)temp3 - 1; |
683 | > | n_cells = (int) temp3 - 1; |
684 | cellx = info[0].boxL[0] / temp3; | |
685 | celly = info[0].boxL[1] / temp3; | |
686 | cellz = info[0].boxL[2] / temp3; | |
687 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
688 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
689 | < | n_per_extra = (int)ceil( temp1 ); |
687 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
688 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
689 | > | n_per_extra = (int) ceil(temp1); |
690 | ||
691 | < | if( n_per_extra > 4){ |
692 | < | sprintf( painCave.errMsg, |
693 | < | "SimSetup error. There has been an error in constructing" |
694 | < | " the non-complete lattice.\n" ); |
691 | > | if (n_per_extra > 4){ |
692 | > | sprintf(painCave.errMsg, |
693 | > | "SimSetup error. There has been an error in constructing" |
694 | > | " the non-complete lattice.\n"); |
695 | painCave.isFatal = 1; | |
696 | simError(); | |
697 | } | |
698 | } | |
699 | else{ | |
700 | < | n_cells = (int)temp3; |
700 | > | n_cells = (int) temp3; |
701 | cellx = info[0].boxL[0] / temp3; | |
702 | celly = info[0].boxL[1] / temp3; | |
703 | cellz = info[0].boxL[2] / temp3; | |
# | Line 462 | Line 708 | void SimSetup::initFromBass( void ){ | |
708 | current_comp = 0; | |
709 | current_atom_ndx = 0; | |
710 | ||
711 | < | for( i=0; i < n_cells ; i++ ){ |
712 | < | for( j=0; j < n_cells; j++ ){ |
713 | < | for( k=0; k < n_cells; k++ ){ |
711 | > | for (i = 0; i < n_cells ; i++){ |
712 | > | for (j = 0; j < n_cells; j++){ |
713 | > | for (k = 0; k < n_cells; k++){ |
714 | > | makeElement(i * cellx, j * celly, k * cellz); |
715 | ||
716 | < | makeElement( i * cellx, |
470 | < | j * celly, |
471 | < | k * cellz ); |
716 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
717 | ||
718 | < | makeElement( i * cellx + 0.5 * cellx, |
474 | < | j * celly + 0.5 * celly, |
475 | < | k * cellz ); |
718 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
719 | ||
720 | < | makeElement( i * cellx, |
478 | < | j * celly + 0.5 * celly, |
479 | < | k * cellz + 0.5 * cellz ); |
480 | < | |
481 | < | makeElement( i * cellx + 0.5 * cellx, |
482 | < | j * celly, |
483 | < | k * cellz + 0.5 * cellz ); |
720 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
721 | } | |
722 | } | |
723 | } | |
724 | ||
725 | < | if( have_extra ){ |
725 | > | if (have_extra){ |
726 | done = 0; | |
727 | ||
728 | int start_ndx; | |
729 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
730 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
729 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
730 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
731 | > | if (i < n_cells){ |
732 | > | if (j < n_cells){ |
733 | > | start_ndx = n_cells; |
734 | > | } |
735 | > | else |
736 | > | start_ndx = 0; |
737 | > | } |
738 | > | else |
739 | > | start_ndx = 0; |
740 | ||
741 | < | if( i < n_cells ){ |
741 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
742 | > | makeElement(i * cellx, j * celly, k * cellz); |
743 | > | done = (current_mol >= tot_nmol); |
744 | ||
745 | < | if( j < n_cells ){ |
746 | < | start_ndx = n_cells; |
747 | < | } |
748 | < | else start_ndx = 0; |
749 | < | } |
502 | < | else start_ndx = 0; |
745 | > | if (!done && n_per_extra > 1){ |
746 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
747 | > | k * cellz); |
748 | > | done = (current_mol >= tot_nmol); |
749 | > | } |
750 | ||
751 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
751 | > | if (!done && n_per_extra > 2){ |
752 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
753 | > | k * cellz + 0.5 * cellz); |
754 | > | done = (current_mol >= tot_nmol); |
755 | > | } |
756 | ||
757 | < | makeElement( i * cellx, |
758 | < | j * celly, |
759 | < | k * cellz ); |
760 | < | done = ( current_mol >= tot_nmol ); |
761 | < | |
762 | < | if( !done && n_per_extra > 1 ){ |
512 | < | makeElement( i * cellx + 0.5 * cellx, |
513 | < | j * celly + 0.5 * celly, |
514 | < | k * cellz ); |
515 | < | done = ( current_mol >= tot_nmol ); |
516 | < | } |
517 | < | |
518 | < | if( !done && n_per_extra > 2){ |
519 | < | makeElement( i * cellx, |
520 | < | j * celly + 0.5 * celly, |
521 | < | k * cellz + 0.5 * cellz ); |
522 | < | done = ( current_mol >= tot_nmol ); |
523 | < | } |
524 | < | |
525 | < | if( !done && n_per_extra > 3){ |
526 | < | makeElement( i * cellx + 0.5 * cellx, |
527 | < | j * celly, |
528 | < | k * cellz + 0.5 * cellz ); |
529 | < | done = ( current_mol >= tot_nmol ); |
530 | < | } |
531 | < | } |
757 | > | if (!done && n_per_extra > 3){ |
758 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
759 | > | k * cellz + 0.5 * cellz); |
760 | > | done = (current_mol >= tot_nmol); |
761 | > | } |
762 | > | } |
763 | } | |
764 | } | |
765 | } | |
766 | ||
767 | < | for( i=0; i<info[0].n_atoms; i++ ){ |
768 | < | info[0].atoms[i]->setVel( vel ); |
767 | > | for (i = 0; i < info[0].n_atoms; i++){ |
768 | > | info[0].atoms[i]->setVel(vel); |
769 | } | |
770 | } | |
771 | ||
772 | < | void SimSetup::makeElement( double x, double y, double z ){ |
542 | < | |
772 | > | void SimSetup::makeElement(double x, double y, double z){ |
773 | int k; | |
774 | AtomStamp* current_atom; | |
775 | DirectionalAtom* dAtom; | |
776 | double rotMat[3][3]; | |
777 | double pos[3]; | |
778 | ||
779 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
780 | < | |
781 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
782 | < | if( !current_atom->havePosition() ){ |
783 | < | sprintf( painCave.errMsg, |
784 | < | "SimSetup:initFromBass error.\n" |
785 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
786 | < | "\tThe initialization routine is unable to give a start" |
787 | < | " position.\n", |
558 | < | comp_stamps[current_comp]->getID(), |
559 | < | current_atom->getType() ); |
779 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
780 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
781 | > | if (!current_atom->havePosition()){ |
782 | > | sprintf(painCave.errMsg, |
783 | > | "SimSetup:initFromBass error.\n" |
784 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
785 | > | "\tThe initialization routine is unable to give a start" |
786 | > | " position.\n", |
787 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
788 | painCave.isFatal = 1; | |
789 | simError(); | |
790 | } | |
791 | < | |
791 | > | |
792 | pos[0] = x + current_atom->getPosX(); | |
793 | pos[1] = y + current_atom->getPosY(); | |
794 | pos[2] = z + current_atom->getPosZ(); | |
567 | – | |
568 | – | info[0].atoms[current_atom_ndx]->setPos( pos ); |
795 | ||
796 | < | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
796 | > | info[0].atoms[current_atom_ndx]->setPos(pos); |
797 | ||
798 | < | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
798 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
799 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
800 | ||
801 | rotMat[0][0] = 1.0; | |
802 | rotMat[0][1] = 0.0; | |
# | Line 583 | Line 810 | void SimSetup::makeElement( double x, double y, double | |
810 | rotMat[2][1] = 0.0; | |
811 | rotMat[2][2] = 1.0; | |
812 | ||
813 | < | dAtom->setA( rotMat ); |
813 | > | dAtom->setA(rotMat); |
814 | } | |
815 | ||
816 | current_atom_ndx++; | |
# | Line 592 | Line 819 | void SimSetup::makeElement( double x, double y, double | |
819 | current_mol++; | |
820 | current_comp_mol++; | |
821 | ||
822 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
596 | < | |
822 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
823 | current_comp_mol = 0; | |
824 | current_comp++; | |
825 | } | |
826 | } | |
827 | ||
828 | ||
829 | < | void SimSetup::gatherInfo( void ){ |
830 | < | int i,j,k; |
829 | > | void SimSetup::gatherInfo(void){ |
830 | > | int i; |
831 | ||
832 | ensembleCase = -1; | |
833 | ffCase = -1; | |
834 | ||
835 | // set the easy ones first | |
836 | ||
837 | < | for( i=0; i<nInfo; i++){ |
837 | > | for (i = 0; i < nInfo; i++){ |
838 | info[i].target_temp = globals->getTargetTemp(); | |
839 | info[i].dt = globals->getDt(); | |
840 | info[i].run_time = globals->getRunTime(); | |
# | Line 618 | Line 844 | void SimSetup::gatherInfo( void ){ | |
844 | ||
845 | // get the forceField | |
846 | ||
847 | < | strcpy( force_field, globals->getForceField() ); |
847 | > | strcpy(force_field, globals->getForceField()); |
848 | ||
849 | < | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
850 | < | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
851 | < | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
849 | > | if (!strcasecmp(force_field, "DUFF")){ |
850 | > | ffCase = FF_DUFF; |
851 | > | } |
852 | > | else if (!strcasecmp(force_field, "LJ")){ |
853 | > | ffCase = FF_LJ; |
854 | > | } |
855 | > | else if (!strcasecmp(force_field, "EAM")){ |
856 | > | ffCase = FF_EAM; |
857 | > | } |
858 | > | else if (!strcasecmp(force_field, "WATER")){ |
859 | > | ffCase = FF_H2O; |
860 | > | } |
861 | else{ | |
862 | < | sprintf( painCave.errMsg, |
863 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
864 | < | force_field ); |
865 | < | painCave.isFatal = 1; |
631 | < | simError(); |
862 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
863 | > | force_field); |
864 | > | painCave.isFatal = 1; |
865 | > | simError(); |
866 | } | |
867 | ||
868 | < | // get the ensemble |
868 | > | // get the ensemble |
869 | ||
870 | < | strcpy( ensemble, globals->getEnsemble() ); |
870 | > | strcpy(ensemble, globals->getEnsemble()); |
871 | ||
872 | < | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
873 | < | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
874 | < | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
872 | > | if (!strcasecmp(ensemble, "NVE")){ |
873 | > | ensembleCase = NVE_ENS; |
874 | > | } |
875 | > | else if (!strcasecmp(ensemble, "NVT")){ |
876 | > | ensembleCase = NVT_ENS; |
877 | > | } |
878 | > | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
879 | ensembleCase = NPTi_ENS; | |
880 | < | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
881 | < | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
882 | < | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
880 | > | } |
881 | > | else if (!strcasecmp(ensemble, "NPTf")){ |
882 | > | ensembleCase = NPTf_ENS; |
883 | > | } |
884 | > | else if (!strcasecmp(ensemble, "NPTxyz")){ |
885 | > | ensembleCase = NPTxyz_ENS; |
886 | > | } |
887 | else{ | |
888 | < | sprintf( painCave.errMsg, |
889 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
890 | < | "reverting to NVE for this simulation.\n", |
891 | < | ensemble ); |
892 | < | painCave.isFatal = 0; |
893 | < | simError(); |
894 | < | strcpy( ensemble, "NVE" ); |
895 | < | ensembleCase = NVE_ENS; |
888 | > | sprintf(painCave.errMsg, |
889 | > | "SimSetup Warning. Unrecognized Ensemble -> %s \n" |
890 | > | "\treverting to NVE for this simulation.\n", |
891 | > | ensemble); |
892 | > | painCave.isFatal = 0; |
893 | > | simError(); |
894 | > | strcpy(ensemble, "NVE"); |
895 | > | ensembleCase = NVE_ENS; |
896 | } | |
655 | – | |
656 | – | for(i=0; i<nInfo; i++){ |
657 | – | |
658 | – | strcpy( info[i].ensemble, ensemble ); |
897 | ||
898 | + | for (i = 0; i < nInfo; i++){ |
899 | + | strcpy(info[i].ensemble, ensemble); |
900 | + | |
901 | // get the mixing rule | |
902 | ||
903 | < | strcpy( info[i].mixingRule, globals->getMixingRule() ); |
903 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
904 | info[i].usePBC = globals->getPBC(); | |
905 | } | |
906 | < | |
906 | > | |
907 | // get the components and calculate the tot_nMol and indvidual n_mol | |
908 | < | |
908 | > | |
909 | the_components = globals->getComponents(); | |
910 | components_nmol = new int[n_components]; | |
911 | ||
912 | ||
913 | < | if( !globals->haveNMol() ){ |
913 | > | if (!globals->haveNMol()){ |
914 | // we don't have the total number of molecules, so we assume it is | |
915 | // given in each component | |
916 | ||
917 | tot_nmol = 0; | |
918 | < | for( i=0; i<n_components; i++ ){ |
918 | > | for (i = 0; i < n_components; i++){ |
919 | > | if (!the_components[i]->haveNMol()){ |
920 | > | // we have a problem |
921 | > | sprintf(painCave.errMsg, |
922 | > | "SimSetup Error. No global NMol or component NMol given.\n" |
923 | > | "\tCannot calculate the number of atoms.\n"); |
924 | > | painCave.isFatal = 1; |
925 | > | simError(); |
926 | > | } |
927 | ||
679 | – | if( !the_components[i]->haveNMol() ){ |
680 | – | // we have a problem |
681 | – | sprintf( painCave.errMsg, |
682 | – | "SimSetup Error. No global NMol or component NMol" |
683 | – | " given. Cannot calculate the number of atoms.\n" ); |
684 | – | painCave.isFatal = 1; |
685 | – | simError(); |
686 | – | } |
687 | – | |
928 | tot_nmol += the_components[i]->getNMol(); | |
929 | components_nmol[i] = the_components[i]->getNMol(); | |
930 | } | |
931 | } | |
932 | else{ | |
933 | < | sprintf( painCave.errMsg, |
934 | < | "SimSetup error.\n" |
935 | < | "\tSorry, the ability to specify total" |
936 | < | " nMols and then give molfractions in the components\n" |
937 | < | "\tis not currently supported." |
938 | < | " Please give nMol in the components.\n" ); |
933 | > | sprintf(painCave.errMsg, |
934 | > | "SimSetup error.\n" |
935 | > | "\tSorry, the ability to specify total" |
936 | > | " nMols and then give molfractions in the components\n" |
937 | > | "\tis not currently supported." |
938 | > | " Please give nMol in the components.\n"); |
939 | painCave.isFatal = 1; | |
940 | simError(); | |
941 | } | |
942 | ||
943 | + | //check whether sample time, status time, thermal time and reset time are divisble by dt |
944 | + | if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
945 | + | sprintf(painCave.errMsg, |
946 | + | "Sample time is not divisible by dt.\n" |
947 | + | "\tThis will result in samples that are not uniformly\n" |
948 | + | "\tdistributed in time. If this is a problem, change\n" |
949 | + | "\tyour sampleTime variable.\n"); |
950 | + | painCave.isFatal = 0; |
951 | + | simError(); |
952 | + | } |
953 | + | |
954 | + | if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){ |
955 | + | sprintf(painCave.errMsg, |
956 | + | "Status time is not divisible by dt.\n" |
957 | + | "\tThis will result in status reports that are not uniformly\n" |
958 | + | "\tdistributed in time. If this is a problem, change \n" |
959 | + | "\tyour statusTime variable.\n"); |
960 | + | painCave.isFatal = 0; |
961 | + | simError(); |
962 | + | } |
963 | + | |
964 | + | if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
965 | + | sprintf(painCave.errMsg, |
966 | + | "Thermal time is not divisible by dt.\n" |
967 | + | "\tThis will result in thermalizations that are not uniformly\n" |
968 | + | "\tdistributed in time. If this is a problem, change \n" |
969 | + | "\tyour thermalTime variable.\n"); |
970 | + | painCave.isFatal = 0; |
971 | + | simError(); |
972 | + | } |
973 | + | |
974 | + | if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
975 | + | sprintf(painCave.errMsg, |
976 | + | "Reset time is not divisible by dt.\n" |
977 | + | "\tThis will result in integrator resets that are not uniformly\n" |
978 | + | "\tdistributed in time. If this is a problem, change\n" |
979 | + | "\tyour resetTime variable.\n"); |
980 | + | painCave.isFatal = 0; |
981 | + | simError(); |
982 | + | } |
983 | + | |
984 | // set the status, sample, and thermal kick times | |
704 | – | |
705 | – | for(i=0; i<nInfo; i++){ |
985 | ||
986 | < | if( globals->haveSampleTime() ){ |
986 | > | for (i = 0; i < nInfo; i++){ |
987 | > | if (globals->haveSampleTime()){ |
988 | info[i].sampleTime = globals->getSampleTime(); | |
989 | info[i].statusTime = info[i].sampleTime; | |
710 | – | info[i].thermalTime = info[i].sampleTime; |
990 | } | |
991 | else{ | |
992 | info[i].sampleTime = globals->getRunTime(); | |
993 | info[i].statusTime = info[i].sampleTime; | |
715 | – | info[i].thermalTime = info[i].sampleTime; |
994 | } | |
995 | < | |
996 | < | if( globals->haveStatusTime() ){ |
995 | > | |
996 | > | if (globals->haveStatusTime()){ |
997 | info[i].statusTime = globals->getStatusTime(); | |
998 | } | |
999 | < | |
1000 | < | if( globals->haveThermalTime() ){ |
999 | > | |
1000 | > | if (globals->haveThermalTime()){ |
1001 | info[i].thermalTime = globals->getThermalTime(); | |
1002 | + | } else { |
1003 | + | info[i].thermalTime = globals->getRunTime(); |
1004 | } | |
1005 | ||
1006 | < | // check for the temperature set flag |
1006 | > | info[i].resetIntegrator = 0; |
1007 | > | if( globals->haveResetTime() ){ |
1008 | > | info[i].resetTime = globals->getResetTime(); |
1009 | > | info[i].resetIntegrator = 1; |
1010 | > | } |
1011 | ||
1012 | < | if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
1012 | > | // check for the temperature set flag |
1013 | ||
1014 | < | // get some of the tricky things that may still be in the globals |
1015 | < | |
1016 | < | double boxVector[3]; |
1017 | < | if( globals->haveBox() ){ |
1018 | < | boxVector[0] = globals->getBox(); |
1019 | < | boxVector[1] = globals->getBox(); |
1020 | < | boxVector[2] = globals->getBox(); |
1021 | < | |
1022 | < | info[i].setBox( boxVector ); |
1023 | < | } |
1024 | < | else if( globals->haveDensity() ){ |
1025 | < | |
1026 | < | double vol; |
1027 | < | vol = (double)tot_nmol / globals->getDensity(); |
1028 | < | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
1029 | < | boxVector[1] = boxVector[0]; |
1030 | < | boxVector[2] = boxVector[0]; |
1031 | < | |
1032 | < | info[i].setBox( boxVector ); |
1033 | < | } |
1034 | < | else{ |
1035 | < | if( !globals->haveBoxX() ){ |
1036 | < | sprintf( painCave.errMsg, |
1037 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
1014 | > | if (globals->haveTempSet()) |
1015 | > | info[i].setTemp = globals->getTempSet(); |
1016 | > | |
1017 | > | // check for the extended State init |
1018 | > | |
1019 | > | info[i].useInitXSstate = globals->getUseInitXSstate(); |
1020 | > | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
1021 | > | |
1022 | > | // check for thermodynamic integration |
1023 | > | if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) { |
1024 | > | if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
1025 | > | info[i].useSolidThermInt = globals->getUseSolidThermInt(); |
1026 | > | info[i].thermIntLambda = globals->getThermIntLambda(); |
1027 | > | info[i].thermIntK = globals->getThermIntK(); |
1028 | > | |
1029 | > | Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK); |
1030 | > | info[i].restraint = myRestraint; |
1031 | > | } |
1032 | > | else { |
1033 | > | sprintf(painCave.errMsg, |
1034 | > | "SimSetup Error:\n" |
1035 | > | "\tKeyword useSolidThermInt was set to 'true' but\n" |
1036 | > | "\tthermodynamicIntegrationLambda (and/or\n" |
1037 | > | "\tthermodynamicIntegrationK) was not specified.\n" |
1038 | > | "\tPlease provide a lambda value and k value in your .bass file.\n"); |
1039 | painCave.isFatal = 1; | |
1040 | < | simError(); |
1040 | > | simError(); |
1041 | } | |
1042 | < | boxVector[0] = globals->getBoxX(); |
1043 | < | |
1044 | < | if( !globals->haveBoxY() ){ |
1042 | > | } |
1043 | > | else if(globals->getUseLiquidThermInt()) { |
1044 | > | if (globals->getUseSolidThermInt()) { |
1045 | sprintf( painCave.errMsg, | |
1046 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
1047 | < | painCave.isFatal = 1; |
1046 | > | "SimSetup Warning: It appears that you have both solid and\n" |
1047 | > | "\tliquid thermodynamic integration activated in your .bass\n" |
1048 | > | "\tfile. To avoid confusion, specify only one technique in\n" |
1049 | > | "\tyour .bass file. Liquid-state thermodynamic integration\n" |
1050 | > | "\twill be assumed for the current simulation. If this is not\n" |
1051 | > | "\twhat you desire, set useSolidThermInt to 'true' and\n" |
1052 | > | "\tuseLiquidThermInt to 'false' in your .bass file.\n"); |
1053 | > | painCave.isFatal = 0; |
1054 | simError(); | |
1055 | } | |
1056 | < | boxVector[1] = globals->getBoxY(); |
1057 | < | |
1058 | < | if( !globals->haveBoxZ() ){ |
1059 | < | sprintf( painCave.errMsg, |
1060 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
1056 | > | if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
1057 | > | info[i].useLiquidThermInt = globals->getUseLiquidThermInt(); |
1058 | > | info[i].thermIntLambda = globals->getThermIntLambda(); |
1059 | > | info[i].thermIntK = globals->getThermIntK(); |
1060 | > | } |
1061 | > | else { |
1062 | > | sprintf(painCave.errMsg, |
1063 | > | "SimSetup Error:\n" |
1064 | > | "\tKeyword useLiquidThermInt was set to 'true' but\n" |
1065 | > | "\tthermodynamicIntegrationLambda (and/or\n" |
1066 | > | "\tthermodynamicIntegrationK) was not specified.\n" |
1067 | > | "\tPlease provide a lambda value and k value in your .bass file.\n"); |
1068 | painCave.isFatal = 1; | |
1069 | < | simError(); |
1069 | > | simError(); |
1070 | } | |
773 | – | boxVector[2] = globals->getBoxZ(); |
774 | – | |
775 | – | info[i].setBox( boxVector ); |
1071 | } | |
1072 | < | |
1072 | > | else if(globals->haveThermIntLambda() || globals->haveThermIntK()){ |
1073 | > | sprintf(painCave.errMsg, |
1074 | > | "SimSetup Warning: If you want to use Thermodynamic\n" |
1075 | > | "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n" |
1076 | > | "\t'true' in your .bass file. These keywords are set to\n" |
1077 | > | "\t'false' by default, so your lambda and/or k values are\n" |
1078 | > | "\tbeing ignored.\n"); |
1079 | > | painCave.isFatal = 0; |
1080 | > | simError(); |
1081 | > | } |
1082 | } | |
1083 | + | |
1084 | + | //setup seed for random number generator |
1085 | + | int seedValue; |
1086 | + | |
1087 | + | if (globals->haveSeed()){ |
1088 | + | seedValue = globals->getSeed(); |
1089 | + | |
1090 | + | if(seedValue / 1E9 == 0){ |
1091 | + | sprintf(painCave.errMsg, |
1092 | + | "Seed for sprng library should contain at least 9 digits\n" |
1093 | + | "OOPSE will generate a seed for user\n"); |
1094 | + | painCave.isFatal = 0; |
1095 | + | simError(); |
1096 | + | |
1097 | + | //using seed generated by system instead of invalid seed set by user |
1098 | + | #ifndef IS_MPI |
1099 | + | seedValue = make_sprng_seed(); |
1100 | + | #else |
1101 | + | if (worldRank == 0){ |
1102 | + | seedValue = make_sprng_seed(); |
1103 | + | } |
1104 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
1105 | + | #endif |
1106 | + | } |
1107 | + | }//end of if branch of globals->haveSeed() |
1108 | + | else{ |
1109 | ||
1110 | + | #ifndef IS_MPI |
1111 | + | seedValue = make_sprng_seed(); |
1112 | + | #else |
1113 | + | if (worldRank == 0){ |
1114 | + | seedValue = make_sprng_seed(); |
1115 | + | } |
1116 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
1117 | + | #endif |
1118 | + | }//end of globals->haveSeed() |
1119 | + | |
1120 | + | for (int i = 0; i < nInfo; i++){ |
1121 | + | info[i].setSeed(seedValue); |
1122 | + | } |
1123 | + | |
1124 | #ifdef IS_MPI | |
1125 | < | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
1125 | > | strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
1126 | MPIcheckPoint(); | |
1127 | #endif // is_mpi | |
784 | – | |
1128 | } | |
1129 | ||
1130 | ||
1131 | < | void SimSetup::finalInfoCheck( void ){ |
1131 | > | void SimSetup::finalInfoCheck(void){ |
1132 | int index; | |
1133 | int usesDipoles; | |
1134 | + | int usesCharges; |
1135 | int i; | |
1136 | ||
1137 | < | for(i=0; i<nInfo; i++){ |
1137 | > | for (i = 0; i < nInfo; i++){ |
1138 | // check electrostatic parameters | |
1139 | < | |
1139 | > | |
1140 | index = 0; | |
1141 | usesDipoles = 0; | |
1142 | < | while( (index < info[i].n_atoms) && !usesDipoles ){ |
1142 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
1143 | usesDipoles = (info[i].atoms[index])->hasDipole(); | |
1144 | index++; | |
1145 | } | |
1146 | < | |
1146 | > | index = 0; |
1147 | > | usesCharges = 0; |
1148 | > | while ((index < info[i].n_atoms) && !usesCharges){ |
1149 | > | usesCharges= (info[i].atoms[index])->hasCharge(); |
1150 | > | index++; |
1151 | > | } |
1152 | #ifdef IS_MPI | |
1153 | int myUse = usesDipoles; | |
1154 | < | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
1154 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
1155 | #endif //is_mpi | |
1156 | < | |
1157 | < | double theEcr, theEst; |
1158 | < | |
1159 | < | if (globals->getUseRF() ) { |
1160 | < | info[i].useReactionField = 1; |
1156 | > | |
1157 | > | double theRcut, theRsw; |
1158 | > | |
1159 | > | if (globals->haveRcut()) { |
1160 | > | theRcut = globals->getRcut(); |
1161 | > | |
1162 | > | if (globals->haveRsw()) |
1163 | > | theRsw = globals->getRsw(); |
1164 | > | else |
1165 | > | theRsw = theRcut; |
1166 | ||
1167 | < | if( !globals->haveECR() ){ |
1168 | < | sprintf( painCave.errMsg, |
1169 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
816 | < | "box length for the electrostaticCutoffRadius.\n" |
817 | < | "I hope you have a very fast processor!\n"); |
818 | < | painCave.isFatal = 0; |
819 | < | simError(); |
820 | < | double smallest; |
821 | < | smallest = info[i].boxL[0]; |
822 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
823 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
824 | < | theEcr = 0.5 * smallest; |
825 | < | } else { |
826 | < | theEcr = globals->getECR(); |
827 | < | } |
1167 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1168 | > | |
1169 | > | } else { |
1170 | ||
1171 | < | if( !globals->haveEST() ){ |
1172 | < | sprintf( painCave.errMsg, |
1173 | < | "SimSetup Warning: using default value of 0.05 * the " |
1174 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
1175 | < | ); |
1176 | < | painCave.isFatal = 0; |
1177 | < | simError(); |
836 | < | theEst = 0.05 * theEcr; |
837 | < | } else { |
838 | < | theEst= globals->getEST(); |
839 | < | } |
1171 | > | the_ff->calcRcut(); |
1172 | > | theRcut = info[i].getRcut(); |
1173 | > | |
1174 | > | if (globals->haveRsw()) |
1175 | > | theRsw = globals->getRsw(); |
1176 | > | else |
1177 | > | theRsw = theRcut; |
1178 | ||
1179 | < | info[i].setEcr( theEcr, theEst ); |
1179 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1180 | > | } |
1181 | > | |
1182 | > | if (globals->getUseRF()){ |
1183 | > | info[i].useReactionField = 1; |
1184 | ||
1185 | < | if(!globals->haveDielectric() ){ |
1186 | < | sprintf( painCave.errMsg, |
1187 | < | "SimSetup Error: You are trying to use Reaction Field without" |
1188 | < | "setting a dielectric constant!\n" |
1189 | < | ); |
1190 | < | painCave.isFatal = 1; |
1191 | < | simError(); |
1185 | > | if (!globals->haveRcut()){ |
1186 | > | sprintf(painCave.errMsg, |
1187 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1188 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
1189 | > | "\tfor the cutoffRadius.\n"); |
1190 | > | painCave.isFatal = 0; |
1191 | > | simError(); |
1192 | > | theRcut = 15.0; |
1193 | } | |
1194 | < | info[i].dielectric = globals->getDielectric(); |
1195 | < | } |
1196 | < | else { |
1197 | < | if (usesDipoles) { |
1194 | > | else{ |
1195 | > | theRcut = globals->getRcut(); |
1196 | > | } |
1197 | > | |
1198 | > | if (!globals->haveRsw()){ |
1199 | > | sprintf(painCave.errMsg, |
1200 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1201 | > | "\tOOPSE will use a default value of\n" |
1202 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1203 | > | painCave.isFatal = 0; |
1204 | > | simError(); |
1205 | > | theRsw = 0.95 * theRcut; |
1206 | > | } |
1207 | > | else{ |
1208 | > | theRsw = globals->getRsw(); |
1209 | > | } |
1210 | > | |
1211 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1212 | > | |
1213 | > | if (!globals->haveDielectric()){ |
1214 | > | sprintf(painCave.errMsg, |
1215 | > | "SimSetup Error: No Dielectric constant was set.\n" |
1216 | > | "\tYou are trying to use Reaction Field without" |
1217 | > | "\tsetting a dielectric constant!\n"); |
1218 | > | painCave.isFatal = 1; |
1219 | > | simError(); |
1220 | > | } |
1221 | > | info[i].dielectric = globals->getDielectric(); |
1222 | > | } |
1223 | > | else{ |
1224 | > | if (usesDipoles || usesCharges){ |
1225 | > | |
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 | > | theRcut = 15.0; |
1234 | > | } |
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 | > | theRsw = 0.95 * theRcut; |
1247 | > | } |
1248 | > | else{ |
1249 | > | theRsw = globals->getRsw(); |
1250 | > | } |
1251 | > | |
1252 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1253 | ||
856 | – | if( !globals->haveECR() ){ |
857 | – | sprintf( painCave.errMsg, |
858 | – | "SimSetup Warning: using default value of 1/2 the smallest " |
859 | – | "box length for the electrostaticCutoffRadius.\n" |
860 | – | "I hope you have a very fast processor!\n"); |
861 | – | painCave.isFatal = 0; |
862 | – | simError(); |
863 | – | double smallest; |
864 | – | smallest = info[i].boxL[0]; |
865 | – | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
866 | – | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
867 | – | theEcr = 0.5 * smallest; |
868 | – | } else { |
869 | – | theEcr = globals->getECR(); |
870 | – | } |
871 | – | |
872 | – | if( !globals->haveEST() ){ |
873 | – | sprintf( painCave.errMsg, |
874 | – | "SimSetup Warning: using default value of 0.05 * the " |
875 | – | "electrostaticCutoffRadius for the " |
876 | – | "electrostaticSkinThickness\n" |
877 | – | ); |
878 | – | painCave.isFatal = 0; |
879 | – | simError(); |
880 | – | theEst = 0.05 * theEcr; |
881 | – | } else { |
882 | – | theEst= globals->getEST(); |
883 | – | } |
884 | – | |
885 | – | info[i].setEcr( theEcr, theEst ); |
1254 | } | |
1255 | < | } |
1255 | > | } |
1256 | } | |
889 | – | |
1257 | #ifdef IS_MPI | |
1258 | < | strcpy( checkPointMsg, "post processing checks out" ); |
1258 | > | strcpy(checkPointMsg, "post processing checks out"); |
1259 | MPIcheckPoint(); | |
1260 | #endif // is_mpi | |
1261 | ||
1262 | + | // clean up the forcefield |
1263 | + | the_ff->cleanMe(); |
1264 | } | |
896 | – | |
897 | – | void SimSetup::initSystemCoords( void ){ |
898 | – | int i; |
1265 | ||
1266 | + | void SimSetup::initSystemCoords(void){ |
1267 | + | int i; |
1268 | + | |
1269 | char* inName; | |
1270 | ||
1271 | < | std::cerr << "Setting atom Coords\n"; |
1271 | > | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
1272 | ||
1273 | < | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
1274 | < | |
1275 | < | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
1276 | < | |
908 | < | if( globals->haveInitialConfig() ){ |
909 | < | |
1273 | > | for (i = 0; i < info[0].n_atoms; i++) |
1274 | > | info[0].atoms[i]->setCoords(); |
1275 | > | |
1276 | > | if (globals->haveInitialConfig()){ |
1277 | InitializeFromFile* fileInit; | |
1278 | #ifdef IS_MPI // is_mpi | |
1279 | < | if( worldRank == 0 ){ |
1279 | > | if (worldRank == 0){ |
1280 | #endif //is_mpi | |
1281 | inName = globals->getInitialConfig(); | |
1282 | < | fileInit = new InitializeFromFile( inName ); |
1282 | > | fileInit = new InitializeFromFile(inName); |
1283 | #ifdef IS_MPI | |
1284 | < | }else fileInit = new InitializeFromFile( NULL ); |
1284 | > | } |
1285 | > | else |
1286 | > | fileInit = new InitializeFromFile(NULL); |
1287 | #endif | |
1288 | < | fileInit->readInit( info ); // default velocities on |
1289 | < | |
1288 | > | fileInit->readInit(info); // default velocities on |
1289 | > | |
1290 | delete fileInit; | |
1291 | } | |
1292 | else{ | |
1293 | ||
925 | – | #ifdef IS_MPI |
926 | – | |
1294 | // no init from bass | |
1295 | ||
1296 | < | sprintf( painCave.errMsg, |
1297 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
1298 | < | painCave.isFatal; |
1296 | > | sprintf(painCave.errMsg, |
1297 | > | "Cannot intialize a simulation without an initial configuration file.\n"); |
1298 | > | painCave.isFatal = 1;; |
1299 | simError(); | |
1300 | ||
934 | – | #else |
935 | – | |
936 | – | initFromBass(); |
937 | – | |
938 | – | |
939 | – | #endif |
1301 | } | |
1302 | < | |
1302 | > | |
1303 | #ifdef IS_MPI | |
1304 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
1304 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
1305 | MPIcheckPoint(); | |
1306 | #endif // is_mpi | |
946 | – | |
1307 | } | |
1308 | ||
1309 | ||
1310 | < | void SimSetup::makeOutNames( void ){ |
951 | < | |
1310 | > | void SimSetup::makeOutNames(void){ |
1311 | int k; | |
1312 | ||
954 | – | |
955 | – | for(k=0; k<nInfo; k++){ |
1313 | ||
1314 | + | for (k = 0; k < nInfo; k++){ |
1315 | #ifdef IS_MPI | |
1316 | < | if( worldRank == 0 ){ |
1316 | > | if (worldRank == 0){ |
1317 | #endif // is_mpi | |
1318 | < | |
1319 | < | if( globals->haveFinalConfig() ){ |
1320 | < | strcpy( info[k].finalName, globals->getFinalConfig() ); |
1318 | > | |
1319 | > | if (globals->haveFinalConfig()){ |
1320 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
1321 | } | |
1322 | else{ | |
1323 | < | strcpy( info[k].finalName, inFileName ); |
1324 | < | char* endTest; |
1325 | < | int nameLength = strlen( info[k].finalName ); |
1326 | < | endTest = &(info[k].finalName[nameLength - 5]); |
1327 | < | if( !strcmp( endTest, ".bass" ) ){ |
1328 | < | strcpy( endTest, ".eor" ); |
1329 | < | } |
1330 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1331 | < | strcpy( endTest, ".eor" ); |
1332 | < | } |
1333 | < | else{ |
1334 | < | endTest = &(info[k].finalName[nameLength - 4]); |
1335 | < | if( !strcmp( endTest, ".bss" ) ){ |
1336 | < | strcpy( endTest, ".eor" ); |
1337 | < | } |
1338 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1339 | < | strcpy( endTest, ".eor" ); |
1340 | < | } |
1341 | < | else{ |
1342 | < | strcat( info[k].finalName, ".eor" ); |
1343 | < | } |
1344 | < | } |
1323 | > | strcpy(info[k].finalName, inFileName); |
1324 | > | char* endTest; |
1325 | > | int nameLength = strlen(info[k].finalName); |
1326 | > | endTest = &(info[k].finalName[nameLength - 5]); |
1327 | > | if (!strcmp(endTest, ".bass")){ |
1328 | > | strcpy(endTest, ".eor"); |
1329 | > | } |
1330 | > | else if (!strcmp(endTest, ".BASS")){ |
1331 | > | strcpy(endTest, ".eor"); |
1332 | > | } |
1333 | > | else{ |
1334 | > | endTest = &(info[k].finalName[nameLength - 4]); |
1335 | > | if (!strcmp(endTest, ".bss")){ |
1336 | > | strcpy(endTest, ".eor"); |
1337 | > | } |
1338 | > | else if (!strcmp(endTest, ".mdl")){ |
1339 | > | strcpy(endTest, ".eor"); |
1340 | > | } |
1341 | > | else{ |
1342 | > | strcat(info[k].finalName, ".eor"); |
1343 | > | } |
1344 | > | } |
1345 | } | |
1346 | < | |
1346 | > | |
1347 | // make the sample and status out names | |
1348 | < | |
1349 | < | strcpy( info[k].sampleName, inFileName ); |
1348 | > | |
1349 | > | strcpy(info[k].sampleName, inFileName); |
1350 | char* endTest; | |
1351 | < | int nameLength = strlen( info[k].sampleName ); |
1351 | > | int nameLength = strlen(info[k].sampleName); |
1352 | endTest = &(info[k].sampleName[nameLength - 5]); | |
1353 | < | if( !strcmp( endTest, ".bass" ) ){ |
1354 | < | strcpy( endTest, ".dump" ); |
1353 | > | if (!strcmp(endTest, ".bass")){ |
1354 | > | strcpy(endTest, ".dump"); |
1355 | } | |
1356 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1357 | < | strcpy( endTest, ".dump" ); |
1356 | > | else if (!strcmp(endTest, ".BASS")){ |
1357 | > | strcpy(endTest, ".dump"); |
1358 | } | |
1359 | else{ | |
1360 | < | endTest = &(info[k].sampleName[nameLength - 4]); |
1361 | < | if( !strcmp( endTest, ".bss" ) ){ |
1362 | < | strcpy( endTest, ".dump" ); |
1363 | < | } |
1364 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1365 | < | strcpy( endTest, ".dump" ); |
1366 | < | } |
1367 | < | else{ |
1368 | < | strcat( info[k].sampleName, ".dump" ); |
1369 | < | } |
1360 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1361 | > | if (!strcmp(endTest, ".bss")){ |
1362 | > | strcpy(endTest, ".dump"); |
1363 | > | } |
1364 | > | else if (!strcmp(endTest, ".mdl")){ |
1365 | > | strcpy(endTest, ".dump"); |
1366 | > | } |
1367 | > | else{ |
1368 | > | strcat(info[k].sampleName, ".dump"); |
1369 | > | } |
1370 | } | |
1371 | < | |
1372 | < | strcpy( info[k].statusName, inFileName ); |
1373 | < | nameLength = strlen( info[k].statusName ); |
1371 | > | |
1372 | > | strcpy(info[k].statusName, inFileName); |
1373 | > | nameLength = strlen(info[k].statusName); |
1374 | endTest = &(info[k].statusName[nameLength - 5]); | |
1375 | < | if( !strcmp( endTest, ".bass" ) ){ |
1376 | < | strcpy( endTest, ".stat" ); |
1375 | > | if (!strcmp(endTest, ".bass")){ |
1376 | > | strcpy(endTest, ".stat"); |
1377 | } | |
1378 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1379 | < | strcpy( endTest, ".stat" ); |
1378 | > | else if (!strcmp(endTest, ".BASS")){ |
1379 | > | strcpy(endTest, ".stat"); |
1380 | } | |
1381 | else{ | |
1382 | < | endTest = &(info[k].statusName[nameLength - 4]); |
1383 | < | if( !strcmp( endTest, ".bss" ) ){ |
1384 | < | strcpy( endTest, ".stat" ); |
1385 | < | } |
1386 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1387 | < | strcpy( endTest, ".stat" ); |
1388 | < | } |
1389 | < | else{ |
1390 | < | strcat( info[k].statusName, ".stat" ); |
1391 | < | } |
1382 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1383 | > | if (!strcmp(endTest, ".bss")){ |
1384 | > | strcpy(endTest, ".stat"); |
1385 | > | } |
1386 | > | else if (!strcmp(endTest, ".mdl")){ |
1387 | > | strcpy(endTest, ".stat"); |
1388 | > | } |
1389 | > | else{ |
1390 | > | strcat(info[k].statusName, ".stat"); |
1391 | > | } |
1392 | } | |
1393 | < | |
1393 | > | |
1394 | > | strcpy(info[k].rawPotName, inFileName); |
1395 | > | nameLength = strlen(info[k].rawPotName); |
1396 | > | endTest = &(info[k].rawPotName[nameLength - 5]); |
1397 | > | if (!strcmp(endTest, ".bass")){ |
1398 | > | strcpy(endTest, ".raw"); |
1399 | > | } |
1400 | > | else if (!strcmp(endTest, ".BASS")){ |
1401 | > | strcpy(endTest, ".raw"); |
1402 | > | } |
1403 | > | else{ |
1404 | > | endTest = &(info[k].rawPotName[nameLength - 4]); |
1405 | > | if (!strcmp(endTest, ".bss")){ |
1406 | > | strcpy(endTest, ".raw"); |
1407 | > | } |
1408 | > | else if (!strcmp(endTest, ".mdl")){ |
1409 | > | strcpy(endTest, ".raw"); |
1410 | > | } |
1411 | > | else{ |
1412 | > | strcat(info[k].rawPotName, ".raw"); |
1413 | > | } |
1414 | > | } |
1415 | > | |
1416 | #ifdef IS_MPI | |
1417 | + | |
1418 | } | |
1419 | #endif // is_mpi | |
1420 | } | |
1421 | } | |
1422 | ||
1423 | ||
1424 | < | void SimSetup::sysObjectsCreation( void ){ |
1425 | < | |
1426 | < | int i,k; |
1046 | < | |
1424 | > | void SimSetup::sysObjectsCreation(void){ |
1425 | > | int i, k; |
1426 | > | |
1427 | // create the forceField | |
1428 | ||
1429 | createFF(); | |
# | Line 1058 | Line 1438 | void SimSetup::sysObjectsCreation( void ){ | |
1438 | ||
1439 | #ifdef IS_MPI | |
1440 | // divide the molecules among the processors | |
1441 | < | |
1441 | > | |
1442 | mpiMolDivide(); | |
1443 | #endif //is_mpi | |
1444 | < | |
1444 | > | |
1445 | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's | |
1446 | < | |
1446 | > | |
1447 | makeSysArrays(); | |
1448 | ||
1449 | // make and initialize the molecules (all but atomic coordinates) | |
1450 | < | |
1450 | > | |
1451 | makeMolecules(); | |
1452 | < | |
1453 | < | for(k=0; k<nInfo; k++){ |
1452 | > | |
1453 | > | for (k = 0; k < nInfo; k++){ |
1454 | info[k].identArray = new int[info[k].n_atoms]; | |
1455 | < | for(i=0; i<info[k].n_atoms; i++){ |
1455 | > | for (i = 0; i < info[k].n_atoms; i++){ |
1456 | info[k].identArray[i] = info[k].atoms[i]->getIdent(); | |
1457 | } | |
1458 | } | |
1459 | } | |
1460 | ||
1461 | ||
1462 | < | void SimSetup::createFF( void ){ |
1462 | > | void SimSetup::createFF(void){ |
1463 | > | switch (ffCase){ |
1464 | > | case FF_DUFF: |
1465 | > | the_ff = new DUFF(); |
1466 | > | break; |
1467 | ||
1468 | < | switch( ffCase ){ |
1468 | > | case FF_LJ: |
1469 | > | the_ff = new LJFF(); |
1470 | > | break; |
1471 | ||
1472 | < | case FF_DUFF: |
1473 | < | the_ff = new DUFF(); |
1474 | < | break; |
1472 | > | case FF_EAM: |
1473 | > | the_ff = new EAM_FF(); |
1474 | > | break; |
1475 | ||
1476 | < | case FF_LJ: |
1477 | < | the_ff = new LJFF(); |
1478 | < | break; |
1476 | > | case FF_H2O: |
1477 | > | the_ff = new WATER(); |
1478 | > | break; |
1479 | ||
1480 | < | case FF_EAM: |
1481 | < | the_ff = new EAM_FF(); |
1482 | < | break; |
1483 | < | |
1484 | < | default: |
1099 | < | sprintf( painCave.errMsg, |
1100 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1101 | < | painCave.isFatal = 1; |
1102 | < | simError(); |
1480 | > | default: |
1481 | > | sprintf(painCave.errMsg, |
1482 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1483 | > | painCave.isFatal = 1; |
1484 | > | simError(); |
1485 | } | |
1486 | ||
1487 | #ifdef IS_MPI | |
1488 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
1488 | > | strcpy(checkPointMsg, "ForceField creation successful"); |
1489 | MPIcheckPoint(); | |
1490 | #endif // is_mpi | |
1109 | – | |
1491 | } | |
1492 | ||
1493 | ||
1494 | < | void SimSetup::compList( void ){ |
1114 | < | |
1494 | > | void SimSetup::compList(void){ |
1495 | int i; | |
1496 | char* id; | |
1497 | LinkedMolStamp* headStamp = new LinkedMolStamp(); | |
1498 | LinkedMolStamp* currentStamp = NULL; | |
1499 | < | comp_stamps = new MoleculeStamp*[n_components]; |
1499 | > | comp_stamps = new MoleculeStamp * [n_components]; |
1500 | > | bool haveCutoffGroups; |
1501 | > | |
1502 | > | haveCutoffGroups = false; |
1503 | ||
1504 | // make an array of molecule stamps that match the components used. | |
1505 | // also extract the used stamps out into a separate linked list | |
1506 | < | |
1507 | < | for(i=0; i<nInfo; i++){ |
1506 | > | |
1507 | > | for (i = 0; i < nInfo; i++){ |
1508 | info[i].nComponents = n_components; | |
1509 | info[i].componentsNmol = components_nmol; | |
1510 | info[i].compStamps = comp_stamps; | |
1511 | info[i].headStamp = headStamp; | |
1512 | } | |
1130 | – | |
1513 | ||
1132 | – | for( i=0; i<n_components; i++ ){ |
1514 | ||
1515 | + | for (i = 0; i < n_components; i++){ |
1516 | id = the_components[i]->getType(); | |
1517 | comp_stamps[i] = NULL; | |
1518 | < | |
1518 | > | |
1519 | // check to make sure the component isn't already in the list | |
1520 | ||
1521 | < | comp_stamps[i] = headStamp->match( id ); |
1522 | < | if( comp_stamps[i] == NULL ){ |
1141 | < | |
1521 | > | comp_stamps[i] = headStamp->match(id); |
1522 | > | if (comp_stamps[i] == NULL){ |
1523 | // extract the component from the list; | |
1524 | < | |
1525 | < | currentStamp = stamps->extractMolStamp( id ); |
1526 | < | if( currentStamp == NULL ){ |
1527 | < | sprintf( painCave.errMsg, |
1528 | < | "SimSetup error: Component \"%s\" was not found in the " |
1529 | < | "list of declared molecules\n", |
1530 | < | id ); |
1531 | < | painCave.isFatal = 1; |
1532 | < | simError(); |
1524 | > | |
1525 | > | currentStamp = stamps->extractMolStamp(id); |
1526 | > | if (currentStamp == NULL){ |
1527 | > | sprintf(painCave.errMsg, |
1528 | > | "SimSetup error: Component \"%s\" was not found in the " |
1529 | > | "list of declared molecules\n", |
1530 | > | id); |
1531 | > | painCave.isFatal = 1; |
1532 | > | simError(); |
1533 | } | |
1534 | < | |
1535 | < | headStamp->add( currentStamp ); |
1536 | < | comp_stamps[i] = headStamp->match( id ); |
1534 | > | |
1535 | > | headStamp->add(currentStamp); |
1536 | > | comp_stamps[i] = headStamp->match(id); |
1537 | } | |
1538 | + | |
1539 | + | if(comp_stamps[i]->getNCutoffGroups() > 0) |
1540 | + | haveCutoffGroups = true; |
1541 | } | |
1542 | + | |
1543 | + | for (i = 0; i < nInfo; i++) |
1544 | + | info[i].haveCutoffGroups = haveCutoffGroups; |
1545 | ||
1546 | #ifdef IS_MPI | |
1547 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1547 | > | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1548 | MPIcheckPoint(); | |
1549 | #endif // is_mpi | |
1550 | + | } |
1551 | ||
1552 | + | void SimSetup::calcSysValues(void){ |
1553 | + | int i, j; |
1554 | + | int ncutgroups, atomsingroups, ngroupsinstamp; |
1555 | ||
1556 | < | } |
1556 | > | int* molMembershipArray; |
1557 | > | CutoffGroupStamp* cg; |
1558 | ||
1167 | – | void SimSetup::calcSysValues( void ){ |
1168 | – | int i, j, k; |
1169 | – | |
1170 | – | int *molMembershipArray; |
1171 | – | |
1559 | tot_atoms = 0; | |
1560 | tot_bonds = 0; | |
1561 | tot_bends = 0; | |
1562 | tot_torsions = 0; | |
1563 | < | for( i=0; i<n_components; i++ ){ |
1564 | < | |
1565 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1566 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1567 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1563 | > | tot_rigid = 0; |
1564 | > | tot_groups = 0; |
1565 | > | for (i = 0; i < n_components; i++){ |
1566 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1567 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1568 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1569 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1570 | + | tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); |
1571 | + | |
1572 | + | ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
1573 | + | atomsingroups = 0; |
1574 | + | for (j=0; j < ncutgroups; j++) { |
1575 | + | cg = comp_stamps[i]->getCutoffGroup(j); |
1576 | + | atomsingroups += cg->getNMembers(); |
1577 | + | } |
1578 | + | ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups; |
1579 | + | tot_groups += components_nmol[i] * ngroupsinstamp; |
1580 | } | |
1581 | ||
1582 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1583 | molMembershipArray = new int[tot_atoms]; | |
1584 | < | |
1585 | < | for(i=0; i<nInfo; i++){ |
1584 | > | |
1585 | > | for (i = 0; i < nInfo; i++){ |
1586 | info[i].n_atoms = tot_atoms; | |
1587 | info[i].n_bonds = tot_bonds; | |
1588 | info[i].n_bends = tot_bends; | |
1589 | info[i].n_torsions = tot_torsions; | |
1590 | info[i].n_SRI = tot_SRI; | |
1591 | info[i].n_mol = tot_nmol; | |
1592 | < | |
1592 | > | info[i].ngroup = tot_groups; |
1593 | info[i].molMembershipArray = molMembershipArray; | |
1594 | < | } |
1594 | > | } |
1595 | } | |
1596 | ||
1597 | #ifdef IS_MPI | |
1598 | ||
1599 | < | void SimSetup::mpiMolDivide( void ){ |
1202 | < | |
1599 | > | void SimSetup::mpiMolDivide(void){ |
1600 | int i, j, k; | |
1601 | int localMol, allMol; | |
1602 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1603 | + | int local_rigid, local_groups; |
1604 | + | vector<int> globalMolIndex; |
1605 | + | int ncutgroups, atomsingroups, ngroupsinstamp; |
1606 | + | CutoffGroupStamp* cg; |
1607 | ||
1608 | < | mpiSim = new mpiSimulation( info ); |
1208 | < | |
1209 | < | globalIndex = mpiSim->divideLabor(); |
1608 | > | mpiSim = new mpiSimulation(info); |
1609 | ||
1610 | + | mpiSim->divideLabor(); |
1611 | + | globalAtomIndex = mpiSim->getGlobalAtomIndex(); |
1612 | + | //globalMolIndex = mpiSim->getGlobalMolIndex(); |
1613 | + | |
1614 | // set up the local variables | |
1615 | < | |
1615 | > | |
1616 | mol2proc = mpiSim->getMolToProcMap(); | |
1617 | molCompType = mpiSim->getMolComponentType(); | |
1618 | < | |
1618 | > | |
1619 | allMol = 0; | |
1620 | localMol = 0; | |
1621 | local_atoms = 0; | |
1622 | local_bonds = 0; | |
1623 | local_bends = 0; | |
1624 | local_torsions = 0; | |
1625 | < | globalAtomIndex = 0; |
1625 | > | local_rigid = 0; |
1626 | > | local_groups = 0; |
1627 | > | globalAtomCounter = 0; |
1628 | ||
1629 | + | for (i = 0; i < n_components; i++){ |
1630 | + | for (j = 0; j < components_nmol[i]; j++){ |
1631 | + | if (mol2proc[allMol] == worldRank){ |
1632 | + | local_atoms += comp_stamps[i]->getNAtoms(); |
1633 | + | local_bonds += comp_stamps[i]->getNBonds(); |
1634 | + | local_bends += comp_stamps[i]->getNBends(); |
1635 | + | local_torsions += comp_stamps[i]->getNTorsions(); |
1636 | + | local_rigid += comp_stamps[i]->getNRigidBodies(); |
1637 | ||
1638 | < | for( i=0; i<n_components; i++ ){ |
1638 | > | ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
1639 | > | atomsingroups = 0; |
1640 | > | for (k=0; k < ncutgroups; k++) { |
1641 | > | cg = comp_stamps[i]->getCutoffGroup(k); |
1642 | > | atomsingroups += cg->getNMembers(); |
1643 | > | } |
1644 | > | ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + |
1645 | > | ncutgroups; |
1646 | > | local_groups += ngroupsinstamp; |
1647 | ||
1648 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1228 | < | |
1229 | < | if( mol2proc[allMol] == worldRank ){ |
1230 | < | |
1231 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
1232 | < | local_bonds += comp_stamps[i]->getNBonds(); |
1233 | < | local_bends += comp_stamps[i]->getNBends(); |
1234 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
1235 | < | localMol++; |
1648 | > | localMol++; |
1649 | } | |
1650 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1651 | < | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1652 | < | globalAtomIndex++; |
1650 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1651 | > | info[0].molMembershipArray[globalAtomCounter] = allMol; |
1652 | > | globalAtomCounter++; |
1653 | } | |
1654 | ||
1655 | < | allMol++; |
1655 | > | allMol++; |
1656 | } | |
1657 | } | |
1658 | local_SRI = local_bonds + local_bends + local_torsions; | |
1659 | + | |
1660 | + | info[0].n_atoms = mpiSim->getNAtomsLocal(); |
1661 | ||
1662 | < | info[0].n_atoms = mpiSim->getMyNlocal(); |
1663 | < | |
1664 | < | if( local_atoms != info[0].n_atoms ){ |
1665 | < | sprintf( painCave.errMsg, |
1666 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1252 | < | " localAtom (%d) are not equal.\n", |
1253 | < | info[0].n_atoms, |
1254 | < | local_atoms ); |
1662 | > | if (local_atoms != info[0].n_atoms){ |
1663 | > | sprintf(painCave.errMsg, |
1664 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1665 | > | "\tlocalAtom (%d) are not equal.\n", |
1666 | > | info[0].n_atoms, local_atoms); |
1667 | painCave.isFatal = 1; | |
1668 | simError(); | |
1669 | } | |
1670 | ||
1671 | + | info[0].ngroup = mpiSim->getNGroupsLocal(); |
1672 | + | if (local_groups != info[0].ngroup){ |
1673 | + | sprintf(painCave.errMsg, |
1674 | + | "SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n" |
1675 | + | "\tlocalGroups (%d) are not equal.\n", |
1676 | + | info[0].ngroup, local_groups); |
1677 | + | painCave.isFatal = 1; |
1678 | + | simError(); |
1679 | + | } |
1680 | + | |
1681 | info[0].n_bonds = local_bonds; | |
1682 | info[0].n_bends = local_bends; | |
1683 | info[0].n_torsions = local_torsions; | |
1684 | info[0].n_SRI = local_SRI; | |
1685 | info[0].n_mol = localMol; | |
1686 | ||
1687 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1687 | > | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1688 | MPIcheckPoint(); | |
1689 | } | |
1690 | < | |
1690 | > | |
1691 | #endif // is_mpi | |
1692 | ||
1693 | ||
1694 | < | void SimSetup::makeSysArrays( void ){ |
1695 | < | int i, j, k, l; |
1694 | > | void SimSetup::makeSysArrays(void){ |
1695 | > | |
1696 | > | #ifndef IS_MPI |
1697 | > | int k, j; |
1698 | > | #endif // is_mpi |
1699 | > | int i, l; |
1700 | ||
1701 | Atom** the_atoms; | |
1702 | Molecule* the_molecules; | |
1277 | – | Exclude** the_excludes; |
1703 | ||
1704 | < | |
1280 | < | for(l=0; l<nInfo; l++){ |
1281 | < | |
1704 | > | for (l = 0; l < nInfo; l++){ |
1705 | // create the atom and short range interaction arrays | |
1706 | < | |
1707 | < | the_atoms = new Atom*[info[l].n_atoms]; |
1706 | > | |
1707 | > | the_atoms = new Atom * [info[l].n_atoms]; |
1708 | the_molecules = new Molecule[info[l].n_mol]; | |
1709 | int molIndex; | |
1710 | ||
1711 | // initialize the molecule's stampID's | |
1712 | < | |
1712 | > | |
1713 | #ifdef IS_MPI | |
1714 | < | |
1715 | < | |
1714 | > | |
1715 | > | |
1716 | molIndex = 0; | |
1717 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1718 | < | |
1719 | < | if(mol2proc[i] == worldRank ){ |
1720 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
1721 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1722 | < | the_molecules[molIndex].setGlobalIndex( i ); |
1300 | < | molIndex++; |
1717 | > | for (i = 0; i < mpiSim->getNMolGlobal(); i++){ |
1718 | > | if (mol2proc[i] == worldRank){ |
1719 | > | the_molecules[molIndex].setStampID(molCompType[i]); |
1720 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1721 | > | the_molecules[molIndex].setGlobalIndex(i); |
1722 | > | molIndex++; |
1723 | } | |
1724 | } | |
1725 | < | |
1725 | > | |
1726 | #else // is_mpi | |
1727 | < | |
1727 | > | |
1728 | molIndex = 0; | |
1729 | < | globalAtomIndex = 0; |
1730 | < | for(i=0; i<n_components; i++){ |
1731 | < | for(j=0; j<components_nmol[i]; j++ ){ |
1732 | < | the_molecules[molIndex].setStampID( i ); |
1733 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1734 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1735 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1736 | < | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1737 | < | globalAtomIndex++; |
1738 | < | } |
1739 | < | molIndex++; |
1729 | > | globalAtomCounter = 0; |
1730 | > | for (i = 0; i < n_components; i++){ |
1731 | > | for (j = 0; j < components_nmol[i]; j++){ |
1732 | > | the_molecules[molIndex].setStampID(i); |
1733 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1734 | > | the_molecules[molIndex].setGlobalIndex(molIndex); |
1735 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1736 | > | info[l].molMembershipArray[globalAtomCounter] = molIndex; |
1737 | > | globalAtomCounter++; |
1738 | > | } |
1739 | > | molIndex++; |
1740 | } | |
1741 | } | |
1320 | – | |
1321 | – | |
1322 | – | #endif // is_mpi |
1742 | ||
1743 | ||
1744 | < | if( info[l].n_SRI ){ |
1326 | < | |
1327 | < | Exclude::createArray(info[l].n_SRI); |
1328 | < | the_excludes = new Exclude*[info[l].n_SRI]; |
1329 | < | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1330 | < | the_excludes[ex] = new Exclude(ex); |
1331 | < | } |
1332 | < | info[l].globalExcludes = new int; |
1333 | < | info[l].n_exclude = info[l].n_SRI; |
1334 | < | } |
1335 | < | else{ |
1336 | < | |
1337 | < | Exclude::createArray( 1 ); |
1338 | < | the_excludes = new Exclude*; |
1339 | < | the_excludes[0] = new Exclude(0); |
1340 | < | the_excludes[0]->setPair( 0,0 ); |
1341 | < | info[l].globalExcludes = new int; |
1342 | < | info[l].globalExcludes[0] = 0; |
1343 | < | info[l].n_exclude = 0; |
1344 | < | } |
1744 | > | #endif // is_mpi |
1745 | ||
1746 | + | info[l].globalExcludes = new int; |
1747 | + | info[l].globalExcludes[0] = 0; |
1748 | + | |
1749 | // set the arrays into the SimInfo object | |
1750 | ||
1751 | info[l].atoms = the_atoms; | |
1752 | info[l].molecules = the_molecules; | |
1753 | info[l].nGlobalExcludes = 0; | |
1351 | – | info[l].excludes = the_excludes; |
1352 | – | |
1353 | – | the_ff->setSimInfo( info ); |
1754 | ||
1755 | + | the_ff->setSimInfo(info); |
1756 | } | |
1757 | } | |
1758 | ||
1759 | < | void SimSetup::makeIntegrator( void ){ |
1359 | < | |
1759 | > | void SimSetup::makeIntegrator(void){ |
1760 | int k; | |
1761 | ||
1762 | < | NVT<RealIntegrator>* myNVT = NULL; |
1763 | < | NPTi<RealIntegrator>* myNPTi = NULL; |
1764 | < | NPTf<RealIntegrator>* myNPTf = NULL; |
1765 | < | NPTim<RealIntegrator>* myNPTim = NULL; |
1766 | < | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1767 | < | |
1768 | < | for(k=0; k<nInfo; k++){ |
1769 | < | |
1770 | < | switch( ensembleCase ){ |
1771 | < | |
1772 | < | case NVE_ENS: |
1773 | < | if (globals->haveZconstraints()){ |
1774 | < | setupZConstraint(info[k]); |
1775 | < | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1762 | > | NVE<RealIntegrator>* myNVE = NULL; |
1763 | > | NVT<RealIntegrator>* myNVT = NULL; |
1764 | > | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1765 | > | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1766 | > | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1767 | > | |
1768 | > | for (k = 0; k < nInfo; k++){ |
1769 | > | switch (ensembleCase){ |
1770 | > | case NVE_ENS: |
1771 | > | if (globals->haveZconstraints()){ |
1772 | > | setupZConstraint(info[k]); |
1773 | > | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1774 | > | } |
1775 | > | else{ |
1776 | > | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1777 | } | |
1778 | + | |
1779 | + | info->the_integrator = myNVE; |
1780 | + | break; |
1781 | ||
1782 | < | else |
1783 | < | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1784 | < | break; |
1785 | < | |
1786 | < | case NVT_ENS: |
1787 | < | if (globals->haveZconstraints()){ |
1788 | < | setupZConstraint(info[k]); |
1385 | < | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1386 | < | } |
1387 | < | else |
1388 | < | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1782 | > | case NVT_ENS: |
1783 | > | if (globals->haveZconstraints()){ |
1784 | > | setupZConstraint(info[k]); |
1785 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1786 | > | } |
1787 | > | else |
1788 | > | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1789 | ||
1790 | < | myNVT->setTargetTemp(globals->getTargetTemp()); |
1391 | < | |
1392 | < | if (globals->haveTauThermostat()) |
1393 | < | myNVT->setTauThermostat(globals->getTauThermostat()); |
1394 | < | |
1395 | < | else { |
1396 | < | sprintf( painCave.errMsg, |
1397 | < | "SimSetup error: If you use the NVT\n" |
1398 | < | " ensemble, you must set tauThermostat.\n"); |
1399 | < | painCave.isFatal = 1; |
1400 | < | simError(); |
1401 | < | } |
1402 | < | break; |
1403 | < | |
1404 | < | case NPTi_ENS: |
1405 | < | if (globals->haveZconstraints()){ |
1406 | < | setupZConstraint(info[k]); |
1407 | < | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1408 | < | } |
1409 | < | else |
1410 | < | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1790 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1791 | ||
1792 | < | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1793 | < | |
1794 | < | if (globals->haveTargetPressure()) |
1795 | < | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1796 | < | else { |
1797 | < | sprintf( painCave.errMsg, |
1798 | < | "SimSetup error: If you use a constant pressure\n" |
1799 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1800 | < | painCave.isFatal = 1; |
1421 | < | simError(); |
1422 | < | } |
1423 | < | |
1424 | < | if( globals->haveTauThermostat() ) |
1425 | < | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1426 | < | else{ |
1427 | < | sprintf( painCave.errMsg, |
1428 | < | "SimSetup error: If you use an NPT\n" |
1429 | < | " ensemble, you must set tauThermostat.\n"); |
1430 | < | painCave.isFatal = 1; |
1431 | < | simError(); |
1432 | < | } |
1433 | < | |
1434 | < | if( globals->haveTauBarostat() ) |
1435 | < | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1436 | < | else{ |
1437 | < | sprintf( painCave.errMsg, |
1438 | < | "SimSetup error: If you use an NPT\n" |
1439 | < | " ensemble, you must set tauBarostat.\n"); |
1440 | < | painCave.isFatal = 1; |
1441 | < | simError(); |
1442 | < | } |
1443 | < | break; |
1444 | < | |
1445 | < | case NPTf_ENS: |
1446 | < | if (globals->haveZconstraints()){ |
1447 | < | setupZConstraint(info[k]); |
1448 | < | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1449 | < | } |
1450 | < | else |
1451 | < | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1792 | > | if (globals->haveTauThermostat()) |
1793 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1794 | > | else{ |
1795 | > | sprintf(painCave.errMsg, |
1796 | > | "SimSetup error: If you use the NVT\n" |
1797 | > | "\tensemble, you must set tauThermostat.\n"); |
1798 | > | painCave.isFatal = 1; |
1799 | > | simError(); |
1800 | > | } |
1801 | ||
1802 | < | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1803 | < | |
1455 | < | if (globals->haveTargetPressure()) |
1456 | < | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1457 | < | else { |
1458 | < | sprintf( painCave.errMsg, |
1459 | < | "SimSetup error: If you use a constant pressure\n" |
1460 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1461 | < | painCave.isFatal = 1; |
1462 | < | simError(); |
1463 | < | } |
1464 | < | |
1465 | < | if( globals->haveTauThermostat() ) |
1466 | < | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1467 | < | else{ |
1468 | < | sprintf( painCave.errMsg, |
1469 | < | "SimSetup error: If you use an NPT\n" |
1470 | < | " ensemble, you must set tauThermostat.\n"); |
1471 | < | painCave.isFatal = 1; |
1472 | < | simError(); |
1473 | < | } |
1474 | < | |
1475 | < | if( globals->haveTauBarostat() ) |
1476 | < | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1477 | < | else{ |
1478 | < | sprintf( painCave.errMsg, |
1479 | < | "SimSetup error: If you use an NPT\n" |
1480 | < | " ensemble, you must set tauBarostat.\n"); |
1481 | < | painCave.isFatal = 1; |
1482 | < | simError(); |
1483 | < | } |
1484 | < | break; |
1485 | < | |
1486 | < | case NPTim_ENS: |
1487 | < | if (globals->haveZconstraints()){ |
1488 | < | setupZConstraint(info[k]); |
1489 | < | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1490 | < | } |
1491 | < | else |
1492 | < | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1802 | > | info->the_integrator = myNVT; |
1803 | > | break; |
1804 | ||
1805 | < | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1806 | < | |
1807 | < | if (globals->haveTargetPressure()) |
1808 | < | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1809 | < | else { |
1810 | < | sprintf( painCave.errMsg, |
1811 | < | "SimSetup error: If you use a constant pressure\n" |
1501 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1502 | < | painCave.isFatal = 1; |
1503 | < | simError(); |
1504 | < | } |
1505 | < | |
1506 | < | if( globals->haveTauThermostat() ) |
1507 | < | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1508 | < | else{ |
1509 | < | sprintf( painCave.errMsg, |
1510 | < | "SimSetup error: If you use an NPT\n" |
1511 | < | " ensemble, you must set tauThermostat.\n"); |
1512 | < | painCave.isFatal = 1; |
1513 | < | simError(); |
1514 | < | } |
1515 | < | |
1516 | < | if( globals->haveTauBarostat() ) |
1517 | < | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1518 | < | else{ |
1519 | < | sprintf( painCave.errMsg, |
1520 | < | "SimSetup error: If you use an NPT\n" |
1521 | < | " ensemble, you must set tauBarostat.\n"); |
1522 | < | painCave.isFatal = 1; |
1523 | < | simError(); |
1524 | < | } |
1525 | < | break; |
1526 | < | |
1527 | < | case NPTfm_ENS: |
1528 | < | if (globals->haveZconstraints()){ |
1529 | < | setupZConstraint(info[k]); |
1530 | < | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1531 | < | } |
1532 | < | else |
1533 | < | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1805 | > | case NPTi_ENS: |
1806 | > | if (globals->haveZconstraints()){ |
1807 | > | setupZConstraint(info[k]); |
1808 | > | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1809 | > | } |
1810 | > | else |
1811 | > | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1812 | ||
1813 | < | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1814 | < | |
1815 | < | if (globals->haveTargetPressure()) |
1816 | < | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1817 | < | else { |
1818 | < | sprintf( painCave.errMsg, |
1819 | < | "SimSetup error: If you use a constant pressure\n" |
1820 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1821 | < | painCave.isFatal = 1; |
1822 | < | simError(); |
1823 | < | } |
1824 | < | |
1825 | < | if( globals->haveTauThermostat() ) |
1826 | < | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1827 | < | else{ |
1828 | < | sprintf( painCave.errMsg, |
1829 | < | "SimSetup error: If you use an NPT\n" |
1830 | < | " ensemble, you must set tauThermostat.\n"); |
1831 | < | painCave.isFatal = 1; |
1832 | < | simError(); |
1833 | < | } |
1834 | < | |
1835 | < | if( globals->haveTauBarostat() ) |
1836 | < | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1837 | < | else{ |
1838 | < | sprintf( painCave.errMsg, |
1839 | < | "SimSetup error: If you use an NPT\n" |
1840 | < | " ensemble, you must set tauBarostat.\n"); |
1841 | < | painCave.isFatal = 1; |
1842 | < | simError(); |
1843 | < | } |
1844 | < | break; |
1845 | < | |
1846 | < | default: |
1847 | < | sprintf( painCave.errMsg, |
1848 | < | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1849 | < | painCave.isFatal = 1; |
1850 | < | simError(); |
1813 | > | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1814 | > | |
1815 | > | if (globals->haveTargetPressure()) |
1816 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1817 | > | else{ |
1818 | > | sprintf(painCave.errMsg, |
1819 | > | "SimSetup error: If you use a constant pressure\n" |
1820 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1821 | > | painCave.isFatal = 1; |
1822 | > | simError(); |
1823 | > | } |
1824 | > | |
1825 | > | if (globals->haveTauThermostat()) |
1826 | > | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1827 | > | else{ |
1828 | > | sprintf(painCave.errMsg, |
1829 | > | "SimSetup error: If you use an NPT\n" |
1830 | > | "\tensemble, you must set tauThermostat.\n"); |
1831 | > | painCave.isFatal = 1; |
1832 | > | simError(); |
1833 | > | } |
1834 | > | |
1835 | > | if (globals->haveTauBarostat()) |
1836 | > | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1837 | > | else{ |
1838 | > | sprintf(painCave.errMsg, |
1839 | > | "SimSetup error: If you use an NPT\n" |
1840 | > | "\tensemble, you must set tauBarostat.\n"); |
1841 | > | painCave.isFatal = 1; |
1842 | > | simError(); |
1843 | > | } |
1844 | > | |
1845 | > | info->the_integrator = myNPTi; |
1846 | > | break; |
1847 | > | |
1848 | > | case NPTf_ENS: |
1849 | > | if (globals->haveZconstraints()){ |
1850 | > | setupZConstraint(info[k]); |
1851 | > | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1852 | > | } |
1853 | > | else |
1854 | > | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1855 | > | |
1856 | > | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1857 | > | |
1858 | > | if (globals->haveTargetPressure()) |
1859 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1860 | > | else{ |
1861 | > | sprintf(painCave.errMsg, |
1862 | > | "SimSetup error: If you use a constant pressure\n" |
1863 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1864 | > | painCave.isFatal = 1; |
1865 | > | simError(); |
1866 | > | } |
1867 | > | |
1868 | > | if (globals->haveTauThermostat()) |
1869 | > | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1870 | > | |
1871 | > | else{ |
1872 | > | sprintf(painCave.errMsg, |
1873 | > | "SimSetup error: If you use an NPT\n" |
1874 | > | "\tensemble, you must set tauThermostat.\n"); |
1875 | > | painCave.isFatal = 1; |
1876 | > | simError(); |
1877 | > | } |
1878 | > | |
1879 | > | if (globals->haveTauBarostat()) |
1880 | > | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1881 | > | |
1882 | > | else{ |
1883 | > | sprintf(painCave.errMsg, |
1884 | > | "SimSetup error: If you use an NPT\n" |
1885 | > | "\tensemble, you must set tauBarostat.\n"); |
1886 | > | painCave.isFatal = 1; |
1887 | > | simError(); |
1888 | > | } |
1889 | > | |
1890 | > | info->the_integrator = myNPTf; |
1891 | > | break; |
1892 | > | |
1893 | > | case NPTxyz_ENS: |
1894 | > | if (globals->haveZconstraints()){ |
1895 | > | setupZConstraint(info[k]); |
1896 | > | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1897 | > | } |
1898 | > | else |
1899 | > | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1900 | > | |
1901 | > | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1902 | > | |
1903 | > | if (globals->haveTargetPressure()) |
1904 | > | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1905 | > | else{ |
1906 | > | sprintf(painCave.errMsg, |
1907 | > | "SimSetup error: If you use a constant pressure\n" |
1908 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1909 | > | painCave.isFatal = 1; |
1910 | > | simError(); |
1911 | > | } |
1912 | > | |
1913 | > | if (globals->haveTauThermostat()) |
1914 | > | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1915 | > | else{ |
1916 | > | sprintf(painCave.errMsg, |
1917 | > | "SimSetup error: If you use an NPT\n" |
1918 | > | "\tensemble, you must set tauThermostat.\n"); |
1919 | > | painCave.isFatal = 1; |
1920 | > | simError(); |
1921 | > | } |
1922 | > | |
1923 | > | if (globals->haveTauBarostat()) |
1924 | > | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1925 | > | else{ |
1926 | > | sprintf(painCave.errMsg, |
1927 | > | "SimSetup error: If you use an NPT\n" |
1928 | > | "\tensemble, you must set tauBarostat.\n"); |
1929 | > | painCave.isFatal = 1; |
1930 | > | simError(); |
1931 | > | } |
1932 | > | |
1933 | > | info->the_integrator = myNPTxyz; |
1934 | > | break; |
1935 | > | |
1936 | > | default: |
1937 | > | sprintf(painCave.errMsg, |
1938 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1939 | > | painCave.isFatal = 1; |
1940 | > | simError(); |
1941 | } | |
1942 | } | |
1943 | } | |
1944 | ||
1945 | < | void SimSetup::initFortran( void ){ |
1578 | < | |
1945 | > | void SimSetup::initFortran(void){ |
1946 | info[0].refreshSim(); | |
1947 | < | |
1948 | < | if( !strcmp( info[0].mixingRule, "standard") ){ |
1949 | < | the_ff->initForceField( LB_MIXING_RULE ); |
1947 | > | |
1948 | > | if (!strcmp(info[0].mixingRule, "standard")){ |
1949 | > | the_ff->initForceField(LB_MIXING_RULE); |
1950 | } | |
1951 | < | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1952 | < | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1951 | > | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1952 | > | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1953 | } | |
1954 | else{ | |
1955 | < | sprintf( painCave.errMsg, |
1956 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1590 | < | info[0].mixingRule ); |
1955 | > | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1956 | > | info[0].mixingRule); |
1957 | painCave.isFatal = 1; | |
1958 | simError(); | |
1959 | } | |
1960 | ||
1961 | ||
1962 | #ifdef IS_MPI | |
1963 | < | strcpy( checkPointMsg, |
1598 | < | "Successfully intialized the mixingRule for Fortran." ); |
1963 | > | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1964 | MPIcheckPoint(); | |
1965 | #endif // is_mpi | |
1601 | – | |
1966 | } | |
1967 | ||
1968 | < | void SimSetup::setupZConstraint(SimInfo& theInfo) |
1969 | < | { |
1970 | < | int nZConstraints; |
1607 | < | ZconStamp** zconStamp; |
1608 | < | |
1609 | < | if(globals->haveZconstraintTime()){ |
1610 | < | |
1611 | < | //add sample time of z-constraint into SimInfo's property list |
1612 | < | DoubleData* zconsTimeProp = new DoubleData(); |
1613 | < | zconsTimeProp->setID(ZCONSTIME_ID); |
1614 | < | zconsTimeProp->setData(globals->getZconsTime()); |
1615 | < | theInfo.addProperty(zconsTimeProp); |
1616 | < | } |
1617 | < | else{ |
1618 | < | sprintf( painCave.errMsg, |
1619 | < | "ZConstraint error: If you use an ZConstraint\n" |
1620 | < | " , you must set sample time.\n"); |
1621 | < | painCave.isFatal = 1; |
1622 | < | simError(); |
1623 | < | } |
1968 | > | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1969 | > | int nZConstraints; |
1970 | > | ZconStamp** zconStamp; |
1971 | ||
1972 | < | // |
1973 | < | nZConstraints = globals->getNzConstraints(); |
1974 | < | zconStamp = globals->getZconStamp(); |
1975 | < | ZConsParaItem tempParaItem; |
1972 | > | if (globals->haveZconstraintTime()){ |
1973 | > | //add sample time of z-constraint into SimInfo's property list |
1974 | > | DoubleData* zconsTimeProp = new DoubleData(); |
1975 | > | zconsTimeProp->setID(ZCONSTIME_ID); |
1976 | > | zconsTimeProp->setData(globals->getZconsTime()); |
1977 | > | theInfo.addProperty(zconsTimeProp); |
1978 | > | } |
1979 | > | else{ |
1980 | > | sprintf(painCave.errMsg, |
1981 | > | "ZConstraint error: If you use a ZConstraint,\n" |
1982 | > | "\tyou must set zconsTime.\n"); |
1983 | > | painCave.isFatal = 1; |
1984 | > | simError(); |
1985 | > | } |
1986 | ||
1987 | < | ZConsParaData* zconsParaData = new ZConsParaData(); |
1988 | < | zconsParaData->setID(ZCONSPARADATA_ID); |
1989 | < | |
1990 | < | for(int i = 0; i < nZConstraints; i++){ |
1987 | > | //push zconsTol into siminfo, if user does not specify |
1988 | > | //value for zconsTol, a default value will be used |
1989 | > | DoubleData* zconsTol = new DoubleData(); |
1990 | > | zconsTol->setID(ZCONSTOL_ID); |
1991 | > | if (globals->haveZconsTol()){ |
1992 | > | zconsTol->setData(globals->getZconsTol()); |
1993 | > | } |
1994 | > | else{ |
1995 | > | double defaultZConsTol = 0.01; |
1996 | > | sprintf(painCave.errMsg, |
1997 | > | "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1998 | > | "\tOOPSE will use a default value of %f.\n" |
1999 | > | "\tTo set the tolerance, use the zconsTol variable.\n", |
2000 | > | defaultZConsTol); |
2001 | > | painCave.isFatal = 0; |
2002 | > | simError(); |
2003 | > | |
2004 | > | zconsTol->setData(defaultZConsTol); |
2005 | > | } |
2006 | > | theInfo.addProperty(zconsTol); |
2007 | > | |
2008 | > | //set Force Subtraction Policy |
2009 | > | StringData* zconsForcePolicy = new StringData(); |
2010 | > | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
2011 | > | |
2012 | > | if (globals->haveZconsForcePolicy()){ |
2013 | > | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
2014 | > | } |
2015 | > | else{ |
2016 | > | sprintf(painCave.errMsg, |
2017 | > | "ZConstraint Warning: No force subtraction policy was set.\n" |
2018 | > | "\tOOPSE will use PolicyByMass.\n" |
2019 | > | "\tTo set the policy, use the zconsForcePolicy variable.\n"); |
2020 | > | painCave.isFatal = 0; |
2021 | > | simError(); |
2022 | > | zconsForcePolicy->setData("BYMASS"); |
2023 | > | } |
2024 | > | |
2025 | > | theInfo.addProperty(zconsForcePolicy); |
2026 | > | |
2027 | > | //set zcons gap |
2028 | > | DoubleData* zconsGap = new DoubleData(); |
2029 | > | zconsGap->setID(ZCONSGAP_ID); |
2030 | > | |
2031 | > | if (globals->haveZConsGap()){ |
2032 | > | zconsGap->setData(globals->getZconsGap()); |
2033 | > | theInfo.addProperty(zconsGap); |
2034 | > | } |
2035 | > | |
2036 | > | //set zcons fixtime |
2037 | > | DoubleData* zconsFixtime = new DoubleData(); |
2038 | > | zconsFixtime->setID(ZCONSFIXTIME_ID); |
2039 | > | |
2040 | > | if (globals->haveZConsFixTime()){ |
2041 | > | zconsFixtime->setData(globals->getZconsFixtime()); |
2042 | > | theInfo.addProperty(zconsFixtime); |
2043 | > | } |
2044 | > | |
2045 | > | //set zconsUsingSMD |
2046 | > | IntData* zconsUsingSMD = new IntData(); |
2047 | > | zconsUsingSMD->setID(ZCONSUSINGSMD_ID); |
2048 | > | |
2049 | > | if (globals->haveZConsUsingSMD()){ |
2050 | > | zconsUsingSMD->setData(globals->getZconsUsingSMD()); |
2051 | > | theInfo.addProperty(zconsUsingSMD); |
2052 | > | } |
2053 | > | |
2054 | > | //Determine the name of ouput file and add it into SimInfo's property list |
2055 | > | //Be careful, do not use inFileName, since it is a pointer which |
2056 | > | //point to a string at master node, and slave nodes do not contain that string |
2057 | > | |
2058 | > | string zconsOutput(theInfo.finalName); |
2059 | > | |
2060 | > | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
2061 | > | |
2062 | > | StringData* zconsFilename = new StringData(); |
2063 | > | zconsFilename->setID(ZCONSFILENAME_ID); |
2064 | > | zconsFilename->setData(zconsOutput); |
2065 | > | |
2066 | > | theInfo.addProperty(zconsFilename); |
2067 | > | |
2068 | > | //setup index, pos and other parameters of z-constraint molecules |
2069 | > | nZConstraints = globals->getNzConstraints(); |
2070 | > | theInfo.nZconstraints = nZConstraints; |
2071 | > | |
2072 | > | zconStamp = globals->getZconStamp(); |
2073 | > | ZConsParaItem tempParaItem; |
2074 | > | |
2075 | > | ZConsParaData* zconsParaData = new ZConsParaData(); |
2076 | > | zconsParaData->setID(ZCONSPARADATA_ID); |
2077 | > | |
2078 | > | for (int i = 0; i < nZConstraints; i++){ |
2079 | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); | |
2080 | tempParaItem.zPos = zconStamp[i]->getZpos(); | |
2081 | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); | |
2082 | tempParaItem.kRatio = zconStamp[i]->getKratio(); | |
2083 | < | |
2083 | > | tempParaItem.havingCantVel = zconStamp[i]->haveCantVel(); |
2084 | > | tempParaItem.cantVel = zconStamp[i]->getCantVel(); |
2085 | zconsParaData->addItem(tempParaItem); | |
2086 | + | } |
2087 | + | |
2088 | + | //check the uniqueness of index |
2089 | + | if(!zconsParaData->isIndexUnique()){ |
2090 | + | sprintf(painCave.errMsg, |
2091 | + | "ZConstraint Error: molIndex is not unique!\n"); |
2092 | + | painCave.isFatal = 1; |
2093 | + | simError(); |
2094 | + | } |
2095 | + | |
2096 | + | //sort the parameters by index of molecules |
2097 | + | zconsParaData->sortByIndex(); |
2098 | + | |
2099 | + | //push data into siminfo, therefore, we can retrieve later |
2100 | + | theInfo.addProperty(zconsParaData); |
2101 | + | } |
2102 | + | |
2103 | + | void SimSetup::makeMinimizer(){ |
2104 | + | |
2105 | + | OOPSEMinimizer* myOOPSEMinimizer; |
2106 | + | MinimizerParameterSet* param; |
2107 | + | char minimizerName[100]; |
2108 | + | |
2109 | + | for (int i = 0; i < nInfo; i++){ |
2110 | + | |
2111 | + | //prepare parameter set for minimizer |
2112 | + | param = new MinimizerParameterSet(); |
2113 | + | param->setDefaultParameter(); |
2114 | + | |
2115 | + | if (globals->haveMinimizer()){ |
2116 | + | param->setFTol(globals->getMinFTol()); |
2117 | } | |
2118 | ||
2119 | < | //sort the parameters by index of molecules |
2120 | < | zconsParaData->sortByIndex(); |
2121 | < | |
1645 | < | //push data into siminfo, therefore, we can retrieve later |
1646 | < | theInfo.addProperty(zconsParaData); |
2119 | > | if (globals->haveMinGTol()){ |
2120 | > | param->setGTol(globals->getMinGTol()); |
2121 | > | } |
2122 | ||
2123 | < | //push zconsTol into siminfo, if user does not specify |
2124 | < | //value for zconsTol, a default value will be used |
1650 | < | DoubleData* zconsTol = new DoubleData(); |
1651 | < | zconsTol->setID(ZCONSTOL_ID); |
1652 | < | if(globals->haveZconsTol()){ |
1653 | < | zconsTol->setData(globals->getZconsTol()); |
2123 | > | if (globals->haveMinMaxIter()){ |
2124 | > | param->setMaxIteration(globals->getMinMaxIter()); |
2125 | } | |
1655 | – | else{ |
1656 | – | double defaultZConsTol = 1E-6; |
1657 | – | sprintf( painCave.errMsg, |
1658 | – | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1659 | – | " , default value %f is used.\n", defaultZConsTol); |
1660 | – | painCave.isFatal = 0; |
1661 | – | simError(); |
2126 | ||
2127 | < | zconsTol->setData(defaultZConsTol); |
2128 | < | } |
2129 | < | theInfo.addProperty(zconsTol); |
2130 | < | |
2131 | < | //Determine the name of ouput file and add it into SimInfo's property list |
2132 | < | //Be careful, do not use inFileName, since it is a pointer which |
2133 | < | //point to a string at master node, and slave nodes do not contain that string |
2127 | > | if (globals->haveMinWriteFrq()){ |
2128 | > | param->setMaxIteration(globals->getMinMaxIter()); |
2129 | > | } |
2130 | > | |
2131 | > | if (globals->haveMinWriteFrq()){ |
2132 | > | param->setWriteFrq(globals->getMinWriteFrq()); |
2133 | > | } |
2134 | ||
2135 | < | string zconsOutput(theInfo.finalName); |
2136 | < | |
2137 | < | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
2138 | < | |
2139 | < | StringData* zconsFilename = new StringData(); |
2140 | < | zconsFilename->setID(ZCONSFILENAME_ID); |
2141 | < | zconsFilename->setData(zconsOutput); |
2142 | < | |
2143 | < | theInfo.addProperty(zconsFilename); |
2135 | > | if (globals->haveMinStepSize()){ |
2136 | > | param->setStepSize(globals->getMinStepSize()); |
2137 | > | } |
2138 | > | |
2139 | > | if (globals->haveMinLSMaxIter()){ |
2140 | > | param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
2141 | > | } |
2142 | > | |
2143 | > | if (globals->haveMinLSTol()){ |
2144 | > | param->setLineSearchTol(globals->getMinLSTol()); |
2145 | > | } |
2146 | > | |
2147 | > | strcpy(minimizerName, globals->getMinimizer()); |
2148 | > | |
2149 | > | if (!strcasecmp(minimizerName, "CG")){ |
2150 | > | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
2151 | > | } |
2152 | > | else if (!strcasecmp(minimizerName, "SD")){ |
2153 | > | //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param); |
2154 | > | myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param); |
2155 | > | } |
2156 | > | else{ |
2157 | > | sprintf(painCave.errMsg, |
2158 | > | "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n"); |
2159 | > | painCave.isFatal = 0; |
2160 | > | simError(); |
2161 | > | |
2162 | > | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
2163 | > | } |
2164 | > | info[i].the_integrator = myOOPSEMinimizer; |
2165 | > | |
2166 | > | //store the minimizer into simInfo |
2167 | > | info[i].the_minimizer = myOOPSEMinimizer; |
2168 | > | info[i].has_minimizer = true; |
2169 | > | } |
2170 | > | |
2171 | } |
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